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Sample records for chemically modified oligonucleotides

  1. Chemically modified oligonucleotides with efficient RNase H response

    DEFF Research Database (Denmark)

    Vester, Birte; Boel, Anne Marie; Lobedanz, Sune;

    2008-01-01

    Ten different chemically modified nucleosides were incorporated into short DNA strands (chimeric oligonucleotides ON3-ON12 and ON15-ON24) and then tested for their capacity to mediate RNAse H cleavage of the complementary RNA strand. The modifications were placed at two central positions directly...... in the RNase H cleaving region. The RNA strand of duplexes with ON3, ON5 and ON12 were cleaved more efficiently than the RNA strand of the DNA:RNA control duplex. There seems to be no correlation between the thermal stability between the duplexes and RNase H cleavage....

  2. Chemically Modified Oligonucleotides Modulate an Epigenetically Varied and Transient Form of Transcription Silencing of HIV-1 in Human Cells

    Directory of Open Access Journals (Sweden)

    Stuart Knowling

    2012-01-01

    Full Text Available Small noncoding RNAs (ncRNAs have been shown to guide epigenetic silencing complexes to target loci in human cells. When targeted to gene promoters, these small RNAs can lead to long-term stable epigenetic silencing of gene transcription. To date, small RNAs have been shown to modulate transcriptional gene silencing (TGS of human immunodeficiency virus type 1 (HIV-1 as well as several other disease-related genes, but it has remained unknown as to what extent particular chemistries can be used to generate single-stranded backbone-modified oligonucleotides that are amenable to this form of gene targeting and regulation. Here, we present data indicating that specific combinations of backbone modifications can be used to generate single-stranded antisense oligonucleotides that can functionally direct TGS of HIV-1 in a manner that is however, independent of epigenetic changes at the target loci. Furthermore, this functionality appears contingent on the absence of a 5′ phosphate in the oligonucleotide. These data suggest that chemically modified oligonucleotide based approaches could be implemented as a means to regulate gene transcription in an epigenetically independent manner.

  3. Negative electrospray ionization mass spectrometry of synthetic and chemically modified oligonucleotides

    NARCIS (Netherlands)

    Potier, N.; Van Dorsselaer, A.; Cordier, Y.; Roch, O.; Bischoff, Rainer

    1994-01-01

    We report here on the analysis of synthetic oligonucleotides by electrospray ionization mass spectrometry (ESI-MS). After intensive removal of salt ions (especially sodium cations), negative ion mass spectra, allowing mass measurement with an accuracy of 0.01%, were obtained on several oligonucleoti

  4. An overview of sugar-modified oligonucleotides for antisense therapeutics.

    Science.gov (United States)

    Prakash, Thazha P

    2011-09-01

    Among the multitude of chemical modifications that have been described over the past two decades, oligonucleotide analogs that are modified at the 2'-position of the furanose sugar have been especially useful for improving the drug-like properties of antisense oligonucleotides (ASOs). These modifications bias the sugar pucker towards the 3'-endo-conformation and improve ASO affinity for its biological target (i.e., mRNA). In addition, antisense drugs incorporating 2'-modified nucleotides exhibit enhanced metabolic stability, and improved pharmacokinetic and toxicological properties. Further conformational restriction of the 2'-substituent to the 4'-position of the furanose ring yielded the 2',4'-bridged nucleic acid (BNA) analogs. ASOs containing BNA modifications showed unprecedented increase in binding affinity for target RNA, while also improved nuclease resistance, in vitro and in vivo potency. Several ASO drug candidates containing 2'-modified nucleotides have entered clinical trials and continue to make progress in the clinic for a variety of therapeutic indications. 2011 Verlag Helvetica Chimica Acta AG, Zürich.

  5. Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles

    DEFF Research Database (Denmark)

    Cogoi, S; Jakobsen, U; Pedersen, E B

    2016-01-01

    KRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription...... factor essential for KRAS transcription. It is based on the use of palmitoyl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with lipid-modified G4-decoy oligonucleotides and a lipid-modified cell penetrating TAT peptide. The potency of the strategy in pancreatic cancer cells is demonstrated...

  6. Delivery of antisense oligonucleotides using cholesterol-modified sense dendrimers and cationic lipids

    NARCIS (Netherlands)

    Chaltin, Patrick; Margineanu, Anca; Marchand, Damien; Aerschot, Arthur Van; Rozenski, Jef; Schryver, Frans De; Herrmann, Andreas; Müllen, Klaus; Juliano, Rudolph; Fisher, Michael H.; Kang, Hyunmin; Feyter, Steven De; Herdewijn, Piet

    2005-01-01

    Cholesterol modified mono-, di-, and tetrameric oligonucleotides were synthesized and hybridized with antisense oligonucleotides to study their incorporation in cationic liposomes together with the influence of this dendrimeric delivery system on biological activity. Electrostatic interactions seem

  7. Synthesis of 3'-, or 5'-, or internal methacrylamido-modified oligonucleotides

    Science.gov (United States)

    Golova, Julia B.; Chernov, Boris K.

    2010-04-27

    New modifiers were synthesized for incorporation of a methacrylic function in 3'-, 5'- and internal positions of oligonucleotides during solid phase synthesis. A modifier was used for synthesis of 5'-methacrylated oligonucleotides for preparation of microarrays by a co-polymerization method.

  8. Correlating In Vitro Splice Switching Activity With Systemic In Vivo Delivery Using Novel ZEN-modified Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Suzan M Hammond

    2014-01-01

    Full Text Available Splice switching oligonucleotides (SSOs induce alternative splicing of pre-mRNA and typically employ chemical modifications to increase nuclease resistance and binding affinity to target pre-mRNA. Here we describe a new SSO non-base modifier (a naphthyl-azo group, “ZEN™” to direct exon exclusion in mutant dystrophin pre-mRNA to generate functional dystrophin protein. The ZEN modifier is placed near the ends of a 2′-O-methyl (2′OMe oligonucleotide, increasing melting temperature and potency over unmodified 2′OMe oligonucleotides. In cultured H2K cells, a ZEN-modified 2′OMe phosphorothioate (PS oligonucleotide delivered by lipid transfection greatly enhanced dystrophin exon skipping over the same 2′OMePS SSO lacking ZEN. However, when tested using free gymnotic uptake in vitro and following systemic delivery in vivo in dystrophin deficient mdx mice, the same ZEN-modified SSO failed to enhance potency. Importantly, we show for the first time that in vivo activity of anionic SSOs is modelled in vitro only when using gymnotic delivery. ZEN is thus a novel modifier that enhances activity of SSOs in vitro but will require improved delivery methods before its in vivo clinical potential can be realized.

  9. A Tandem Oligonucleotide Approach for SNP-Selective RNA Degradation Using Modified Antisense Oligonucleotides.

    Science.gov (United States)

    Magner, Dorota; Biala, Ewa; Lisowiec-Wachnicka, Jolanta; Kierzek, Elzbieta; Kierzek, Ryszard

    2015-01-01

    Antisense oligonucleotides have been studied for many years as a tool for gene silencing. One of the most difficult cases of selective RNA silencing involves the alleles of single nucleotide polymorphisms, in which the allele sequence is differentiated by a single nucleotide. A new approach to improve the performance of allele selectivity for antisense oligonucleotides is proposed. It is based on the simultaneous application of two oligonucleotides. One is complementary to the mutated form of the targeted RNA and is able to activate RNase H to cleave the RNA. The other oligonucleotide, which is complementary to the wild type allele of the targeted RNA, is able to inhibit RNase H cleavage. Five types of SNPs, C/G, G/C, G/A, A/G, and C/U, were analyzed within the sequence context of genes associated with neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, ALS (Amyotrophic Lateral Sclerosis), and Machado-Joseph disease. For most analyzed cases, the application of the tandem approach increased allele-selective RNA degradation 1.5-15 fold relative to the use of a single antisense oligonucleotide. The presented study proves that differentiation between single substitution is highly dependent on the nature of the SNP and surrounding nucleotides. These variables are crucial for determining the proper length of the inhibitor antisense oligonucleotide. In the tandem approach, the comparison of thermodynamic stability of the favorable duplexes WT RNA-inhibitor and Mut RNA-gapmer with the other possible duplexes allows for the evaluation of chances for the allele-selective degradation of RNA. A larger difference in thermodynamic stability between favorable duplexes and those that could possibly form, usually results in the better allele selectivity of RNA degradation.

  10. Improved Performance of Anti-miRNA Oligonucleotides Using a Novel Non-Nucleotide Modifier

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    Kim A Lennox

    2013-01-01

    Full Text Available Anti-microRNA oligonucleotides (AMOs are steric blocking antisense reagents that inhibit microRNA (miRNA function by hybridizing and repressing the activity of a mature miRNA. First generation AMOs employed 2′-O-Methyl RNA nucleotides (2′OMe with phosphorothioate (PS internucleotide linkages positioned at both ends to block exonuclease attack. Second generation AMOs improved potency through the use of chemical modifications that increase binding affinity to the target, such as locked nucleic acid (LNA residues. However, this strategy can reduce specificity as high binding affinity compounds can bind to and suppress function of related sequences even if one or more mismatches are present. Further, unnatural modified nucleic acid residues can have toxic side effects. In the present study, a variety of non-nucleotide modifiers were screened for utility in steric blocking antisense applications. A novel compound, N,N-diethyl-4-(4-nitronaphthalen-1-ylazo-phenylamine (“ZEN”, was discovered that increased binding affinity and blocked exonuclease degradation when placed at or near each end of a single-stranded oligonucleotide. This new modification was combined with the 2′OMe RNA backbone to make ZEN-AMOs. The new ZEN-AMOs have high potency and can effectively inhibit miRNA function in vitro at low nanomolar concentrations, show high specificity, and have low toxicity in cell culture.

  11. Effect of 2'-O-methyl/thiophosphonoacetate-modified antisense oligonucleotides on huntingtin expression in patient-derived cells.

    Science.gov (United States)

    Matsui, Masayuki; Threlfall, Richard N; Caruthers, Marvin H; Corey, David R

    2014-12-15

    Optimizing oligonucleotides as therapeutics will require exploring how chemistry can be used to enhance their effects inside cells. To achieve this goal it will be necessary to fully explore chemical space around the native DNA/RNA framework to define the potential of diverse chemical modifications. In this report we examine the potential of thiophosphonoacetate (thioPACE)-modified 2'-O-methyl oligoribonucleotides as inhibitors of human huntingtin (HTT) expression. Inhibition occurred, but was less than with analogous locked nucleic acid (LNA)-substituted oligomers lacking the thioPACE modification. These data suggest that thioPACE oligonucleotides have the potential to control gene expression inside cells. However, advantages relative to other modifications were not demonstrated. Additional modifications are likely to be necessary to fully explore any potential advantages of thioPACE substitutions.

  12. 2-O-[2-(Methylthio)ethyl]-Modified Oligonucleotide: An Analog of 2-O-[2-(Methoxy)ethyl]-Modified Oligonucleotide with Improved Protein Binding Properties and High Binding Affinity to Target RNA

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, T.P.; Manoharan, M.; Fraser, A.S.; Kawasaki, A.M.; Lesnik, E.; Sioufi, N.; Leeds, J.M.; Teplova, M.; Egli, M.

    2010-03-08

    A novel 2'-modification, 2'-O-[2-(methylthio)ethyl] or 2'-O-MTE, has been incorporated into oligonucleotides and evaluated for properties relevant to antisense activity. The results were compared with the previously characterized 2'-O-[2-(methoxy)ethyl] 2'-O-MOE modification. As expected, the 2'-O-MTE modified oligonucleotides exhibited improved binding to human serum albumin compared to the 2'-O-MOE modified oligonucleotides. The 2'-O-MTE oligonucleotides maintained high binding affinity to target RNA. Nuclease digestion of 2'-O-MTE oligonucleotides showed that they have limited resistance to exonuclease degradation. We analyzed the crystal structure of a decamer DNA duplex containing the 2'-O-MTE modifcation. Analysis of the crystal structure provides insight into the improved RNA binding affinity, protein binding affinity and limited resistance of 2'-O-MTE modified oligonucleotides to exonuclease degradation.

  13. LNA-modified isothermal oligonucleotide microarray for differentiating bacilli of similar origin.

    Science.gov (United States)

    Yan, Jing; Yuan, Ying; Mu, Runqing; Shang, Hong; Guan, Yifu

    2014-12-01

    Oligonucleotide microarray has been one of the most powerful tools in the 'Post-Genome Era' for its high sensitivity, high throughput and parallel processing capability. To achieve high detection specificity, we fabricated an isothermal microarray using locked nucleic acid (LNA)-modified oligonucleotide probes, since LNA has demonstrated the advanced ability to enhance the binding affinity toward their complementary nucleotides. After designing the nucleotide sequences of these oligonucleotide probes for gram-positive bacilli of similar origin (Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus megaterium and Bacillus circulans), we unified the melting temperatures of these oligonucleotide probes by modifying some nucleotides using LNA. Furthermore, we optimized the experimental procedures of hydrating microarray slides, blocking side surface as well as labelling the PCR products. Experimental results revealed that KOD Dash DNA polymerase could efficiently incorporate Cy3-dCTP into the PCR products, and the LNA-isothermal oligonucleotide microarray were able to distinguish the bacilli of similar origin with a high degree of accuracy and specificity under the optimized experimental condition.

  14. LNA-modified isothermal oligonucleotide microarray for differentiating bacilli of similar origin

    Indian Academy of Sciences (India)

    Jing Yan; Ying Yuan; Runqing Mu; Hong Shang; Yifu Guan

    2014-12-01

    Oligonucleotide microarray has been one of the most powerful tools in the ‘Post-Genome Era’ for its high sensitivity, high throughput and parallel processing capability. To achieve high detection specificity, we fabricated an isothermal microarray using locked nucleic acid (LNA)-modified oligonucleotide probes, since LNA has demonstrated the advanced ability to enhance the binding affinity toward their complementary nucleotides. After designing the nucleotide sequences of these oligonucleotide probes for gram-positive bacilli of similar origin (Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus megaterium and Bacillus circulans), we unified the melting temperatures of these oligonucleotide probes by modifying some nucleotides using LNA. Furthermore, we optimized the experimental procedures of hydrating microarray slides, blocking side surface as well as labelling the PCR products. Experimental results revealed that KOD Dash DNA polymerase could efficiently incorporate Cy3-dCTP into the PCR products, and the LNA-isothermal oligonucleotide microarray were able to distinguish the bacilli of similar origin with a high degree of accuracy and specificity under the optimized experimental condition.

  15. Sequence selective naked-eye detection of DNA harnessing extension of oligonucleotide-modified nucleotides.

    Science.gov (United States)

    Verga, Daniela; Welter, Moritz; Marx, Andreas

    2016-02-01

    DNA polymerases can efficiently and sequence selectively incorporate oligonucleotide (ODN)-modified nucleotides and the incorporated oligonucleotide strand can be employed as primer in rolling circle amplification (RCA). The effective amplification of the DNA primer by Φ29 DNA polymerase allows the sequence-selective hybridisation of the amplified strand with a G-quadruplex DNA sequence that has horse radish peroxidase-like activity. Based on these findings we develop a system that allows DNA detection with single-base resolution by naked eye.

  16. Synthesis and antisense properties of 2'-O-(2S-methoxypropyl)-RNA-modified gapmer antisense oligonucleotides.

    Science.gov (United States)

    Yu, Jinghua; Pandey, Sanjay K; Khatri, Hetal; Prakash, Thazha P; Swayze, Eric E; Seth, Punit P

    2014-09-01

    To ascertain whether increasing hydrophobicity can enhance the activity of second-generation antisense oligonucleotides (ASOs) in muscle, we investigated the antisense properties of 2'-O-(2S-methoxypropyl)-RNA (2S-MOP)-modified ASOs. Synthesis of the 2S-MOP 5-methyl uridine phosphoramidite was accomplished on a multi-gram scale by Lewis-acid-catalyzed ring opening of 5'-O-tert-butyldiphenylsilyl ether-protected 2,2'-anhydro-5-methyl uridine with 2S-methoxy-1-propanol. Synthesis of the 2S-MOP 5-methyl cytidine nucleoside from the corresponding 5-methyl uridine nucleoside was accomplished by formation and displacement of a 4-triazolide intermediate with aqueous ammonia. 2S-MOP-modified oligonucleotides were prepared on an automated DNA synthesizer and showed similar enhancements in duplex thermal stability as 2'-O-methoxyethyl RNA (MOE)-modified oligonucleotides. 2S-MOP-containing antisense oligonucleotides were evaluated in Balb-c mice and showed good activity for decreasing the expression levels of scavenger receptor B1 (Srb1) and phosphatase and tensin homologue (PTEN) mRNA in liver and muscle tissue. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Stable gene targeting in human cells using single-strand oligonucleotides with modified bases.

    Directory of Open Access Journals (Sweden)

    Xavier Rios

    Full Text Available Recent advances allow multiplexed genome engineering in E. coli, employing easily designed oligonucleotides to edit multiple loci simultaneously. A similar technology in human cells would greatly expedite functional genomics, both by enhancing our ability to test how individual variants such as single nucleotide polymorphisms (SNPs are related to specific phenotypes, and potentially allowing simultaneous mutation of multiple loci. However, oligo-mediated targeting of human cells is currently limited by low targeting efficiencies and low survival of modified cells. Using a HeLa-based EGFP-rescue reporter system we show that use of modified base analogs can increase targeting efficiency, in part by avoiding the mismatch repair machinery. We investigate the effects of oligonucleotide toxicity and find a strong correlation between the number of phosphorothioate bonds and toxicity. Stably EGFP-corrected cells were generated at a frequency of ~0.05% with an optimized oligonucleotide design combining modified bases and reduced number of phosphorothioate bonds. We provide evidence from comparative RNA-seq analysis suggesting cellular immunity induced by the oligonucleotides might contribute to the low viability of oligo-corrected cells. Further optimization of this method should allow rapid and scalable genome engineering in human cells.

  18. Chemical phosphorylation of deoxyribonucleosides and thermolytic DNA oligonucleotides.

    Science.gov (United States)

    Ausín, Cristina; Grajkowski, Andrzej; Cieślak, Jacek; Beaucage, Serge L

    2006-10-01

    The phosphorylating reagent bis[S-(4,4'-dimethoxytrityl)-2-mercaptoethyl]-N,N-diisopropylphosphoramidite is prepared in three steps from commercial methyl thioglycolate and diisopropylphosphoramidous dichloride. The phosphorylating reagent has been used successfully in the solid-phase synthesis of deoxyribonucleoside 5'-/3'-phosphate or -thiophosphate monoesters and oligonucleotide 5'-phosphate/-thiophosphate monoesters. Bis[S-(4,4'-dimethoxytrityl)-2-mercaptoethyl]-N,N-diisopropylphosphoramidite has also been employed in the construction of a thermolytic dinucleotide prodrug model to evaluate the ability of the reagent to produce thermosentive oligonucleotide prodrugs under mild temperature conditions ( approximately 25 degrees C) for potential therapeutic applications.

  19. Photoswitchable oligonucleotide-modified gold nanoparticles: controlling hybridization stringency with photon dose.

    Science.gov (United States)

    Yan, Yunqi; Chen, Jennifer I L; Ginger, David S

    2012-05-09

    We describe a new class of stimulus-responsive DNA-functionalized gold nanoparticles that incorporate azobenzene-modified oligonucleotides. Beyond the classic directed assembly and sensing behaviors associated with oligonucleotide-modified nanoparticles, these particles also exhibit reversible photoswitching of their assembly behavior. Exposure to UV light induces a trans-cis isomerization of the azobenzene which destabilizes the DNA duplex, resulting in dissociation of the nanoparticle assemblies. The isomerization is reversible upon exposure to blue light, resulting in rehybridization and reassembly of the DNA-linked nanoparticle clusters. We show that perfectly complementary and partially mismatched strands exhibit clearly distinguishable photoinduced melting properties, and we demonstrate that photon dose can thus be used in place of temperature or ionic strength to control hybridization stringency with the ability to discriminate single-base mismatches.

  20. A High-Fidelity Codon Set for the T4 DNA Ligase-Catalyzed Polymerization of Modified Oligonucleotides.

    Science.gov (United States)

    Lei, Yi; Kong, Dehui; Hili, Ryan

    2015-12-14

    In vitro selection of nucleic acid polymers can readily deliver highly specific receptors and catalysts for a variety of applications; however, it is suspected that the functional group deficit of nucleic acids has limited their potential with respect to proteinogenic polymers. This has stimulated research toward expanding their chemical diversity to bridge the functional gap between nucleic acids and proteins to develop a superior biopolymer. In this study, we investigate the effect of codon library size and composition on the sequence specificity of T4 DNA ligase in the DNA-templated polymerization of both unmodified and modified oligonucleotides. Using high-throughput DNA sequencing of duplex pairs, we have uncovered a 256-membered codon set that yields sequence-defined modified ssDNA polymers in high yield and with high fidelity.

  1. Oligonucleotides conjugated with short chemically defined polyethylene glycol chains are efficient antisense agents.

    Science.gov (United States)

    Shokrzadeh, Nasrin; Winkler, Anna-Maria; Dirin, Mehrdad; Winkler, Johannes

    2014-12-15

    Ligand conjugation is an attractive approach to rationally modify the poor pharmacokinetic behavior and cellular uptake properties of antisense oligonucleotides. Polyethylene glycol (PEG) attachment is a method to increase solubility of oligonucleotides and prevent the rapid elimination, thus increasing tissue distribution. On the other hand, the attachment of long PEG chains negatively influences the pharmacodynamic effect by reducing the hybridization efficiency. We examined the use of short PEG ligands on the in vitro effect of antisense agents. Circular dichroism showed that the tethering of PEG12-chains to phosphodiester and phosphorothioate oligonucleotides had no influence on their secondary structure and did not reduce the affinity to the counter strand. In an in vitro tumor model, a luciferase reporter assay indicated unchanged gene silencing activity compared to unmodified compounds, and even slightly superior target down regulation was found after treatment with a phosphorothioate modified conjugate. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  2. The Role of Fluorinated Alcohols as Mobile Phase Modifiers for LC-MS Analysis of Oligonucleotides

    Science.gov (United States)

    Basiri, Babak; van Hattum, Hilde; van Dongen, William D.; Murph, Mandi M.; Bartlett, Michael G.

    2016-09-01

    Hexafluoroisopropanol (HFIP) has been widely used as an acidic modifier for mobile phases for liquid chromatography-mass spectrometry (LC-MS) analysis of oligonucleotides ever since the first report of its use for this purpose. This is not surprising, considering the exceptional performance of HFIP compared with carboxylic acids, which cause significant MS signal suppression in electrospray ionization. However, we have found that other fluorinated alcohols can also be utilized for mobile phase preparation and the choice of optimal fluorinated alcohol is determined by the ion-pairing (IP) agent. Although HFIP is a very good choice to be used alongside less hydrophobic IP agents, other fluorinated alcohols such as 1,1,1,3,3,3-hexafluoro-2-methyl-2-propanol (HFMIP) can significantly outperform HFIP when used with more hydrophobic IP agents. We also found that more acidic fluorinated alcohols assist with the transfer of oligonucleotides with secondary structure (e.g., folded strands and hairpins) into the gas phase.

  3. A novel route for immobilization of oligonucleotides onto modified silica nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Kota Sreenivasa [Institute of Scientific and Industrial Research, Sanken, Osaka University, Osaka (Japan)]. E-mail: kotas_1999@yahoo.com; Rani, Sikhakolli Usha [Institute of Scientific and Industrial Research, Sanken, Osaka University, Osaka (Japan); Charyulu, Devarayapalli Kamakshaiah [Institute of Advanced Energy, Kyoto University, Gokasho, Uji (Japan); Kumar, Kamisetty Nagendra [Institute of Advanced Energy, Kyoto University, Gokasho, Uji (Japan); Lee, Bong-Kuk [Institute of Scientific and Industrial Research, Sanken, Osaka University, Osaka (Japan); Lee, Hea-Yeon [Institute of Scientific and Industrial Research, Sanken, Osaka University, Osaka (Japan); Kawai, Tomoji [Institute of Scientific and Industrial Research, Sanken, Osaka University, Osaka (Japan)

    2006-08-25

    A novel approach for immobilization of probe oligonucleotides that uses zirconium phosphate modified silica nanoparticles is proposed. The surface modification of nanoparticles was carried out in two stages. Initially binding of Zr{sup 4+} to the surface of silica nanoparticles and later treated with phosphoric acid for terminal phosphate groups. Oligonucleotide probes modified with amine group at 5'-end were strongly binds to the phosphate terminated silica nanoparticles with imidazole in presence of 0.1 mol L{sup -1} EDC [N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide], as phosphate groups are more reactive towards amine group. Various studies, i.e., synthesis of silica nanoparticles, their surface modification, probe immobilization, measurement of hybridization and effect of bovine serum albumin (BSA) were carried out during optimization of reaction conditions. The significant reduction in the background signal was observed by treating the probe modified silica nanoparticles with bovine serum albumin prior to hybridization. The probe modified silica nanoparticles were retained their properties and the hybridization was induced by exposure of single-stranded DNA (ssDNA) containing silica nanoparticles to the complementary DNA in solution. The decrease in the fluorescence signal for one mismatch and three mismatch was observed upon hybridization of probe with target DNAs, while there was no response for the random target ssDNA under the same experimental conditions. The intensity of fluorescence signal was linear to the concentration of target DNA ranging from 3.9 x 10{sup -9} to 3.0 x 10{sup -6} mol L{sup -1}. A detection limit of 1.22 x 10{sup -9} mol L{sup -1} of oligonucleotides can be estimated. The proposed hybridization assay is simple and possesses good analytical characteristics and it can provide an effective and efficient route in the development of DNA biosensors and biochips.

  4. Oligonucleotide-templated chemical reactions: pushing the boundaries of a nature-inspired process.

    Science.gov (United States)

    Percivalle, Claudia; Bartolo, Jean-François; Ladame, Sylvain

    2013-01-07

    Widespread in nature, oligonucleotide-templated reactions of phosphodiester bond formation have inspired chemists who are now applying this elegant strategy to the catalysis of a broad range of otherwise inefficient reactions. This review highlights the increasing diversity of chemical reactions that can be efficiently catalysed by an oligonucleotide template, using Watson-Crick base-pairing to bring both reagents in close enough proximity to react, thus increasing significantly their effective molarity. The applications of this elegant concept for nucleic acid sensing and controlled organic synthesis will also be discussed.

  5. Lipid-modified oligonucleotide conjugates: Insights into gene silencing, interaction with model membranes and cellular uptake mechanisms.

    Science.gov (United States)

    Ugarte-Uribe, Begoña; Grijalvo, Santiago; Pertíñez, Samuel Núñez; Busto, Jon V; Martín, César; Alagia, Adele; Goñi, Félix M; Eritja, Ramón; Alkorta, Itziar

    2017-01-01

    The ability of oligonucleotides to silence specific genes or inhibit the biological activity of specific proteins has generated great interest in their use as research tools and therapeutic agents. Unfortunately, their biological applications meet the limitation of their poor cellular accessibility. Developing an appropriate delivery system for oligonucleotides is essential to achieve their efficient cellular uptake. In the present work a series of phosphorothioate lipid-oligonucleotide hybrids were synthesized introducing covalently single or double lipid tails at both 3'- and 5'-termini of an antisense oligonucleotide. Gene transfections in cultured cells showed antisense luciferase inhibition without the use of a transfecting agent for conjugates modified with the double-lipid tail at 5'-termini. The effect of the double lipid-tailed modification was further studied in detail in several model membrane systems as well as in cellular uptake experiments. During these studies the spontaneous formation of self-assembled microstructures is clearly observed. Lipidation allowed the efficient incorporation of the oligonucleotide in HeLa cells by a macropinocytosis mechanism without causing cytotoxicity in cells or altering the binding properties of the oligonucleotide conjugates. In addition, both single- and double-tailed compounds showed a similar behavior in lipid model membranes, making them useful in nucleotide-based technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases.

    Science.gov (United States)

    Renaud, Jean-Baptiste; Boix, Charlotte; Charpentier, Marine; De Cian, Anne; Cochennec, Julien; Duvernois-Berthet, Evelyne; Perrouault, Loïc; Tesson, Laurent; Edouard, Joanne; Thinard, Reynald; Cherifi, Yacine; Menoret, Séverine; Fontanière, Sandra; de Crozé, Noémie; Fraichard, Alexandre; Sohm, Frédéric; Anegon, Ignacio; Concordet, Jean-Paul; Giovannangeli, Carine

    2016-03-08

    Genome editing has now been reported in many systems using TALEN and CRISPR-Cas9 nucleases. Precise mutations can be introduced during homology-directed repair with donor DNA carrying the wanted sequence edit, but efficiency is usually lower than for gene knockout and optimal strategies have not been extensively investigated. Here, we show that using phosphorothioate-modified oligonucleotides strongly enhances genome editing efficiency of single-stranded oligonucleotide donors in cultured cells. In addition, it provides better design flexibility, allowing insertions more than 100 bp long. Despite previous reports of phosphorothioate-modified oligonucleotide toxicity, clones of edited cells are readily isolated and targeted sequence insertions are achieved in rats and mice with very high frequency, allowing for homozygous loxP site insertion at the mouse ROSA locus in particular. Finally, when detected, imprecise knockin events exhibit indels that are asymmetrically positioned, consistent with genome editing taking place by two steps of single-strand annealing.

  7. Sequence motifs associated with hepatotoxicity of locked nucleic acid--modified antisense oligonucleotides.

    Science.gov (United States)

    Burdick, Andrew D; Sciabola, Simone; Mantena, Srinivasa R; Hollingshead, Brett D; Stanton, Robert; Warneke, James A; Zeng, Ming; Martsen, Elena; Medvedev, Alexander; Makarov, Sergei S; Reed, Lori A; Davis, John W; Whiteley, Laurence O

    2014-04-01

    Fully phosphorothioate antisense oligonucleotides (ASOs) with locked nucleic acids (LNAs) improve target affinity, RNase H activation and stability. LNA modified ASOs can cause hepatotoxicity, and this risk is currently not fully understood. In vitro cytotoxicity screens have not been reliable predictors of hepatic toxicity in non-clinical testing; however, mice are considered to be a sensitive test species. To better understand the relationship between nucleotide sequence and hepatotoxicity, a structure-toxicity analysis was performed using results from 2 week repeated-dose-tolerability studies in mice administered LNA-modified ASOs. ASOs targeting human Apolipoprotien C3 (Apoc3), CREB (cAMP Response Element Binding Protein) Regulated Transcription Coactivator 2 (Crtc2) or Glucocorticoid Receptor (GR, NR3C1) were classified based upon the presence or absence of hepatotoxicity in mice. From these data, a random-decision forest-classification model generated from nucleotide sequence descriptors identified two trinucleotide motifs (TCC and TGC) that were present only in hepatotoxic sequences. We found that motif containing sequences were more likely to bind to hepatocellular proteins in vitro and increased P53 and NRF2 stress pathway activity in vivo. These results suggest in silico approaches can be utilized to establish structure-toxicity relationships of LNA-modified ASOs and decrease the likelihood of hepatotoxicity in preclinical testing.

  8. Sequence motifs associated with hepatotoxicity of locked nucleic acid—modified antisense oligonucleotides

    Science.gov (United States)

    Burdick, Andrew D.; Sciabola, Simone; Mantena, Srinivasa R.; Hollingshead, Brett D.; Stanton, Robert; Warneke, James A.; Zeng, Ming; Martsen, Elena; Medvedev, Alexander; Makarov, Sergei S.; Reed, Lori A.; Davis, John W.; Whiteley, Laurence O.

    2014-01-01

    Fully phosphorothioate antisense oligonucleotides (ASOs) with locked nucleic acids (LNAs) improve target affinity, RNase H activation and stability. LNA modified ASOs can cause hepatotoxicity, and this risk is currently not fully understood. In vitro cytotoxicity screens have not been reliable predictors of hepatic toxicity in non-clinical testing; however, mice are considered to be a sensitive test species. To better understand the relationship between nucleotide sequence and hepatotoxicity, a structure–toxicity analysis was performed using results from 2 week repeated-dose-tolerability studies in mice administered LNA-modified ASOs. ASOs targeting human Apolipoprotien C3 (Apoc3), CREB (cAMP Response Element Binding Protein) Regulated Transcription Coactivator 2 (Crtc2) or Glucocorticoid Receptor (GR, NR3C1) were classified based upon the presence or absence of hepatotoxicity in mice. From these data, a random-decision forest-classification model generated from nucleotide sequence descriptors identified two trinucleotide motifs (TCC and TGC) that were present only in hepatotoxic sequences. We found that motif containing sequences were more likely to bind to hepatocellular proteins in vitro and increased P53 and NRF2 stress pathway activity in vivo. These results suggest in silico approaches can be utilized to establish structure–toxicity relationships of LNA-modified ASOs and decrease the likelihood of hepatotoxicity in preclinical testing. PMID:24550163

  9. DETECTING LOW-LEVEL SYNTHESIS IMPURITIES IN MODIFIED PHOSPHOROTHIOATE OLIGONUCLEOTIDES USING LIQUID CHROMATOGRAPHY - HIGH RESOLUTION MASS SPECTROMETRY.

    Science.gov (United States)

    Nikcevic, Irena; Wyrzykiewicz, Tadeusz K; Limbach, Patrick A

    2011-07-01

    An LC-MS method based on the use of high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS) for profiling oligonucleotides synthesis impurities is described.Oligonucleotide phosphorothioatediesters (phosphorothioate oligonucleotides), in which one of the non-bridging oxygen atoms at each phosphorus center is replaced by a sulfur atom, are now one of the most popular oligonucleotide modifications due to their ease of chemical synthesis and advantageous pharmacokinetic properties. Despite significant progress in the solid-phase oligomerization chemistry used in the manufacturing of these oligonucleotides, multiple classes of low-level impurities always accompany synthetic oligonucleotides. Liquid chromatography-mass spectrometry has emerged as a powerful technique for the identification of these synthesis impurities. However, impurity profiling, where the entire complement of low-level synthetic impurities is identified in a single analysis, is more challenging. Here we present an LC-MS method based the use of high resolution-mass spectrometry, specifically Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS or FTMS). The optimal LC-FTMS conditions, including the stationary phase and mobile phases for the separation and identification of phosphorothioate oligonucleotides, were found. The characteristics of FTMS enable charge state determination from single m/z values of low-level impurities. Charge state information then enables more accurate modeling of the detected isotopic distribution for identification of the chemical composition of the detected impurity. Using this approach, a number of phosphorothioate impurities can be detected by LC-FTMS including failure sequences carrying 3'-terminal phosphate monoester and 3'-terminal phosphorothioate monoester, incomplete backbone sulfurization and desulfurization products, high molecular weight impurities, and chloral, isobutyryl, and N(3) (2-cyanoethyl) adducts of the full

  10. Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides

    Science.gov (United States)

    Bertoni, Carmen; Rustagi, Arjun; Rando, Thomas A.

    2009-01-01

    Gene editing mediated by oligonucleotides has been shown to induce stable single base alterations in genomic DNA in both prokaryotic and eukaryotic organisms. However, the low frequencies of gene repair have limited its applicability for both basic manipulation of genomic sequences and for the development of therapeutic approaches for genetic disorders. Here, we show that single-stranded oligodeoxynucleotides (ssODNs) containing a methyl-CpG modification and capable of binding to the methyl-CpG binding domain protein 4 (MBD4) are able to induce >10-fold higher levels of gene correction than ssODNs lacking the specific modification. Correction was stably inherited through cell division and was confirmed at the protein, transcript and genomic levels. Downregulation of MBD4 expression using RNAi prevented the enhancement of gene correction efficacy obtained using the methyl-CpG-modified ssODN, demonstrating the specificity of the repair mechanism being recruited. Our data demonstrate that efficient manipulation of genomic targets can be achieved and controlled by the type of ssODN used and by modulation of the repair mechanism involved in the correction process. This new generation of ssODNs represents an important technological advance that is likely to have an impact on multiple applications, especially for gene therapy where permanent correction of the genetic defect has clear advantages over viral and other nonviral approaches currently being tested. PMID:19854937

  11. The Preparation of New Phosphorus-Centered Functional Groups for Modified Oligonucleotides and Other Natural Phosphates

    Directory of Open Access Journals (Sweden)

    S. Piettre

    2005-09-01

    Full Text Available Efforts to develop synthetic methodologies allowing the preparation of α,α– difluorophosphonothioates, α,α–difluorophosphonodithioates, α,α–difluorophosphono- trithioates, and α,α–difluorophosphinates are reviewed in the light of applications in the field of modified oligonucleotides and cyclitol phosphates. Two successful approaches have been developed, based either on the addition of phosphorus-centered radicals onto gem–difluoroalkenes or on a process involving the addition of lithiodifluorophosphono- thioates 91 onto a ketone and the subsequent deoxygenation reaction of the adduct. The radical route successfully developed a practical route to α,α–difluoro–H–phosphinates which proved to be useful intermediates to a variety of phosphate isosters. The ionic route led to the first preparation of phosphonodifluoromethyl analogues of nucleoside– 3’–phosphates.

  12. [Identification of genetically modified vegetable sources in food and feed using hydrogel oligonucleotide microchip].

    Science.gov (United States)

    Griadunov, D A; Getman, I A; Chizhova, S I; Mikhaĭlovich, V M; Zasedatelev, A S; Romanov, G A

    2011-01-01

    A method of multiplex polymerase chain reaction (PCR) followed by the hybridization on a hydrogel oligonucleotide biochip was developed for simultaneous identification of ten different transgenic elements of plant DNA in feed and food products. The biochip contained 22 immobilized probes intended for (i) detection of plant DNA; (ii) plant species determination (soybean, maize, potato, rice); (iii) identification of transgenic elements, including 35S CaMV, 35S FMV, rice actine gene promoters, nos, 35S CaMV, ocs, pea rbcS1 gene terminators, and bar, gus, nptII marker genes. The limit of detection was 0.5% of genetically modified (GM) soybean and maize in analyzed samples. Identification of transgenic DNA in food and feed products using either the developed approach or real-time PCR led to virtually identical results. The assay can be used for selection of GM samples by screening food and feed products for subsequent quantitative determination of the GM component based on the identified transgene.

  13. SINGLE CELL DEGENERATE OLIGONUCLEOTIDE PRIMER-PCR AND COMPARATIVE GENOMIC HYBRIDIZATION WITH MODIFIED CONTROL REFERENCE

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    For investigating the possibility of applying degenerate oligonucleotide primer PCR (DOP-PCR) and comparative genomic hybridization (CGH) technique to analyses of genomic genetics in a single cell, the whole genomic DNA of a single cell with XX, XY, XO, XXY, +13 or +21 was amplified by DOP-PCR. Single cell DOP-PCR CGHs with conventional and modified control references, the genomic DNA and a single cell DOP-PCR product from normal male, were carried out respectively. The results showed that the average profile of the fluorescence intensity ratio in CGH with the genomic DNA as reference fluctuates much and that the standard deviation in about 30% haploid is beyond the normal limits. False positive hyper-representation was found to exist in X chromosome while trisomy 13 and 21 were not detected. However, the distributions of the mean and the standard deviation of the ratio in the CGH with DOP-PCR product as reference were quite acceptable. The copy number changes of chromosome X,Y,13 and 21 were revealed. Those results suggested that there is unrandom unequal amplification in a single cell DOP-PCR. Using a single DOP-PCR product as reference can decrease its influence on CGH. Single cell DOP-PCR-CGH and its application in the genetic analyses of preimplantation embryo or fetal cell in maternal blood may be possible.

  14. Transfection and mutagenesis of target genes in mosquito cells by locked nucleic acid-modified oligonucleotides.

    Science.gov (United States)

    Pakpour, Nazzy; Cheung, Kong Wai; Souvannaseng, Lattha; Concordet, Jean-Paul; Luckhart, Shirley

    2010-12-26

    Plasmodium parasites, the causative agent of malaria, are transmitted through the bites of infected Anopheles mosquitoes resulting in over 250 million new infections each year. Despite decades of research, there is still no vaccine against malaria, highlighting the need for novel control strategies. One innovative approach is the use of genetically modified mosquitoes to effectively control malaria parasite transmission. Deliberate alterations of cell signaling pathways in the mosquito, via targeted mutagenesis, have been found to regulate parasite development (1). From these studies, we can begin to identify potential gene targets for transformation. Targeted mutagenesis has traditionally relied upon the homologous recombination between a target gene and a large DNA molecule. However, the construction and use of such complex DNA molecules for generation of stably transformed cell lines is costly, time consuming and often inefficient. Therefore, a strategy using locked nucleic acid-modified oligonucleotides (LNA-ONs) provides a useful alternative for introducing artificial single nucleotide substitutions into episomal and chromosomal DNA gene targets (reviewed in (2)). LNA-ON-mediated targeted mutagenesis has been used to introduce point mutations into genes of interest in cultured cells of both yeast and mice (3,4). We show here that LNA-ONs can be used to introduce a single nucleotide change in a transfected episomal target that results in a switch from blue fluorescent protein (BFP) expression to green fluorescent protein (GFP) expression in both Anopheles gambiae and Anopheles stephensi cells. This conversion demonstrates for the first time that effective mutagenesis of target genes in mosquito cells can be mediated by LNA-ONs and suggests that this technique may be applicable to mutagenesis of chromosomal targets in vitro and in vivo.

  15. Exploiting Protected Maleimides to Modify Oligonucleotides, Peptides and Peptide Nucleic Acids

    Directory of Open Access Journals (Sweden)

    Clément Paris

    2015-04-01

    Full Text Available This manuscript reviews the possibilities offered by 2,5-dimethylfuran-protected maleimides. Suitably derivatized building blocks incorporating the exo Diels-Alder cycloadduct can be introduced at any position of oligonucleotides, peptide nucleic acids, peptides and peptoids, making use of standard solid-phase procedures. Maleimide deprotection takes place upon heating, which can be followed by either Michael-type or Diels-Alder click conjugation reactions. However, the one-pot procedure in which maleimide deprotection and conjugation are simultaneously carried out provides the target conjugate more quickly and, more importantly, in better yield. This procedure is compatible with conjugates involving oligonucleotides, peptides and peptide nucleic acids. A variety of cyclic peptides and oligonucleotides can be obtained from peptide and oligonucleotide precursors incorporating protected maleimides and thiols.

  16. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases

    Directory of Open Access Journals (Sweden)

    Jean-Baptiste Renaud

    2016-03-01

    Full Text Available Genome editing has now been reported in many systems using TALEN and CRISPR-Cas9 nucleases. Precise mutations can be introduced during homology-directed repair with donor DNA carrying the wanted sequence edit, but efficiency is usually lower than for gene knockout and optimal strategies have not been extensively investigated. Here, we show that using phosphorothioate-modified oligonucleotides strongly enhances genome editing efficiency of single-stranded oligonucleotide donors in cultured cells. In addition, it provides better design flexibility, allowing insertions more than 100 bp long. Despite previous reports of phosphorothioate-modified oligonucleotide toxicity, clones of edited cells are readily isolated and targeted sequence insertions are achieved in rats and mice with very high frequency, allowing for homozygous loxP site insertion at the mouse ROSA locus in particular. Finally, when detected, imprecise knockin events exhibit indels that are asymmetrically positioned, consistent with genome editing taking place by two steps of single-strand annealing.

  17. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

    DEFF Research Database (Denmark)

    El-Sayed, Ahmed Ali; Pedersen, Erik B.; Khaireldin, Nahid Y.

    2016-01-01

    In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion of naphtha......In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion...... of naphthalimide (1H-benzo[de]isoquinoline-1,3(2H)-dione) as the intercalating nucleic acid. The stabilities of i-motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding...... and non-crowding). This study indicated a positive effect of the naphthalimide intercalating nucleotides on the stabilities of the i-motif structures compared to the wild-type structure which is in contrast to a previous observation for a pyrene-intercalating nucleotide showing a decrease in Tm values....

  18. 2'-O-[2-[2-(N,N-Dimethylamino)ethoxy]ethyl] Modified Antisense Oligonucleotides: Symbiosis of Charge Interaction Factors and Stereoelectronic Effects

    Energy Technology Data Exchange (ETDEWEB)

    Prhavc, M.; Prakash, T.P.; Minasov, G.; Egli, M.; Manoharan, M. (Vanderbilt)

    2010-03-08

    Oligonucleotides with a novel, 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] (2'-O-DMAEOE) modification have been synthesized. This modification, a cationic analogue of the 2'-O-(2-methoxyethyl) (2'-O-MOE) modification, exhibits high binding affinity to target RNA (but not to DNA) and exceptional resistance to nuclease degradation. Analysis of the crystal structure of a self-complementary oligonucleotide containing a single 2'-O-DMAEOE modification explains the importance of charge factors and gauche effects on the observed antisense properties. 2'-O-DMAEOE modified oligonucleotides are ideal candidates for antisense drugs.

  19. Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes

    Indian Academy of Sciences (India)

    Ying Yan; Jing Yan; Xianyu Piao; Tianbiao Zhang; Yifu Guan

    2012-06-01

    Locked nucleic acid (LNA) and 2′--methyl nucleotide (OMeN) are the most extensively studied nucleotide analogues. Although both LNA and OMeN are characterized by the C3′-endo sugar pucker conformation, which is dominant in A-form DNA and RNA nucleotides, they demonstrate different binding behaviours. Previous studies have focused attention on their properties of duplex stabilities, hybridization kinetics and resistance against nuclease digestion; however, their ability to discriminate mismatched hybridizations has been explored much less. In this study, LNA- and OMeN-modified oligonucleotide probes have been prepared and their effects on the DNA duplex stability have been examined: LNA modifications can enhance the duplex stability, whereas OMeN modifications reduce the duplex stability. Next, we studied how the LNA:DNA and OMeN:DNA mismatches reduced the duplex stability. Melting temperature measurement showed that different LNA:DNA or OMeN:DNA mismatches indeed influence the duplex stability differently. LNA purines can discriminate LNA:DNA mismatches more effectively than LNA pyrimidines as well as DNA nucleotides. Furthermore, we designed five LNA- and five OMeN-modified oligonucleotide probes to simulate realistic situations where target–probe duplexes contain a complementary LNA:DNA or OMeN:DNA base pairs and a DNA:DNA mismatch simultaneously. The measured collective effect showed that the duplex stability was enhanced by the complementary LNA:DNA base pair but decreased by the DNA:DNA mismatch in a position-dependent manner regardless of the chemical identity and position of the complementary LNA:DNA base pair. On the other hand, the OMeN-modified probes also showed that the duplex stability was reduced by both the OMeN modification and the OMeN:DNA mismatch in a position-dependent manner.

  20. Synthesis, hybridization characteristics, and fluorescence properties of oligonucleotides modified with nucleobase-functionalized locked nucleic acid adenosine and cytidine monomers.

    Science.gov (United States)

    Kaura, Mamta; Kumar, Pawan; Hrdlicka, Patrick J

    2014-07-03

    Conformationally restricted nucleotides such as locked nucleic acid (LNA) are very popular as affinity-, specificity-, and stability-enhancing modifications in oligonucleotide chemistry to produce probes for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. Considerable efforts have been devoted in recent years to optimize the biophysical properties of LNA through additional modification of the sugar skeleton. We recently introduced C5-functionalization of LNA uridines as an alternative and synthetically more straightforward approach to improve the biophysical properties of LNA. In the present work, we set out to test the generality of this concept by studying the characteristics of oligonucleotides modified with four different C5-functionalized LNA cytidine and C8-functionalized LNA adenosine monomers. The results strongly suggest that C5-functionalization of LNA pyrimidines is indeed a viable approach for improving the binding affinity, target specificity, and/or enzymatic stability of LNA-modified ONs, whereas C8-functionalization of LNA adenosines is detrimental to binding affinity and specificity. These insights will impact the future design of conformationally restricted nucleotides for nucleic acid targeting applications.

  1. Inhibitory effect of 2 '-o-methoxyethyl-modified antisense oligonucleotides targeting vascular endothelial growth factor A on SKOV3 human ovarian cancer cells

    Institute of Scientific and Technical Information of China (English)

    FU Yi-bing; WEN Ze-qing; ZHAO Xing-bo; YAN Lei; ZHANG Chun-hua; WANG Fei

    2011-01-01

    Background Ovarian cancers are often at an advanced stage at diagnosis because early detection is difficult. The poor prognosis of ovarian cancers highlights the crucial need to develop better therapeutic agents and strategies. The objective of this study was to investigate the inhibitory effects of a new modified antisense oligonucleotides targeting vascular endothelial growth factor A (VEGF-A) in SKOV3 ovarian cancer cells.Methods Antisense oligonucleotides targeting VEGF-A was designed, synthesized and transfected into SKOV3ovarian cancer cells. Western blotting and real-time RT-PCR were used to analyze the inhibitory effects of antisense oligonucleotides on VEGF-A protein and mRNA expression. Transwell matrix assay was used to detect cell migration inhibition.Results The antisense oligonucleotides targeting VEGF-A significantly decreased VEGF-A protein and mRNA expression and inhibited cell migration in SKOV3 ovarian cancer cells.Conclusions This new modified antisense oligonucleotides targeting VEGF-A can decrease VEGF-A expression and inhibit cell migration in SKOV3 ovarian cancer cells. This new oligonucleotides may be a promising therapeutic agent for ovarian cancers.

  2. Optical Properties and In Vitro Biological Studies of Oligonucleotide-Modified Quantum Dots

    Directory of Open Access Journals (Sweden)

    Valérie A. Gérard

    2013-01-01

    Full Text Available Water-soluble semiconducting nanocrystals or quantum dots (QDs have attracted much interest in recent years due to their tuneable emission and potential applications in photonics and biological imaging. Fluorescence resonance energy transfer (FRET processes are very important for elucidating biochemical mechanisms in vitro, and QDs constitute an excellent substrate for this purpose. In this work, new oligonucleotide-functionalised CdTe-based QDs were prepared, characterised and biologically tested. These QDs demonstrated interesting optical properties as well as remarkable in vitro behaviour and potential for a range of biological applications.

  3. Chemically robust fluoroalkyl phthalocyanine-oligonucleotide bioconjugates and their GRP78 oncogene photocleavage activity.

    Science.gov (United States)

    Patel, Pradeepkumar; Patel, Hemantbhai H; Borland, Emily; Gorun, Sergiu M; Sabatino, David

    2014-06-18

    The first representative of functionalized fluoroalkyl phthalocyanines, F48H7(COOH)PcZn, is reported. The complex generates (1)O2 affording long-lasting photooxidation of an external substrate without self-decomposition. The carboxylic group couples with an antisense oligonucleotide targeting GRP78 oncogenes, resulting in the F48H7PcZn-cancer targeting oligonucleotide (CTO). The bioconjugated fluorophthalocyanine effectively hybridizes complementary GRP78 DNA and mRNA sequences. Piperidine cleavage assays reveal desired photochemical oligonucleotide oxidative degradation for both F48H7PcZn-CTO:DNA and F48H7PcZn-CTO:mRNA hybrids. This new materials strategy could be extended to other functional fluorinated phthalocyanines-antisense oligonucleotide combinations for long-lasting oncogene-targeting photodynamic therapy.

  4. Selective binding of oligonucleotide on TiO{sub 2} surfaces modified by swift heavy ion beam lithography

    Energy Technology Data Exchange (ETDEWEB)

    Vicente Pérez-Girón, J. [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Emerging Viruses Department Heinrich Pette Institute, Hamburg 20251 (Germany); Hirtz, M. [Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology - KIT, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); McAtamney, C.; Bell, A.P. [Advanced Microscopy Laboratory, CRANN, Trinity College Dublin, Dublin 2 (Ireland); Antonio Mas, J. [Laboratorio de Genómica del Centro de Apoyo Tecnológico, Universidad Rey Juan Carlos, Campus de Alcorcón 28922, Madrid (Spain); Jaafar, M. [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain); Luis, O. de [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Departamento de Bioquímica, Fisiología y Genética Molecular, Facultad de Ciencias de la Salud, Universidad Rey Juan Carlos, Campus de Alcorcón, 28922 Madrid (Spain); Fuchs, H. [Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology - KIT, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Physical Institute and Center for Nanotechnology (CeNTech), Wilhelm-Klemm-Straße 10, University of Münster (Germany); and others

    2014-11-15

    We have used swift heavy-ion beam based lithography to create patterned bio-functional surfaces on rutile TiO{sub 2} single crystals. The applied lithography method generates a permanent and well defined periodic structure of micrometre sized square holes having nanostructured TiO{sub 2} surfaces, presenting different physical and chemical properties compared to the surrounding rutile single crystal surface. On the patterned substrates selective binding of oligonucleotides molecules is possible at the surfaces of the holes. This immobilisation process is only being controlled by UV light exposure. The patterned transparent substrates are compatible with fluorescence detection techniques, are mechanically robust, have a high tolerance to extreme chemical and temperature environments, and apparently do not degrade after ten cycles of use. These qualities make the patterned TiO{sub 2} substrates useful for potential biosensor applications.

  5. Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

    Science.gov (United States)

    Samuelsen, Simone V.; Solov'Yov, Ilia A.; Balboni, Imelda M.; Mellins, Elizabeth; Nielsen, Christoffer Tandrup; Heegaard, Niels H. H.; Astakhova, Kira

    2016-10-01

    New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies.

  6. Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

    Science.gov (United States)

    Samuelsen, Simone V.; Solov’yov, Ilia A.; Balboni, Imelda M.; Mellins, Elizabeth; Nielsen, Christoffer Tandrup; Heegaard, Niels H. H.; Astakhova, Kira

    2016-01-01

    New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies. PMID:27775006

  7. Universal strategies for the DNA-encoding of libraries of small molecules using the chemical ligation of oligonucleotide tags.

    Science.gov (United States)

    Litovchick, Alexander; Clark, Matthew A; Keefe, Anthony D

    2014-01-01

    The affinity-mediated selection of large libraries of DNA-encoded small molecules is increasingly being used to initiate drug discovery programs. We present universal methods for the encoding of such libraries using the chemical ligation of oligonucleotides. These methods may be used to record the chemical history of individual library members during combinatorial synthesis processes. We demonstrate three different chemical ligation methods as examples of information recording processes (writing) for such libraries and two different cDNA-generation methods as examples of information retrieval processes (reading) from such libraries. The example writing methods include uncatalyzed and Cu(I)-catalyzed alkyne-azide cycloadditions and a novel photochemical thymidine-psoralen cycloaddition. The first reading method "relay primer-dependent bypass" utilizes a relay primer that hybridizes across a chemical ligation junction embedded in a fixed-sequence and is extended at its 3'-terminus prior to ligation to adjacent oligonucleotides. The second reading method "repeat-dependent bypass" utilizes chemical ligation junctions that are flanked by repeated sequences. The upstream repeat is copied prior to a rearrangement event during which the 3'-terminus of the cDNA hybridizes to the downstream repeat and polymerization continues. In principle these reading methods may be used with any ligation chemistry and offer universal strategies for the encoding (writing) and interpretation (reading) of DNA-encoded chemical libraries.

  8. Diffusion of Oligonucleotides from within Iron-Crosslinked Polyelectrolyte-Modified Alginate Beads: A Model System for Drug Release

    CERN Document Server

    Privman, Vladimir; Luz, Roberto A S; Guz, Nataliia; Glasser, M Lawrence; Katz, Evgeny

    2016-01-01

    We developed and experimentally verified an analytical model to describe diffusion of oligonucleotides from stable hydrogel beads. The synthesized alginate beads are Fe3+-cross-linked as well as polyelectrolyte-doped for uniformity and stability at physiological pH. Data on diffusion of oligonucleotides from inside the beads provide physical insights into the volume nature of the immobilization of a fraction of oligonucleotides due to polyelectrolyte cross-linking, i.e., the absence of the surface-layer barrier in this case. Furthermore, our results suggest a new simple approach to measuring the diffusion coefficient of the mobile oligonucleotide molecules inside hydrogel. The considered alginate beads provide a model for a well-defined component in drug release systems and for the oligonucleotide-release transduction steps in drug-delivering and biocomputing applications. This is illustrated by destabilizing the beads with citrate that induces full oligonucleotide release with non-diffusional kinetics.

  9. Systematic evaluation and optimization of modification reactions of oligonucleotides with amines and carboxylic acids for the synthesis of DNA-encoded chemical libraries.

    Science.gov (United States)

    Franzini, Raphael M; Samain, Florent; Abd Elrahman, Maaly; Mikutis, Gediminas; Nauer, Angela; Zimmermann, Mauro; Scheuermann, Jörg; Hall, Jonathan; Neri, Dario

    2014-08-20

    DNA-encoded chemical libraries are collections of small molecules, attached to DNA fragments serving as identification barcodes, which can be screened against multiple protein targets, thus facilitating the drug discovery process. The preparation of large DNA-encoded chemical libraries crucially depends on the availability of robust synthetic methods, which enable the efficient conjugation to oligonucleotides of structurally diverse building blocks, sharing a common reactive group. Reactions of DNA derivatives with amines and/or carboxylic acids are particularly attractive for the synthesis of encoded libraries, in view of the very large number of building blocks that are commercially available. However, systematic studies on these reactions in the presence of DNA have not been reported so far. We first investigated conditions for the coupling of primary amines to oligonucleotides, using either a nucleophilic attack on chloroacetamide derivatives or a reductive amination on aldehyde-modified DNA. While both methods could be used for the production of secondary amines, the reductive amination approach was generally associated with higher yields and better purity. In a second endeavor, we optimized conditions for the coupling of a diverse set of 501 carboxylic acids to DNA derivatives, carrying primary and secondary amine functions. The coupling efficiency was generally higher for primary amines, compared to secondary amine substituents, but varied considerably depending on the structure of the acids and on the synthetic methods used. Optimal reaction conditions could be found for certain sets of compounds (with conversions >80%), but multiple reaction schemes are needed when assembling large libraries with highly diverse building blocks. The reactions and experimental conditions presented in this article should facilitate the synthesis of future DNA-encoded chemical libraries, while outlining the synthetic challenges that remain to be overcome.

  10. Electrochemical biosensors for detection of point mutation based on surface ligation reaction and oligonucleotides modified gold nanoparticles.

    Science.gov (United States)

    Wang, Qing; Yang, Lijuan; Yang, Xiaohai; Wang, Kemin; He, Leiliang; Zhu, Jinqing

    2011-03-04

    An electrochemical method for point mutation detection based on surface ligation reaction and oligonucleotides (ODNs) modified gold nanoparticles (AuNPs) was demonstrated. Point mutation identification was achieved using Escherichia coli DNA ligase. This system for point mutation detection relied on a sandwich assay comprising capture ODN immobilized on Au electrodes, target ODN and ligation ODN. Because of the sequence-specific surface reactions of E. coli DNA ligase, the ligation ODN covalently linked to the capture ODN only in the presence of a perfectly complementary target ODN. The presence of ligation products on Au electrode was detected using chronocoulometry through hybridization with reporter ODN modified AuNPs. The use of AuNPs improved the sensitivity of chronocoulometry in this approach, a detection limit of 0.9 pM complementary ODN was obtained. For single base mismatched ODN (smODN), a negligible signal was observed. Even if the concentration ratio of complementary ODN to smODN was decreased to 1:1000, a detectable signal was observed. This work may provide a specific, sensitive and cost-efficient approach for point mutant detection.

  11. Pharmacokinetics, biodistribution and cell uptake of antisense oligonucleotides.

    Science.gov (United States)

    Geary, Richard S; Norris, Daniel; Yu, Rosie; Bennett, C Frank

    2015-06-29

    Pharmacokinetic properties of oligonucleotides are largely driven by chemistry of the backbone and thus are sequence independent within a chemical class. Tissue bioavailability (% of administered dose) is assisted by plasma protein binding that limits glomerular filtration and ultimate urinary excretion of oligonucleotides. The substitution of one non-bridging oxygen with the more hydrophobic sulfur atom (phosphorothioate) increases both plasma stability and plasma protein binding and thus, ultimately, tissue bioavailability. Additional modifications of the sugar at the 2' position, increase RNA binding affinity and significantly increase potency, tissue half-life and prolong RNA inhibitory activity. Oligonucleotides modified in this manner consistently exhibit the highest tissue bioavailability (>90%). Systemic biodistribution is broad, and organs typically with highest concentrations are liver and kidney followed by bone marrow, adipocytes, and lymph nodes. Cell uptake is predominantly mediated by endocytosis. Both size and charge for most oligonucleotides prevents distribution across the blood brain barrier. However, modified single-strand oligonucleotides administered by intrathecal injection into the CSF distribute broadly in the CNS. The majority of intracellular oligonucleotide distribution following systemic or local administration occurs rapidly in just a few hours following administration and is facilitated by rapid endocytotic uptake mechanisms. Further understanding of the intracellular trafficking of oligonucleotides may provide further enhancements in design and ultimate potency of antisense oligonucleotides in the future. Copyright © 2015. Published by Elsevier B.V.

  12. Evaluation of Amphiphilic Peptide Modified Antisense Morpholino Oligonucleotides In Vitro and in Dystrophic mdx Mice

    OpenAIRE

    Mingxing Wang; Bo Wu; Peijuan Lu; Shah, Sapana N.; Jason D. Tucker; Lauren E. Bollinger; Qilong Lu

    2017-01-01

    A series of amphiphilic peptides modified PMO (Pt-PMO) were prepared, and their antisense effect and toxicity were evaluated both in vitro and in mdx mice. The results showed that the exon-skipping performance of Pt-PMO are relative to the structure of the conjugated peptide: the Pt3/Pt4 composed of six/seven arginines and one myristoylation modified PMO showed more efficacy and with less toxicity as compared to others, confirming that appropriate hydrophilic-lipophilic balance (HLB) and cati...

  13. Synthesis and properties of carbohydrate-phosphate backbone-modified oligonucleotide analogues and nucleic acid mimetics

    Energy Technology Data Exchange (ETDEWEB)

    Abramova, Tatyana V; Silnikov, Vladimir N [Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (Russian Federation)

    2011-05-31

    Advances in the synthesis of oligo(deoxy)ribonucleotide analogues and nucleic acid mimetics made in the last decade are summarized. Attention is focused on new methods for the synthesis of derivatives with a modified ribose-phosphate backbone (phosphorothioate, boranophosphate, and nucleoside phosphonate derivatives) and derivatives devoid of the phosphate group. Among nucleic acid mimetics, conformationally restricted modified peptide nucleic acids, including those bearing a negative or positive charge, and morpholino oligomers are considered. Advantages and drawbacks of the main types of analogues as regards the complexity of the synthesis and the possibility of their application as antisense agents or reagents for hybridization analysis are compared.

  14. Synthesis and properties of carbohydrate-phosphate backbone-modified oligonucleotide analogues and nucleic acid mimetics

    Science.gov (United States)

    Abramova, Tatyana V.; Silnikov, Vladimir N.

    2011-05-01

    Advances in the synthesis of oligo(deoxy)ribonucleotide analogues and nucleic acid mimetics made in the last decade are summarized. Attention is focused on new methods for the synthesis of derivatives with a modified ribose-phosphate backbone (phosphorothioate, boranophosphate, and nucleoside phosphonate derivatives) and derivatives devoid of the phosphate group. Among nucleic acid mimetics, conformationally restricted modified peptide nucleic acids, including those bearing a negative or positive charge, and morpholino oligomers are considered. Advantages and drawbacks of the main types of analogues as regards the complexity of the synthesis and the possibility of their application as antisense agents or reagents for hybridization analysis are compared.

  15. Synthesis and Structural Characterization of 2'-Fluoro-α-L-RNA-Modified Oligonucleotides

    DEFF Research Database (Denmark)

    Bundgaard Jensen, Troels; Pasternak, Anna; Stahl Madsen, Andreas

    2011-01-01

    -α-L-RNA monomer was designed as a monocyclic mimic of the bicyclic α-L-LNA, and molecular modeling showed that this indeed is the case as the 2'-fluoro monomer adopts a C3'-endo/C2'-exo sugar pucker. Molecular modeling of modified duplexes show that the 2'-fluoro-α-L-RNA nucleotides partake in Watson-Crick base...

  16. Gene suppression via U1 small nuclear RNA interference (U1i) machinery using oligonucleotides containing 2'-modified-4'-thionucleosides.

    Science.gov (United States)

    Kikuchi, Yusaku; Yamazaki, Naoshi; Tarashima, Noriko; Furukawa, Kazuhiro; Takiguchi, Yoshiharu; Itoh, Kohji; Minakawa, Noriaki

    2013-09-01

    Gene suppression via U1 small nuclear RNA interference (U1i) is considered to be one of the most attractive approaches, and takes the place of general antisense, RNA interference (RNAi), and anti-micro RNA machineries. Since the U1i can be induced by short oligonucleotides (ONs), namely U1 adaptors consisting of a 'target domain' and a 'U1 domain', we prepared adaptor ONs using 2'-modified-4'-thionucleosides developed by our group, and evaluated their U1i activity. As a result, the desired gene suppression via U1i was observed in ONs prepared as a combination of 2'-fluoro-4'-thionucleoside and 2'-fluoronucleoside units as well as only 2'-fluoronucleoside units, while those prepared as combination of 2'-OMe nucleoside/2'-OMe-4'-thionucleoside and 2'-fluoronucleoside units did not show significant activity. Measurement of Tm values indicated that a higher hybridization ability of adaptor ONs with complementary RNA is one of the important factors to show potent U1i activity.

  17. Binding specificity and stability of duplexes formed by modified oligonucleotides with a 4096-hexanucleotide microarray

    Science.gov (United States)

    Timofeev, Edward; Mirzabekov, Andrei

    2001-01-01

    The binding of oligodeoxynucleotides modified with adenine 2′-O-methyl riboside, 2,6-diaminopurine 2′-O-methyl riboside, cytosine 2′-O-methyl riboside, 2,6-diaminopurine deoxyriboside or 5-bromodeoxyuridine was studied with a microarray containing all possible (4096) polyacrylamide-bound hexadeoxynucleotides (a generic microchip). The generic microchip was manufactured by using reductive immobilization of aminooligonucleotides in the activated copolymer of acrylamide, bis-acrylamide and N-(2,2-dimethoxyethyl) acrylamide. The binding of the fluorescently labeled modified octanucleotides to the array was analyzed with the use of both melting profiles and the fluorescence distribution at selected temperatures. Up to three substitutions of adenosines in the octamer sequence by adenine 2′-O-methyl ribosides (Am), 2,6-diaminopurine 2′-O-methyl ribosides (Dm) or 2,6-diaminopurine deoxyribosides (D) resulted in increased mismatch discrimination measured at the melting temperature of the corresponding perfect duplex. The stability of complexes formed by 2′-O-methyl-adenosine-modified oligodeoxynucleotides was slightly decreased with every additional substitution, yielding ∼4°C of total loss in melting temperature for three modifications, as followed from microchip thermal denaturation experiments. 2,6-Diaminopurine 2′-O-methyl riboside modifications led to considerable duplex stabilization. The cytosine 2′-O-methyl riboside and 5-bromodeoxyuridine modifications generally did not change either duplex stability or mismatch resolution. Denaturation experiments conducted with selected perfect duplexes on microchips and in solution showed similar results on thermal stabilities. Some hybridization artifacts were observed that might indicate the formation of parallel DNA. PMID:11410672

  18. Screening genetically modified organisms using multiplex-PCR coupled with oligonucleotide microarray.

    Science.gov (United States)

    Xu, Jia; Miao, Haizhen; Wu, Houfei; Huang, Wensheng; Tang, Rong; Qiu, Minyan; Wen, Jianguo; Zhu, Shuifang; Li, Yao

    2006-07-15

    In this research, we developed a multiplex polymerase chain reaction (multiplex-PCR) coupled with a DNA microarray system simultaneously aiming at many targets in a consecutive reaction to detect a genetically modified organism (GMO). There are a total of 20 probes for detecting a GMO in a DNA microarray which can be classified into three categories according to their purpose: the first for screening GMO from un-transgenic plants based on the common elements such as promoter, reporter and terminator genes; the second for specific gene confirmation based on the target gene sequences such as herbicide-resistance or insect-resistance genes; the third for species-specific genes which the sequences are unique for different plant species. To ensure the reliability of this method, different kinds of positive and negative controls were used in DNA microarray. Commercial GM soybean, maize, rapeseed and cotton were identified by means of this method and further confirmed by PCR analysis and sequencing. The results indicate that this method discriminates between the GMOs very quickly and in a cost-saving and more time efficient way. It can detect more than 95% of currently commercial GMO plants and the limits of detection are 0.5% for soybean and 1% for maize. This method is proved to be a new method for routine analysis of GMOs.

  19. Quality of chemically modified hemp fibers.

    Science.gov (United States)

    Kostic, Mirjana; Pejic, Biljana; Skundric, Petar

    2008-01-01

    Hemp fibers are very interesting natural material for textile and technical applications now. Applying hemp fibers to the apparel sector requires improved quality fibers. In this paper, hemp fibers were modified with sodium hydroxide solutions (5% and 18% w/v), at room and boiling temperature, for different periods of time, and both under tension and slack, in order to partially extract noncellulosic substances, and separate the fiber bundles. The quality of hemp fibers was characterised by determining their chemical composition, fineness, mechanical and sorption properties. The modified hemp fibers were finer, with lower content of lignin, increased flexibility, and in some cases tensile properties were improved. An original method for evaluation of tensile properties of hemp fibers was developed.

  20. Encoded libraries of chemically modified peptides.

    Science.gov (United States)

    Heinis, Christian; Winter, Greg

    2015-06-01

    The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries.

  1. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies.

    Science.gov (United States)

    Lipi, Farhana; Chen, Suxiang; Chakravarthy, Madhuri; Rakesh, Shilpa; Veedu, Rakesh N

    2016-12-01

    Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.

  2. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore

    Science.gov (United States)

    Cao, Chan; Ying, Yi-Lun; Hu, Zheng-Li; Liao, Dong-Fang; Tian, He; Long, Yi-Tao

    2016-08-01

    Protein nanopores offer an inexpensive, label-free method of analysing single oligonucleotides. The sensitivity of the approach is largely determined by the characteristics of the pore-forming protein employed, and typically relies on nanopores that have been chemically modified or incorporate molecular motors. Effective, high-resolution discrimination of oligonucleotides using wild-type biological nanopores remains difficult to achieve. Here, we show that a wild-type aerolysin nanopore can resolve individual short oligonucleotides that are 2 to 10 bases long. The sensing capabilities are attributed to the geometry of aerolysin and the electrostatic interactions between the nanopore and the oligonucleotides. We also show that the wild-type aerolysin nanopores can distinguish individual oligonucleotides from mixtures and can monitor the stepwise cleavage of oligonucleotides by exonuclease I.

  3. Functionalization of silicon oxide using supercritical fluid deposition of 3,4-epoxybutyltrimethoxysilane for the immobilization of amino-modified oligonucleotide

    Science.gov (United States)

    Rull, Jordi; Nonglaton, Guillaume; Costa, Guillaume; Fontelaye, Caroline; Marchi-Delapierre, Caroline; Ménage, Stéphane; Marchand, Gilles

    2015-11-01

    The functionalization of silicon oxide based substrates using silanes is generally performed through liquid phase methodologies. These processes involve a huge quantity of potentially toxic solvents and present some important disadvantages for the functionalization of microdevices or porous materials, for example the low diffusion. To overcome this drawback, solvent-free methodologies like molecular vapor deposition (MVD) or supercritical fluid deposition (SFD) have been developed. In this paper, the deposition process of 3,4-epoxybutyltrimethoxysilane (EBTMOS) on silicon oxide using supercritical carbon dioxide (scCO2) as a solvent is studied for the first time. The oxirane ring of epoxy silanes readily reacts with amine group and is of particular interest for the grafting of amino-modified oligonucleotides or antibodies for diagnostic application. Then the ability of this specific EBTMOS layer to react with amine functions has been evaluated using the immobilization of amino-modified oligonucleotide probes. The presence of the probes is revealed by fluorescence using hybridization with a fluorescent target oligonucleotide. The performances of SFD of EBTMOS have been optimized and then compared with the dip coating and molecular vapor deposition methods, evidencing a better grafting efficiency and homogeneity, a lower reaction time in addition to the eco-friendly properties of the supercritical carbon dioxide. The epoxysilane layers have been characterized by surface enhanced ellipsometric contrast optical technique, atomic force microscopy, multiple internal reflection infrared spectroscopy and X-ray photoelectron spectroscopy. The shelf life of the 3,4-epoxybutyltrimethoxysilane coating layer has also been studied. Finally, two different strategies of NH2-oligonucleotide grafting on EBTMOS coating layer have been compared, i.e. reductive amination and nucleophilic substitution, SN2. This EBTMOS based coating layer can be used for a wide range of applications

  4. Antitumor activity of chemical modified natural compounds

    Directory of Open Access Journals (Sweden)

    Marilda Meirelles de Oliveira

    1991-01-01

    Full Text Available Search of new activity substances starting from chemotherapeutic agents, continously appears in international literature. Perhaps this search has been done more frequently in the field of anti-tumor chemotherapy on account of the unsuccess in saving advanced stage patients. The new point in this matter during the last decade was computer aid in planning more rational drugs. In near future "the accessibility of supercomputers and emergence of computer net systems, willopen new avenues to rational drug design" (Portoghese, P. S. J. Med. Chem. 1989, 32, 1. Unknown pharmacological active compounds synthetized by plants can be found even without this eletronic devices, as tradicional medicine has pointed out in many contries, and give rise to a new drug. These compounds used as found in nature or after chemical modifications have produced successful experimental medicaments as FAA, "flavone acetic acid" with good results as inibitors of slow growing animal tumors currently in preclinical evaluation for human treatment. In this lecture some international contributions in the field of chemical modified compounds as antineoplasic drugs will be examined, particularly those done by Brazilian researches.

  5. Inhibition of microRNA with antisense oligonucleotides.

    Science.gov (United States)

    Esau, Christine C

    2008-01-01

    Antisense inhibition of microRNA (miRNA) function has been an important tool for uncovering miRNA biology. Chemical modification of anti-miRNA oligonucleotides (AMOs) is necessary to improve affinity for target miRNA, stabilize the AMO to nuclease degradation, and to promote tissue uptake for in vivo delivery. Here I summarize the work done to evaluate the effectiveness of various chemically modified AMOs for use in cultured cells and rodent models, and outline important issues to consider when inhibiting miRNAs with antisense oligonucleotides.

  6. Cellular uptake of modified oligonucleotides enhanced by porphyrins studied by time-resolved microspectrofluorimetry and fluorescence imaging techniques

    Science.gov (United States)

    Praus, P.; Kočišová, E.; Mojzeš, P.; Štěpánek, J.; Turpin, P.-Y.; Sureau, F.

    2011-05-01

    Fluorescence microimaging and homodyne phase-resolved confocal microspectrofluorimetry were used to monitor the transport of antisense oligonucleotide into 3T3 living cells and its subsequent intracellular distribution. Phosphorothioate analog of 15-mer oligothymidylate labeled by ATTO 425 was complexed with 5,10,15,20-tetrakis (1-methyl-4-pyridyl) porphyrin (H 2TMPyP4) as an uptake-mediating agent. High frequency (up to 180 MHz) analog modulation of both exciting diode laser and the detector image intensifier gain was used to record time-resolved fluorescence spectra. Fluorescence lifetime data within a broad spectral range have revealed preservation of oligonucleotide/porphyrin complex integrity and binding properties of both components inside the cell.

  7. New Concepts of Fluorescent Probes for Specific Detection of DNA Sequences: Bis-Modified Oligonucleotides in Excimer and Exciplex Detection

    Directory of Open Access Journals (Sweden)

    Gbaj A

    2009-01-01

    Full Text Available The detection of single base mismatches in DNA is important for diagnostics, treatment of genetic diseases, and identification of single nucleotide polymorphisms. Highly sensitive, specific assays are needed to investigate genetic samples from patients. The use of a simple fluorescent nucleoside analogue in detection of DNA sequence and point mutations by hybridisation in solution is described in this study. The 5’-bispyrene and 3’-naphthalene oligonucleotide probes form an exciplex on hybridisation to target in water and the 5’-bispyrene oligonucleotide alone is an adequate probe to determine concentration of target present. It was also indicated that this system has a potential to identify mismatches and insertions. The aim of this work was to investigate experimental structures and conditions that permit strong exciplex emission for nucleic acid detectors, and show how such exciplexes can register the presence of mismatches as required in SNP analysis. This study revealed that the hybridisation of 5'-bispyrenyl fluorophore to a DNA target results in formation of a fluorescent probe with high signal intensity change and specificity for detecting a complementary target in a homogeneous system. Detection of SNP mutations using this split-probe system is a highly specific, simple, and accessible method to meet the rigorous requirements of pharmacogenomic studies. Thus, it is possible for the system to act as SNP detectors and it shows promise for future applications in genetic testing.

  8. Versatile functionalization of nanoelectrodes by oligonucleotides via pyrrole electrochemistry.

    Science.gov (United States)

    Descamps, Emeline; Nguyen, Khoa; Bouchain-Gautier, Christelle; Filoramo, Arianna; Goux-Capes, Laurence; Goffman, Marcello; Bourgoin, Jean-Philippe; Mailley, Pascal; Livache, Thierry

    2010-11-15

    Surface modification at the nanometer scale is a challenge for the future of molecular electronics. In particular, the precise anchoring and electrical addressing of biological scaffolds such as complex DNA nanonetworks is of importance for generating bio-directed assemblies of nano-objects for nanocircuit purposes. Herein, we consider the individual modification of nanoelectrodes with different oligonucleotide sequences by an electrochemically driven co-polymerization process of pyrrole and modified oligonucleotide sequences bearing pyrrole monomers. We demonstrate that this one-step technique presents the advantages of simplicity, localization of surface modification, mechanical, biological and chemical stability of the coatings, and high lateral resolution.

  9. Cyclic Voltammetric Responses of Nitrate Reductase on Chemical Modified Electrodes

    Institute of Scientific and Technical Information of China (English)

    YaRuSONG; HuiBoSHAO; 等

    2002-01-01

    Electrochemistry of nitrate reductases (NR) incorporated into 2-aminoethanethiol self-assembled on the gold electrode and polyacrylamide cast on the pyrolytic graphite electrode was examined. NR on chemical modified electrode showed electrochemical cyclic voltammetric responses in phosphate buffers.

  10. Chemically modified field effect transistors with nitrite or fluoride selectivity

    NARCIS (Netherlands)

    Antonisse, Martijn M.G.; Snellink-Ruël, Bianca H.M.; Engbersen, Johan F.J.; Reinhoudt, David N.

    1998-01-01

    Polysiloxanes with different types of polar substituents are excellent membrane materials for nitrite and fluoride selective chemically modified field effect transistors (CHEMFETs). Nitrite selectivity has been introduced by incorporation of a cobalt porphyrin into the membrane; fluoride selectivity

  11. Chemically modified field effect transistors with nitrite or fluoride selectivity

    NARCIS (Netherlands)

    Antonisse, M.M.G.; Ruel, Bianca H.M.; Engbersen, Johannes F.J.; Reinhoudt, David

    1998-01-01

    Polysiloxanes with different types of polar substituents are excellent membrane materials for nitrite and fluoride selective chemically modified field effect transistors (CHEMFETs). Nitrite selectivity has been introduced by incorporation of a cobalt porphyrin into the membrane; fluoride selectivity

  12. Chemical and semisynthesis of modified histones.

    Science.gov (United States)

    Maity, Suman Kumar; Jbara, Muhammad; Brik, Ashraf

    2016-05-01

    Post-translational modifications (PTMs) of histones play critical roles in the epigenetic regulation of eukaryotic genome by directly altering the biophysical properties of chromatin or by recruiting effector proteins. The large number of PTMs and the inherent complexity in their population and signaling processes make it highly challenging to understand epigenetics-related processes. To address these challenges, accesses to homogeneously modified histones are obligatory. Over the last decade, synthetic protein chemists have been devising novel synthetic tools and applying state-of-the-art chemoselective ligation strategies to prepare precious materials useful in answering fundamental questions in this area. In this short review, we cover some of the recent breakthroughs in these directions in particular the synthesis and semi-synthesis of modified histones and their use to unravel the mysteries of epigenetics. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

  13. Antisense oligonucleotides in cancer.

    Science.gov (United States)

    Castanotto, Daniela; Stein, Cy A

    2014-11-01

    Over the past several dozen years, regardless of the substantial effort directed toward developing rational oligonucleotide strategies to silence gene expression, antisense oligonucleotide-based cancer therapy has not been successful. This review focuses on the most likely reasons for this lack of success, and on the barriers that still need to be overcome to make a clinical cancer treatment reality out of the promise of antisense therapy. Considerable progress has been made in the design and delivery of nucleic acid fragments. Chemical modifications have considerably improved oligonucleotide absorption, distribution and metabolism while at the same time reducing toxicity. Nevertheless, the delivery and the cellular uptake of these molecules are still not adequate to provide the desired therapeutic outcome. Recent therapeutic interventional phase III trials of antisense oligodeoxyribonucleotides for a cancer indication will be discussed, in addition to those studies that markedly improve the scientific understanding of the properties of these molecules. We still do not have a marketed antisense oligonucleotide for a cancer indication. This is because critical aspects of the cellular, tumor pharmacology and delivery properties of these agents are still not well understood.

  14. Development of a Method for Profiling Protein Interactions with LNA-Modified Antisense Oligonucleotides Using Protein Microarrays.

    Science.gov (United States)

    Kakiuchi-Kiyota, Satoko; Whiteley, Lawrence O; Ryan, Anne M; Mathialagan, Nagappan

    2016-04-01

    Development of locked nucleic acid (LNA) gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by nontarget-mediated hepatotoxicity. Increased binding of hepatocellular proteins to toxic LNA gapmers may be one of the mechanisms contributing to LNA gapmer-induced hepatotoxicity in vivo. In the present study, we investigated the protein binding propensity of nontoxic sequence-1 (NTS-1), toxic sequence-2 (TS-2), and severely highly toxic sequence-3 (HTS-3) LNA gapmers using human protein microarrays. We previously demonstrated by the transcription profiling analysis of liver RNA isolated from mice that TS-2 and HTS-3 gapmers modulate different transcriptional pathways in mice leading to hepatotoxicity. Our protein array profiling demonstrated that a greater number of proteins, including ones associated with hepatotoxicity, hepatic system disorder, and cell functions, were bound by TS-2 and HTS-3 compared with NTS-1. However, the profiles of proteins bound by TS-2 and HTS-3 were similar and did not distinguish proteins contributing to severe in vivo toxicity. These results, together with the previous transcription profiling analysis, indicate that the combination of sequence-dependent transcription modulation and increased protein binding of toxic LNA gapmers contributes to hepatotoxicity.

  15. Synthesis and application of a triazene-ferrocene modifier for immobilization and characterization of oligonucleotides at electrodes.

    Science.gov (United States)

    Hansen, Majken N; Farjami, Elaheh; Kristiansen, Martin; Clima, Lilia; Pedersen, Steen Uttrup; Daasbjerg, Kim; Ferapontova, Elena E; Gothelf, Kurt V

    2010-04-16

    A new DNA modifier containing triazene, ferrocene, and activated ester functionalities was synthesized and applied for electrochemical grafting and characterization of DNA at glassy carbon (GC) and gold electrodes. The modifier was synthesized from ferrocenecarboxylic acid by attaching a phenyltriazene derivative to one of the ferrocene Cp rings, while the other Cp ring containing the carboxylic acid was converted to an activated ester. The modifier was conjugated to an amine-modified DNA sequence. For immobilization of the conjugate at Au or GC electrodes, the triazene was activated by dimethyl sulfate for release of the diazonium salt. The salt was reductively converted to the aryl radical which was readily immobilized at the surface. DNA grafted onto electrodes exhibited remarkable hybridization properties, as detected through a reversible shift in the redox potential of the Fc redox label upon repeated hybridization/denaturation procedures with a complementary target DNA sequence. By using a methylene blue (MB) labeled target DNA sequence the hybridization could also be followed through the MB redox potential. Electrochemical studies demonstrated that grafting through the triazene modifier can successfully compete with existing protocols for DNA immobilization through the commonly used alkanethiol linkers and diazonium salts. Furthermore, the triazene modifier provides a practical one-step immobilization procedure.

  16. Increasing the analytical sensitivity by oligonucleotides modified with para- and ortho-twisted intercalating nucleic acids--TINA.

    Directory of Open Access Journals (Sweden)

    Uffe V Schneider

    Full Text Available The sensitivity and specificity of clinical diagnostic assays using DNA hybridization techniques are limited by the dissociation of double-stranded DNA (dsDNA antiparallel duplex helices. This situation can be improved by addition of DNA stabilizing molecules such as nucleic acid intercalators. Here, we report the synthesis of a novel ortho-Twisted Intercalating Nucleic Acid (TINA amidite utilizing the phosphoramidite approach, and examine the stabilizing effect of ortho- and para-TINA molecules in antiparallel DNA duplex formation. In a thermal stability assay, ortho- and para-TINA molecules increased the melting point (Tm of Watson-Crick based antiparallel DNA duplexes. The increase in Tm was greatest when the intercalators were placed at the 5' and 3' termini (preferable or, if placed internally, for each half or whole helix turn. Terminally positioned TINA molecules improved analytical sensitivity in a DNA hybridization capture assay targeting the Escherichia coli rrs gene. The corresponding sequence from the Pseudomonas aeruginosa rrs gene was used as cross-reactivity control. At 150 mM ionic strength, analytical sensitivity was improved 27-fold by addition of ortho-TINA molecules and 7-fold by addition of para-TINA molecules (versus the unmodified DNA oligonucleotide, with a 4-fold increase retained at 1 M ionic strength. Both intercalators sustained the discrimination of mismatches in the dsDNA (indicated by ΔTm, unless placed directly adjacent to the mismatch--in which case they partly concealed ΔTm (most pronounced for para-TINA molecules. We anticipate that the presented rules for placement of TINA molecules will be broadly applicable in hybridization capture assays and target amplification systems.

  17. Increasing the Analytical Sensitivity by Oligonucleotides Modified with Para- and Ortho-Twisted Intercalating Nucleic Acids – TINA

    Science.gov (United States)

    Schneider, Uffe V.; Géci, Imrich; Jøhnk, Nina; Mikkelsen, Nikolaj D.; Pedersen, Erik B.; Lisby, Gorm

    2011-01-01

    The sensitivity and specificity of clinical diagnostic assays using DNA hybridization techniques are limited by the dissociation of double-stranded DNA (dsDNA) antiparallel duplex helices. This situation can be improved by addition of DNA stabilizing molecules such as nucleic acid intercalators. Here, we report the synthesis of a novel ortho-Twisted Intercalating Nucleic Acid (TINA) amidite utilizing the phosphoramidite approach, and examine the stabilizing effect of ortho- and para-TINA molecules in antiparallel DNA duplex formation. In a thermal stability assay, ortho- and para-TINA molecules increased the melting point (Tm) of Watson-Crick based antiparallel DNA duplexes. The increase in Tm was greatest when the intercalators were placed at the 5′ and 3′ termini (preferable) or, if placed internally, for each half or whole helix turn. Terminally positioned TINA molecules improved analytical sensitivity in a DNA hybridization capture assay targeting the Escherichia coli rrs gene. The corresponding sequence from the Pseudomonas aeruginosa rrs gene was used as cross-reactivity control. At 150 mM ionic strength, analytical sensitivity was improved 27-fold by addition of ortho-TINA molecules and 7-fold by addition of para-TINA molecules (versus the unmodified DNA oligonucleotide), with a 4-fold increase retained at 1 M ionic strength. Both intercalators sustained the discrimination of mismatches in the dsDNA (indicated by ΔTm), unless placed directly adjacent to the mismatch – in which case they partly concealed ΔTm (most pronounced for para-TINA molecules). We anticipate that the presented rules for placement of TINA molecules will be broadly applicable in hybridization capture assays and target amplification systems. PMID:21673988

  18. In vitro correction of a pseudoexon-generating deep intronic mutation in LGMD2A by antisense oligonucleotides and modified small nuclear RNAs.

    Science.gov (United States)

    Blázquez, Lorea; Aiastui, Ana; Goicoechea, Maria; Martins de Araujo, Mafalda; Avril, Aurélie; Beley, Cyriaque; García, Luis; Valcárcel, Juan; Fortes, Puri; López de Munain, Adolfo

    2013-10-01

    Limb-girdle muscular dystrophy type 2A (LGMD2A) is the most frequent autosomal recessive muscular dystrophy. It is caused by mutations in the calpain-3 (CAPN3) gene. The majority of the mutations described to date are located in the coding sequence of the gene. However, it is estimated that 25% of the mutations are present at exon-intron boundaries and modify the pre-mRNA splicing of the CAPN3 transcript. We have previously described the first deep intronic mutation in the CAPN3 gene: c.1782+1072G>C mutation. This mutation causes the pseudoexonization of an intronic sequence of the CAPN3 gene in the mature mRNA. In the present work, we show that the point mutation generates the inclusion of the pseudoexon in the mRNA using a minigene assay. In search of a treatment that restores normal splicing, splicing modulation was induced by RNA-based strategies, which included antisense oligonucleotides and modified small-nuclear RNAs. The best effect was observed with antisense sequences, which induced pseudoexon skipping in both HeLa cells cotransfected with mutant minigene and in fibroblasts from patients. Finally, transfection of antisense sequences and siRNA downregulation of serine/arginine-rich splicing factor 1 (SRSF1) indicate that binding of this factor to splicing enhancer sequences is involved in pseudoexon activation. © 2013 WILEY PERIODICALS, INC.

  19. Lubricants from chemically modified vegetable oils.

    Science.gov (United States)

    Campanella, Alejandrina; Rustoy, Eduardo; Baldessari, Alicia; Baltanás, Miguel A

    2010-01-01

    This work reports laboratory results obtained from the production of polyols with branched ether and ester compounds from epoxidized vegetable oils pertaining to annual, temperate climate crops (soybean, sunflower and high-oleic sunflower oils), focusing on their possible use as components of lubricant base stocks. To this end, two different opening reactions of the epoxide ring were studied. The first caused by the attack with glacial acetic acid (exclusively in a single organic phase) and the second using short-chain aliphatic alcohols, methanol and ethanol, in acid media. Both reactions proceed under mild conditions: low synthesis temperature and short reaction times and with conversions above 99%. Spectroscopic (NMR), thermal (DSC) and rheological techniques were used to characterize the oils, their epoxides and polyols, to assess the impact of the nature of the vegetable oil and the chemical modifications introduced, including long-term storage conditions. Several correlations were employed to predict the viscosity of the vegetable oils with temperature, and good agreement with the experimental data was obtained.

  20. [Adsorption of phenol chemicals by surfactant-modified zeolites].

    Science.gov (United States)

    Xie, Jie; Wang, Zhe; Wu, De-Yi; Li, Chun-Jie

    2012-12-01

    Two kinds of zeolites were prepared from fly ash and modified by surfactant subsequently. Surfactant-modified zeolites were studied for adsorption of phenol chemicals (phenol, p-chlorphenol, bisphenol A). It showed that the adsorption affinity of zeolite to phenol chemicals was significantly improved after surfactant modification. The adsorption isotherms of phenol chemicals were well fitted by the Langmuir isotherm. For the two surfactant-surfactant modified zeolites, the maximum adsorption amounts of phenol, p-chlorphenol, and bisphenol A calculated from the Langmuir equation were 37.7, 52.36, 90.9 mg x g(-1) and 10.7, 22.83, 56.8 mg x g(-1), respectively. When pH values of solutions were higher than the pK(a) values of phenol chemicals, the removal efficiencies were getting higher with the increase of pH values. The octanol/water partition coefficient (K(ow)) was also found to be an important factor affecting adsorption of phenol chemicals by the modified zeolites. Higher K(ow) value, which means the greater hydrophobicity of the chemicals, resulted in a higher removal.

  1. Identification and characterization of modified antisense oligonucleotides targeting DMPK in mice and nonhuman primates for the treatment of myotonic dystrophy type 1.

    Science.gov (United States)

    Pandey, Sanjay K; Wheeler, Thurman M; Justice, Samantha L; Kim, Aneeza; Younis, Husam S; Gattis, Danielle; Jauvin, Dominic; Puymirat, Jack; Swayze, Eric E; Freier, Susan M; Bennett, C Frank; Thornton, Charles A; MacLeod, A Robert

    2015-11-01

    Myotonic dystrophy type 1 (DM1) is the most common form of muscular dystrophy in adults. DM1 is caused by an expanded CTG repeat in the 3'-untranslated region of DMPK, the gene encoding dystrophia myotonica protein kinase (DMPK). Antisense oligonucleotides (ASOs) containing 2',4'-constrained ethyl-modified (cEt) residues exhibit a significantly increased RNA binding affinity and in vivo potency relative to those modified with other 2'-chemistries, which we speculated could translate to enhanced activity in extrahepatic tissues, such as muscle. Here, we describe the design and characterization of a cEt gapmer DMPK ASO (ISIS 486178), with potent activity in vitro and in vivo against mouse, monkey, and human DMPK. Systemic delivery of unformulated ISIS 486718 to wild-type mice decreased DMPK mRNA levels by up to 90% in liver and skeletal muscle. Similarly, treatment of either human DMPK transgenic mice or cynomolgus monkeys with ISIS 486178 led to up to 70% inhibition of DMPK in multiple skeletal muscles and ∼50% in cardiac muscle in both species. Importantly, inhibition of DMPK was well tolerated and was not associated with any skeletal muscle or cardiac toxicity. Also interesting was the demonstration that the inhibition of DMPK mRNA levels in muscle was maintained for up to 16 and 13 weeks post-treatment in mice and monkeys, respectively. These results demonstrate that cEt-modified ASOs show potent activity in skeletal muscle, and that this attractive therapeutic approach warrants further clinical investigation to inhibit the gain-of-function toxic RNA underlying the pathogenesis of DM1. Copyright © 2015 by The American Society for Pharmacology and Experimental Therapeutics.

  2. Chemically-Modified Cellulose Paper as a Microstructured Catalytic Reactor

    Directory of Open Access Journals (Sweden)

    Hirotaka Koga

    2015-01-01

    Full Text Available We discuss the successful use of chemically-modified cellulose paper as a microstructured catalytic reactor for the production of useful chemicals. The chemical modification of cellulose paper was achieved using a silane-coupling technique. Amine-modified paper was directly used as a base catalyst for the Knoevenagel condensation reaction. Methacrylate-modified paper was used for the immobilization of lipase and then in nonaqueous transesterification processes. These catalytic paper materials offer high reaction efficiencies and have excellent practical properties. We suggest that the paper-specific interconnected microstructure with pulp fiber networks provides fast mixing of the reactants and efficient transport of the reactants to the catalytically-active sites. This concept is expected to be a promising route to green and sustainable chemistry.

  3. High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers

    DEFF Research Database (Denmark)

    Hansen, Mads E; Bentin, Thomas; Nielsen, Peter E

    2009-01-01

    While sequence-selective dsDNA targeting by triplex forming oligonucleotides has been studied extensively, only very little is known about the properties of PNA-dsDNA triplexes-mainly due to the competing invasion process. Here we show that when appropriately modified using pseudoisocytosine subs...

  4. Stabilin-1 and Stabilin-2 are specific receptors for the cellular internalization of phosphorothioate-modified antisense oligonucleotides (ASOs) in the liver.

    Science.gov (United States)

    Miller, Colton M; Donner, Aaron J; Blank, Emma E; Egger, Andrew W; Kellar, Brianna M; Østergaard, Michael E; Seth, Punit P; Harris, Edward N

    2016-04-07

    Phosphorothioate (PS)-modified antisense oligonucleotides (ASOs) have been extensively investigated over the past three decades as pharmacological and therapeutic agents. One second generation ASO, Kynamro™, was recently approved by the FDA for the treatment of homozygous familial hypercholesterolemia and over 35 second generation PS ASOs are at various stages of clinical development. In this report, we show that the Stabilin class of scavenger receptors, which were not previously thought to bind DNA, do bind and internalize PS ASOs. With the use of primary cells from mouse and rat livers and recombinant cell lines each expressing Stabilin-1 and each isoform of Stabilin-2 (315-HARE and 190-HARE), we have determined that PS ASOs bind with high affinity and these receptors are responsible for bulk, clathrin-mediated endocytosis within the cell. Binding is primarily dependent on salt-bridge formation and correct folding of the intact protein receptor. Increased internalization rates also enhanced ASO potency for reducing expression of the non-coding RNA Malat-1, in Stabilin-expressing cell lines. A more thorough understanding of mechanisms by which ASOs are internalized in cells and their intracellular trafficking pathways will aid in the design of next generation antisense agents with improved therapeutic properties. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Molecular Dynamics Investigations of the Local Structural Characteristics of DNA Oligonucleotides: Studies of Helical Axis Deformations, Conformational Sequence Dependence and Modified Nucleoside Perturbations.

    Science.gov (United States)

    Louise-May, Shirley

    The present DNA studies investigate the local structure of DNA oligonucleotides in order to characterize helical axis deformations, sequence dependent fine structure and modified nucleoside perturbations of selected oligonucleotide sequences. The molecular dynamics method is used to generate an ensemble of energetically feasible DNA conformations which can then be analyzed for dynamical conformational properties, some of which can be compared to experimentally derived values. A theory and graphical presentation for the analysis of helical deformations of DNA based on the configurational statistics of polymers, called "Persistence Analysis", was designed. The results of the analysis on prototype forms, static crystal structures and two solvated MD simulations of the sequence d(CGCGAATTCGCG) indicate that all of the expected features of bending can be sensitively and systematically identified by this approach. Comparison of the relative performance of three molecular dynamics potential functions commonly used for dynamical modeling of biological macromolecules; CHARMm, AMBER and GROMOS was investigated via in vacuo MD simulations on the dodecamer sequence d(CGCGAATTCGCG)_2 with respect to the conformational properties of each dynamical model and their ability to support A and B families of DNA. Vacuum molecular dynamics simulations using the CHARMm force field carried out on simple homo- and heteropolymers of DNA led to the conclusion that sequence dependent fine structure appears to be well defined for adenine-thymine rich sequences both at the base pair and base step level whereas much of the the fine structure found in cytosine -guanine rich sequences appears to be context dependent. The local conformational properties of the homopolymer poly (dA) -poly (dT) revealed one dynamical model which was found in general agreement with fiber models currently available. Investigation of the relative structural static and dynamical effect of the misincorporation of

  6. Structure and biological activity of chemically modified nisin A species

    NARCIS (Netherlands)

    Rollema, Harry S.; Metzger, Jörg W.; Both, Paula; Kuipers, Oscar P.; Siezen, Roland J.

    1996-01-01

    Nisin, a 34-residue peptide bacteriocin, contains the less common amino acids lanthionine, β-methyllanthionine, dehydroalanine (Dha), and dehydrobutyrine (Dhb). Several chemically modified nisin A species were purified by reverse-phase HPLC and characterized by two-dimensional NMR and electrospray m

  7. Modified NASA-Lewis Chemical Equilibrium Code for MHD applications

    Energy Technology Data Exchange (ETDEWEB)

    Sacks, R. A.; Geyer, H. K.; Grammel, S. J.; Doss, E. D.

    1979-12-01

    A substantially modified version of the NASA-Lewis Chemical Equilibrium Code has recently been developed. The modifications were designed to extend the power and convenience of the Code as a tool for performing combustor analysis for MHD systems studies. This report describes the effect of the programming details from a user point of view, but does not describe the Code in detail.

  8. Structure and biological activity of chemically modified nisin A species

    NARCIS (Netherlands)

    Rollema, Harry S.; Metzger, Jörg W.; Both, Paula; Kuipers, Oscar P.; Siezen, Roland J.

    1996-01-01

    Nisin, a 34-residue peptide bacteriocin, contains the less common amino acids lanthionine, β-methyllanthionine, dehydroalanine (Dha), and dehydrobutyrine (Dhb). Several chemically modified nisin A species were purified by reverse-phase HPLC and characterized by two-dimensional NMR and electrospray m

  9. Chemical composition of silica-based biocidal modifier

    Directory of Open Access Journals (Sweden)

    Grishina Anna Nikolaevna

    2016-11-01

    Full Text Available Increase of the amount of fungi spores and micotixines causes the increase in the number of different diseases. Because of this, ensuring the biological safety in buildings is becoming more and more important today. The preferred way to guarantee the biological safety of a building is to employ modern building materials that prevent the settlement of the fungi colonies on the inner surfaces of walls. Such building materials can be produced using novel biocidal modifiers that allow controlling the number of microorganisms on the surface and in the bulk of a composite construction. The precipitation product of zinc hydrosilicates and sodium sulfate is one of the mentioned modifiers. Till now, the exact chemical composition of such precipitation product is controversial; it is obvious, though, that the efficacy of the biocidal modifier is mostly determined by the type of the copper compounds. In the present work an integrated approach is used for the investigation of the chemical composition of the biocidal modifier. Such an approach consists in the examination of the modifier’s composition by means of different, yet complementary, research methods: X-ray diffraction, infrared spectroscopy and DTA. It is shown that the chemical composition of the modifier mainly depends on the amount of precipitant. X-ray diffraction reveals that the major part of the modifier is represented by amorphous phase. Along with the increase of the precipitant’s amount the crystalline phase Zn4SO4(OH6•xH2O formation takes place. Such a crystalline phase is not appropriate as a component of the biocidal modifier. Another two methods - DTA and IR spectroscopy - reveal that the amorphous phase consists essentially of zinc hydrosilicates.

  10. Chemical sensors based on molecularly modified metallic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Haick, Hossam [Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 32000 (Israel)

    2007-12-07

    This paper presents a concise, although admittedly non-exhaustive, didactic review of some of the main concepts and approaches related to the use of molecularly modified metal nanoparticles in or as chemical sensors. This paper attempts to pull together different views and terminologies used in sensors based on molecularly modified metal nanoparticles, including those established upon electrochemical, optical, surface Plasmon resonance, piezoelectric and electrical transduction approaches. Finally, this paper discusses briefly the main advantages and disadvantages of each of the presented class of sensors. (review article)

  11. Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities

    Science.gov (United States)

    Brunet, Erika; Corgnali, Maddalena; Perrouault, Loïc; Roig, Victoria; Asseline, Ulysse; Sørensen, Mads D.; Babu, B. Ravindra; Wengel, Jesper; Giovannangeli, Carine

    2005-01-01

    Triplex-forming oligonucleotides (TFOs) are powerful tools to interfere sequence-specifically with DNA-associated biological functions. (A/T,G)-containing TFOs are more commonly used in cells than (T,C)-containing TFOs, especially C-rich sequences; indeed the low intracellular stability of the non-covalent pyrimidine triplexes make the latter less active. In this work we studied the possibility to enhance DNA binding of (T,C)-containing TFOs, aiming to reach cellular activities; to this end, we used locked nucleic acid-modified TFOs (TFO/LNAs) in association with 5′-conjugation of an intercalating agent, an acridine derivative. In vitro a stable triplex was formed with the TFO-acridine conjugate: by SPR measurements at 37°C and neutral pH, the dissociation equilibrium constant was found in the nanomolar range and the triplex half-life ∼10 h (50-fold longer compared with the unconjugated TFO/LNA). Moreover to further understand DNA binding of (T,C)-containing TFO/LNAs, hybridization studies were performed at different pH values: triplex stabilization associated with pH decrease was mainly due to a slower dissociation process. Finally, biological activity of pyrimidine TFO/LNAs was evaluated in a cellular context: it occurred at concentrations ∼0.1 μM for acridine-conjugated TFO/LNA (or ∼2 μM for the unconjugated TFO/LNA) whereas the corresponding phosphodiester TFO was inactive, and it was demonstrated to be triplex-mediated. PMID:16049028

  12. Gene silencing by chemically modified siRNAs.

    Science.gov (United States)

    Engels, Joachim W

    2013-03-25

    RNA interference (RNAi) has not only already risen as a gold standard for validating gene function in basic science studies, but also holds great promise as a new therapeutic paradigm. Advantages of RNAi-based therapeutics include relatively fast initial screening and the ability to target proteins not yet addressable by traditional drug design strategies. In this review we describe the development of chemically modified small inhibiting siRNAs and their application as potential therapeutics during the past decade. Focus is on proper siRNA design, choice of chemical modification and how to circumvent immunogenicity as well as off-target effects.

  13. THE INDUSTRIAL UTILIZATION OF CHEMICAL MODIFIED AGRICULTURAL RESIDUES

    Institute of Scientific and Technical Information of China (English)

    Feng Xu; Runcang Sun; Huaiyu Zhan

    2004-01-01

    Various lignocellulosic materials such as wood,agricultural and forest residues has the potential to be valuable substitute for, or complement to,commercial sorbents for removing heavy metal ions or dyes from waste water or spilled oil from inland water or sea. More than 9 million tons of straw pulp are produced annually in china, which account for about 90% of the world′s total straw pulp. However,huge quantity of remain straw is not used as industrial raw material and is burnt in the fields or on the side of road. These resources can be chemical modified such as acetylation. Modified straws have the characteristics of low cost, high capacity, quick uptake, and easy to desorb. This paper reviews the current status of the technology for modified agricultural residues, which focus on hemicellulose and cellulose. The potential of these natural sorbents in main industry is also indicated.

  14. THE INDUSTRIAL UTILIZATION OF CHEMICAL MODIFIED AGRICULTURAL RESIDUES

    Institute of Scientific and Technical Information of China (English)

    FengXu; RuncangSun; HuaiyuZhan

    2004-01-01

    Various lignocellulosic materials such as wood, agricultural and forest residues has the potential to be valuable substitute for, or complement to, commercial sorbents for removing heavy metal ions or dyes from waste water or spilled oil from inland water or sea. More than 9 million tons of straw pulp are produced annually in china, which account for about 90% of the world's total straw pulp. However, huge quantity of remain straw is not used as industrial raw material and is burnt in the fields or on the side of road. These resources can be chemical modified such as acetylation. Modified straws have the characteristics of low cost, high capacity, quick uptake, and easy to desorb. This paper reviews the current status of the technology for modified agricultural residues, which focus on hemicellulose and cellulose. The potential of these natural sorbents in main industry is also indicated.

  15. Chemical characteristics and volatile profile of genetically modified peanut cultivars.

    Science.gov (United States)

    Ng, Ee Chin; Dunford, Nurhan T; Chenault, Kelly

    2008-10-01

    Genetic engineering has been used to modify peanut cultivars for improving agronomic performance and pest resistance. Food products developed through genetic engineering have to be assessed for their safety before approval for human consumption. Preservation of desirable chemical, flavor and aroma attributes of the peanut cultivars during the genetic modifications is critical for acceptance of genetically modified peanuts (GMP) by the food industry. Hence, the main objective of this study is to examine chemical characteristics and volatile profile of GMP. The genetically modified peanut cultivars, 188, 540 and 654 were obtained from the USDA-ARS in Stillwater, Oklahoma. The peanut variety Okrun was examined as a control. The volatile analysis was performed using a gas chromatograph/mass spectrometer (GC/MS) equipped with an olfactory detector. The peanut samples were also analyzed for their moisture, ash, protein, sugar and oil compositions. Experimental results showed that the variations in nutritional composition of peanut lines examined in this study were within the values reported for existing cultivars. There were minor differences in volatile profile among the samples. The implication of this study is significant, since it shows that peanut cultivars with greater pest and fungal resistance were successfully developed without major changes in their chemical characteristics.

  16. Gene expression visualisation with antisense oligonucleotides; Visualisation de l'expression d'un gene: la strategie antisens

    Energy Technology Data Exchange (ETDEWEB)

    Brard, P.Y.; Gauchez, A.S.; Vuillez, J.P. [Universite Joseph-Fourier, Grenoble I, INSERM E 03-40, Radiopharmaceutiques Biocliniques, Faculte de Medecine, 38 (France); Defrancq, E. [Universite Joseph-Fourier, Grenoble I, UMR CNRS 5616 - LEDSS, Faculte de Medecine, 38 (France)

    2004-08-01

    Using radiolabelled antisense oligonucleotides to target mRNAs is a very promising method to study gene expression in vivo. This molecular imaging technique has the aim to identify cellular modifications in a very early stage of disease. During the last ten years, the number of published studies concerning in vivo tumor specific imaging is small. This fact depends on numerous biological challenges. In fact, gene specific oligonucleotides must be chemically modified to increase nuclease resistance and permit labelling with radionuclide. To be used as imaging radiopharmaceutical agent, a good antisense oligonucleotide need to valid a lot of steps: in vivo stability, cell membrane passage and durable hybridization to mRNA to obtain a kinetic which depends directly on gene expression level. We can get over these difficulties, we will illustrate with our experience on chemo-resistance imaging with antisense oligonucleotides which target h-mdr 1, in vitro and in vivo. (author)

  17. Solid-phase synthesis of siRNA oligonucleotides.

    Science.gov (United States)

    Beaucage, Serge L

    2008-03-01

    Since the discovery of RNA interference (RNAi) as a means to silence the expression of specific genes, small interfering RNA (siRNA) oligonucleotides have been recognized as powerful tools for targeting therapeutically important mRNAs and eliciting their destruction. This discovery has created a high demand for synthetic oligoribonucleotides as potential therapeutics and has spurred a renaissance in the development of rapid, efficient methods for solid-phase RNA synthesis. The design and implementation of 2'-hydroxyl protecting groups that provide ribonucleoside phosphoramidites with coupling kinetics and coupling efficiencies comparable to those of deoxyribonucleoside phosphoramidites are key to the production of RNA oligonucleotides in sufficient quantity and purity for pharmaceutical applications. In this context, various siRNAs were chemically modified to identify the biophysical and biochemical parameters necessary for effective and stable RNAi-mediated gene-silencing activities.

  18. Chemically modified cellulose paper as a thin film microextraction phase.

    Science.gov (United States)

    Saraji, Mohammad; Farajmand, Bahman

    2013-11-01

    In this paper, chemically modified cellulose paper was introduced as a novel extracting phase for thin film microextraction (TFME). Different reagents (Octadecyltrichlorosilane, diphenyldichlorosilane, cyclohexyl isocyanate and phenyl isocyanate) were used to modify the cellulose papers. The modified papers were evaluated as a sorbent for the extraction of some synthetic and natural estrogenic hormones (17α-ethynylestradiol, estriol and estradiol) from aqueous samples. Liquid chromatography-fluorescence detection was used for the quantification of the extracted compounds. The cellulose paper modified with phenyl isocyanate showed the best affinity to the target compounds. TEME parameters such as desorption condition, shaking rate, sample ionic strength and extraction time were investigated and optimized. Limit of detections were between 0.05 and 0.23μgL(-1) and relative standard deviations were less than 11.1% under the optimized condition. The calibration curves were obtained in the range of 0.2-100μgL(-1) with a good linearity (r(2)>0.9935). Wastewater, human urine, pool and river water samples were studied as real samples for the evaluation of the method. Relative recoveries were found to be between 75% and 101%.

  19. Recovery of palladium using chemically modified cedar wood powder.

    Science.gov (United States)

    Parajuli, Durga; Hirota, Koichi

    2009-10-15

    Japanese cedar wood powder (CWP) was chemically modified to a tertiary-amine-type adsorbent and studied for the selective recovery of Pd(II) from various industrial waters. Batch adsorption tests performed from 0.1 M to 5 M HCl and HNO3 systems reveal stable performance with better results in HNO3 medium. The maximum loading capacity for Pd(II) was studied in HCl as well as in HNO3. A continuous-flow experiment taking a real industrial solution revealed the feasibility of using modified CWP for the selective uptake and preconcentration of traces of palladium contained in acidic effluents. In addition, stable adsorption performance even on long exposure to gamma-irradiation and selective recovery of palladium from simulated high-level liquid waste (HLW) are important outcomes of the study.

  20. Chemically modified tetracyclines: The novel host modulating agents

    Directory of Open Access Journals (Sweden)

    Devulapalli Narasimha Swamy

    2015-01-01

    Full Text Available Periodontal pathogens and destructive host responses are involved in the initiation and progression of periodontitis. The emergence of host response modulation as a treatment concept has resulted from our improved understanding of the pathogenesis of periodontal disease. A variety of drugs have been evaluated as host modulation agents (HMA, including Non Steroidal Anti Inflammatory Drugs (NSAIDS, bisphosphonates, tetracyclines, enamel matrix proteins and bone morphogenetic proteins. Chemically modified tetracyclines (CMTs are one such group of drugs which have been viewed as potential host modulating agents by their anticollagenolytic property. The CMTs are designed to be more potent inhibitors of pro inflammatory mediators and can increase the levels of anti inflammatory mediators.

  1. Mechano-sorptive creep of Portuguese pinewood chemically modified

    Directory of Open Access Journals (Sweden)

    Barroso Lopes Duarte

    2014-03-01

    Full Text Available The effect of chemical modification on mechano-sorptive creep in bending was studied by experimental work. Stakes with 20 × 20 × 400 mm RTL of Portuguese wood species (Pinus pinaster Aiton modified with 1,3-dimethylol-4,5- dihydroxyethyleneurea (DMDHEU, m-methylated melamine resin (MMF, tetraethoxysilane (TEOS and amid wax (WA were measured under asymmetric moistening conditions over a period of 42 days (app. 1000 hours with stress level (SL of 12 MPa, according to ENV 1156.

  2. Probing Chromatin-modifying Enzymes with Chemical Tools

    KAUST Repository

    Fischle, Wolfgang

    2016-02-04

    Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins.

  3. Detecting Chemically Modified DNA Bases Using Surface Enhanced Raman Spectroscopy.

    Science.gov (United States)

    Barhoumi, Aoune; Halas, Naomi J

    2011-12-15

    Post-translational modifications of DNA- changes in the chemical structure of individual bases that occur without changes in the DNA sequence- are known to alter gene expression. They are believed to result in frequently deleterious phenotypic changes, such as cancer. Methylation of adenine, methylation and hydroxymethylation of cytosine, and guanine oxidation are the primary DNA base modifications identified to date. Here we show it is possible to use surface enhanced Raman spectroscopy (SERS) to detect these primary DNA base modifications. SERS detection of modified DNA bases is label-free and requires minimal additional sample preparation, reducing the possibility of additional chemical modifications induced prior to measurement. This approach shows the feasibility of DNA base modification assessment as a potentially routine analysis that may be further developed for clinical diagnostics.

  4. Reduced chemically modified graphene oxide for supercapacitor electrode.

    Science.gov (United States)

    Rajagopalan, Balasubramaniyan; Chung, Jin Suk

    2014-01-01

    An efficient active material for supercapacitor electrodes is prepared by reacting potassium hydroxide (KOH) with graphene oxide followed by chemical reduction with hydrazine. The electrochemical performance of KOH treated graphene oxide reduced for 24 h (reduced chemically modified graphene oxide, RCMGO-24) exhibits a specific capacitance of 253 F g(-1) at 0.2 A g(-1) in 2 M H2SO4 compared to a value of 141 F g(-1) for graphene oxide reduced for 24 h (RGO-24), and good cyclic stability up to 3,000 cycles. Interestingly, RCMGO-24 demonstrated a higher specific capacitance and excellent cycle stability due to its residual oxygen functional groups that accelerate the faradaic reactions and aid in faster wetting. This non-annealed strategy offers the potential for simple and cost-effective preparation of an active material for a supercapacitor electrode.

  5. Chemically modified solid state nanopores for high throughput nanoparticle separation

    Energy Technology Data Exchange (ETDEWEB)

    Prabhu, Anmiv S; Kim, Min Jun [School of Biomedical Engineering and Health Science, Drexel University, Philadelphia, PA 19104 (United States); Jubery, Talukder Zaki N; Dutta, Prashanta [School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164 (United States); Freedman, Kevin J; Mulero, Rafael, E-mail: mkim@coe.drexel.ed [Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA 19104 (United States)

    2010-11-17

    The separation of biomolecules and other nanoparticles is a vital step in several analytical and diagnostic techniques. Towards this end we present a solid state nanopore-based set-up as an efficient separation platform. The translocation of charged particles through a nanopore was first modeled mathematically using the multi-ion model and the surface charge density of the nanopore membrane was identified as a critical parameter that determines the selectivity of the membrane and the throughput of the separation process. Drawing from these simulations a single 150 nm pore was fabricated in a 50 nm thick free-standing silicon nitride membrane by focused-ion-beam milling and was chemically modified with (3-aminopropyl)triethoxysilane to change its surface charge density. This chemically modified membrane was then used to separate 22 and 58 nm polystyrene nanoparticles in solution. Once optimized, this approach can readily be scaled up to nanopore arrays which would function as a key component of next-generation nanosieving systems.

  6. Band bending and electrical transport at chemically modified silicon surfaces

    Science.gov (United States)

    Lopinski, Greg; Ward, Tim; Hul'Ko, Oleksa; Boukherroub, Rabah

    2002-03-01

    High resolution electron energy loss spectroscopy (HREELS) and electrical transport measurements have been used to investigate how various chemical modifications give rise to band bending and alter the conductivity of Si(111) surfaces. HREELS is a sensitive probe of band bending through observations of the low frequency free carrier plasmon mode. For hydrogen terminated surfaces, prepared by the standard etch in ammonium flouride, HREELS measurements on both n and n+ substrates are consistent with nearly flat bands. Chlorination of these surfaces results in substantial upward band bending due to the strong electron withdrawing nature of the chlorine, driving the surface into inversion. The presence of this inversion layer on high resistivity n-type samples is observed through a substantial enhancement of the surface conductivity (relative to the H-terminated surface), as well as through broadening of the quasi-elastic peak in the HREELS measurements. We have also begun to examine organically modified silicon surfaces, prepared by various wet chemical reactions with the H-terminated surface. Decyl modified Si(111) surfaces are seen to exhibit a small degree of band bending, attributed to extrinsic defect states cause by a small degree of oxidation accompanying the modification reaction. The prospects of using conductivity as an in-situ monitor of the rate of these reactions will be discussed.

  7. Preparation of calcium stannate by modified wet chemical method

    Institute of Scientific and Technical Information of China (English)

    何则强; 李新海; 刘恩辉; 侯朝辉; 邓凌峰; 胡传跃

    2003-01-01

    A modified wet chemical route for low-temperature synthesis of the calcium stannate CaSnO3, a potentialmaterial for dielectric applications is reported. Firstly, a precursor CaSn(OH)6 was prepared using tin tetrachloride,calcium chloride and sodium hydroxide at room temperature. Then the precursor was annealed at relatively low tem-perature of 600 ℃ to obtain CaSnO3. The phase identification, thermal behavior and surface morphology of the sam-ples were characterized by element analysis, X-ray diffraction (XRD), thermo-gravimetric (TG) analysis and deriva-tive thermo-gravimetric (DTG) analysis, Fourier transform infrared spectroscopy (FTIR) and scanning electron mi-croscopy (SEM) in detail. The results show that CaSnO3 obtained by this method possesses a cubic perovskitestructure with average grain size of 5 μm.

  8. 12-Tungstophosphates Immobilized on Chemically Modified Mesoporous Silica SBA-15

    Institute of Scientific and Technical Information of China (English)

    ZHU Jing; YOU Wan-sheng; ZHU Zai-ming; SUN Zhen-gang; ZHANG Lan-cui; GU Yuan-peng

    2005-01-01

    A functionalized material, PW/SBA-15m, was prepared successfully in diluted H2SO4 aqueous solutions by immobilizing 12-tungstophosphates on chemically modified mesoporous silica SBA-15 and characterized by elemental analysis, FTIR, 31P MAS NMR, XRD and TEM. The results indicate that the framework of SBA-15 and the Keggin structure of PW12O3-40 were retained, and that 23%-33%(mass fraction) of PW12O3-40 was immobilized; the PW12O3-40 anions were finely dispersed on the pore wall of SBA-15. Having been leached in ethanol at 60 ℃ for 7 h, the loss of PW12O3-40 anions was not found.

  9. The Chemistry and Biology of Oligonucleotide Conjugates

    Science.gov (United States)

    Juliano, R.L.; Ming, Xin; Nakagawa, Osamu

    2012-01-01

    CONSPECTUS Short DNA or RNA oligonucleotides have tremendous potential as therapeutic agents. Because of their ability to engage in Watson-Crick base pairing they can interact with messenger mRNA or pre-mRNA targets with high selectivity and thus offer the possibility of precise manipulation of gene expression. This possibility has engendered extensive efforts to develop oligonucleotides as drugs, with many candidates already in clinical trials. However, a major impediment to the maturation of oligonucleotide-based therapeutics is the fact that these relatively large and usually highly charged molecules have great difficulty crossing cellular membranes and thus in penetrating to their sites of action in the cytosol or nucleus. In this Account we first summarize some basic aspects of the biology of antisense and siRNA oligonucleotides and then discuss chemical conjugation as an approach to improving the intracellular delivery and therapeutic potential of these agents. Our emphasis will be on the pharmacological ramifications of oligonucleotide conjugates rather than the details of conjugation chemistry. One important approach has been conjugation with ligands designed to bind to particular receptors and thus provide specificity to the interaction of cells with oligonucleotides. Another approach has been to couple antisense or siRNA with agents such as cell penetrating peptides that are designed to provoke escape of the conjugate from intracellular vesicular compartments. Both of these approaches have enjoyed some success. However, there remains much to be learned before oligonucleotide conjugates can find an important place in human therapeutics. PMID:22353142

  10. Highly efficient adsorption of chlorophenols onto chemically modified chitosan

    Science.gov (United States)

    Zhou, Liang-Chun; Meng, Xiang-Guang; Fu, Jing-Wei; Yang, Yu-Chong; Yang, Peng; Mi, Chun

    2014-02-01

    A novel chemically modified chitosan CS-SA-CD with phenol and β-cyclodextrin groups was prepared. The adsorptions of phenol, 2-chlorophenol (2-CP), 4-chlorophenol (4-CP), 2,4-dichlorophenol (DCP) and 2,4,6-trichlorophenol (TCP) on the functional chitosan from aqueous solution were investigated. CS-SA-CD exhibited excellent adsorption ability for chlorophenols especially for DCP and TCP. The maximum adsorption capacities of phenol, 2-CP, 4-CP, DCP and TCP on CS-SA-CD were 59.74, 70.52, 96.43, 315.46 and 375.94 mg/g, respectively. The scanning electron microscope and Brunauer-Emmett-Teller analyses revealed that the introduction of phenol group changed the surface morphology and surface properties of chitosan. The modified chitosan CS-SA-CD possesses larger surface areas (4.72 m2/g), pore volume (7.29 × 10-3 mL/g) and average pore diameter (59.99 Å) as compared to those of chitosan 3.27 m2/g, 2.00 × 10-3 mL/g and 15.95 Å, respectively. The enhanced adsorption of chlorophenols was also attributed to the interaction of hydrogen bond between Cl atom and sbnd OH group. The adsorption of chlorophenols on CS-SA-CD followed the pseudo-second-order kinetic model. Adsorbent could be regenerated easily and the regenerated CS-SA-CD remained 80-91% adsorption efficiency.

  11. Pharmacology of a Central Nervous System Delivered 2′-O-Methoxyethyl–Modified Survival of Motor Neuron Splicing Oligonucleotide in Mice and Nonhuman Primates

    OpenAIRE

    Rigo, Frank; Chun, Seung J.; Norris, Daniel A.; Hung, Gene; Lee, Sam; Matson, John; Fey, Robert A.; Gaus, Hans; Hua, Yimin; Grundy, John S.; Krainer, Adrian R; Henry, Scott P.; Bennett, C. Frank

    2014-01-01

    Spinal muscular atrophy (SMA) is a debilitating neuromuscular disease caused by the loss of survival of motor neuron (SMN) protein. Previously, we demonstrated that ISIS 396443, an antisense oligonucleotide (ASO) targeted to the SMN2 pre-mRNA, is a potent inducer of SMN2 exon 7 inclusion and SMN protein expression, and improves function and survival of mild and severe SMA mouse models. Here, we demonstrate that ISIS 396443 is the most potent ASO in central nervous system (CNS) tissues of adul...

  12. Functionalization of magnetic gold/iron-oxide composite nanoparticles with oligonucleotides and magnetic separation of specific target

    Energy Technology Data Exchange (ETDEWEB)

    Kinoshita, Takuya [Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan)]. E-mail: t-kinoshita@mit.eng.osaka-u.ac.jp; Seino, Satoshi [Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Mizukoshi, Yoshiteru [Faculty of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521 (Japan); Nakagawa, Takashi [Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Yamamoto, Takao A. [Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan)

    2007-04-15

    Magnetic composite nanoparticles of gold and iron-oxide synthesized with gamma-rays or ultrasonics were functionalized with thiol-modified oligonucleotides. The amount of oligonucleotides bound to the functionalized nanoparticle probes via hybridization was quantified with fluorescently-labeled target oligonucleotides. Our composite nanoparticles magnetically separated the specific target oligonucleotides without the non-specific adsorption.

  13. G-Quadruplex Forming Oligonucleotides as Anti-HIV Agents.

    Science.gov (United States)

    Musumeci, Domenica; Riccardi, Claudia; Montesarchio, Daniela

    2015-09-22

    Though a variety of different non-canonical nucleic acids conformations have been recognized, G-quadruplex structures are probably the structural motifs most commonly found within known oligonucleotide-based aptamers. This could be ascribed to several factors, as their large conformational diversity, marked responsiveness of their folding/unfolding processes to external stimuli, high structural compactness and chemo-enzymatic and thermodynamic stability. A number of G-quadruplex-forming oligonucleotides having relevant in vitro anti-HIV activity have been discovered in the last two decades through either SELEX or rational design approaches. Improved aptamers have been obtained by chemical modifications of natural oligonucleotides, as terminal conjugations with large hydrophobic groups, replacement of phosphodiester linkages with phosphorothioate bonds or other surrogates, insertion of base-modified monomers, etc. In turn, detailed structural studies have elucidated the peculiar architectures adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. An overview of the state-of-the-art knowledge of the relevance of putative G-quadruplex forming sequences within the viral genome and of the most studied G-quadruplex-forming aptamers, selectively targeting HIV proteins, is here presented.

  14. Highly efficient adsorption of chlorophenols onto chemically modified chitosan

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Liang-Chun [Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 (China); National Center for Packaging Material Quality Supervision and Inspection, Chengdu Institute of Product Quality Supervision and Inspection, Chengdu 610064 (China); Meng, Xiang-Guang, E-mail: mengxgchem@163.com [Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 (China); Fu, Jing-Wei [National Center for Packaging Material Quality Supervision and Inspection, Chengdu Institute of Product Quality Supervision and Inspection, Chengdu 610064 (China); Yang, Yu-Chong; Yang, Peng; Mi, Chun [Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 (China)

    2014-02-15

    A novel chemically modified chitosan CS-SA-CD with phenol and β-cyclodextrin groups was prepared. The adsorptions of phenol, 2-chlorophenol (2-CP), 4-chlorophenol (4-CP), 2,4-dichlorophenol (DCP) and 2,4,6-trichlorophenol (TCP) on the functional chitosan from aqueous solution were investigated. CS-SA-CD exhibited excellent adsorption ability for chlorophenols especially for DCP and TCP. The maximum adsorption capacities of phenol, 2-CP, 4-CP, DCP and TCP on CS-SA-CD were 59.74, 70.52, 96.43, 315.46 and 375.94 mg/g, respectively. The scanning electron microscope and Brunauer–Emmett–Teller analyses revealed that the introduction of phenol group changed the surface morphology and surface properties of chitosan. The modified chitosan CS-SA-CD possesses larger surface areas (4.72 m{sup 2}/g), pore volume (7.29 × 10{sup −3} mL/g) and average pore diameter (59.99 Å) as compared to those of chitosan 3.27 m{sup 2}/g, 2.00 × 10{sup −3} mL/g and 15.95 Å, respectively. The enhanced adsorption of chlorophenols was also attributed to the interaction of hydrogen bond between Cl atom and -OH group. The adsorption of chlorophenols on CS-SA-CD followed the pseudo-second-order kinetic model. Adsorbent could be regenerated easily and the regenerated CS-SA-CD remained 80–91% adsorption efficiency.

  15. Enhanced fluorescence of silver nanoclusters stabilized with branched oligonucleotides.

    Science.gov (United States)

    Latorre, Alfonso; Lorca, Romina; Zamora, Félix; Somoza, Álvaro

    2013-05-28

    DNA stabilized silver nanoclusters (AgNCs) are promising optical materials, whose fluorescence properties can be tuned by the selection of the DNA sequence employed. In this work we have used modified oligonucleotides in the preparation of AgNCs. The fluorescent intensity obtained was 60 times higher than that achieved with standard oligonucleotides.

  16. Synthesis of triazole-linked oligonucleotides with high affinity to DNA complements and an analysis of their compatibility with biosystems.

    Science.gov (United States)

    Varizhuk, Anna M; Kaluzhny, Dmitry N; Novikov, Roman A; Chizhov, Alexandr O; Smirnov, Igor P; Chuvilin, Andrey N; Tatarinova, Olga N; Fisunov, Gleb Y; Pozmogova, Galina E; Florentiev, Vladimir L

    2013-06-21

    New oligonucleotide analogues with triazole internucleotide linkages were synthesized, and their hybridization properties were studied. The analogues demonstrated DNA binding affinities similar to those of unmodified oligonucleotides. The modification was shown to protect the oligonucleotides from nuclease hydrolysis. The modified oligonucleotides were tested as PCR primers. Modifications remote from the 3'-terminus were tolerated by polymerases. Our results suggest that these new oligonucleotide analogues are among the most promising triazole DNA mimics characterized to date.

  17. Why Carba-LNA-modified oligonucleotides show considerably improved 3'-exonuclease stability compared to that of the LNA modified or the native counterparts: A Michaelis-Menten kinetic analysis.

    Science.gov (United States)

    Zhou, Chuanzheng; Chattopadhyaya, Jyoti

    2010-04-02

    In this study, 12 different native or LNA, carba-LNA-modified dinucleoside phosphates were designed as simple chemical models to study how carba-LNA modifications improve the 3'-exonuclease (SVPDE in this study) resistance of internucleotidic phosphate compared to those exhibited by LNA-modified and the native counterparts. Michaelis-Menten kinetic studies for dimers 3 - 7, in which the LNA or carba-LNA modifications are located at the 5'-end, showed that (i) increased 3'-exonuclease resistance of (5')[LNA-T](p)T (3) compared to the native (5')T(p)T (1) was mainly attributed to steric hindrance imposed by the LNA modification that retards the nuclease binding (K(M)) and (ii) digestion of (5')[carba-LNA-dT](p)T (4) and (5')[LNA-T](p)T (3), however, exhibit similar K(M)s, whereas the former shows a 100x decrease in K(cat) and is hence more stable than the latter. By studying the correlation between log k(cat) and pK(a) of the departing 3'(or 6')-OHs for 3-7, we found the pK(a) of 3'-OH of carba-LNA-T was 1.4 pK(a) units higher than that of LNA-T, and this relatively less acidic character of the 3'-OH in the former leads to the 100x decrease in the catalytic efficiency for the digestion of (5')[carba-LNA-T](p)T (4). In contrast, Michaelis-Menten kinetic studies for dimers 9-12, with the LNA or carba-LNA modifications at the 3'-end, showed that the digestion of (5')T(p)[LNA-T] (9) exhibited similar K(M) but k(cat) decreased around 40 times compared to that of the native (5')T(p)T (1). Similar k(cat) values have been observed for digestion of (5')T(p)[carba-LNA-T] (10) and (5')T(p)[LNA-T] (9). The higher stability of carba-LNA modified dimer 10 compared with LNA modified dimer 9 comes solely from the increased K(M).

  18. Reference field effect transistor based on chemically modified ISFETs

    NARCIS (Netherlands)

    Skowronska-Ptasinska, Maria; Wal, van der Peter D.; Berg, van den Albert; Bergveld, Piet; Sudhölter, Ernst J.R.; Reinhoudt, David N.

    1990-01-01

    Different hydrophobic polymers were used for chemical modification of ion-sensitive field effect transistors (ISFETs) in order to prepare a reference FET (REFET). Chemical attachment of the polymer to the ISFET gate results in a long lifetime of the device. Properties of polyacrylate (polyACE) REFET

  19. Comparison of small molecules and oligonucleotides that target a toxic, non-coding RNA.

    Science.gov (United States)

    Costales, Matthew G; Rzuczek, Suzanne G; Disney, Matthew D

    2016-06-01

    Potential RNA targets for chemical probes and therapeutic modalities are pervasive in the transcriptome. Oligonucleotide-based therapeutics are commonly used to target RNA sequence. Small molecules are emerging as a modality to target RNA structures selectively, but their development is still in its infancy. In this work, we compare the activity of oligonucleotides and several classes of small molecules that target the non-coding r(CCUG) repeat expansion (r(CCUG)(exp)) that causes myotonic dystrophy type 2 (DM2), an incurable disease that is the second-most common cause of adult onset muscular dystrophy. Small molecule types investigated include monomers, dimers, and multivalent compounds synthesized on-site by using RNA-templated click chemistry. Oligonucleotides investigated include phosphorothioates that cleave their target and vivo-morpholinos that modulate target RNA activity via binding. We show that compounds assembled on-site that recognize structure have the highest potencies amongst small molecules and are similar in potency to a vivo-morpholino modified oligonucleotide that targets sequence. These studies are likely to impact the design of therapeutic modalities targeting other repeats expansions that cause fragile X syndrome and amyotrophic lateral sclerosis, for example.

  20. Evaluation of the effects of chemically different linkers on hepatic accumulations, cell tropism and gene silencing ability of cholesterol-conjugated antisense oligonucleotides.

    Science.gov (United States)

    Wada, Shunsuke; Yasuhara, Hidenori; Wada, Fumito; Sawamura, Motoki; Waki, Reiko; Yamamoto, Tsuyoshi; Harada-Shiba, Mariko; Obika, Satoshi

    2016-03-28

    Cholesterol conjugation of oligonucleotides is an attractive way to deliver the oligonucleotides specifically to the liver. However cholesterol-conjugated antisense oligonucleotides (ASOs) mainly accumulate in non-parenchymal cells (NPCs) such as Kupffer cells. In this study, to increase the hepatic accumulation of cholesterol-conjugated ASOs, we prepared a variety of linkers for cholesterol conjugation to anti-Pcsk9 ASOs and examined their effects on pharmacological parameters. Hepatic accumulation of ASO was dramatically increased with cholesterol conjugation. The increase in hepatic accumulation depended largely on the linker chemistry of each cholesterol-conjugated ASO. In addition to hepatic accumulation, the cell tropism of each cholesterol-conjugated ASO tended to depend on their linker. Although a linker bearing a disulfide bond accumulated mainly in NPCs, hexamethylene succinimide linker accumulated mainly in hepatocytes. To estimate the benefits of releasing ASO from the conjugated cholesterol in hepatocyte, we designed another linker based on hexamethylene succinimide, which has a phosphodiester bond between the linker and the ASO. The cholesterol-conjugated ASO bearing such a phosphodiester bond showed a significantly improved Pcsk9 mRNA inhibitory effect compared to its counterpart, cholesterol-conjugated ASO with a phosphorothioate bond, while the hepatic accumulation of both cholesterol-conjugated ASOs was comparable, indicating the effectiveness of removing the conjugated cholesterol for ASO activity. In toxicity analysis, some of the linkers induced lethal toxicities when they were injected at high concentrations (>600μM). These toxicities were attributed to decreased platelet levels in the blood, suggesting an interaction between cholesterol-conjugated ASO and platelets. Our findings may provide a guideline for the design of molecule-conjugated ASOs. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Noncoding oligonucleotides: the belle of the ball in gene therapy.

    Science.gov (United States)

    Shum, Ka-To; Rossi, John J

    2015-01-01

    Gene therapy carries the promise of cures for many diseases based on manipulating the expression of a person's genes toward the therapeutic goal. The relevance of noncoding oligonucleotides to human disease is attracting widespread attention. Noncoding oligonucleotides are not only involved in gene regulation, but can also be modified into therapeutic tools. There are many strategies that leverage noncoding oligonucleotides for gene therapy, including small interfering RNAs, antisense oligonucleotides, aptamers, ribozymes, decoys, and bacteriophage phi 29 RNAs. In this chapter, we will provide a broad, comprehensive overview of gene therapies that use noncoding oligonucleotides for disease treatment. The mechanism and development of each therapeutic will be described, with a particular focus on its clinical development. Finally, we will discuss the challenges associated with developing nucleic acid therapeutics and the prospects for future success.

  2. Predicting oligonucleotide-directed mutagenesis failures in protein engineering.

    Science.gov (United States)

    Wassman, Christopher D; Tam, Phillip Y; Lathrop, Richard H; Weiss, Gregory A

    2004-01-01

    Protein engineering uses oligonucleotide-directed mutagenesis to modify DNA sequences through a two-step process of hybridization and enzymatic synthesis. Inefficient reactions confound attempts to introduce mutations, especially for the construction of vast combinatorial protein libraries. This paper applied computational approaches to the problem of inefficient mutagenesis. Several results implicated oligonucleotide annealing to non-target sites, termed 'cross-hybridization', as a significant contributor to mutagenesis reaction failures. Test oligonucleotides demonstrated control over reaction outcomes. A novel cross-hybridization score, quickly computable for any plasmid and oligonucleotide mixture, directly correlated with yields of deleterious mutagenesis side products. Cross-hybridization was confirmed conclusively by partial incorporation of an oligonucleotide at a predicted cross-hybridization site, and by modification of putative template secondary structure to control cross-hybridization. Even in low concentrations, cross-hybridizing species in mixtures poisoned reactions. These results provide a basis for improved mutagenesis efficiencies and increased diversities of cognate protein libraries.

  3. The delivery of therapeutic oligonucleotides.

    Science.gov (United States)

    Juliano, Rudolph L

    2016-08-19

    The oligonucleotide therapeutics field has seen remarkable progress over the last few years with the approval of the first antisense drug and with promising developments in late stage clinical trials using siRNA or splice switching oligonucleotides. However, effective delivery of oligonucleotides to their intracellular sites of action remains a major issue. This review will describe the biological basis of oligonucleotide delivery including the nature of various tissue barriers and the mechanisms of cellular uptake and intracellular trafficking of oligonucleotides. It will then examine a variety of current approaches for enhancing the delivery of oligonucleotides. This includes molecular scale targeted ligand-oligonucleotide conjugates, lipid- and polymer-based nanoparticles, antibody conjugates and small molecules that improve oligonucleotide delivery. The merits and liabilities of these approaches will be discussed in the context of the underlying basic biology. © The Author 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Biophysical and RNA Interference Inhibitory Properties of Oligonucleotides Carrying Tetrathiafulvalene Groups at Terminal Positions

    Directory of Open Access Journals (Sweden)

    Sónia Pérez-Rentero

    2013-01-01

    Full Text Available Oligonucleotide conjugates carrying a single functionalized tetrathiafulvalene (TTF unit linked through a threoninol molecule to the 3′ or 5′ ends were synthesized together with their complementary oligonucleotides carrying a TTF, pyrene, or pentafluorophenyl group. TTF-oligonucleotide conjugates formed duplexes with higher thermal stability than the corresponding unmodified oligonucleotides and pyrene- and pentafluorophenyl-modified oligonucleotides. TTF-modified oligonucleotides are able to bind to citrate-stabilized gold nanoparticles (AuNPs and produce stable gold AuNPs functionalized with oligonucleotides. Finally, TTF-oligoribonucleotides have been synthesized to produce siRNA duplexes carrying TTF units. The presence of the TTF molecule is compatible with the RNA interference mechanism for gene inhibition.

  5. CHEMICALLY MODIFIED FIELD-EFFECT TRANSISTORS - POTENTIOMETRIC AG+ SELECTIVITY OF PVC MEMBRANES BASED ON MACROCYCLIC THIOETHERS

    NARCIS (Netherlands)

    BRZOZKA, Z; COBBEN, PLHM; REINHOUDT, DN; EDEMA, JJH; KELLOGG, RM

    1993-01-01

    A chemically modified field-effect transistor (CHEMFET) with satisfactory Ag+ selectivity is described. The potentiometric Ag+ selectivities of CHEMFETs with plasticized PVC membranes based on macrocyclic thioethers have been determined. All the macrocyclic thioethers tested showed silver response a

  6. A NOVEL METHOD TO SYNTHESIZE N-DOPED CNTs ARRAYS VIA CHEMICAL MODIFYING POROUS ALUMINA MEMBRANE

    OpenAIRE

    CHENGYONG LI; LEI HE

    2014-01-01

    N-doped carbon nanotubes (CNTs) arrays were fabricated via simply chemical modifying porous alumina membrane (PAM) with dopamine. The diameter of N-doped CNTs is about 60–70 nm. The N/C atomic ratio is calculated to be 0.05 and the main functionality is pyridone/pyrrole N. This chemical modifying method can be used to fabricate mass of N-doped CNTs arrays in one step with single raw material.

  7. a Novel Method to Synthesize N-DOPED CNTs Arrays via Chemical Modifying Porous Alumina Membrane

    Science.gov (United States)

    Li, Chengyong; He, Lei

    2014-01-01

    N-doped carbon nanotubes (CNTs) arrays were fabricated via simply chemical modifying porous alumina membrane (PAM) with dopamine. The diameter of N-doped CNTs is about 60-70 nm. The N/C atomic ratio is calculated to be 0.05 and the main functionality is pyridone/pyrrole N. This chemical modifying method can be used to fabricate mass of N-doped CNTs arrays in one step with single raw material.

  8. Correlation between dynamic wetting behavior and chemical components of thermally modified wood

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Wang; Zhu, Yuan; Cao, Jinzhen, E-mail: caoj@bjfu.edu.cn; Sun, Wenjing

    2015-01-01

    Highlights: • We studied the dynamic wetting behavior of thermally modified wood by wetting models. • We found lower wetting speed of water droplets on thermally modified wood surface. • Dynamic wetting behavior and surface chemical components show a strong correlation. - Abstract: In order to investigate the dynamic wetting behavior of thermally modified wood, Cathay poplar (Populus cathayana Rehd.) and Scots pine (Pinus sylvestris L.) samples were thermally modified in an oven at 160, 180, 200, 220 or 240 °C for 4 h in this study. The dynamic contact angles and droplet volumes of water droplets on modified and unmodified wood surfaces were measured by sessile drop method, and their changing rates (expression index: K value and wetting slope) calculated by wetting models were illustrated for mapping the dynamic wetting process. The surface chemical components were also measured by X-ray photoelectron spectroscopy analysis (XPS), thus the relationship between dynamic wetting behavior and chemical components of thermally modified wood were determined. The results indicated that thermal modification was capable of decreasing the dynamic wettability of wood, expressed in lowing spread and penetration speed of water droplets on wood surfaces. This change was more obvious with the increased heating temperature. The K values varied linearly with the chemical components parameter (mass loss, O/C ratio, and C{sub 1}/C{sub 2} ratio), indicating a strong correlation between dynamic wetting behavior and chemical components of thermally modified wood.

  9. DIMENSIONAL STABILITY AND WATER REPELLENT EFFICIENCY MEASUREMENT OF CHEMICALLY MODIFIED TROPICAL LIGHT HARDWOOD

    OpenAIRE

    Md. Saiful Islam; Sinin Hamdan; Mohamad Rusop; Md. Rezaur Rahman; Abu Saleh Ahmed; M. A. M. Mohd Idrus

    2012-01-01

    Chemical modification is an often-followed route to improve physical and mechanical properties of solid wood materials. In this study five kinds of tropical light hardwoods species, namely jelutong (Dyera costulata), terbulan (Endospermum diadenum), batai (Paraserianthes moluccana), rubberwood (Hevea brasiliensis), and pulai (Alstonia pneumatophora), were chemically modified with benzene diazonium salt to improve their dimensional stability and water repellent efficiency. The dimensional stab...

  10. Antisense Oligonucleotides: Translation from Mouse Models to Human Neurodegenerative Diseases.

    Science.gov (United States)

    Schoch, Kathleen M; Miller, Timothy M

    2017-06-21

    Multiple neurodegenerative diseases are characterized by single-protein dysfunction and aggregation. Treatment strategies for these diseases have often targeted downstream pathways to ameliorate consequences of protein dysfunction; however, targeting the source of that dysfunction, the affected protein itself, seems most judicious to achieve a highly effective therapeutic outcome. Antisense oligonucleotides (ASOs) are small sequences of DNA able to target RNA transcripts, resulting in reduced or modified protein expression. ASOs are ideal candidates for the treatment of neurodegenerative diseases, given numerous advancements made to their chemical modifications and delivery methods. Successes achieved in both animal models and human clinical trials have proven ASOs both safe and effective. With proper considerations in mind regarding the human applicability of ASOs, we anticipate ongoing in vivo research and clinical trial development of ASOs for the treatment of neurodegenerative diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. The use of modified phenol for chemical face peeling.

    Science.gov (United States)

    Stone, P A

    1998-01-01

    This article reviews the results of 59 consecutive, modified phenol facial peels on 627 anatomic areas for the purpose of reducing fine to coarse rhytides, hyperpigmentation, and actinic keratoses. This work discusses the Venner-Kellson concentrated Lysol saponated formula containing 62.5% phenol; the Maschek-Truppman 53% phenol, nonsaponated glycerin formula; and the previously unpublished Gradé formulae I, II, and III with 49.5%, 60%, and 70% phenol, respectively. The new Stone formulae I, II, and III are introduced here. These new formulae are mixed from available reagents, thus obviating the need to melt potentially toxic phenol crystals, and are designed to achieve a range of clinical peel results on a wide variety of skin types. The ingredients, methods of preparation and application, as well as three postpeel occlusion techniques are presented. Clinical data including pH measurements, croton oil ratios, phenol concentrations, and preliminary biopsy data also are presented.

  12. Radiation modification of swollen and chemically modified cellulose

    Science.gov (United States)

    Borsa, J.; Tóth, T.; Takács, E.; Hargittai, P.

    2003-06-01

    Effect of accessibility of cellulose molecules on development of crosslinks during high-energy irradiation was investigated. Accessibility of cellulose was improved by swelling (NaOH, tetramethylammonium hydroxide), carboxymethylation, coating with water-soluble carboxymethylcellulose, respectively. Irradiation of samples (10 kGy) was carried out in wet state of the fabric as mobility of cellulose molecules is much higher in the presence of water and high mobility of molecular chains is advantageous for development of crosslinks. Change in molecular size was followed by degree of polymerization. The structure modified by crosslinks was characterized by increase in the absorbance assigned to the intermolecular hydrogen bonds (FTIR), and by decrease of fiber swelling (water vapor sorption, water retention). Thew highest values both for water vapor sorption and water retention were found in sample of highest accessibility (carboxymethylated cotton fabric coated with carboxymethylcellulose).

  13. Mthfd1 is a modifier of chemically induced intestinal carcinogenesis.

    Science.gov (United States)

    MacFarlane, Amanda J; Perry, Cheryll A; McEntee, Michael F; Lin, David M; Stover, Patrick J

    2011-03-01

    The causal metabolic pathways underlying associations between folate and risk for colorectal cancer (CRC) have yet to be established. Folate-mediated one-carbon metabolism is required for the de novo synthesis of purines, thymidylate and methionine. Methionine is converted to S-adenosylmethionine (AdoMet), the major one-carbon donor for cellular methylation reactions. Impairments in folate metabolism can modify DNA synthesis, genomic stability and gene expression, characteristics associated with tumorigenesis. The Mthfd1 gene product, C1-tetrahydrofolate synthase, is a trifunctional enzyme that generates one-carbon substituted tetrahydrofolate cofactors for one-carbon metabolism. In this study, we use Mthfd1(gt/+) mice, which demonstrate a 50% reduction in C1-tetrahydrofolate synthase, to determine its influence on tumor development in two mouse models of intestinal cancer, crosses between Mthfd1(gt/+) and Apc(min)(/+) mice and azoxymethane (AOM)-induced colon cancer in Mthfd1(gt/+) mice. Mthfd1 hemizygosity did not affect colon tumor incidence, number or load in Apc(min/+) mice. However, Mthfd1 deficiency increased tumor incidence 2.5-fold, tumor number 3.5-fold and tumor load 2-fold in AOM-treated mice. DNA uracil content in the colon was lower in Mthfd1(gt/+) mice, indicating that thymidylate biosynthesis capacity does not play a significant role in AOM-induced colon tumorigenesis. Mthfd1 deficiency-modified cellular methylation potential, as indicated by the AdoMet: S-adenosylhomocysteine ratio and gene expression profiles, suggesting that changes in the transcriptome and/or decreased de novo purine biosynthesis and associated mutability cause cellular transformation in the AOM CRC model. This study emphasizes the impact and complexity of gene-nutrient interactions with respect to the relationships among folate metabolism and colon cancer initiation and progression.

  14. Interfacial characterization and analytical applications of chemically-modified surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jianhong [Iowa State Univ., Ames, IA (United States)

    1998-02-23

    The goal of this work is to explore several new strategies and approaches to the surface modification and the microscopic characterization of interfaces in the areas mainly targeting sensor technologies that are of interest to environmental control or monitoring, and scanning probe microscopies techniques that can monitor interfacial chemical reactions in real time. Centered on the main theme, four specific topics are presented as four chapters in this dissertation following the general introduction. Chapter 1 describes the development of two immobilization schemes for covalently immobilizing fluoresceinamine at cellulose acetate and its application as a pH sensing film. Chapter 2 investigates the applicability of SFM to following the base-hydrolysis of a dithio-bis(succinimidylundecanoate) monolayer at gold in situ. Chapter 3 studies the mechanism for the accelerated rate of hydrolysis of the dithio-bis(succinimidylundecanoate) monolayer at Au(111) surface. Chapter 4 focuses on the development of an electrochemical approach to the elimination of chloride interference in Chemical Oxygen Demand (COD) analysis of waste water. The procedures, results and conclusions are described in each chapter. This report contains the introduction, references, and general conclusions. Chapters have been processed separately for inclusion on the data base. 95 refs.

  15. Antisense oligonucleotide induction of progerin in human myogenic cells.

    Directory of Open Access Journals (Sweden)

    Yue-Bei Luo

    Full Text Available We sought to use splice-switching antisense oligonucleotides to produce a model of accelerated ageing by enhancing expression of progerin, translated from a mis-spliced lamin A gene (LMNA transcript in human myogenic cells. The progerin transcript (LMNA Δ150 lacks the last 150 bases of exon 11, and is translated into a truncated protein associated with the severe premature ageing disease, Hutchinson-Gilford progeria syndrome (HGPS. HGPS arises from de novo mutations that activate a cryptic splice site in exon 11 of LMNA and result in progerin accumulation in tissues of mesodermal origin. Progerin has also been proposed to play a role in the 'natural' ageing process in tissues. We sought to test this hypothesis by producing a model of accelerated muscle ageing in human myogenic cells. A panel of splice-switching antisense oligonucleotides were designed to anneal across exon 11 of the LMNA pre-mRNA, and these compounds were transfected into primary human myogenic cells. RT-PCR showed that the majority of oligonucleotides were able to modify LMNA transcript processing. Oligonucleotides that annealed within the 150 base region of exon 11 that is missing in the progerin transcript, as well as those that targeted the normal exon 11 donor site induced the LMNA Δ150 transcript, but most oligonucleotides also generated variable levels of LMNA transcript missing the entire exon 11. Upon evaluation of different oligomer chemistries, the morpholino phosphorodiamidate oligonucleotides were found to be more efficient than the equivalent sequences prepared as oligonucleotides with 2'-O-methyl modified bases on a phosphorothioate backbone. The morpholino oligonucleotides induced nuclear localised progerin, demonstrated by immunostaining, and morphological nuclear changes typical of HGPS cells. We show that it is possible to induce progerin expression in myogenic cells using splice-switching oligonucleotides to redirect splicing of LMNA. This may offer a model

  16. WATER-BLOWN POLYURETHANE RIGID FOAMS MODIFIED BY CHEMICAL PLASTICATION

    Institute of Scientific and Technical Information of China (English)

    YU Ming; XU Qiang

    2006-01-01

    Water-blown polyurethane rigid foams are getting more and more attention, because the traditional blowing agent HCFC141b has already been abolished to prevent the ozone layer from destruction. However, the polyurethane rigid foams blown by water have serious defects, i.e. friability and resulting lower adhesion strength. Thus, the purpose of this study is to resolve the problems by chemical plastication. The maleate was added to polyol-premix containing water or to polyisocyanate,with both of which maleate does not react. To prove the reaction when polyol-premix and polyisocyanate were mixed, the model composite was synthesized and analyzed by IR, NMR and ESI (MS). Furthermore, a series of water-blown polyurethane rigid foams added different amount maleate were successfully prepared. By testing impact strength and adhesion strength of the foams, the actual effect of adding maleate was obtained.

  17. CO2 adsorption on chemically modified activated carbon.

    Science.gov (United States)

    Caglayan, Burcu Selen; Aksoylu, A Erhan

    2013-05-15

    CO2 adsorption capacity of a commercial activated carbon was improved by using HNO3 oxidation, air oxidation, alkali impregnation and heat treatment under helium gas atmosphere. The surface functional groups produced were investigated by diffuse reflectance infrared Fourier transform spectrometer (DRIFTS). CO2 adsorption capacities of the samples were determined by gravimetric analyses for 25-200°C temperature range. DRIFTS studies revealed the formation of carboxylic acid groups on the HNO3 oxidized adsorbents. Increased aromatization and uniform distribution of the Na particles were observed on the samples prepared by Na2CO3 impregnation onto HNO3 oxidized AC support. The adsorption capacities of the nonimpregnated samples were increased by high temperature helium treatments or by increasing the adsorption temperature; both leading to decomposition of surface oxygen groups, forming sites that can easily adsorb CO2. The adsorption capacity loss due to cyclic adsorption/desorption procedures was overcome with further surface stabilization of Na2CO3 modified samples with high temperature He treatments. With Na2CO3 impregnation the mass uptakes of the adsorbents at 20 bars and 25 °C were improved by 8 and 7 folds and at 1 bar were increased 15 and 16 folds, on the average, compared to their air oxidized and nitric acid oxidized supports, respectively.

  18. Basic analytical investigation of plasma-chemically modified carbon fibers

    Energy Technology Data Exchange (ETDEWEB)

    Bubert, H.; Ai, X.; Haiber, S.; Heintze, M.; Brueser, V.; Pasch, E.; Brandl, W.; Marginean, G

    2002-10-15

    The background of the present investigation is to enhance the overall adherence of vapor grown carbon fibers (VGCF) to the surrounding polymer matrix in different applications by forming polar groups at their surfaces and by modifying the surface morphology. This has been done by plasma treatments using a low-pressure plasma with different gases, flow rates, pressures and powers. Two different types of carbon fibers were investigated: carbon microfibers and carbon nanofibers. The characterization of fiber surfaces was achieved by photoelectron spectroscopy (XPS), contact angle measurements and titration. These investigations were accompanied by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The oxygen plasma treatment of the fibers changes the surfaces by forming a layer with a thickness of the order of one nanometer mainly consisting of functional groups like hydroxyl, carbonyl and carboxyl. After functionalization of the complete surface, a further plasma treatment does not enhance the superficial oxygen content but changes slightly the portions of the functional groups. A comparison of the methods applied provides a largely consistent image of the effect of plasma treatment.

  19. Biosorption of Methylene Blue by Chemically Modified Cellulose Waste

    Institute of Scientific and Technical Information of China (English)

    JIN Yanqiao; ZHANG Yizhuan; Lü Qiufeng; CHENG Xiansu

    2014-01-01

    Citric acid modified cellulose waste (CMCW) was prepared via esterification and used as a low-cost biosorbent for the removal of methylene blue (MB) from aqueous solutions. The effects of biosorbent concentration, initial pH of MB solution, biosorption temperature, contact time, and initial MB concentration on the biosorption of MB were investigated using batch biosorption technique under static conditions. The experimental results showed that CMCW exhibited excellent biosorption characteristics for MB. The maximum biosorption capacity of MB was up to 214.5 mg/g at an adsorption temperature of 293 K. The removal rate of MB onto CMCW reached the maximum at pH>4 and the biosorption reached an equilibrium at about 50 min. The kinetic data can be described well with the pseudo-second-order model and the isotherm data was found to fit the Langmuir isotherm with a monolayer adsorption capacity of 211.42 mg/g. The biosorption appears to be controlled by chemisorption and may be involved in surface adsorption and pore diffusion during the whole biosorption process.

  20. Chitosan and chemically modified chitosan beads for acid dyes sorption

    Institute of Scientific and Technical Information of China (English)

    AZLAN Kamari; WAN SAIME Wan Ngah; LAI KEN Liew

    2009-01-01

    The capabilities of chitosan and chitosan-EGDE (ethylene glycol diglycidyl ether) beads for removing Acid Red 37 (AR 37) and Acid Blue 25 (AB 25) from aqueous solution were examined. Chitosan beads were cross-linked with EGDE to enhance its chemical resistance and mechanical strength. Experiments were performed as a function of pH, agitation period and concentration of AR 37 and AB 25. It was shown that the adsorption capacities of chitosan were comparatively higher than chitosan-EGDE for both acid dyes. This is mainly because cross-linking using EGDE reduces the major adsorption sites -NH3+ on chitosan. Langmuir isotherm model showed best conformity compared to Freundlich and BET. The kinetic experimental data agreed very well to the pseudo second-order kinetic model. The desorption study revealed that after three cycles of adsorption and desorption by NaOH and HCl, both adsorbents retained their promising adsorption abilities. FT-IR analysis proved that the adsorption of acid dyes onto chitosan-based adsorbents was a physical adsorption. Results also showed that chitosan and chitosan-EGDE beads were favourable adsorbers and could be employed as low-cost alternatives for the removal of acid dyes in wastewater treatment.

  1. Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity

    Science.gov (United States)

    Netzer, Nir; Goodenbour, Jeffrey M.; David, Alexandre; Dittmar, Kimberly A.; Jones, Richard B.; Schneider, Jeffrey R.; Boone, David; Eves, Eva M.; Rosner, Marsha R.; Gibbs, James S.; Embry, Alan; Dolan, Brian; Das, Suman; Hickman, Heather; Berglund, Peter; Bennink, Jack R.; Yewdell, Jonathan W.; Pan, Tao

    2009-01-01

    Translational fidelity, essential for protein and cell function, requires accurate tRNA aminoacylation. Purified aminoacyl-tRNA synthetases exhibit a fidelity of 1 error per 10,000 to 100,000 couplings 1, 2. The accuracy of tRNA aminoacylation in vivo is uncertain, however, and might be considerably lower 3–6. Here, we show that in mammalian cells, approximately 1% of methionine (Met) residues used in protein synthesis are aminoacylated to non-methionyl-tRNAs. Remarkably, Met-misacylation increases up to 10-fold upon exposing cells to live or non-infectious viruses, toll-like receptor ligands, or chemically induced oxidative stress. Met is misacylated to specific non-methionyl-tRNA families, and these Met-misacylated tRNAs are used in translation. Met-misacylation is blocked by an inhibitor of cellular oxidases, implicating reactive oxygen species (ROS) as the misacylation trigger. Among six amino acids tested, tRNA misacylation occurs exclusively with Met. As Met residues are known to protect proteins against ROS-mediated damage 7, we propose that Met-misacylation functions adaptively to increase Met incorporation into proteins to protect cells against oxidative stress. In demonstrating an unexpected conditional aspect of decoding mRNA, our findings illustrate the importance of considering alternative iterations of the genetic code. PMID:19940929

  2. Mechanical and chemical properties of cysteine-modified kinesin molecules.

    Science.gov (United States)

    Iwatani, S; Iwane, A H; Higuchi, H; Ishii, Y; Yanagida, T

    1999-08-10

    To probe the structural changes within kinesin molecules, we made the mutants of motor domains of two-headed kinesin (4-411 aa) in which either all the five cysteines or all except Cys45 were mutated. A residual cysteine (Cys45) of the kinesin mutant was labeled with an environment-sensitive fluorescent probe, acrylodan. ATPase activity, mechanical properties, and fluorescence intensity of the mutants were measured. Upon acrylodan-labeled kinesin binding to microtubules in the presence of 1 mM AMPPNP, the peak intensity was enhanced by 3.4-fold, indicating the structural change of the kinesin head by the binding. Substitution of cysteines decreased both the maximum microtubule-activated ATPase and the sliding velocity to the same extent. However, the maximum force and the step size were not affected; the force produced by a single molecule was 6-6.5 pN, and a step size due to the hydrolysis of one ATP molecule by kinesin molecules was about 10 nm for all kinesins. This step size was close to a unitary step size of 8 nm. Thus, the mechanical events of kinesin are tightly coupled with the chemical events.

  3. Design and analysis of mismatch probes for long oligonucleotide microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  4. Design and analysis of mismatch probes for long oligonucleotide microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  5. Food preparation characteristics of potato starch pastes containing a proportion of chemically-modified starch

    OpenAIRE

    菊地, 和美; 高橋 セツ子; 吉田 訓子; 山本 未穂; 知地 英征; Kazumi, KIKUCHI; Takahashi, Setsuko; Yoshida, Kuniko; Yamamoto, Miho; Chiji, Hideyuki; 藤女子大学人間生活学部食物栄養学科; 藤女子大学人間生活学部食物栄養学科藤女子大学大学院人間生活学研究科食物栄養学専攻

    2011-01-01

    Hokkaido potatoes are widely used as a source of starch. Potato starch is used for various purposes,particularly for the production of fish paste products,livestock products, and confectionery. Moreover, modified starch, which is produced by processing potato starch chemically and physically, is used in a variety of forms. This study examines the properties of modified starch gels produced by further enhancing the starch functions of potato starch. To study the primary properties of starch ge...

  6. Correlation between dynamic wetting behavior and chemical components of thermally modified wood

    Science.gov (United States)

    Wang, Wang; Zhu, Yuan; Cao, Jinzhen; Sun, Wenjing

    2015-01-01

    In order to investigate the dynamic wetting behavior of thermally modified wood, Cathay poplar (Populus cathayana Rehd.) and Scots pine (Pinus sylvestris L.) samples were thermally modified in an oven at 160, 180, 200, 220 or 240 °C for 4 h in this study. The dynamic contact angles and droplet volumes of water droplets on modified and unmodified wood surfaces were measured by sessile drop method, and their changing rates (expression index: K value and wetting slope) calculated by wetting models were illustrated for mapping the dynamic wetting process. The surface chemical components were also measured by X-ray photoelectron spectroscopy analysis (XPS), thus the relationship between dynamic wetting behavior and chemical components of thermally modified wood were determined. The results indicated that thermal modification was capable of decreasing the dynamic wettability of wood, expressed in lowing spread and penetration speed of water droplets on wood surfaces. This change was more obvious with the increased heating temperature. The K values varied linearly with the chemical components parameter (mass loss, O/C ratio, and C1/C2 ratio), indicating a strong correlation between dynamic wetting behavior and chemical components of thermally modified wood.

  7. Applicability of chemically modified capillaries in chiral capillary electrophoresis for methamphetamine profiling.

    Science.gov (United States)

    Iwata, Yuko T; Mikuma, Toshiyasu; Kuwayama, Kenji; Tsujikawa, Kenji; Miyaguchi, Hajime; Kanamori, Tatsuyuki; Inoue, Hiroyuki

    2013-03-10

    We examined the applicability of chemically modified capillaries on the chiral capillary electrophoresis of essential compounds for methamphetamine (MA) profiling (MA, amphetamine, ephedrine, pseudoephedrine, norephedrine, and norpseudoephedrine) using highly sulfated γ-cyclodextrin as a chiral selector. Four types of chemically modified capillaries, namely, FunCap-CE/Type D (possessing diol groups), Type A (amino groups), Type C (carboxyl groups), and Type S (sulfate groups), were evaluated. Repeatability, speed, and good chiral resolution sufficient for routine MA profiling were achieved with the Type S capillary.

  8. Hepatotoxic Potential of Therapeutic Oligonucleotides Can Be Predicted from Their Sequence and Modification Pattern

    Science.gov (United States)

    Hagedorn, Peter H.; Yakimov, Victor; Ottosen, Søren; Kammler, Susanne; Nielsen, Niels F.; Høg, Anja M.; Hedtjärn, Maj; Meldgaard, Michael; Møller, Marianne R.; Ørum, Henrik; Koch, Troels

    2013-01-01

    Antisense oligonucleotides that recruit RNase H and thereby cleave complementary messenger RNAs are being developed as therapeutics. Dose-dependent hepatic changes associated with hepatocyte necrosis and increases in serum alanine-aminotransferase levels have been observed after treatment with certain oligonucleotides. Although general mechanisms for drug-induced hepatic injury are known, the characteristics of oligonucleotides that determine their hepatotoxic potential are not well understood. Here, we present a comprehensive analysis of the hepatotoxic potential of locked nucleic acid-modified oligonucleotides in mice. We developed a random forests classifier, in which oligonucleotides are regarded as being composed of dinucleotide units, which distinguished between 206 oligonucleotides with high and low hepatotoxic potential with 80% accuracy as estimated by out-of-bag validation. In a validation set, 17 out of 23 oligonucleotides were correctly predicted (74% accuracy). In isolation, some dinucleotide units increase, and others decrease, the hepatotoxic potential of the oligonucleotides within which they are found. However, a complex interplay between all parts of an oligonucleotide can influence the hepatotoxic potential. Using the classifier, we demonstrate how an oligonucleotide with otherwise high hepatotoxic potential can be efficiently redesigned to abate hepatotoxic potential. These insights establish analysis of sequence and modification patterns as a powerful tool in the preclinical discovery process for oligonucleotide-based medicines. PMID:23952551

  9. Antisense oligonucleotides in therapy for neurodegenerative disorders.

    Science.gov (United States)

    Evers, Melvin M; Toonen, Lodewijk J A; van Roon-Mom, Willeke M C

    2015-06-29

    Antisense oligonucleotides are synthetic single stranded strings of nucleic acids that bind to RNA and thereby alter or reduce expression of the target RNA. They can not only reduce expression of mutant proteins by breakdown of the targeted transcript, but also restore protein expression or modify proteins through interference with pre-mRNA splicing. There has been a recent revival of interest in the use of antisense oligonucleotides to treat several neurodegenerative disorders using different approaches to prevent disease onset or halt disease progression and the first clinical trials for spinal muscular atrophy and amyotrophic lateral sclerosis showing promising results. For these trials, intrathecal delivery is being used but direct infusion into the brain ventricles and several methods of passing the blood brain barrier after peripheral administration are also under investigation. Copyright © 2015. Published by Elsevier B.V.

  10. Antisense Oligonucleotide-Based Therapy for Neuromuscular Disease.

    Science.gov (United States)

    Sardone, Valentina; Zhou, Haiyan; Muntoni, Francesco; Ferlini, Alessandra; Falzarano, Maria Sofia

    2017-04-05

    Neuromuscular disorders such as Duchenne Muscular Dystrophy and Spinal Muscular Atrophy are neurodegenerative genetic diseases characterized primarily by muscle weakness and wasting. Until recently there were no effective therapies for these conditions, but antisense oligonucleotides, a new class of synthetic single stranded molecules of nucleic acids, have demonstrated promising experimental results and are at different stages of regulatory approval. The antisense oligonucleotides can modulate the protein expression via targeting hnRNAs or mRNAs and inducing interference with splicing, mRNA degradation, or arrest of translation, finally, resulting in rescue or reduction of the target protein expression. Different classes of antisense oligonucleotides are being tested in several clinical trials, and limitations of their clinical efficacy and toxicity have been reported for some of these compounds, while more encouraging results have supported the development of others. New generation antisense oligonucleotides are also being tested in preclinical models together with specific delivery systems that could allow some of the limitations of current antisense oligonucleotides to be overcome, to improve the cell penetration, to achieve more robust target engagement, and hopefully also be associated with acceptable toxicity. This review article describes the chemical properties and molecular mechanisms of action of the antisense oligonucleotides and the therapeutic implications these compounds have in neuromuscular diseases. Current strategies and carrier systems available for the oligonucleotides delivery will be also described to provide an overview on the past, present and future of these appealing molecules.

  11. Evaluating Zeolite-Modified Sensors: towards a faster set of chemical sensors

    Science.gov (United States)

    Berna, A. Z.; Vergara, A.; Trincavelli, M.; Huerta, R.; Afonja, A.; Parkin, I. P.; Binions, R.; Trowell, S.

    2011-09-01

    The responses of zeolite-modified sensors, prepared by screen printing layers of chromium titanium oxide (CTO), were compared to unmodified tin oxide sensors using amplitude and transient responses. For transient responses we used a family of features, derived from the exponential moving average (EMA), to characterize chemo-resistive responses. All sensors were tested simultaneously against 20 individual volatile compounds from four chemical groups. The responses of the two types of sensors showed some independence. The zeolite-modified CTO sensors discriminated compounds better using either amplitude response or EMA features and CTO-modified sensors also responded three times faster.

  12. Chemical treatment of the intra-canal dentin surface: a new approach to modify dentin hydrophobicity

    Directory of Open Access Journals (Sweden)

    Cesar GAITAN-FONSECA

    2013-01-01

    Full Text Available Objective This study evaluated the hydrophobicity of dentin surfaces that were modified through chemical silanization with octadecyltrichlorosilane (OTS. Material and Methods An in vitro experimental study was performed using 40 human permanent incisors that were divided into the following two groups: non-silanized and silanized. The specimens were pretreated and chemically modified with OTS. After the chemical modification, the dentin hydrophobicity was examined using a water contact angle measurement (WCA. The effectiveness of the modification of hydrophobicity was verified by the fluid permeability test (FPT. Results and Conclusions Statistically significant differences were found in the values of WCA and FPT between the two groups. After silanization, the hydrophobic intraradicular dentin surface exhibited in vitro properties that limit fluid penetration into the sealed root canal. This chemical treatment is a new approach for improving the sealing of the root canal system.

  13. Modified clay minerals efficiency against chemical and biological warfare agents for civil human protection.

    Science.gov (United States)

    Plachá, Daniela; Rosenbergová, Kateřina; Slabotínský, Jiří; Kutláková, Kateřina Mamulová; Studentová, Soňa; Martynková, Gražyna Simha

    2014-04-30

    Sorption efficiencies of modified montmorillonite and vermiculite of their mono ionic Na and organic HDTMA and HDP forms were studied against chemical and biological warfare agents such as yperite and selected bacterial strains. Yperite interactions with modified clay minerals were observed through its capture in low-density polyethylene foil-modified clay composites by measuring yperite gas permeation with using chemical indication and gas chromatography methods. The antibacterial activities of synthetized organoclays were tested against selected Gram-positive and Gram-negative bacterial species in minimum inhibitory concentration tests. The obtained results showed a positive influence of modified clay minerals on the significant yperite breakthrough-time increase. The most effective material was the polyethylene-Na form montmorillonite, while the polyethylene-Na form vermiculite showed the lowest efficiency. With increasing organic cations loading in the interlayer space the montmorillonite efficiency decreased, and in the case of vermiculite an opposite effect was observed. Generally the modified montmorillonites were more effective than modified vermiculites. The HDP cations seem to be more effective compare to the HDTMA. The antibacterial activity tests confirmed efficiency of all organically modified clay minerals against Gram-positive bacteria. The confirmation of antibacterial activity against Y. pestis, plague bacteria, is the most interesting result of this part of the study.

  14. X-Ray Photoelectron Spectroscopic Characterization of Chemically Modified Electrodes Used as Chemical Sensors and Biosensors: A Review

    Directory of Open Access Journals (Sweden)

    Elio Desimoni

    2015-04-01

    Full Text Available The characterization of chemically modified sensors and biosensors is commonly performed by cyclic voltammetry and electron microscopies, which allow verifying electrode mechanisms and surface morphologies. Among other techniques, X-ray photoelectron spectroscopy (XPS plays a unique role in giving access to qualitative, quantitative/semi-quantitative and speciation information concerning the sensor surface. Nevertheless, XPS remains rather underused in this field. The aim of this paper is to review selected articles which evidence the useful performances of XPS in characterizing the top surface layers of chemically modified sensors and biosensors. A concise introduction to X-ray Photoelectron Spectroscopy gives to the reader the essential background. The application of XPS for characterizing sensors suitable for food and environmental analysis is highlighted.

  15. The "Clickable" Method for Oligonucleotide Immobilization Onto Azide-Functionalized Microarrays.

    Science.gov (United States)

    Ratajczak, Tomasz; Uszczyńska, Barbara; Frydrych-Tomczak, Emilia; Chmielewski, Marcin K

    2016-01-01

    The DNA microarray technique was supposed to help identifying and analyzing the expression level of tens of thousands of genes in the whole genome. But there is a serious problem concerning fabrication of the microarrays by chemical synthesis, such as specific and efficient linking of probes to a solid support. Therefore, we reckon that applying "click" chemistry to covalently anchor oligonucleotides on chemically modified supports may help construct microarrays in applications such as gene identification. Silanization of the glass support with organofunctional silane makes it possible to link azide groups on glass surface and the nucleic acid probe that is equipped with a pentynyl group. This is followed by direct spotting of the nucleic acid on the azide-modified glass support in the presence of copper ions, and this is a frequently applied method of "click" chemistry.

  16. Synthesis of Peptide-Oligonucleotide Conjugates Using a Heterobifunctional Crosslinker

    Science.gov (United States)

    Williams, Berea A.R.; Chaput, John C.

    2010-01-01

    Peptide-oligonucleotide conjugates (POCs) are molecular chimeras composed of a nucleic acid moiety covalently attached to a polypeptide moiety. POCs have been used in numerous applications from therapeutics to nanotechnology, and most recently as combinatorial agents in the assembly of bivalent protein affinity reagents. This unit describes the synthesis and purification of POC molecules using the heterobifunctional crosslinking reagent succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC), which enables amine-modified oligonucleotides to become covalently linked to cysteine-modified polypeptides. This solution-based protocol consists of a two-step synthesis followed by a single purification step. PMID:20827717

  17. Novel Nanostructures based on Modified Oligonucleotides

    OpenAIRE

    Lorca Contreras, Romina Andrea

    2016-01-01

    Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química Inorgánica Los oligonucleótidos han mostrado una gran versatilidad en nanotecnología, debido principalmente a sus propiedades únicas de reconocimiento y auto-ensamblaje, su tamaño nanométrico y su gran estabilidad. Estas características hacen de ellos unos elementos singulares para la construcción en la nanoescala. En este sentido los oligonucleótidos se han utilizado para gener...

  18. Chemically modified tetracyclines stimulate matrix metalloproteinase-2 production by periodontal ligament cells.

    NARCIS (Netherlands)

    Bildt, M.M.; Snoek-van Beurden, A.M.; Groot, J. de; El, B. van; Kuijpers-Jagtman, A.M.; Hoff, J.W. Von den

    2006-01-01

    BACKGROUND AND OBJECTIVE: The purpose of this study was to investigate the effects of chemically modified tetracyclines (CMTs) on the production of gelatinases [matrix metalloproteinase (MMP)-2 and -9] by human periodontal ligament (PDL) cells, and on the activity of recombinant gelatinases. MATERIA

  19. Chemical modifiers in electrothermal atomic absorption determination of Platinum and Palladium containing preparations in blood serum

    Directory of Open Access Journals (Sweden)

    Аntonina Alemasova

    2012-11-01

    Full Text Available The biological liquids matrixes influence on the characteristic masses and repeatability of Pt and Pd electrothermal atomic absorption spectroscopy (ETAAS determination was studied. The chemical modifiers dimethylglyoxime and ascorbic acid for matrix interferences elimination and ETAAS results repeatability improvement were proposed while bioliquids ETAAS analysis, and their action mechanism was discussed.

  20. Biomechanical properties of acellular sciatic nerves treated with a modified chemical method

    Institute of Scientific and Technical Information of China (English)

    Xinlong Ma; Zhao Yang; Xiaolei Sun; Jianxiong Ma; Xiulan Li; Zhenzhen Yuan; Yang Zhang; Honggang Guo

    2011-01-01

    Nerve grafts are able to adapt to surrounding biomechanical environments if the nerve graft itself exhibits appropriate biomechanical properties (load, elastic modulus, etc.). The present study was designed to determine the differences in biomechanical properties between fresh and chemically acellularized sciatic nerve grafts. Two different chemical methods were used to establish acellular nerve grafts. The nerve was chemically extracted in the Sondell method with a combination of Triton X-100 (nonionic detergent) and sodium deoxycholate (anionic detergent), and in the modified method with a combination of Triton X-200 (anionic detergent), sulfobetaine-10 (SB-10, amphoteric detergents), and sulfobetaine-16 (SB-16, amphoteric detergents). Following acellularization, hematoxylin-eosin staining and scanning electron microscopy demonstrated that the effect of acellularization via the modified method was similar to the traditional Sondell method. However, effects of demyelination and nerve fiber tube integrity were superior to the traditional Sondell method. Biomechanical testing showed that peripheral nerve graft treated using the chemical method resulted in decreased biomechanical properties (ultimate load, ultimate stress, ultimate strain, and mechanical work to fracture) compared with fresh nerves, but the differences had no statistical significance (P > 0.05). These results demonstrated no significant effect on biomechanical properties of nerves treated using the chemical method. In conclusion, nerve grafts treated via the modified method removed Schwann cells, preserved neural structures, and ensured biomechanical properties of the nerve graft, which could be more appropriate for implantation studies.

  1. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function

    Directory of Open Access Journals (Sweden)

    Ville Y. P. Väre

    2017-03-01

    Full Text Available RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA’s cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.

  2. Chemical functionalization of ceramic tile surfaces by silane coupling agents: polymer modified mortar adhesion mechanism implications

    Directory of Open Access Journals (Sweden)

    Alexandra Ancelmo Piscitelli Mansur

    2008-09-01

    Full Text Available Adhesion between tiles and mortars are crucial to the stability of ceramic tile systems. From the chemical point of view, weak forces such as van der Waals forces and hydrophilic interactions are expected to be developed preferably at the tiles and polymer modified Portland cement mortar interface. The main goal of this paper was to use organosilanes as primers to modify ceramic tile hydrophilic properties to improve adhesion between ceramic tiles and polymer modified mortars. Glass tile surfaces were treated with several silane derivatives bearing specific functionalities. Contact angle measurements and Fourier Transform Infrared Spectroscopy (FTIR were used for evaluating the chemical changes on the tile surface. In addition, pull-off tests were conducted to assess the effect on adhesion properties between tile and poly(ethylene-co-vinyl acetate, EVA, modified mortar. The bond strength results have clearly shown the improvement of adherence at the tile-polymer modified mortar interface, reflecting the overall balance of silane, cement and polymer interactions.

  3. Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays

    Directory of Open Access Journals (Sweden)

    Khan Shehnaz

    2004-02-01

    Full Text Available Abstract Background Spotted 70-mer oligonucleotide arrays offer potentially greater specificity and an alternative to expensive cDNA library maintenance and amplification. Since microarray fabrication is a considerable source of data variance, we previously directly tagged cDNA probes with a third fluorophore for prehybridization quality control. Fluorescently modifying oligonucleotide sets is cost prohibitive, therefore, a co-spotted Staphylococcus aureus-specific fluorescein-labeled "tracking" oligonucleotide is described to monitor fabrication variables of a Mycobacterium tuberculosis oligonucleotide microarray. Results Significantly (p M. tuberculosis H37Rv and M. tuberculosis mprA. Linearity between the mean log Cy3/Cy5 ratios of genes differentially expressed from arrays either possessing or lacking the tracking oligonucleotide was observed (R2 = 0.90, p Conclusions This novel approach enables prehybridization array visualization for spotted oligonucleotide arrays and sets the stage for more sophisticated slide qualification and data filtering applications.

  4. Osteogenesis ability of biomimetic modified 3Y-TZP ceramic using chemical treatment

    Energy Technology Data Exchange (ETDEWEB)

    Hsu, Shih-Kuang [Department of Dental Technology and Materials Science, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan, ROC (China); Chang, Pai-Ling [Taoyuan General Hospital, Taoyuan 33004, Taiwan, ROC (China); Ho, Wen-Fu [Department of Chemical and Materials Engineering, National University of Kaohsiung, Kaohsiung 81148, Taiwan, ROC (China); Hsu, Hsueh-Chuan; Liao, Huei-Jyuan [Department of Dental Technology and Materials Science, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan, ROC (China); Wu, Shih-Ching, E-mail: scwu@ctust.edu.tw [Department of Dental Technology and Materials Science, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan, ROC (China)

    2015-12-01

    In this study, RGD peptide derived from extracellular matrix proteins was employed to modify the surface of yttria-tetragonal zirconia polycrystal (3Y-TZP) to promote cell adhesion. The surface of 3Y-TZP ceramic specimens was first modified using chemical treatment with aqueous solutions of H{sub 3}PO{sub 4}, CH{sub 3}COOH, and NaOH, for the formation of Zr–OH surface functional groups. Then, the RGD peptide was immobilized on the surface of the 3Y-TZP through silanization method, with covalent bonding via the Zr–OH surface functional groups. From this study, the RGD peptide can successfully be grafted onto the chemical modified 3Y-TZP surface. The –OH functional groups formed on the surface of 3Y-TZP after acid/alkaline chemical treatment contribute to the grafting reaction of RGD peptides. The use of phosphoric acid solution in 3Y-TZP surface treatment before RGD peptide grafting for biomimetic modification can significantly enhance cell adhesion, proliferation, and differentiation. - Highlights: • This study successfully immobilized the peptides onto the surface of zirconia. • Acid/alkaline chemical treatment promotes the formation of − OH functional groups. • The use of phosphoric acid solution produced the formation of most − OH. • Peptides can significantly enhance cell adhesion, proliferation, and differentiation.

  5. The 5' binding MID domain of human Argonaute2 tolerates chemically modified nucleotide analogues.

    Science.gov (United States)

    Deleavey, Glen F; Frank, Filipp; Hassler, Matthew; Wisnovsky, Simon; Nagar, Bhushan; Damha, Masad J

    2013-02-01

    Small interfering RNAs (siRNAs) can trigger potent gene silencing through the RNA interference (RNAi) pathway. The RNA-induced silencing complex (RISC) is key to this targeted mRNA degradation, and the human Argonaute2 (hAGO2) endonuclease component of RISC is responsible for the actual mRNA cleavage event. During RNAi, hAGO2 becomes loaded with the siRNA guide strand, making several key nucleic acid-enzyme interactions. Chemically modified siRNAs are now widely used in place of natural double-stranded RNAs, and understanding the effects chemical modifications have on guide strand-hAGO2 interactions has become particularly important. Here, interactions between the 5' nucleotide binding domain of hAGO2, MID, and chemically modified nucleotide analogues are investigated. Measured dissociation constants reveal that hAGO2 does not discriminate between nucleotide analogues during binding, regardless of the preferred sugar conformation of the nucleotide analogues. These results correlate well with cell-based gene silencing results employing siRNAs with 5'-modified guide strands. Additionally, chemical modification with 2'-deoxy-2'-fluoroarabino nucleic acid (2'F-ANA) and 2'-deoxy-2'-fluororibonucleic acid (2'F-RNA) at the passenger strand cleavage site of siRNAs has been shown to prevent hAGO2-mediated strand cleavage, an observation that appears to have little impact on overall gene silencing potency.

  6. Polynuclear Nickel Hexacyanoferrate/Graphitized Mesoporous Carbon Hybrid Chemically Modified Electrode for Selective Hydrazine Detection

    OpenAIRE

    Palani Barathi; Annamalai Senthil Kumar; Minnal Ranjan Babu Karthick

    2011-01-01

    A hybrid polynuclear nickel hexacyanoferrate (NiHCFe)/graphitized mesoporous carbon- (GMC-) modified glassy carbon electrode (GCE/NiHCFe@GMC) has been prepared by a sequential method using electrodeposited Ni on a GMC-modified glassy carbon electrode (GCE/Ni@GMC) as a template and [Fe(CN)6]3− as an in-situ chemical precipitant, without any additional interlinking agent. Physicochemical and electrochemical characterizations reveal the presence of NiHCFe units within the porous sites of the GM...

  7. Near-infrared silver cluster optically signaling oligonucleotide hybridization and assembling two DNA hosts.

    Science.gov (United States)

    Petty, Jeffrey T; Nicholson, David A; Sergev, Orlin O; Graham, Stuart K

    2014-09-16

    Silver clusters with ~10 atoms form within DNA strands, and the conjugates are chemical sensors. The DNA host hybridizes with short oligonucleotides, and the cluster moieties optically respond to these analytes. Our studies focus on how the cluster adducts perturb the structure of their DNA hosts. Our sensor is comprised of an oligonucleotide with two components: a 5'-cluster domain that complexes silver clusters and a 3'-recognition site that hybridizes with a target oligonucleotide. The single-stranded sensor encapsulates an ~11 silver atom cluster with violet absorption at 400 nm and with minimal emission. The recognition site hybridizes with complementary oligonucleotides, and the violet cluster converts to an emissive near-infrared cluster with absorption at 730 nm. Our key finding is that the near-infrared cluster coordinates two of its hybridized hosts. The resulting tertiary structure was investigated using intermolecular and intramolecular variants of the same dimer. The intermolecular dimer assembles in concentrated (~5 μM) DNA solutions. Strand stoichiometries and orientations were chromatographically determined using thymine-modified complements that increase the overall conjugate size. The intramolecular dimer develops within a DNA scaffold that is founded on three linked duplexes. The high local cluster concentrations and relative strand arrangements again favor the antiparallel dimer for the near-infrared cluster. When the two monomeric DNA/violet cluster conjugates transform to one dimeric DNA/near-infrared conjugate, the DNA strands accumulate silver. We propose that these correlated changes in DNA structure and silver stoichiometry underlie the violet to near-infrared cluster transformation.

  8. Modified Nucleoside Triphosphates for in-vitro Selection Techniques

    Science.gov (United States)

    Iribarren, Adolfo; Dellafiore, María; Montserrat, Javier

    2016-05-01

    The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the selection of natural DNA or RNA molecules but, in order to improve chemical and structural diversity as well as for particular applications where further chemical or biological stability is necessary, the extension of this strategy to modified oligonucleotides is desirable. Taking into account these needs, this review intends to collect the research carried out during the past years, focusing mainly on the use of modified nucleotides in SELEX and the development of mutant enzymes for broadening nucleoside triphosphates acceptance. In addition, comments regarding the synthesis of modified nucleoside triphosphate will be briefly discussed.

  9. Adhesion mapping of chemically modified and poly(ethylene oxide)-grafted glass surfaces

    OpenAIRE

    Jogikalmath, G.; Stuart, J.K.; Pungor, A.; Hlady, V.

    1999-01-01

    Two-dimensional mapping of the adhesion pull-off forces was used to study the origin of surface heterogeneity in the grafted poly(ethylene oxide) (PEO) layer. The variance of the pull-off forces measured over the μm-sized regions after each chemical step of modifying glass surfaces was taken to be a measure of the surface chemical heterogeneity. The attachment of γ-glycidoxypropyltrimethoxy silane (GPS) to glass decreased the pull-off forces relative to the clean glass and made the surface mo...

  10. Highly improved chromium (III uptake capacity in modified sugarcane bagasse using different chemical treatments

    Directory of Open Access Journals (Sweden)

    Vanessa Cristina Gonçalves Dos Santos

    2012-01-01

    Full Text Available The present paper focuses on improving chromium (III uptake capacity of sugarcane bagasse through its chemical modification with citric acid and/or sodium hydroxide. The chemical modifications were confirmed by infrared spectroscopy, with an evident peak observed at 1730 cm-1, attributed to carbonyl groups. Equilibrium was reached after 24 h, and the kinetics followed the pseudo-second-order model. The highest chromium (III maximum adsorption capacity (MAC value was found when using sugarcane bagasse modified with sodium hydroxide and citric acid (58.00 mg g-1 giving a MAC value about three times greater (20.34 mg g-1 than for raw sugarcane bagasse.

  11. Research on the chemical mechanism in the polyacrylate latex modified cement system

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Min [The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi' an 710072 (China); Wang, Rumin, E-mail: wangmin19@mail.nwpu.edu.cn [The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi' an 710072 (China); Zheng, Shuirong [The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi' an 710072 (China); Northwestern Polytechnical University–East China University of Science and Technology Combined Research Institute of New High Speed Railway Materials (China); Farhan, Shameel; Yao, Hao; Jiang, Hao [The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi' an 710072 (China)

    2015-10-15

    In this paper, the chemical mechanism in the polyacrylate latex modified cement system was investigated by Fourier transform infrared spectra (FT-IR), X-ray photoelectron spectroscopy (XPS), gel permeation chromatography (GPC) and compact pH meter. All results have shown that the chemical reactions in the polyacrylate modified system can be divided into three stages. The hydration reactions of cement can produce large amounts of Ca(OH){sub 2} (calcium hydroxide) and lead the whole system to be alkali-rich and exothermic at the first stage. Subsequently, this environment can do great contributions to the hydrolysis of ester groups in the polyacrylate chains, resulting in the formation of carboxyl groups at the second stage. At the third stage, the final crosslinked network structure of the product was obtained by the reaction between the carboxyl groups in the polyacrylate latex chains and Ca(OH){sub 2}.

  12. Chemically Modified Ordered Mesoporous Carbon/Polyaniline Composites for Electrochemical Capacitors

    Institute of Scientific and Technical Information of China (English)

    KONG Ling-bin; ZHANG Jing; CAI Jian-jun; YANG Zhen-sheng; LUO Yong-chun; KANG Long

    2011-01-01

    Chemically modified ordered mesoporous carbon CMK-3 materials were prepared by means of an easy wet-oxidative method in 2 mol/L nitric acid aqueous solution. A large amount of oxygen-containing functional groups were introduced onto the CMK-3 surface. Modified CMK-3(m-CMK-3) and aniline monomer were polymerized via an in situ chemical oxidative polymerization method. Morphological characterizations of m-CMK-3/PANI (polyaniline) composites were carried out via field emission scanning electron microscopy(SEM). Their electrochemical properties were investigated with cyclic voltammetry, galvanostatic charge-discharge, and electrochemical impedance spectroscopy. The m-CMK-3/PANI composites have excellent properties in capacitance, and the highest specific capacitance(SC) value was up to 489 F/g, suggesting their potential application in the electrode material for electrochemical capacitors.

  13. Splice-switching antisense oligonucleotides as therapeutic drugs

    National Research Council Canada - National Science Library

    Havens, Mallory A; Hastings, Michelle L

    2016-01-01

    Splice-switching oligonucleotides (SSOs) are short, synthetic, antisense, modified nucleic acids that base-pair with a pre-mRNA and disrupt the normal splicing repertoire of the transcript by blocking the RNA-RNA base-pairing or protein-RNA...

  14. Chemically modified STM tips for atomic-resolution imaging of ultrathin NaCI films

    Institute of Scientific and Technical Information of China (English)

    Zhe Li[1; Koen Schouteden[1; Violeta lancu[1; Ewald Janssens[1; Peter Lievens[1; Chris Van Haesendonck[1; Jorge I. Cerda[2

    2015-01-01

    Cl-functionalized scanning tunneling microscopy (STM) tips are fabricated by modifying a tungsten STM tip in situ on islands of ultrathin NaCI(100) films on Au(111) surfaces. The functionalized tips are used to achieve clear atomic- resolution imaging of NaCI(100) islands. In comparison with bare metal tips, the chemically modified tips yield drastically enhanced spatial resolution as well as contrast reversal in STM topographs, implying that Na atoms, rather than C1 atoms, are imaged as protrusions. STM simulations based on a Green's function formalism reveal that the experimentally observed contrast reversal in the STM topographs is due to the highly localized character of the Cl-pz states at the tip apex. An additional remarkable characteristic of the modified tips is that in dI/dV maps, a Na atom appears as a ring with a diameter that depends crucially on the tip-sample distance.

  15. Chemically modified bitumens with enhanced rheology and adhesion properties to siliceous aggregates

    OpenAIRE

    Cuadri Vega, Antonio Abad; Partal López, Pedro; Ahmad, Naveed; Grenfell, James; Airey, Gordon

    2015-01-01

    Moisture damage is one of the major premature failures that worsens the performance and shortens service life of pavements. This research assesses the effect that two chemical modifiers (thiourea and an isocyanate-functionalized castor oil prepolymer) exerts on the bitumen rheology and on the resistance to potential moisture damage of asphalt mixtures based on siliceous aggregates. Both thiourea and the isocyanate-based prepolymer improve the viscous and viscoelastic behaviours of bitumen at ...

  16. Applicability and Optimal Parameters Analysis for Chemical Phosphorus Removal in a Modified Carrousel Oxidation Ditch

    OpenAIRE

    Tao Zhang; Yonghong Zhao

    2017-01-01

    In order to confine the aqua-eutrophication problem arising from phosphorus pollution, many municipal wastewater treatment plants have to improve their executive drainage standard for total phosphorus (TP). In this study, a municipal wastewater treatment plant employing modified Carrousel oxidation ditch as main biological treatment unit was selected as a representative case. Technical necessity for adding a chemically enhanced phosphorus removal unit was analysed, and process feasibility was...

  17. Fabrication of Rare Earth-Doped Transparent Glass Ceramic Optical Fibers by Modified Chemical Vapor Deposition

    OpenAIRE

    2011-01-01

    International audience; Rare earth (RE) doped silica-based optical fibers with transparent glass ceramic (TGC) core was fabricated through the well-known modified chemical vapor deposition (MCVD) process without going through the commonly used stage of post-ceramming. The main characteristics of the RE-doped oxyde nanoparticles namely, their density and mean diameter in the fibers are dictated by the concentration of alkaline earth element used as phase separating agent. Magnesium and erbium ...

  18. Chemically modified bitumens with enhanced rheology and adhesion properties to siliceous aggregates

    OpenAIRE

    Cuadri Vega, Antonio Abad; Partal López, Pedro; Ahmad, Naveed; Grenfell, James; Airey, Gordon

    2015-01-01

    Moisture damage is one of the major premature failures that worsens the performance and shortens service life of pavements. This research assesses the effect that two chemical modifiers (thiourea and an isocyanate-functionalized castor oil prepolymer) exerts on the bitumen rheology and on the resistance to potential moisture damage of asphalt mixtures based on siliceous aggregates. Both thiourea and the isocyanate-based prepolymer improve the viscous and viscoelastic behaviours of bitumen at ...

  19. Chemical modifiers in arsenic determination in biological materials by tungsten coil electrothermal atomic absorption spectrometry.

    Science.gov (United States)

    Bruhn, C G; Huerta, V N; Neira, J Y

    2004-01-01

    Palladium, iridium, and rhodium are evaluated as possible chemical modifiers in the determination of As in digest solutions of biological materials (human hair and clam) by tungsten coil electrothermal atomic absorption spectrophotometry (TCA-AAS). The modifier in solution was applied onto the coil and thermally pre-reduced; the pre-reduction conditions, the amount of modifier, and the thermal program were optimized. Palladium was not satisfactory, whereas Ir and Rh were effective modifiers and rendered better relative sensitivity for As by a factor of 1.4 and 1.9, respectively compared to the case without modifier. Upon optimization of thermal conditions for As in pre-reduced Ir (2.0 microg) and Rh (2.0 microg) modifiers and in the digest solutions of the study matrices, Rh (2.0 microg) was more effective modifier and was selected as such. The mean within-day repeatability was 2.8% in consecutive measurements (25-100 microg L(-1)) (3 cycles, each of n=6) and confirmed good short-term stability of the absorbance measurements. The mean reproducibility was 4.4% (n=20 in a 3-day period) and the detection limit (3 sigmablank/slope) was 29 pg (n=15). The useful coil lifetime in Rh modifier was extended to 300-400 firings. Validation was by determination of As in the certified reference material (CRM) of "Oyster tissue" solution with a percentage relative error (Erel%) of 2% and percentage relative standard deviation (RSD%) of 3% (n=4), and by analytical recovery of As spiked in CRM of human hair [94 +/- 8% (n=4)]. The methodology is simple, fast (sample readout frequency 21 h(-1)), reliable, of low cost, and was applied to the determination of As in hair samples of exposed and unexposed workers.

  20. Chemical modifiers in arsenic determination in biological materials by tungsten coil electrothermal atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Bruhn, C.G.; Huerta, V.N.; Neira, J.Y. [Departamento de Analisis Instrumental, Facultad de Farmacia, Universidad de Concepcion, P.O. Box 237, Concepcion (Chile)

    2004-01-01

    Palladium, iridium, and rhodium are evaluated as possible chemical modifiers in the determination of As in digest solutions of biological materials (human hair and clam) by tungsten coil electrothermal atomic absorption spectrophotometry (TCA-AAS). The modifier in solution was applied onto the coil and thermally pre-reduced; the pre-reduction conditions, the amount of modifier, and the thermal program were optimized. Palladium was not satisfactory, whereas Ir and Rh were effective modifiers and rendered better relative sensitivity for As by a factor of 1.4 and 1.9, respectively compared to the case without modifier. Upon optimization of thermal conditions for As in pre-reduced Ir (2.0 {mu}g) and Rh (2.0 {mu}g) modifiers and in the digest solutions of the study matrices, Rh (2.0 {mu}g) was more effective modifier and was selected as such. The mean within-day repeatability was 2.8% in consecutive measurements (25-100 {mu}g L{sup -1}) (3 cycles, each of n=6) and confirmed good short-term stability of the absorbance measurements. The mean reproducibility was 4.4% (n=20 in a 3-day period) and the detection limit (3{sigma}{sub blank}/slope) was 29 pg (n=15). The useful coil lifetime in Rh modifier was extended to 300-400 firings. Validation was by determination of As in the certified reference material (CRM) of ''Oyster tissue'' solution with a percentage relative error (E{sub rel}%) of 2% and percentage relative standard deviation (RSD%) of 3% (n=4), and by analytical recovery of As spiked in CRM of human hair [94{+-}8% (n=4)]. The methodology is simple, fast (sample readout frequency 21 h{sup -1}), reliable, of low cost, and was applied to the determination of As in hair samples of exposed and unexposed workers. (orig.)

  1. Radiolabeled oligonucleotides for antisense imaging

    Science.gov (United States)

    Iyer, Arun K; He, Jiang

    2011-01-01

    Oligonucleotides radiolabeled with isotopes emitting γ-rays (for SPECT imaging) or positrons (for PET imaging) can be useful for targeting messenger RNA (mRNA) thereby serving as non-invasive imaging tools for detection of gene expression in vivo (antisense imaging). Radiolabeled oligonucleotides may also be used for monitoring their in vivo fate, thereby helping us better understand the barriers to its delivery for antisense targeting. These developments have led to a new area of molecular imaging and targeting, utilizing radiolabeled antisense oligonucleotides. However, the success of antisense imaging relies heavily on overcoming the barriers for its targeted delivery in vivo. Furthermore, the low ability of the radiolabeled antisense oligonucleotide to subsequently internalize into the cell and hybridize with its target mRNA poses additional challenges in realizing its potentials. This review covers the advances in the antisense imaging probe development for PET and SPECT, with an emphasis on radiolabeling strategies, stability, delivery and in vivo targeting. PMID:21822406

  2. Peptide-LNA oligonucleotide conjugates

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Hansen, Lykke Haastrup; Vester, Birte

    2013-01-01

    properties, peptides were introduced into oligonucleotides via a 2'-alkyne-2'-amino-LNA scaffold. Derivatives of methionine- and leucine-enkephalins were chosen as model peptides of mixed amino acid content, which were singly and doubly incorporated into LNA/DNA strands using highly efficient copper......Although peptide-oligonucleotide conjugates (POCs) are well-known for nucleic acids delivery and therapy, reports on internal attachment of peptides to oligonucleotides are limited in number. To develop a convenient route for preparation of internally labeled POCs with improved biomedical......(i)-catalyzed azide-alkyne cycloaddition (CuAAC) "click" chemistry. DNA/RNA target binding affinity and selectivity of the resulting POCs were improved in comparison to LNA/DNA mixmers and unmodified DNA controls. This clearly demonstrates that internal attachment of peptides to oligonucleotides can significantly...

  3. Characterizing the effect of GalNAc and phosphorothioate backbone on binding of antisense oligonucleotides to the asialoglycoprotein receptor.

    Science.gov (United States)

    Schmidt, Karsten; Prakash, Thazha P; Donner, Aaron J; Kinberger, Garth A; Gaus, Hans J; Low, Audrey; Østergaard, Michael E; Bell, Melanie; Swayze, Eric E; Seth, Punit P

    2017-03-17

    Targeted delivery of antisense oligonucleotides (ASO) to hepatocytes via the asialoglycoprotein receptor (ASGR) has improved the potency of ASO drugs ∼30-fold in the clinic (1). In order to fully characterize the effect of GalNAc valency, oligonucleotide length, flexibility and chemical composition on ASGR binding, we tested and validated a fluorescence polarization competition binding assay. The ASGR binding, and in vitro and in vivo activities of 1, 2 and 3 GalNAc conjugated single stranded and duplexed ASOs were studied. Two and three GalNAc conjugated single stranded ASOs bind the ASGR with the strongest affinity and display optimal in vitro and in vivo activities. 1 GalNAc conjugated ASOs showed 10-fold reduced ASGR binding affinity relative to three GalNAc ASOs but only 2-fold reduced activity in mice. An unexpected observation was that the ASGR also appears to play a role in the uptake of unconjugated phosphorothioate modified ASOs in the liver as evidenced by the loss of activity of GalNAc conjugated and unconjugated ASOs in ASGR knockout mice. Our results provide insights into how backbone charge and chemical composition assist in the binding and internalization of highly polar anionic single stranded oligonucleotides into cells and tissues. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Aminosilane functionalizations of mesoporous oxidized silicon for oligonucleotide synthesis and detection.

    Science.gov (United States)

    De Stefano, Luca; Oliviero, Giorgia; Amato, Jussara; Borbone, Nicola; Piccialli, Gennaro; Mayol, Luciano; Rendina, Ivo; Terracciano, Monica; Rea, Ilaria

    2013-06-06

    Direct solid phase synthesis of peptides and oligonucleotides (ONs) requires high chemical stability of the support material. In this work, we have investigated the passivation ability of porous oxidized silicon multilayered structures by two aminosilane compounds, 3-aminopropyltriethoxysilane and 3-aminopropyldimethylethoxysilane (APDMES), for optical label-free ON biosensor fabrication. We have also studied by spectroscopic reflectometry the hybridization between a 13 bases ON, directly grown on the aminosilane modified porous oxidized silicon by in situ synthesis, and its complementary sequence. Even if the results show that both devices are stable to the chemicals (carbonate/methanol) used, the porous silica structure passivated by APDMES reveals higher functionalization degree due to less steric hindrance of pores.

  5. Deposition of carbon nanotubes onto aramid fibers using as-received and chemically modified fibers

    Energy Technology Data Exchange (ETDEWEB)

    Rodríguez-Uicab, O. [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburna de Hidalgo, C.P. 97200 Mérida, Yucatán (Mexico); Avilés, F., E-mail: faviles@cicy.mx [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburna de Hidalgo, C.P. 97200 Mérida, Yucatán (Mexico); Gonzalez-Chi, P.I; Canché-Escamilla, G.; Duarte-Aranda, S. [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburna de Hidalgo, C.P. 97200 Mérida, Yucatán (Mexico); Yazdani-Pedram, M. [Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, S. Livingstone 1007, Independencia, Santiago (Chile); Toro, P. [Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Av. Beauchef 850, Santiago (Chile); Gamboa, F. [Centro de Investigacion y de Estudios Avanzados del IPN, Unidad Mérida, Depto. de Física Aplicada, Km. 6 Antigua Carretera a Progreso, 97310 Mérida, Yucatán (Mexico); Mazo, M.A.; Nistal, A.; Rubio, J. [Instituto de Cerámica y Vidrio (ICV-CSIC), Kelsen 5, 28049 Madrid (Spain)

    2016-11-01

    Highlights: • The surface of aramid fibers was functionalized by two acid treatments. • The treatment based on HNO{sub 3}/H{sub 2}SO{sub 4} reduced the mechanical properties of the fibers. • CNTs were deposited on the aramid fibers, reaching electrical conductivity. • Homogeneous CNT distribution was achieved by using pristine fibers or chlorosulfonic acid. - Abstract: Multiwall carbon nanotubes (MWCNTs) oxidized by an acid treatment were deposited on the surface of as-received commercial aramid fibers containing a surface coating (“sizing”), and fibers modified by either a chlorosulfonic treatment or a mixture of nitric and sulfuric acids. The surface of the aramid fiber activated by the chemical treatments presents increasing density of CO, COOH and OH functional groups. However, these chemical treatments reduced the tensile mechanical properties of the fibers, especially when the nitric and sulfuric acid mixture was used. Characterization of the MWCNTs deposited on the fiber surface was conducted by scanning electron microscopy, Raman spectroscopy mapping and X-ray photoelectron spectroscopy. These characterizations showed higher areal concentration and more homogeneous distribution of MWCNTs over the aramid fibers for as-received fibers and for those modified with chlorosulfonic acid, suggesting the existence of interaction between the oxidized MWCNTs and the fiber coating. The electrical resistance of the MWCNT-modified aramid yarns comprising ∼1000 individual fibers was in the order of MΩ/cm, which renders multifunctional properties.

  6. Deposition of carbon nanotubes onto aramid fibers using as-received and chemically modified fibers

    Science.gov (United States)

    Rodríguez-Uicab, O.; Avilés, F.; Gonzalez-Chi, P. I.; Canché-Escamilla, G.; Duarte-Aranda, S.; Yazdani-Pedram, M.; Toro, P.; Gamboa, F.; Mazo, M. A.; Nistal, A.; Rubio, J.

    2016-11-01

    Multiwall carbon nanotubes (MWCNTs) oxidized by an acid treatment were deposited on the surface of as-received commercial aramid fibers containing a surface coating ("sizing"), and fibers modified by either a chlorosulfonic treatment or a mixture of nitric and sulfuric acids. The surface of the aramid fiber activated by the chemical treatments presents increasing density of CO, COOH and OH functional groups. However, these chemical treatments reduced the tensile mechanical properties of the fibers, especially when the nitric and sulfuric acid mixture was used. Characterization of the MWCNTs deposited on the fiber surface was conducted by scanning electron microscopy, Raman spectroscopy mapping and X-ray photoelectron spectroscopy. These characterizations showed higher areal concentration and more homogeneous distribution of MWCNTs over the aramid fibers for as-received fibers and for those modified with chlorosulfonic acid, suggesting the existence of interaction between the oxidized MWCNTs and the fiber coating. The electrical resistance of the MWCNT-modified aramid yarns comprising ∼1000 individual fibers was in the order of MΩ/cm, which renders multifunctional properties.

  7. A novel catechol-based universal support for oligonucleotide synthesis.

    Science.gov (United States)

    Anderson, Keith M; Jaquinod, Laurent; Jensen, Michael A; Ngo, Nam; Davis, Ronald W

    2007-12-21

    A novel universal support for deoxyribo- and ribonucleic acid synthesis has been developed. The support, constructed from 1,4-dimethoxycatechol, represents an improvement over existing universal supports because of its ability to cleave and deprotect under mild conditions in standard reagents. Because no nonvolatile additives are required for cleavage and deprotection, the synthesized oligonucleotides do not require purification prior to use in biochemical assays. Using reverse phase HPLC and electrospray mass spectroscopy, it was determined that oligonucleotides synthesized on the universal support (UL1) 3'-dephosphorylate quickly (9 h in 28-30% ammonium hydroxide (NH4OH) at 55 degrees C, 2 h in 28-30% NH4OH at 80 degrees C, or <1 h in ammonium hydroxide/methylamine (1:1) (AMA) at 80 degrees C). Oligonucleotides used as primers for the polymerase chain reaction (PCR) assay were found to perform identically to control primers, demonstrating full biological compatibility. In addition, a method was developed for sintering the universal support directly into a filter plug which can be pressure fit into the synthesis column of a commercial synthesizer. The universal support plugs allow the synthesis of high-quality oligonucleotides at least 120 nucleotides in length, with purity comparable to non-universal commercial supports and approximately 50% lower reagent consumption. The universal support plugs are routinely used to synthesize deoxyribo-, ribo-, 3'-modified, 5'-modified, and thioated oligonucleotides. The flexibility of the universal support and the efficiency of 3'-dephosphorylation are expected to increase the use of universal supports in oligonucleotide synthesis.

  8. Biominetic High Density Lipoproteins for the Delivery of Therapeutic Oligonucleotides

    Science.gov (United States)

    Tripathy, Sushant

    Advances in nanotechnology have brought about novel inorganic and hybrid nanoparticles with unique physico-chemical properties that make them suitable for a broad range of applications---from nano-circuitry to drug delivery. A significant part of those advancements have led to ground-breaking discoveries that have changed the approaches to formulation of therapeutics against diseases, such as cancer. Now-a-days the focus does not lie solely on finding a candidate small-molecule therapeutic with minimal adverse effects, but researchers are looking up to nanoparticles to improve biodistribution and biocompatibility profile of clinically proven therapeutics. The plethora of conjugation chemistries offered by currently extant inorganic nanoparticles have, in recent years, led to great leaps in the field of biomimicry---a modality that promises high biocompatibility. Further, in the pursuit of highly specific therapeutic molecules, researchers have turned to silencing oligonucleotides and some have already brought together the strengths of nanoparticles and silencing oligonucleotides in search of an efficacious therapy for cancer with minimal adverse effects. This dissertation work focuses on such a biomimetic platform---a gold nanoparticle based high density lipoprotein biomimetic (HDL NP), for the delivery of therapeutic oligonucleotides. The first chapter of this body of work introduces the molecular target of the silencing oligonucleotides---VEGFR2, and its role in the progression of solid tumor cancers. The background information also covers important aspects of natural high density lipoproteins (HDL), especially their innate capacity to bind and deliver exogenous and endogenous silencing oligonucleotides to tissues that express their high affinity receptor SRB1. We subsequently describe the synthesis of the biomimetic HDL NP and its oligonucleotide conjugates, and establish their biocompatibility. Further on, experimental data demonstrate the efficacy of silencing

  9. A new modified-rate approach for gas-grain chemical simulations

    CERN Document Server

    Garrod, R T

    2008-01-01

    Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new modified-rate method for solving grain-surface chemical systems is presented. Its purpose is accurately to model highly complex systems that can otherwise only be treated using the sometimes inadequate rate-equation approach. In contrast to previous rate-modification techniques, the functional form of the surface production rates was modified, and not simply the rate coefficient. This form is appropriate to the extreme "small-grain" limit, and can be verified using an analytical master-equation approach. Various further modifications were made to this basic form, to account for competition between processes, to improve estimates of surface occupation probabilities, and to allow a switch-over to the normal rate equations where these are applicable. The new method was tested against sys...

  10. A modified method for estimation of chemical oxygen demand for samples having high suspended solids.

    Science.gov (United States)

    Yadvika; Yadav, Asheesh Kumar; Sreekrishnan, T R; Satya, Santosh; Kohli, Sangeeta

    2006-03-01

    Determination of chemical oxygen demand (COD) of samples having high suspended solids concentration such as cattle dung slurry with open reflux method of APHA-AWWA-WPCF did not give consistent results. This study presents a modification of the open reflux method (APHA-AWWA-WPCF) to make it suitable for samples with high percentage of suspended solids. The new method is based on a different technique of sample preparation, modified quantities of reagents and higher reflux time as compared to the existing open reflux method. For samples having solids contents of 14.0 g/l or higher, the modified method was found to give higher value of COD with much higher consistency and accuracy as compared to the existing open reflux method.

  11. The Use of Aryl Hydrazide Linkers for the Solid Phase Synthesis of Chemically Modified Peptides

    Energy Technology Data Exchange (ETDEWEB)

    Woo, Y; Mitchell, A R; Camarero, J A

    2006-11-03

    Since Merrifield introduced the concept of solid phase synthesis in 1963 for the rapid preparation of peptides, a large variety of different supports and resin-linkers have been developed that improve the efficiency of peptide assembly and expand the myriad of synthetically feasible peptides. The aryl hydrazide is one of the most useful resin-linkers for the synthesis of chemically modified peptides. This linker is completely stable during Boc- and Fmoc-based solid phase synthesis and yet it can be cleaved under very mild oxidative conditions. The present article reviews the use of this valuable linker for the rapid and efficient synthesis of C-terminal modified peptides, head-to-tail cyclic peptides and lipidated peptides.

  12. Silencing of Inducible Immunoproteasome Subunit Expression by Chemically Modified siRNA and shRNA.

    Science.gov (United States)

    Gvozdeva, Olga V; Prassolov, Vladimir S; Zenkova, Marina A; Vlassov, Valentin V; Chernolovskaya, Elena L

    2016-08-01

    Overexpression of inducible subunits of immunoproteasome is related to pathogenesis of some chronic diseases. Specific inhibition of the immunosubunits may be used for the treatment of these diseases and RNA interference is one of the potent methods used in this area. We designed 2'-O-methyl modified siRNAs with selectively protected nuclease-sensitive sites, which efficiently silence LMP2, LMP7, and MECL-1 genes expression. To provide stable long-lasting inhibition of target genes, short-hairpin RNAs (shRNA) expressed by lentiviral vectors were constructed. Our results demonstrated that chemically modified siRNAs inhibited the expression of target genes with similar efficiency or with efficiency exceeding that of corresponding shRNAs and provide silencing effect for 5 days.

  13. Highly dispersed Pd nanoparticles on chemically modified graphene with aminophenyl groups for formic acid oxidation

    Science.gov (United States)

    Yang, Su-Dong; Shen, Cheng-Min; Tong, Hao; He, Wei; Zhang, Xiao-Gang; Gao, Hong-Jun

    2011-11-01

    A novel electrode material based on chemically modified graphene (CMG) with aminophenyl groups is covalently functionalized by a nucleophilic ring-opening reaction between the epoxy groups of graphene oxide and the aminophenyl groups of p-phenylenediamine. Palladium nanoparticles with an average diameter of 4.2 nm are deposited on the CMG by a liquid-phase borohydride reduction. The electrocatalytic activity and stability of the Pd/CMG composite towards formic acid oxidation are found to be higher than those of reduced graphene oxide and commercial carbon materials such as Vulcan XC-72 supported Pd electrocatalysts.

  14. Retention of proteins and metalloproteins in open tubular capillary electrochromatography with etched chemically modified columns.

    Science.gov (United States)

    Pesek, Joseph J; Matyska, Maria T; Salgotra, Vasudha

    2008-09-01

    Etched chemically modified capillaries with two different bonded groups (pentyl and octadecyl) are compared for their migration behavior of several common proteins and metalloproteins as well as metalloproteinases. Migration times, efficiency and peak shape are evaluated over the pH range of 2.1-8.1 to determine any effects of the bonded group on the electrochromatographic behavior of these compounds. One goal was to determine if the relative hydrophobicity of the stationary phase has a significant effect on proteins in the open tubular format of capillary electrochromatography as it does in HPLC. Reproducibility of the migration times is also investigated.

  15. Retention of Proteins and Metalloproteins in Open Tubular Capillary Electrochromatography with Etched Chemically Modified Columns

    Science.gov (United States)

    Pesek, Joseph J.; Matyska, Maria T.; Salgotra, Vasudha

    2010-01-01

    Etched chemically modified capillaries with two different bonded groups (pentyl and octadecyl) are compared for their migration behavior of several common proteins and metalloproteins as well as metalloproteinases. Migration times, efficiency and peak shape are evaluated over the pH range of 2.1 to 8.1 to determine any effects of the bonded group on the electrochromatographic behavior of these compounds. One goal was to determine if the relative hydrophobicity of the stationary phase has a significant effect on proteins in the open tubular format of capillary electrochromatography as it does in HPLC. Reproducibility of the migration times is also investigated. PMID:18850653

  16. Modified Augmented Lagrange Multiplier Methods for Large-Scale Chemical Process Optimization

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Chemical process optimization can be described as large-scale nonlinear constrained minimization. The modified augmented Lagrange multiplier methods (MALMM) for large-scale nonlinear constrained minimization are studied in this paper. The Lagrange function contains the penalty terms on equality and inequality constraints and the methods can be applied to solve a series of bound constrained sub-problems instead of a series of unconstrained sub-problems. The steps of the methods are examined in full detail. Numerical experiments are made for a variety of problems, from small to very large-scale, which show the stability and effectiveness of the methods in large-scale problems.

  17. Size-dependent mobility of gold nano-clusters during growth on chemically modified graphene

    Energy Technology Data Exchange (ETDEWEB)

    Bell, Gavin R., E-mail: gavin.bell@warwick.ac.uk; Dawson, Peter M.; Pandey, Priyanka A.; Wilson, Neil R. [Department of Physics, University of Warwick, Coventry CV4 7AL (United Kingdom); Mulheran, Paul A. [Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose St., Glasgow G1 1XJ (United Kingdom)

    2014-01-01

    Gold nano-clusters were grown on chemically modified graphene by direct sputter deposition. Transmission electron microscopy of the nano-clusters on these electron-transparent substrates reveals an unusual bimodal island size distribution (ISD). A kinetic Monte Carlo model of growth incorporating a size-dependent cluster mobility rule uniquely reproduces the bimodal ISD, providing strong evidence for the mobility of large clusters during surface growth. The cluster mobility exponent of −5/3 is consistent with cluster motion via one-dimensional diffusion of gold atoms around the edges of the nano-clusters.

  18. Size-dependent mobility of gold nano-clusters during growth on chemically modified graphene

    Directory of Open Access Journals (Sweden)

    Gavin R. Bell

    2014-01-01

    Full Text Available Gold nano-clusters were grown on chemically modified graphene by direct sputter deposition. Transmission electron microscopy of the nano-clusters on these electron-transparent substrates reveals an unusual bimodal island size distribution (ISD. A kinetic Monte Carlo model of growth incorporating a size-dependent cluster mobility rule uniquely reproduces the bimodal ISD, providing strong evidence for the mobility of large clusters during surface growth. The cluster mobility exponent of −5/3 is consistent with cluster motion via one-dimensional diffusion of gold atoms around the edges of the nano-clusters.

  19. Peroxide-modified titanium dioxide: a chemical analog of putative Martian soil oxidants

    Science.gov (United States)

    Quinn, R. C.; Zent, A. P.

    1999-01-01

    Hydrogen peroxide chemisorbed on titanium dioxide (peroxide-modified titanium dioxide) is investigated as a chemical analog to the putative soil oxidants responsible for the chemical reactivity seen in the Viking biology experiments. When peroxide-modified titanium dioxide (anatase) was exposed to a solution similar to the Viking labeled release (LR) experiment organic medium, CO2 gas was released into the sample cell headspace. Storage of these samples at 10 degrees C for 48 hr prior to exposure to organics resulted in a positive response while storage for 7 days did not. In the Viking LR experiment, storage of the Martian surface samples for 2 sols (approximately 49 hr) resulted in a positive response while storage for 141 sols essentially eliminated the initial rapid release of CO2. Heating the peroxide-modified titanium dioxide to 50 degrees C prior to exposure to organics resulted in a negative response. This is similar to, but not identical to, the Viking samples where heating to approximately 46 degrees C diminished the response by 54-80% and heating to 51.5 apparently eliminated the response. When exposed to water vapor, the peroxide-modified titanium dioxide samples release O2 in a manner similar to the release seen in the Viking gas exchange experiment (GEx). Reactivity is retained upon heating at 50 degrees C for three hours, distinguishing this active agent from the one responsible for the release of CO2 from aqueous organics. The release of CO2 by the peroxide-modified titanium dioxide is attributed to the decomposition of organics by outer-sphere peroxide complexes associated with surface hydroxyl groups, while the release of O2 upon humidification is attributed to more stable inner-sphere peroxide complexes associated with Ti4+ cations. Heating the peroxide-modified titanium dioxide to 145 degrees C inhibited the release of O2, while in the Viking experiments heating to this temperature diminished but did not eliminated the response. Although the

  20. A Mechanistic Study of Chemically Modified Inorganic Membranes for Gas and Liquid Separations

    Energy Technology Data Exchange (ETDEWEB)

    Way, J Douglas

    2011-01-21

    This final report will summarize the progress made during the period August 1, 1993 - October 31, 2010 with support from DOE grant number DE-FG03-93ER14363. The objectives of the research have been to investigate the transport mechanisms in micro- and mesoporous, metal oxide membranes and to examine the relationship between the microstructure of the membrane, the membrane surface chemistry, and the separation performance of the membrane. Examples of the membrane materials under investigation are the microporous silica hollow fiber membrane manufactured by PPG Industries, chemically modified mesoporous oxide membranes, and polymer membranes containing microporous oxides (mixed matrix membranes). Analytical techniques such as NMR, FTIR and Raman spectroscopy, thermal analysis, and gas adsorption were used to investigate membrane microstructure and to probe the chemical interactions occurring at the gas-membrane interface.

  1. Free-radical-promoted conversion of graphite oxide into chemically modified graphene.

    Science.gov (United States)

    Chai, Na-Na; Zeng, Jing; Zhou, Kai-Ge; Xie, Yu-Long; Wang, Hang-Xing; Zhang, Hao-Li; Xu, Chen; Zhu, Ji-Xin; Yan, Qing-Yu

    2013-05-01

    The preparation of chemically modified graphene (CMG) generally involves the reduction of graphite oxide (GO) by using various reducing reagents. Herein, we report a free-radical-promoted synthesis of CMG, which does not require any conventional reductant. We demonstrated that the phenyl free radical can efficiently promote the conversion of GO into CMG under mild conditions and produces phenyl-functionalized CMG. This pseudo-"reduction" process is attributed to a free-radical-mediated elimination of the surface-attached oxygen-containing functionalities. This work illustrates a new strategy for preparing CMG that is alternative to the conventional means of chemical reduction. Furthermore, the phenyl-functionalized graphene shows an excellent performance as an electrode material for lithium-battery applications.

  2. DIMENSIONAL STABILITY AND WATER REPELLENT EFFICIENCY MEASUREMENT OF CHEMICALLY MODIFIED TROPICAL LIGHT HARDWOOD

    Directory of Open Access Journals (Sweden)

    Md Saiful Islam,

    2012-01-01

    Full Text Available Chemical modification is an often-followed route to improve physical and mechanical properties of solid wood materials. In this study five kinds of tropical light hardwoods species, namely jelutong (Dyera costulata, terbulan (Endospermum diadenum, batai (Paraserianthes moluccana, rubberwood (Hevea brasiliensis, and pulai (Alstonia pneumatophora, were chemically modified with benzene diazonium salt to improve their dimensional stability and water repellent efficiency. The dimensional stability of treated samples in terms of volumetric swelling coefficient (S and anti-swelling-efficiency (ASE were found to improve with treatment. The water repellent efficiency (WRE values also seemed to improve considerably with treatment of wood samples. Furthermore, treated wood samples had lower water and moisture absorption compared to that of untreated ones.

  3. Facile Synthesis of Mono-Dispersed Polystyrene (PS/Ag Composite Microspheres via Modified Chemical Reduction

    Directory of Open Access Journals (Sweden)

    Wen Zhu

    2013-12-01

    Full Text Available A modified method based on in situ chemical reduction was developed to prepare mono-dispersed polystyrene/silver (PS/Ag composite microspheres. In this approach; mono-dispersed PS microspheres were synthesized through dispersion polymerization using poly-vinylpyrrolidone (PVP as a dispersant at first. Then, poly-dopamine (PDA was fabricated to functionally modify the surfaces of PS microspheres. With the addition of [Ag(NH32]+ to the PS dispersion, [Ag(NH32]+ complex ions were absorbed and reduced to silver nanoparticles on the surfaces of PS-PDA microspheres to form PS/Ag composite microspheres. PVP acted both as a solvent of the metallic precursor and as a reducing agent. PDA also acted both as a chemical protocol to immobilize the silver nanoparticles at the PS surface and as a reducing agent. Therefore, no additional reducing agents were needed. The resulting composite microspheres were characterized by TEM, field emission scanning electron microscopy (FESEM, energy-dispersive X-ray spectroscopy (EDS, XRD, UV-Vis and surface-enhanced Raman spectroscopy (SERS. The results showed that Ag nanoparticles (NPs were homogeneously immobilized onto the PS microspheres’ surface in the presence of PDA and PVP. PS/Ag composite microspheres were well formed with a uniform and compact shell layer and were adjustable in terms of their optical property.

  4. Aqueous dispersions of few-layer-thick chemically modified magnesium diboride nanosheets by ultrasonication assisted exfoliation

    Science.gov (United States)

    Das, Saroj Kumar; Bedar, Amita; Kannan, Aadithya; Jasuja, Kabeer

    2015-01-01

    The discovery of graphene has led to a rising interest in seeking quasi two-dimensional allotropes of several elements and inorganic compounds. Boron, carbon’s neighbour in the periodic table, presents a curious case in its ability to be structured as graphene. Although it cannot independently constitute a honeycomb planar structure, it forms a graphenic arrangement in association with electron-donor elements. This is exemplified in magnesium diboride (MgB2): an inorganic layered compound comprising boron honeycomb planes alternated by Mg atoms. Till date, MgB2 has been primarily researched for its superconducting properties; it hasn’t been explored for the possibility of its exfoliation. Here we show that ultrasonication of MgB2 in water results in its exfoliation to yield few-layer-thick Mg-deficient hydroxyl-functionalized nanosheets. The hydroxyl groups enable an electrostatically stabilized aqueous dispersion and create a heterogeneity leading to an excitation wavelength dependent photoluminescence. These chemically modified MgB2 nanosheets exhibit an extremely small absorption coefficient of 2.9 ml mg−1 cm−1 compared to graphene and its analogs. This ability to exfoliate MgB2 to yield nanosheets with a chemically modified lattice and properties distinct from the parent material presents a fundamentally new perspective to the science of MgB2 and forms a first foundational step towards exfoliating metal borides. PMID:26041686

  5. Adhesion mapping of chemically modified and poly(ethylene oxide)-grafted glass surfaces

    Science.gov (United States)

    Jogikalmath, G.; Stuart, J.K.; Pungor, A.; Hlady, V.

    2012-01-01

    Two-dimensional mapping of the adhesion pull-off forces was used to study the origin of surface heterogeneity in the grafted poly(ethylene oxide) (PEO) layer. The variance of the pull-off forces measured over the μm-sized regions after each chemical step of modifying glass surfaces was taken to be a measure of the surface chemical heterogeneity. The attachment of γ-glycidoxypropyltrimethoxy silane (GPS) to glass decreased the pull-off forces relative to the clean glass and made the surface more uniform. The subsequent hydrolysis of the terminal epoxide groups resulted in a larger surface heterogeneity which was modeled by two populations of the terminal hydroxyl groups, each with its own distribution of adhesion forces and force variance. The activation of the hydroxyls with carbonyldiimmidazole (CDI) healed the surface and lowered its adhesion, however, the force variance remained rather large. Finally, the grafting of the α,ω-diamino poly(ethyleneoxide) chains to the CDI-activated glass largely eliminated adhesion except at a few discrete regions. The adhesion on the PEO grafted layer followed the Poisson distribution of the pull-off forces. With the exception of the glass surface, a correlation between the water contact angles and the mean pull-off forces measured with the Si3N4 tip surfaces was found for all modified glass surfaces. PMID:22267896

  6. Determination of bisphenol A in food-simulating liquids using LCED with a chemically modified electrode.

    Science.gov (United States)

    D'Antuono, A; Dall'Orto, V C; Lo Balbo, A; Sobral, S; Rezzano, I

    2001-03-01

    Liquid chromatography with electrochemical detector (LC-ED), using a chemically modified electrode coated with a metalloporphyrin film, is reported for determination of bisphenol A (BPA) migration from polycarbonate baby bottles. The extraction process of the samples was performed according to regulations of the Southern Common Market (MERCOSUR), where certain food-simulating liquids [(A) distilled water, (B) acetic acid 3% V/V in distilled water, and (C) ethanol 15% V/V in distilled water] are defined along with controlled time and temperature conditions. The baseline obtained using the naked electrode showed a considerable drift which increased the detection limit. This effect was suppressed with the chemically modified electrode. A linear range up to 450 ppb along with a detection limit of 20 ppb for the amperometric detection technique was observed. The procedure described herein allowed lowering the detection limit of the method to 0.2 ppb. The value found for BPA in the food-simulating liquid is 1.2 ppb, which is below the tolerance limit for specific migration (4.8 ppm).

  7. Chemically modified inulin microparticles serving dual function as a protein antigen delivery vehicle and immunostimulatory adjuvant.

    Science.gov (United States)

    Gallovic, Matthew D; Montjoy, Douglas G; Collier, Michael A; Do, Clement; Wyslouzil, Barbara E; Bachelder, Eric M; Ainslie, Kristy M

    2016-03-01

    To develop a new subunit vaccine adjuvant, we chemically modified a naturally-occurring, immunostimulatory inulin polysaccharide to produce an acid-sensitive biopolymer (acetalated inulin, Ace-IN). Various hydrophobic Ace-IN polymers were formed into microparticles (MPs) by oil-in-water emulsions followed by solvent evaporation These Ace-IN MPs possessed tunable degradation characteristics that, unlike polyesters used in FDA-approved microparticulate formulations, had only pH-neutral hydrolytic byproducts. Macrophages were passively targeted with cytocompatible Ace-IN MPs. TNF-α production by macrophages treated with Ace-IN MPs could be altered by adjusting the polymers' chemistry. Mice immunized with Ace-IN MPs encapsulating a model ovalbumin (OVA) antigen showed higher production of anti-OVA IgG antibody levels relative to soluble antigen. The antibody titers were also comparable to an alum-based formulation. This proof-of-concept establishes the potential for chemically-modified inulin MPs to simultaneously enable dual functionality as a stimuli-controlled antigen delivery vehicle and immunostimulatory adjuvant.

  8. Molecular Mechanisms of Antisense Oligonucleotides.

    Science.gov (United States)

    Crooke, Stanley T

    2017-04-01

    In 1987, when I became interested in the notion of antisense technology, I returned to my roots in RNA biochemistry and began work to understand how oligonucleotides behave in biological systems. Since 1989, my research has focused primarily on this topic, although I have been involved in most areas of research in antisense technology. I believe that the art of excellent science is to frame large important questions that are perhaps not immediately answerable with existing knowledge and methods, and then conceive a long-term (multiyear) research strategy that begins by answering the most pressing answerable questions on the path to the long-term goals. Then, a step-by-step research pathway that will address the strategic questions posed must be implemented, adjusting the plan as new things are learned. This is the approach we have taken at Ionis. Obviously, to create antisense technology, we have had to address a wide array of strategic questions, for example, the medicinal chemistry of oligonucleotides, manufacturing and analytical methods, pharmacokinetics and toxicology, as well as questions about the molecular pharmacology of antisense oligonucleotides (ASOs). Each of these endeavors has consumed nearly three decades of scientific effort, is still very much a work-in-progress, and has resulted in hundreds of publications. As a recipient of the Lifetime Achievement Award 2016 granted by the Oligonucleotide Therapeutic Society, in this note, my goal is to summarize the contributions of my group to the efforts to understand the molecular mechanisms of ASOs.

  9. Thermodynamics of Oligonucleotide Duplex Melting

    Science.gov (United States)

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-01-01

    Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply…

  10. Sensory and rheological properties of transgenically and chemically modified starch ingredients as evaluated in a food product model

    DEFF Research Database (Denmark)

    Ahmt, T.; Wischmann, Bente; Blennow, A.

    2004-01-01

    Starches derived from five genetically modified potato lines, two chemically modified potato starches and two native starches from potato and maize were subjected to physical and chemical analyses and their functionality evaluated in a milk-based food product model. The transgenic starches were...... gels with a higher tendency to retrograde and a low freeze/thaw stability as compared to starches with shorter amylopectin chains and lower phosphorous content. The textural properties of the food product model prepared from genetically and chemically modified starches were characterised by sensory...... and rheological analyses. To clearly visualise the effects of the modifications, data was evaluated by radar plots and multiple regression analysis (chemometrics). Genetically modified potato starches with longer amylopectin chains and increased phosphorous content gave a more gelled and a shorter texture...

  11. Dual-tracer method to estimate coral reef response to a plume of chemically modified seawater

    Science.gov (United States)

    Maclaren, J. K.; Caldeira, K.

    2013-12-01

    We present a new method, based on measurement of seawater samples, to estimate the response of a reef ecosystem to a plume of an additive (for example, a nutrient or other chemical). In the natural environment, where there may be natural variability in concentrations, it can be difficult to distinguish between changes in concentrations that would occur naturally and changes in concentrations that result from a chemical addition. Furthermore, in the unconfined natural environment, chemically modified water can mix with waters that have not been modified, making it difficult to distinguish between effects of dilution and effects of chemical fluxes or transformations. We present a dual-tracer method that extracts signals from observations that may be affected by both natural variability and dilution. In this dual-tracer method, a substance (in our example case, alkalinity) is added to the water in known proportion to a passive conservative tracer (in our example case, Rhodamine WT dye). The resulting plume of seawater is allowed to flow over the study site. Two transects are drawn across the plume at the front and back of the study site. If, in our example, alkalinity is plotted as a function of dye concentration for the front transect, the slope of the resulting mixing line is the ratio of alkalinity to dye in the added fluid. If a similar mixing line is measured and calculated for the back transect, the slope of this mixing line will indicate the amount of added alkalinity that remains in the water flowing out of the study site per unit of added dye. The ratio of the front and back slopes indicates the fraction of added alkalinity that was taken up by the reef. The method is demonstrated in an experiment performed on One Tree Reef (Queensland, Australia) aimed at showing that ocean acidification is already affecting coral reef growth. In an effort to chemically reverse some of the changes to seawater chemistry that have occurred over the past 200 years, we added

  12. The performance of chemically and physically modified local kaolinite in methanol dehydration to dimethyl ether

    Directory of Open Access Journals (Sweden)

    Sanaa M. Solyman

    2014-09-01

    Full Text Available The catalytic activity of modified natural kaolinite as a solid acid catalyst for dimethyl ether (DME preparation was investigated by following up the conversion% of methanol and the yield% of DME. Natural kaolinite (KN was treated chemically with H2O2 (KT followed by thermal treatment at 500 °C (KC and then mechano-chemically by ball milling with and without CaSO4 (KB-Ca and KB, respectively. These samples were characterized by XRD, FTIR, SEM, HRTEM, TGA and NH3-TPD techniques. The different techniques showed that the chemical treatment of kaolinite with H2O2 resulted in partial exfoliation/delamination of kaolinite, decreased the amount of acidic sites which is accompanied by increasing their strength. Calcination only decreased the acidic strength and slightly enlarged the particle size mostly due to heat effect. Ball milling resulted in multitude randomly-oriented crystals and increased the amount of acidic sites with the same strength of KT sample. CaSO4 mostly produced ordered monocrystalline kaolinite and created new acidic sites with slightly lower strength relative to KB. The catalytic activity and selectivity depend on the reaction temperature, the space velocity and the strength of acid sites. The most active sample is KB-Ca, which gives 84% DME due to its high amount and strength of acidic sites. The different modification methods resulted in 100% selectivity for DME.

  13. Physico-Chemical Properties and Biodegradability of Genetically Modified Populus trichocarpa and Pinus taeda

    Science.gov (United States)

    Edmunds, Charles Warren

    Increasing concerns over greenhouse gas emissions and the finite supply of fossil fuels lead to the goal of utilizing lignocellulosic feedstocks for biofuels, platform chemicals, and biocomposites. Lignin is responsible for the recalcitrance of lignocellulosic biomass and is a major barrier to its deconstruction. Great progress has been made in mapping and modifying the lignin biosynthetic pathway. However, the link between the genetic modification, resulting chemical and physical properties of the wood, and how these properties influence the thermomechanical and recalcitrance to biological and chemical degradation needs further investigation. In this dissertation, the study of modified Populus trichocarpa and Pinus taeda were utilized to accomplish this goal. Thermo-mechanical properties of genetically modified P. trichocarpa with altered lignin content and/or lignin structure were measured with a series of tools including; dynamic mechanical analysis, nuclear magnetic resonance, and wet chemistry techniques. Results demonstrated lignin content and lignin structure likely influence the glass transition temperature (Tg), and that decreased lignin content and the corresponding higher proportion of cell wall carbohydrates may contribute to increased molecular mobility in the wood polymer structure. The effect of lignin biosynthetic pathway modification on biological degradation of these transgenic wood specimens was of interest. However, experimental methods for fungal treatment on small young greenhouse-grown wood specimens are not well established. Therefore, a project was undertaken to develop a method for fungal inoculation and incubation for these unique specimens. Several parameters were tested, and a fungal treatment method was identified with sufficient weight loss after decay and significant reduction in variation of weight loss between replicates compared to previous experiments by direct inoculation of wood with liquid malt extract fungal culture

  14. Highly Sensitive Nuclease Assays Based on Chemically Modified DNA or RNA

    Directory of Open Access Journals (Sweden)

    Shinobu Sato

    2014-07-01

    Full Text Available Nucleolytic enzymes are associated with various diseases, and several methods have been developed for their detection. DNase expression is modulated in such diseases as acute myocardial infarction, transient myocardial ischemia, oral cancer, stomach cancer, and malignant lymphoma, and DNase I is used in cystic fibroma therapy. RNase is used to treat mesothelial cancer because of its antiproliferative, cytotoxic, and antineoplastic activities. Angiogenin, an angiogenic factor, is a member of the RNase A family. Angiogenin inhibitors are being developed as anticancer drugs. In this review, we describe fluorometric and electrochemical techniques for detecting DNase and RNase in disease. Oligonucleotides having fluorescence resonance energy transfer (FRET-causing chromophores are non-fluorescent by themselves, yet become fluorescent upon cleavage by DNase or RNase. These oligonucleotides serve as a powerful tool to detect activities of these enzymes and provide a basis for drug discovery. In electrochemical techniques, ferrocenyl oligonucleotides with or without a ribonucleoside unit are used for the detection of RNase or DNase. This technique has been used to monitor blood or serum samples in several diseases associated with DNase and RNase and is unaffected by interferents in these sample types.

  15. Cellular uptake and trafficking of antisense oligonucleotides.

    Science.gov (United States)

    Crooke, Stanley T; Wang, Shiyu; Vickers, Timothy A; Shen, Wen; Liang, Xue-Hai

    2017-03-01

    Antisense oligonucleotides (ASOs) modified with phosphorothioate (PS) linkages and different 2' modifications can be used either as drugs (e.g., to treat homozygous familial hypercholesterolemia and spinal muscular atrophy) or as research tools to alter gene expression. PS-ASOs can enter cells without additional modification or formulation and can be designed to mediate sequence-specific cleavage of different types of RNA (including mRNA and non-coding RNA) targeted by endogenous RNase H1. Although PS-ASOs function in both the cytoplasm and nucleus, localization to different subcellular regions can affect their therapeutic potency. Cellular uptake and intracellular distribution of PS ASOs are mediated by protein interactions. The main proteins involved in these processes have been identified, and intracellular sites in which PS ASOs are active, or inactive, cataloged.

  16. Conjugation of fluorescent proteins with DNA oligonucleotides.

    Science.gov (United States)

    Lapiene, Vidmantas; Kukolka, Florian; Kiko, Kathrin; Arndt, Andreas; Niemeyer, Christof M

    2010-05-19

    This work describes the synthesis of covalent ssDNA conjugates of six fluorescent proteins, ECFP, EGFP, E(2)GFP, mDsRed, Dronpa, and mCherry, which were cloned with an accessible C-terminal cystein residue to enable site-selective coupling using a heterobispecific cross-linker. The resulting conjugates revealed similar fluorescence emission intensity to the unconjugated proteins, and the functionality of the tethered oligonucleotide was proven by specific Watson-Crick base pairing to cDNA-modified gold nanoparticles. Fluorescence spectroscopy analysis indicated that the fluorescence of the FP is quenched by the gold particle, and the extent of quenching varied with the intrinsic spectroscopic properties of FP as well as with the configuration of surface attachment. Since this study demonstrates that biological fluorophores can be selectively incorporated into and optically coupled with nanoparticle-based devices, applications in DNA-based nanofabrication can be foreseen.

  17. Oligonucleotide Therapy for Obstructive and Restrictive Respiratory Diseases

    Directory of Open Access Journals (Sweden)

    Wupeng Liao

    2017-01-01

    Full Text Available Inhaled oligonucleotide is an emerging therapeutic modality for various common respiratory diseases, including obstructive airway diseases like asthma and chronic obstructive pulmonary disease (COPD and restrictive airway diseases like idiopathic pulmonary fibrosis (IPF. The advantage of direct accessibility for oligonucleotide molecules to the lung target sites, bypassing systemic administration, makes this therapeutic approach promising with minimized potential systemic side effects. Asthma, COPD, and IPF are common chronic respiratory diseases, characterized by persistent airway inflammation and dysregulated tissue repair and remodeling, although each individual disease has its unique etiology. Corticosteroids have been widely prescribed for the treatment of asthma, COPD, and IPF. However, the effectiveness of corticosteroids as an anti-inflammatory drug is limited by steroid resistance in severe asthma, the majority of COPD cases, and pulmonary fibrosis. There is an urgent medical need to develop target-specific drugs for the treatment of these respiratory conditions. Oligonucleotide therapies, including antisense oligonucleotide (ASO, small interfering RNA (siRNA, and microRNA (miRNA are now being evaluated both pre-clinically and clinically as potential therapeutics. The mechanisms of action of ASO and siRNA are highly target mRNA specific, ultimately leading to target protein knockdown. miRNA has both biomarker and therapeutic values, and its knockdown by a miRNA antagonist (antagomir has a broader but potentially more non-specific biological outcome. This review will compile the current findings of oligonucleotide therapeutic targets, verified in various respiratory disease models and in clinical trials, and evaluate different chemical modification approaches to improve the stability and potency of oligonucleotides for the treatment of respiratory diseases.

  18. Oligonucleotide Therapy for Obstructive and Restrictive Respiratory Diseases.

    Science.gov (United States)

    Liao, Wupeng; Dong, Jinrui; Peh, Hong Yong; Tan, Lay Hong; Lim, Kah Suan; Li, Li; Wong, Wai-Shiu Fred

    2017-01-17

    Inhaled oligonucleotide is an emerging therapeutic modality for various common respiratory diseases, including obstructive airway diseases like asthma and chronic obstructive pulmonary disease (COPD) and restrictive airway diseases like idiopathic pulmonary fibrosis (IPF). The advantage of direct accessibility for oligonucleotide molecules to the lung target sites, bypassing systemic administration, makes this therapeutic approach promising with minimized potential systemic side effects. Asthma, COPD, and IPF are common chronic respiratory diseases, characterized by persistent airway inflammation and dysregulated tissue repair and remodeling, although each individual disease has its unique etiology. Corticosteroids have been widely prescribed for the treatment of asthma, COPD, and IPF. However, the effectiveness of corticosteroids as an anti-inflammatory drug is limited by steroid resistance in severe asthma, the majority of COPD cases, and pulmonary fibrosis. There is an urgent medical need to develop target-specific drugs for the treatment of these respiratory conditions. Oligonucleotide therapies, including antisense oligonucleotide (ASO), small interfering RNA (siRNA), and microRNA (miRNA) are now being evaluated both pre-clinically and clinically as potential therapeutics. The mechanisms of action of ASO and siRNA are highly target mRNA specific, ultimately leading to target protein knockdown. miRNA has both biomarker and therapeutic values, and its knockdown by a miRNA antagonist (antagomir) has a broader but potentially more non-specific biological outcome. This review will compile the current findings of oligonucleotide therapeutic targets, verified in various respiratory disease models and in clinical trials, and evaluate different chemical modification approaches to improve the stability and potency of oligonucleotides for the treatment of respiratory diseases.

  19. Chemically modified and nanostructured porous silicon as a drug delivery material and device

    Science.gov (United States)

    Anglin, Emily Jessica

    This thesis describes the fabrication, chemical modification, drug release, and toxicity studies of nanostructured porous silicon for the purposes of developing a smart drug delivery device. The first chapter is an introductory chapter, presenting the chemical and physical properties of porous silicon, the concepts and issues of current drug delivery devices and materials, and how porous silicon can address the issues regarding localized and controlled drug therapies. The second chapter discusses chemical modifications of nanostructured porous Si for stabilizing the material in biologically relevant media while providing an extended release of a therapeutic in vitro. This chapter also demonstrates the utility of the porous silicon optical signatures for effectively monitoring drug release from the system and its applications for development of a self-reporting drug delivery device. In chapter three, the concept of providing a triggered release of a therapeutic from porous silicon microparticles through initiation by an external stimulus is demonstrated. The microparticles are chemically modified, and the release is enhanced by a short application of ultrasound to the particulate system. The effect of ultrasound on the drug release and particle size is discussed. Chapter four presents a new method for sustaining the release of a monoclonal antibody from the porous matrix of porous SiO2. The therapeutic is incorporated into the films through electrostatic adsorption and a slow release is observed in vitro. A new method of quantifying the extent of drug loading is monitored with interferometry. The last chapter of the thesis provides a basic in vivo toxicity study of various porous Si microparticles for intraocular applications. Three types of porous Si particles are fabricated and studied in a rabbit eye model. The toxicity studies were conducted by collaborators at the Shiley Eye Center, La Jolla, CA. This work, demonstrates the feasibility of developing a self

  20. Covalent incorporation of non-chemically modified gelatin into degradable PVA-tyramine hydrogels.

    Science.gov (United States)

    Lim, Khoon S; Alves, Marie H; Poole-Warren, Laura A; Martens, Penny J

    2013-09-01

    Development of tissue engineering solutions for biomedical applications has driven the need for integration of biological signals into synthetic materials. Approaches to achieve this typically require chemical modification of the biological molecules. Examples include chemical grafting of synthetic polymers onto protein backbones and covalent modification of proteins using crosslinkable functional groups. However, such chemical modification processes can cause protein degradation, denaturation or loss of biological activity due to side chain disruption. This study exploited the observation that native tyrosine rich proteins could be crosslinked via radical initiated bi-phenol bond formation without any chemical modification of the protein. A new, tyramine functionalised poly(vinyl alcohol) (PVA) polymer was synthesised and characterised. The tyramine modified PVA (PVA-Tyr) was fabricated into hydrogels using a visible light initiated crosslinking system. Mass loss studies showed that PVA-Tyr hydrogels were completely degraded within 19 days most likely via degradation of ester linkages in the network. Protein incorporation to form a biosynthetic hydrogel was achieved using unmodified gelatin, a protein derived from collagen and results showed that 75% of gelatin was retained in the gel post-polymerisation. Incorporation of gelatin did not alter the sol fraction, swelling ratio and degradation profile of the hydrogels, but did significantly improve the cellular interactions. Moreover, incorporation of as little as 0.01 wt% gelatin was sufficient to facilitate fibroblast adhesion onto PVA-Tyr/gelatin hydrogels. Overall, this study details the synthesis of a new functionalised PVA macromer and demonstrates that tyrosine containing proteins can be covalently incorporated into synthetic hydrogels using this innovative PVA-Tyr system. The resultant degradable biosynthetic hydrogels hold great promise as matrices for tissue engineering applications.

  1. Interactions of zearalenone with native and chemically modified cyclodextrins and their potential utilization.

    Science.gov (United States)

    Poór, Miklós; Kunsági-Máté, Sándor; Sali, Nikolett; Kőszegi, Tamás; Szente, Lajos; Peles-Lemli, Beáta

    2015-10-01

    Zearalenone (ZEA) is a widespread xenoestrogenic mycotoxin produced by several Fusarium species. ZEA can cause reproductive disorders in farm animals and hyperoestrogenic syndromes in humans; therefore, development of more sensitive analytical methods (to quantify the mycotoxin) as well as strategies for prevention of its toxic impacts is highly important. In this study, the interactions of ZEA with native and chemically modified cyclodextrins (CDs) were investigated using fluorescence spectroscopy. Furthermore, in vitro experiments on liver cells were also performed to test the potential effect of CDs on toxin uptake. Our results demonstrate that ZEA forms stable complexes with CDs (logK values are approximately 3.7-4.7) resulting in the considerable elevation of its fluorescence signal. In addition, some of the CDs show ability to inhibit the cellular uptake of ZEA, suggesting their potential suitability to develop new CD-based preventive/detoxification strategies against ZEA in the future. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Immobilization of chemically modified horse radish peroxidase within activated alginate beads

    Directory of Open Access Journals (Sweden)

    Spasojević Dragica

    2014-01-01

    Full Text Available Immobilization of horse radish peroxidase (HRP within alginate beads was improved by chemical modification of the enzyme and polysaccharide chains. HRP and alginate were oxidized by periodate and subsequently modified with ethylenediamine. Highest specific activity of 0.43 U/ml of gel and 81 % of bound enzyme activity was obtained using aminated HRP and alginate oxidized by periodate. Immobilized enzyme retained 75 % of original activity after 2 days of incubation in 80 % (v/v dioxane and had increased activity at basic pH values compared to native enzyme. During repeated use in batch reactor for pyrogallol oxidation immobilized peroxidase retained 75 % of original activity. [Projekat Ministarstva nauke Republike Srbije, br. ON173017 i br. ON172049

  3. Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides.

    Science.gov (United States)

    Leikoski, Niina; Liu, Liwei; Jokela, Jouni; Wahlsten, Matti; Gugger, Muriel; Calteau, Alexandra; Permi, Perttu; Kerfeld, Cheryl A; Sivonen, Kaarina; Fewer, David P

    2013-08-22

    Ribosomal peptides are produced through the posttranslational modification of short precursor peptides. Cyanobactins are a growing family of cyclic ribosomal peptides produced by cyanobacteria. However, a broad systematic survey of the genetic capacity to produce cyanobactins is lacking. Here we report the identification of 31 cyanobactin gene clusters from 126 genomes of cyanobacteria. Genome mining suggested a complex evolutionary history defined by horizontal gene transfer and rapid diversification of precursor genes. Extensive chemical analyses demonstrated that some cyanobacteria produce short linear cyanobactins with a chain length ranging from three to five amino acids. The linear peptides were N-prenylated and O-methylated on the N and C termini, respectively, and named aeruginosamide and viridisamide. These findings broaden the structural diversity of the cyanobactin family to include highly modified linear peptides with rare posttranslational modifications.

  4. A modified next reaction method for simulating chemical systems with time dependent propensities and delays.

    Science.gov (United States)

    Anderson, David F

    2007-12-01

    Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the Gillespie algorithm or the next reaction method. In this paper we make explicit use of the fact that the initiation times of the reactions can be represented as the firing times of independent, unit rate Poisson processes with internal times given by integrated propensity functions. Using this representation we derive a modified next reaction method and, in a way that achieves efficiency over existing approaches for exact simulation, extend it to systems with time dependent propensities as well as to systems with delays.

  5. Fabrication of Rare Earth-Doped Transparent Glass Ceramic Optical Fibers by Modified Chemical Vapor Deposition

    CERN Document Server

    Blanc, Wilfried; Nguyen, Luan; Bhaktha, S N B; Sebbah, Patrick; Pal, Bishnu P; Dussardier, Bernard

    2011-01-01

    Rare earth (RE) doped silica-based optical fibers with transparent glass ceramic (TGC) core was fabricated through the well-known modified chemical vapor deposition (MCVD) process without going through the commonly used stage of post-ceramming. The main characteristics of the RE-doped oxyde nanoparticles namely, their density and mean diameter in the fibers are dictated by the concentration of alkaline earth element used as phase separating agent. Magnesium and erbium co-doped fibers were fabricated. Optical transmission in term of loss due to scattering as well as some spectroscopic characteristics of the erbium ions was studied. For low Mg content, nano-scale particles could be grown with and relatively low scattering losses were obtained, whereas large Mg-content causes the growth of larger particles resulting in much higher loss. However in the latter case, certain interesting alteration of the spectroscopic properties of the erbium ions were observed. These initial studies should be useful in incorporati...

  6. Biosilica from Living Diatoms: Investigations on Biocompatibility of Bare and Chemically Modified Thalassiosira weissflogii Silica Shells

    Directory of Open Access Journals (Sweden)

    Stefania Roberta Cicco

    2016-12-01

    Full Text Available In the past decade, mesoporous silica nanoparticles (MSNs with a large surface area and pore volume have attracted considerable attention for their application in drug delivery and biomedicine. Here we propose biosilica from diatoms as an alternative source of mesoporous materials in the field of multifunctional supports for cell growth: the biosilica surfaces were chemically modified by traditional silanization methods resulting in diatom silica microparticles functionalized with 3-mercaptopropyl-trimethoxysilane (MPTMS and 3-aminopropyl-triethoxysilane (APTES. Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy analyses revealed that the –SH or –NH2 were successfully grafted onto the biosilica surface. The relationship among the type of functional groups and the cell viability was established as well as the interaction of the cells with the nanoporosity of frustules. These results show that diatom microparticles are promising natural biomaterials suitable for cell growth, and that the surfaces, owing to the mercapto groups, exhibit good biocompatibility.

  7. Thermoplastic polymers surfaces for Dip-Pen Nanolithography of oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Suriano, Raffaella [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Biella, Serena, E-mail: serena.biella@polimi.it [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Cesura, Federico; Levi, Marinella; Turri, Stefano [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2013-05-15

    Different thermoplastic polymers were spin-coated to prepare smooth surfaces for the direct deposition of end-group modified oligonucleotides by Dip-Pen Nanolithography. A study of the diffusion process was done in order to investigate the dependence of calibration coefficient and quality of deposited features on environmental parameters (temperature, relative humidity) and ink's molecular weight and functionality. The optimization of the process parameters led to the realization of high quality and density nanoarrays on plastics.

  8. A factorial analysis of silanization conditions for the immobilization of oligonucleotides on glass surfaces.

    Science.gov (United States)

    Halliwell, C M; Cass, A E

    2001-06-01

    The modification of glass surfaces with (3-mercaptopropyl)trimethoxysilane and the application of this to DNA chip technology are described. A range of factors influencing the silanization method, and hence the number of surface-bound, chemically active thiol groups, were investigated using a design of experiment approach based on analysis of variance. The number of thiol groups introduced on glass substrates were measured directly using a specific radiolabel, [14C]cysteamine hydrochloride. For liquid-phase silanization, the number of surface-bound thiol groups was found to be dependent on both postsilanization thermal curing and silanization time and relatively independent of silane concentration, reaction temperature, and sample pretreatment. Depending on the conditions used in liquid-phase silanization, (1.3-9.0) x 10(12) thiol groups/cm2 on the glass samples were bound. The reliability and repeatability of liquid- and vacuum-phase silanization were also investigated. Eighteen-base oligonucleotide probes were covalently attached to the modified surfaces via a 3'-amino modification on the DNA and subsequent reaction with the cross-linking reagent N-(gamma-maleimidobutyryloxy) succinimide ester (GMBS). The resulting probe levels were determined and found to be stoichiometric with that of the introduced thiol groups. These results demonstrate that silanization of glass surfaces under specific conditions, prior to probe attachment, is of great importance in the development of DNA chips that use the simple concept of the covalent attachment of presynthesized oligonucleotides to silicon oxide surfaces.

  9. Structural resistance of chemically modified 1-D nanostructured titanates in inorganic acid environment

    Energy Technology Data Exchange (ETDEWEB)

    Marinkovic, Bojan A., E-mail: bojan@puc-rio.br [Departamento de Engenharia de Materiais, Pontificia Universidade Catolica de Rio de Janeiro-PUC-Rio, Rua Marques de Sao Vicente 225, Gavea, RJ (Brazil); Fredholm, Yann C. [Nanogavea-Nanotecnologia Sustentavel Ltda, Av. Padre Leonel Franca 150, Gavea, RJ (Brazil); Morgado, Edisson [PETROBRAS S.A./CENPES, Research and Development Centre, Av. Horacio Macedo, 950, Cidade Universitaria, 21941-915, Rio de Janeiro, RJ (Brazil); Jardim, Paula M.; Rizzo, Fernando [Departamento de Engenharia de Materiais, Pontificia Universidade Catolica de Rio de Janeiro-PUC-Rio, Rua Marques de Sao Vicente 225, Gavea, RJ (Brazil)

    2010-10-15

    Sodium containing one-dimensional nanostructured layered titanates (1-D NSLT) were produced both from commercial anatase powder and Brazilian natural rutile mineral sands by alkali hydrothermal process. The 1-D NSLT were chemically modified with proton, cobalt or iron via ionic exchange and all products were additionally submitted to intensive inorganic acid aging (pH = 0.5) for 28 days. The morphology and crystal structure transformations of chemically modified 1-D NSLT were followed by transmission electron microscopy, powder X-ray diffraction, selected area electron diffraction and energy dispersive spectroscopy. It was found that the original sodium rich 1-D NSLT and cobalt substituted 1-D NSLT were completely converted to rutile nanoparticles, while the protonated form was transformed in a 70%-30% (by weight) anatase-rutile nanoparticles mixture, very similar to that of the well-known TiO{sub 2}-photocatalyst P25 (Degussa). The iron substituted 1-D NSLT presented better acid resistance as 13% of the original structure and morphology remained, the rest being converted in rutile. A significant amount of remaining 1-D NSLT was also observed after the acid treatment of the product obtained from rutile sand. The results showed that phase transformation of NSLT into titanium dioxide polymorph in inorganic acid conditions were controllable by varying the exchanged cations. Finally, the possibility to transform, through acid aging, 1-D NSLT obtained from Brazilian natural rutile sand into TiO{sub 2}-polymorphs was demonstrated for the first time to the best of authors' knowledge, opening path for producing TiO{sub 2}-nanoproducts with different morphologies through a simple process and from a low cost precursor.

  10. Genetic and chemical modifiers of a CUG toxicity model in Drosophila.

    Directory of Open Access Journals (Sweden)

    Amparo Garcia-Lopez

    Full Text Available Non-coding CUG repeat expansions interfere with the activity of human Muscleblind-like (MBNL proteins contributing to myotonic dystrophy 1 (DM1. To understand this toxic RNA gain-of-function mechanism we developed a Drosophila model expressing 60 pure and 480 interrupted CUG repeats in the context of a non-translatable RNA. These flies reproduced aspects of the DM1 pathology, most notably nuclear accumulation of CUG transcripts, muscle degeneration, splicing misregulation, and diminished Muscleblind function in vivo. Reduced Muscleblind activity was evident from the sensitivity of CUG-induced phenotypes to a decrease in muscleblind genetic dosage and rescue by MBNL1 expression, and further supported by the co-localization of Muscleblind and CUG repeat RNA in ribonuclear foci. Targeted expression of CUG repeats to the developing eye and brain mushroom bodies was toxic leading to rough eyes and semilethality, respectively. These phenotypes were utilized to identify genetic and chemical modifiers of the CUG-induced toxicity. 15 genetic modifiers of the rough eye phenotype were isolated. These genes identify putative cellular processes unknown to be altered by CUG repeat RNA, and they include mRNA export factor Aly, apoptosis inhibitor Thread, chromatin remodelling factor Nurf-38, and extracellular matrix structural component Viking. Ten chemical compounds suppressed the semilethal phenotype. These compounds significantly improved viability of CUG expressing flies and included non-steroidal anti-inflammatory agents (ketoprofen, muscarinic, cholinergic and histamine receptor inhibitors (orphenadrine, and drugs that can affect sodium and calcium metabolism such as clenbuterol and spironolactone. These findings provide new insights into the DM1 phenotype, and suggest novel candidates for DM1 treatments.

  11. Chemically Modified Plastic Tube for High Volume Removal and Collection of Circulating Tumor Cells.

    Directory of Open Access Journals (Sweden)

    Angelo Gaitas

    Full Text Available In this preliminary effort, we use a commercially available and chemically modified tube to selectively capture circulating tumor cells (CTCs from the blood stream by immobilizing human anti-EpCAM antibodies on the tube's interior surface. We describe the requisite and critical steps required to modify a tube into a cancer cell-capturing device. Using these simple modifications, we were able to capture or entrap about 85% of cancer cells from suspension and 44% of cancer cells from spiked whole blood. We also found that the percentage of cells captured was dependent on the tube's length and also the number of cancer cells present. It is our strong belief that with the utilization of appropriate tube lengths and procedures, we can ensure capture and removal of nearly the entire CTC population in whole blood. Importantly after a patient's entire blood volume has circulated through the tube, the tube can then be trypsinized to release the captured live CTCs for further analysis and testing.

  12. New Inorganic-organic Hybrid Tetravanadate:Preparation, Characterization and Application in Chemically Modified Electrode

    Institute of Scientific and Technical Information of China (English)

    SUN Ying-hua; LI Xiao-ping; MEI Ze-min; ZHU Yu; NIU Li

    2011-01-01

    A new inorganic-organic hybrid tetravanadate [Co(2,2'-bpy)3]2V4O12.llH2O(l) has been prepared and characterized. X-Ray diffraction study reveals that compound 1 contains classical cluster anions [V4O12]4-, coordi nated cations [Co(2,2'-bpy)3]2+ and eleven water molecules, in which an interesting decamer water cluster is formed.The hybrid nanoparticles were firstly used as a bulk-modifier to fabricate a chemically modified paste electrode (1-CPE). The electrochemical behavior and electrocatalysis of 1-CPE have been studied in detail. The results indicate that 1-CPE has a good electrocatalytic activity toward the reduction of bromate in a 0.5 mol/L H2SO4 aqueous solu tion. I-CPE shows remarkable stability that be ascribed to the hydrogen bonding interactions between V4O12 cluster and water cluster, which are very important for practical application in electrode modification.

  13. Kinetic and thermodynamic studies on biosorption of Cu(Ⅱ) by chemically modified orange peel

    Institute of Scientific and Technical Information of China (English)

    FENG Ning-chuan; GUO Xue-yi; LIANG Sha

    2009-01-01

    Cu(H) biosorption by orange peel that was chemically modified with sodium hydroxide and calcium chloride was investigated. The effects of temperature, contact time, initial concentration of metal ions and pH on the biosorption of Cu( II) ions were assessed. Thermodynamic parameters including change of free energy(△G~Θ), enthalpy (△H~Θ) and entropy(△S~Θ) during the biosorption were determined. The results show that the biosorption process of Cu( II) ions by chemically treated orange peel is feasible, spontaneous and exothermic under studied conditions. Equilibrium is well described by Langmuir equation with the maximum biosorption capacity(q_m) for Cu( II) as 72.73 mg/g and kinetics is found to fit pseudo-second order type biosorption kinetics. As the temperature increases from 16 ℃ to 60 ℃, copper biosorption decreases. The loaded biosorbent is regenerated using HC1 solution for repeatedly use for five times with little loss of biosorption capacity.

  14. On the structure and topography of free-standing chemically modified graphene

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, N R; Pandey, P A; Beanland, R; Lupo, U; Rowlands, G; Roemer, R A [Department of Physics, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL (United Kingdom); Rourke, J P, E-mail: Neil.Wilson@Warwick.ac.uk [Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL (United Kingdom)

    2010-12-15

    The mechanical, electrical and chemical properties of chemically modified graphene (CMG) are intrinsically linked to its structure. Here, we report on our study of the topographic structure of free-standing CMG using atomic force microscopy (AFM) and electron diffraction. We find that, unlike graphene, suspended sheets of CMG are corrugated and distorted on nanometre length scales. AFM reveals not only long-range (100 nm) distortions induced by the support, as previously observed for graphene, but also short-range corrugations with length scales down to the resolution limit of 10 nm. These corrugations are static not dynamic, and are significantly diminished on CMG supported on atomically smooth substrates. Evidence for even shorter-range distortions, down to a few nanometres or less, is found by electron diffraction of suspended CMG. Comparison of the experimental data with simulations reveals that the mean atomic displacement from the nominal lattice position is of order 10% of the carbon-carbon bond length. Taken together, these results suggest a complex structure for CMG where heterogeneous functionalization creates local strain and distortion.

  15. On the structure and topography of free-standing chemically modified graphene

    Science.gov (United States)

    Wilson, N. R.; Pandey, P. A.; Beanland, R.; Rourke, J. P.; Lupo, U.; Rowlands, G.; Römer, R. A.

    2010-12-01

    The mechanical, electrical and chemical properties of chemically modified graphene (CMG) are intrinsically linked to its structure. Here, we report on our study of the topographic structure of free-standing CMG using atomic force microscopy (AFM) and electron diffraction. We find that, unlike graphene, suspended sheets of CMG are corrugated and distorted on nanometre length scales. AFM reveals not only long-range (100 nm) distortions induced by the support, as previously observed for graphene, but also short-range corrugations with length scales down to the resolution limit of 10 nm. These corrugations are static not dynamic, and are significantly diminished on CMG supported on atomically smooth substrates. Evidence for even shorter-range distortions, down to a few nanometres or less, is found by electron diffraction of suspended CMG. Comparison of the experimental data with simulations reveals that the mean atomic displacement from the nominal lattice position is of order 10% of the carbon-carbon bond length. Taken together, these results suggest a complex structure for CMG where heterogeneous functionalization creates local strain and distortion.

  16. High-affinity integration of hydroxyapatite nanoparticles with chemically modified silk fibroin

    Energy Technology Data Exchange (ETDEWEB)

    Wang Li; Li Chunzhong [East China University of Science and Technology, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering (China)], E-mail: czli@ecust.edu.cn; Senna, Mamoru [Keio University, Department of Applied Chemistry, Faculty of Science and Technology (Japan)

    2007-10-15

    Hydroxyapatite (HA)-based nanocomposites were prepared by a co-precipitation method with silk fibroin (SF) serving as organic matrix. Silk fibroin was chemically modified with an alkali solution or an enzyme attempting to improve the interface between the mineral and the organic matrix. The influences of the alkali and enzyme pretreatments on microstructure and physicochemical properties of HA-SF composite were examined and compared. The results reveal that both the two kinds of pretreatments facilitate the formation of highly ordered three-dimensional porous network throughout the composites, increase the microhardness of the composite, and promote the preferential growth of HA crystallites along c-axis. Among all the as-prepared samples, the composite containing the enzyme pretreated SF shows desirable hierarchical microstructure with higher degree of organization and more uniform pore size distribution. Due to the enzyme pretreatment, HA crystallites undergo obvious changes in morphology from rod-like to whisker-like and in crystal growth towards more apparent epitaxy along c-axis. The alkali pretreatment induces the stronger chemical interactions between HA and SF and thus to strengthen the inorganic-organic interfacial adhesion. The newly developed HA-SF composites are expected to be attractive biomedical materials for bone repair and remodeling.

  17. The effects of space radiation on a chemically modified graphite-epoxy composite material

    Science.gov (United States)

    Reed, S. M.; Herakovich, C. T.; Sykes, G. F.

    1986-01-01

    The effects of the space environment on the engineering properties and chemistry of a chemically modified T300/934 graphite-epoxy composite system are characterized. The material was subjected to 1.0 x 10 to the 10th power rads of 1.0 MeV electron irradiation under vacuum to simulate 30 years in geosynchronous earth orbit. Monotonic tension tests were performed at room temperature (75 F/24 C) and elevated temperature (250 F/121 C) on 4-ply unidirectional laminates. From these tests, inplane engineering and strength properties (E sub 1, E sub 2, Nu sub 12, G sub 12, X sub T, Y sub T) were determined. Cyclic tests were also performed to characterize energy dissipation changes due to irradiation and elevated temperature. Large diameter graphite fibers were tested to determine the effects of radiation on their stiffness and strength. No significant changes were observed. Dynamic-mechanical analysis demonstrated that the glass transition temperature was reduced by 50 F(28 C) after irradiation. Thermomechanical analysis showed the occurrence of volatile products generated upon heating of the irradiated material. The chemical modification of the epoxy did not aid in producing a material which was more radiation resistant than the standard T300/934 graphite-epoxy system. Irradiation was found to cause crosslinking and chain scission in the polymer. The latter produced low molecular weight products which plasticize the material at elevated temperatures and cause apparent material stiffening at low stresses at room temperature.

  18. Applicability and Optimal Parameters Analysis for Chemical Phosphorus Removal in a Modified Carrousel Oxidation Ditch

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    2017-07-01

    Full Text Available In order to confine the aqua-eutrophication problem arising from phosphorus pollution, many municipal wastewater treatment plants have to improve their executive drainage standard for total phosphorus (TP. In this study, a municipal wastewater treatment plant employing modified Carrousel oxidation ditch as main biological treatment unit was selected as a representative case. Technical necessity for adding a chemically enhanced phosphorus removal unit was analysed, and process feasibility was verified by batch and continuous experiments as well. The study results were summarized as follows. Because the organic carbon source in influent wastewater is not enough, it is impossible to satisfy the national drainage standard of TP by individual biological phosphorus removal processes, therefore, aided chemical phosphorus removal is essential. The polymeric aluminium chloride (PAC is preferable to be used as precipitant for phosphorus removal. The molar ratio of agent dosage to TP removal is preferable to be about 2.0. Under these conditions, the effluent TP concentration can be lower than 1.0 mg l−1.

  19. Chemically and biologically modified activated carbon sorbents for the removal of lead ions from aqueous media.

    Science.gov (United States)

    Mahmoud, Mohamed E; Abdel-Fattah, Tarek M; Osman, Maher M; Ahmed, Somia B

    2012-01-01

    A method is described for hybridization of the adsorption and biosorption characteristics of chemically treated commercial activated carbon and baker's yeast, respectively, for the formation of environmental friendly multifunctional sorbents. Activated carbon was loaded with baker's yeast after acid-base treatment. Scanning Electron Microscopy (SEM) and Fourier Transform Infrared (FTIR) Spectroscopy were used to characterize these sorbents. Moreover, the sorption capabilities for lead (II) ions were evaluated. A value of 90 μmol g(-1) was identified as the maximum sorption capacity of activated carbon. Acid-base treatment of activated carbon was found to double the sorption capacity (140-180 μmol g(-1)). Immobilization of baker's yeast on the surface of activated carbon sorbents was found to further improve the sorption capacity efficiency of lead to 360, 510 and 560 μmol g(-1), respectively. Several important factors such as pH, contact time, sorbent dose, lead concentration and interfering ions were examined. Lead sorption process was studied and evaluated by several adsorption isotherms and found to follow the Langmuir and BET models. The potential applications of various chemically and biologically modified sorbents and biosorbents for removal of lead from real water matrices were also investigated via multistage micro-column technique and the results referred to excellent recovery values of lead (95.0-99.0 ± 3.0-5.0 %).

  20. Selective recovery of precious metals by persimmon waste chemically modified with dimethylamine.

    Science.gov (United States)

    Xiong, Ying; Adhikari, Chaitanya Raj; Kawakita, Hidetaka; Ohto, Keisuke; Inoue, Katsutoshi; Harada, Hiroyuki

    2009-09-01

    Persimmon waste was chemically modified with dimethylamine (DMA) to obtain a tertiary-amine-type gel, named DMA persimmon waste gel (DMA-PW). It was found to be effective for the adsorption of Au(III), Pd(II), and Pt(IV) in hydrochloric acid medium. In contrast, base metals such as Cu(II), Zn(II), Fe(III), and Ni(II) were not practically adsorbed. The formation of ion pairs of the metal chloro complex anions with the protonated adsorption gels was proposed as the main adsorption process. The gel exhibited selectivity only for precious metals with a remarkably high capacity for Au(III), i.e., 5.63 mol/kg dry gel and comparable capacities, i.e., 0.42 and 0.28 mol/kg for Pd(II) and Pt(IV), respectively. According to the kinetic and electrochemical studies, the adsorption rate of Au(III) was greatly enhanced by the chemical modification. Also, its excellent adsorption characteristics for the precious metals were confirmed by adsorption and elution tests using a column packed with the DMA-PW gel.

  1. Growth of aligned ZnO nanowires via modified atmospheric pressure chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Yuping; Li, Chengchen [Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu, 212013 (China); Chen, Mingming, E-mail: andychain@live.cn [Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu, 212013 (China); Yu, Xiao; Chang, Yunwei [Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu, 212013 (China); Chen, Anqi [State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics & Information Technology, Sun Yat-Sen University, Guangzhou Higher Education Mega Center (University Town), Guangzhou, 510006 (China); Zhu, Hai, E-mail: zhuhai5@mail.sysu.edu.cn [State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics & Information Technology, Sun Yat-Sen University, Guangzhou Higher Education Mega Center (University Town), Guangzhou, 510006 (China); Tang, Zikang, E-mail: zktang@umac.mo [State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics & Information Technology, Sun Yat-Sen University, Guangzhou Higher Education Mega Center (University Town), Guangzhou, 510006 (China); The Institute of Applied Physics and Materials Engineering, University of Macau, Avenida da Universidade, Taipa, Macau (China)

    2016-12-09

    In this work, we report the growth of high-quality aligned ZnO nanowires via a facile atmospheric pressure chemical vapor deposition (CVD) method. The CVD reactor chamber used was more complicated than a conventional one due to the quartz boats loaded with sources (ZnO/C) and substrates being inserted into a semi-open quartz tube, and then placed inside the CVD reactor. The semi-open quartz tube played a very important role in growing the ZnO nanowires, and demonstrated that the transportation properties of Zn and O vapor differ from those in the conventional CVD reactor chamber. Aligned ZnO nanowires were successfully obtained, though they were only found at substrates located upstream. The very high crystalline quality of the obtained ZnO nanowires was demonstrated by high-resolution transmission electron microscopy and room temperature photoluminescence investigations. Such ZnO nanowires with high crystalline quality may provide opportunities for the fabrication of ZnO-based nano-devices in future. - Highlights: • High-quality aligned ZnO nanowires were obtained via modified chemical vapor deposition under atmospheric pressure. • The semi-open quartz tube plays very important roles in growing ZnO nanowires. • The transportation properties of Zn and O vapor differ from those in the conventional CVD reactor chamber.

  2. Efficiency of modified chemical remediation techniques for soil contaminated by organochlorine pesticides

    Science.gov (United States)

    Correa-Torres, S. N.; Kopytko, M.; Avila, S.

    2016-07-01

    This study reports the optimization of innovation chemical techniques in order to improve the remediation of soils contaminated with organochloride pesticides. The techniques used for remediation were dehalogenation and chemical oxidation in soil contaminated by pesticides. These techniques were applied sequentially and combined to evaluate the design optimize the concentration and contact time variables. The soil of this study was collect in cotton crop zone in Agustin Codazzi municipality, Colombia, and its physical properties was measure. The modified dehalogenation technique of EPA was applied on the contaminated soil by adding Sodium Bicarbonate solution at different concentrations and rates during 4, 7 and 14 days, subsequently oxidation technique was implemented by applying a solution of KMnO4 at different concentration and reaction times. Organochlorine were detected by Gas Chromatography analysis coupled Mass Spectrometry and its removals were between 85.4- 90.0% of compounds such as 4, 4’-DDT, 4,4’-DDD, 4,4-DDE, trans-Clordane y Endrin. These results demonstrate that the technique of dehalogenation with oxidation chemistry can be used for remediation soils contaminated by organochloride pesticides.

  3. A Novel Family of Small Molecules that Enhance the Intracellular Delivery and Pharmacological Effectiveness of Antisense and Splice Switching Oligonucleotides.

    Science.gov (United States)

    Wang, Ling; Ariyarathna, Yamuna; Ming, Xin; Yang, Bing; James, Lindsey I; Kreda, Silvia M; Porter, Melissa; Janzen, William; Juliano, Rudolph L

    2017-08-18

    The pharmacological effectiveness of oligonucleotides has been hampered by their tendency to remain entrapped in endosomes, thus limiting their access to cytosolic or nuclear targets. We have previously reported a group of small molecules that enhance the effects of oligonucleotides by causing their release from endosomes. Here, we describe a second novel family of oligonucleotide enhancing compounds (OECs) that is chemically distinct from the compounds reported previously. We demonstrate that these molecules substantially augment the actions of splice switching oligonucleotides (SSOs) and antisense oligonucleotides (ASOs) in cell culture. We also find enhancement of SSO effects in a murine model. These new compounds act by increasing endosome permeability and causing partial release of entrapped oligonucleotides. While they also affect the permeability of lysosomes, they are clearly different from typical lysosomotropic agents. Current members of this compound family display a relatively narrow window between effective dose and toxic dose. Thus, further improvements are necessary before these agents can become suitable for therapeutic use.

  4. [The influence of chemically-modified SLA on bone defect healing around implants in dogs].

    Science.gov (United States)

    Lv, Xiao-fei; Zhuang, Long-fei; Liu, Xin; Zhang, Zhi-yong; Lai, Hong-chang

    2010-06-01

    The study was designed to investigate the effect of surface chemical modification on the process of bone defect healing around implants in dogs. Six Beagle dogs were used in this study. The mandibular premolars and first molars were extracted bilaterally. Three months after tooth extraction the procedure of implant placement was performed. Four canals with a diameter of 2.8 mm and 10 mm in depth were prepared at the third premolar (P3) and the first molar (M1) sites of both sides of the mandible, of which the coronal 5 mm portion were further widened with the 5.3 mm diameter twist drill. In each side of the mandible one modSLA (chemically-modified SLA) implant and one SLA (sandblasted, large-grit, acid-etched) implant with a diameter of 3.3 mm and 10 mm in length were installed, respectively. Thus, the circumferential defect that was 5mm deep and 1mm wide created between the implant surface and the bony wall. Four implants placed in both sides of the mandible were allowed for non-submerged healing. Two dogs were sacrificed at the week 2, 4 and 8 following implant placement, respectively, and the specimens were prepared and stained with trinitrophenol- fuchsin for histological and histomorphometric analyses to acquire the bone-to-implant contact (BIC%), new bone fill (NBF%) and the distance between the most coronal level of bone-to-implant contact and the bottom of the surgically created bone defect(B-D). Statistical analysis was conducted with SPSS13.0 software package. No implant was loosen or lost during the study. The histomorphometric results demonstrated that new bone formation was observed in the defect region around both groups of implants at all time points and the newly formed bone occurred initially from the apical and lateral bony wall of the defect region, the bone defect almost was filled at week 8. At 2 and 4 weeks of healing, the BIC%, NBF% and B-D values were significantly higher for modSLA implants (P0.05). The SLA implants processed by means of

  5. Surface chemical and biological characterization of flax fabrics modified with silver nanoparticles for biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Paladini, F., E-mail: federica.paladini@unisalento.it [Department of Engineering for Innovation, University of Salento, Via per Monteroni, 73100 Lecce (Italy); Picca, R.A.; Sportelli, M.C.; Cioffi, N. [Department of Chemistry, University of Bari “Aldo Moro”, Via Orabona 4, 70126 Bari (Italy); Sannino, A.; Pollini, M. [Department of Engineering for Innovation, University of Salento, Via per Monteroni, 73100 Lecce (Italy)

    2015-07-01

    Silver nanophases are increasingly used as effective antibacterial agent for biomedical applications and wound healing. This work aims to investigate the surface chemical composition and biological properties of silver nanoparticle-modified flax substrates. Silver coatings were deposited on textiles through the in situ photo-reduction of a silver solution, by means of a large-scale apparatus. The silver-coated materials were characterized through X-ray Photoelectron Spectroscopy (XPS), to assess the surface elemental composition of the coatings, and the chemical speciation of both the substrate and the antibacterial nanophases. A detailed investigation of XPS high resolution regions outlined that silver is mainly present on nanophases' surface as Ag{sub 2}O. Scanning electron microscopy and energy dispersive X-ray spectroscopy were also carried out, in order to visualize the distribution of silver particles on the fibers. The materials were also characterized from a biological point of view in terms of antibacterial capability and cytotoxicity. Agar diffusion tests and bacterial enumeration tests were performed on Gram positive and Gram negative bacteria, namely Staphylococcus aureus and Escherichia coli. In vitro cytotoxicity tests were performed through the extract method on murine fibroblasts in order to verify if the presence of the silver coating affected the cellular viability and proliferation. Durability of the coating was also assessed, thus confirming the successful scaling up of the process, which will be therefore available for large-scale production. - Highlights: • Silver nanophases are increasingly used as effective antibacterial agent for biomedical applications. • Silver coatings were deposited on textiles through the in situ photo-reduction of a silver solution. • Flax fabrics were characterized from a biological and surface chemical point of view. • Scaling up of the process was confirmed.

  6. Adhesion force interactions between cyclopentane hydrate and physically and chemically modified surfaces.

    Science.gov (United States)

    Aman, Zachary M; Sloan, E Dendy; Sum, Amadeu K; Koh, Carolyn A

    2014-12-07

    Interfacial interactions between liquid-solid and solid-solid phases/surfaces are of fundamental importance to the formation of hydrate deposits in oil and gas pipelines. This work establishes the effect of five categories of physical and chemical modification to steel on clathrate hydrate adhesive force: oleamide, graphite, citric acid ester, nonanedithiol, and Rain-X anti-wetting agent. Hydrate adhesive forces were measured using a micromechanical force apparatus, under both dry and water-wet surface conditions. The results show that the graphite coating reduced hydrate-steel adhesion force by 79%, due to an increase in the water wetting angle from 42 ± 8° to 154 ± 7°. Two chemical surface coatings (nonanedithiol and the citric acid ester) induced rapid hydrate growth in the hydrate particles; nonanedithiol increased hydrate adhesive force by 49% from the baseline, while the citric acid ester coating reduced hydrate adhesion force by 98%. This result suggests that crystal growth may enable a strong adhesive pathway between hydrate and other crystalline structures, however this effect may be negated in cases where water-hydrocarbon interfacial tension is minimised. When a liquid water droplet was placed on the modified steel surfaces, the graphite and citric acid ester became less effective at reducing adhesive force. In pipelines containing a free water phase wetting the steel surface, chemical or physical surface modifications alone may be insufficient to eliminate hydrate deposition risk. In further tests, the citric acid ester reduced hydrate cohesive forces by 50%, suggesting mild activity as a hybrid anti-agglomerant suppressing both hydrate deposition and particle agglomeration. These results demonstrate a new capability to develop polyfunctional surfactants, which simultaneously limit the capability for hydrate particles to aggregate and deposit on the pipeline wall.

  7. A bridged nucleic acid, 2',4'-BNA COC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNA COC monomers and RNA-selective nucleic-acid recognition.

    Science.gov (United States)

    Mitsuoka, Yasunori; Kodama, Tetsuya; Ohnishi, Ryo; Hari, Yoshiyuki; Imanishi, Takeshi; Obika, Satoshi

    2009-03-01

    Recently, we synthesized pyrimidine derivatives of the 2'-O,4'-C-methylenoxymethylene-bridged nucleic-acid (2',4'-BNA(COC)) monomer, the sugar conformation of which is restricted in N-type conformation by a seven-membered bridged structure. Oligonucleotides (BNA(COC)) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. Here, BNA(COC) consisting of 2',4'-BNA(COC) monomers bearing all four bases, namely thymine, 5-methylcytosine, adenine and guanine was efficiently synthesized and properties of duplexes containing the 2',4'-BNA(COC) monomers were investigated by UV melting experiments and circular dichroism (CD) spectroscopy. The UV melting curve analyses showed that the BNA(COC)/BNA(COC) duplex possessed excellent thermal stability and that the BNA(COC) increased thermal stability with a complementary RNA strand. On the other hand, BNA(COC)/DNA heteroduplexes showed almost the same thermal stability as RNA/DNA heteroduplexes. Furthermore, mismatched sequence studies showed that BNA(COC) generally improved the sequence selectivity with Watson-Crick base-pairing compared to the corresponding natural DNA and RNA. A CD spectroscopic analysis indicated that the BNA(COC) formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.

  8. Pd0-Catalyzed Methyl Transfer on Nucleosides and Oligonucleotides, Envisaged as a PET Tracer

    Directory of Open Access Journals (Sweden)

    Eric Fouquet

    2013-11-01

    Full Text Available The methyl transfer reaction from activated monomethyltin, via a modified Stille coupling reaction, was studied under “ligandless” conditions on fully deprotected 5'-modified nucleosides and one dinucleotide. The reaction was optimized to proceed in a few minutes and quantitative yield, even under dilute conditions, thus affording a rapid and efficient new method for oligonucleotide labelling with carbon-11.

  9. Effect of emulsifiers on complexation and retrogradation characteristics of native and chemically modified White sorghum (Sorghum bicolor) starch

    Energy Technology Data Exchange (ETDEWEB)

    Ali, Tahira Mohsin, E-mail: tahira.mohsin@uok.edu.pk [Department of Food Science and Technology, University of Karachi, 75270 Karachi (Pakistan); Hasnain, Abid, E-mail: abidhasnain@uok.edu.pk [Department of Food Science and Technology, University of Karachi, 75270 Karachi (Pakistan)

    2013-01-20

    Highlights: Black-Right-Pointing-Pointer Sorghum starches were chemically modified. Black-Right-Pointing-Pointer Starch-lipid complexes were studied in the presence of emulsifiers. Black-Right-Pointing-Pointer Type II complexes were also detected in native and oxidized starches on adding GMS. Black-Right-Pointing-Pointer Starch-lipid complexes sharply reduced retrogradation in modified starches. - Abstract: The effect of emulsifiers on complexation and retrogradation characteristics of native and chemically modified white sorghum starches was studied. Complex forming tendency of white sorghum starch with commercially available emulsifiers GMS and DATEM improved after acetylation. Presence of emulsifiers reduced {lambda}{sub max} (wavelength of maximum absorbance) both for native and modified sorghum starches suggesting lower availability of amylose chains to complex with iodine. In native white sorghum starch (NWSS) and oxidized white sorghum starch (OWSS), both Type I and Type II starch-lipid complexes were observed on addition of 1.0% GMS prior to gelatinization. Acetylated-oxidized white sorghum starch (AOWSS) formed weakest complexes among all the modified starches. The results revealed that antistaling characteristics of modified sorghum starches were enhanced when used in combination with emulsifiers. The most prominent decline in reassociative capability among modified starches was observed for acetylated starches.

  10. Release of DNA oligonucleotides and their conjugates from controlled-pore glass under thermolytic conditions.

    Science.gov (United States)

    Grajkowski, Andrzej; Cieślak, Jacek; Norris, Scott; Freedberg, Darón I; Kauffman, Jon S; Duff, Robert J; Beaucage, Serge L

    2008-12-01

    The sequential functionalization of long-chain alkylamine controlled-pore glass (CPG) with a 3-hydroxypropyl-(2-cyanoethyl)thiophosphoryl linker and a dinucleoside phosphorotetrazolide leads to a uniquely engineered support for solid-phase synthesis. Unlike conventional succinylated-CPG supports, this support is designed to allow oligonucleotide deprotection and elimination of deprotection side-products to proceed without release of the oligonucleotide. When needed, the DNA oligonucleotide can be thermolytically released in 2 hr under essentially neutral conditions. The modified CPG support has been successfully employed in the synthesis of both native and fully phosphorothioated DNA 20-mers. On the basis of reversed-phase HPLC and electrophoretic analyses, the purity of the released oligonucleotides is comparable to that of identical oligonucleotides synthesized from succinylated-CPG supports, in terms of both shorter-than-full-length oligonucleotide contaminants and overall yields. The detailed preparation of DNA oligonucleotides conjugated with exemplary reporter or functional groups, either at the 3'-terminus or at both 3'- and 5'-termini, is also described.

  11. Adsorption Studies of Phenol Using Thermally and Chemically Modified Rice Husk as Adsorbents

    Directory of Open Access Journals (Sweden)

    *M. M. Yousaf

    2014-03-01

    Full Text Available Most of the Phenols are hazardous substances and some are supposed to have carcinogenic activity. Thus it is necessary to remove Phenolics and other aromatics from the aqueous ecosystem. Traditional processes for the removal of Phenolics compounds are extraction, adsorption on granulated activated carbon, steam distillation, chemical and bacterial techniques. Literature survey show a number of methods like oxidation, ion exchange, reverse osmosis, electrochemical oxidation and adsorption. Phenol removal by process like, adsorption is the best method of choice as it can remove most of phenols in simple and easy way. In recent past; agricultural by-products such as, maize cob, date stone, apricot Stones, rice bran, and bagass pith have been extensively studied and used as adsorbents for the adsorption of hazardous substances from wastewater. In the present study we tried modified rice husks as potential adsorbents for the removal of Phenol from aqueous system. Batch mode studies were carried out. Isotherm data was generated and fitted in Freundlich and Langmuir equation to explain the phenomenon of adsorption. The adsorption capacities based on Langmuir model (Qm of the 3 adsorbents were found to be 0.81 for raw husk (RH, 0.395 for the Grafted (G and 2.306 mg/g for the Charred (C. The R2 values were 0.92 for raw husk, 0.97 for grafted and 0.91 for charred husk. Based on Freundlich model the adsorption capacities (K were 2.94, 2.29 and 1.25mg/g for Raw husk, grafted husk and charred husk. The R2 values were found to be 0.72, 0.95 and 0.83 for the raw husk, grafted husk and charred husk respectively. Our result showed that modified rice husks could be used as potential adsorbents for Phenol removal from aqueous system.

  12. A modified parallel artificial membrane permeability assay for evaluating the bioconcentration of highly hydrophobic chemicals in fish.

    Science.gov (United States)

    Kwon, Jung-Hwan; Escher, Beate I

    2008-03-01

    Low cost in vitro tools are needed at the screening stage of assessment of bioaccumulation potential of new and existing chemicals because the number of chemical substances that needs to be tested highly exceeds the capacity of in vivo bioconcentration tests. Thus, the parallel artificial membrane permeability assay (PAMPA) system was modified to predict passive uptake/ elimination rate in fish. To overcome the difficulties associated with low aqueous solubility and high membrane affinity of highly hydrophobic chemicals, we measured the rate of permeation from the donor poly(dimethylsiloxane)(PDMS) disk to the acceptor PDMS disk through aqueous and PDMS membrane boundary layers and term the modified PAMPA system "PDMS-PAMPA". Twenty chemicals were selected for validation of PDMS-PAMPA. The measured permeability is proportional to the passive elimination rate constant in fish and was used to predict the "minimum" in vivo elimination rate constant. The in vivo data were very close to predicted values except for a few polar chemicals and metabolically active chemicals, such as pyrene and benzo[a]pyrene. Thus, PDMS-PAMPA can be an appropriate in vitro system for nonmetabolizable chemicals. Combination with metabolic clearance rates using a battery of metabolic degradation assays would enhance the applicability for metabolizable chemicals.

  13. Supported liquid membrane stability in chiral resolution by chemically and physically modified membranes

    Energy Technology Data Exchange (ETDEWEB)

    Molinari, R.; Argurio, P. [Arcavata di Rende Univ. of Calabria, Arcavata di Rende, CS (Italy). Dept. of Chemical and Materials Engineering

    2001-04-01

    In the present work some stability studies on Supported Liquid Membranes (SLMs) to be used for chiral separations were realized. In particular, primary aim was to determine how a modification of the support surface influences the SLM stability. First, the procedure for support modification was optimised, making a screening of various compounds (sulphuric acid, nitric acid, chromic acid, sodium dodecyl sulphate (SDS), glycerol, oleic alcohol, propylene glycol (PPG), bovine serum albumin (BSA)) and testing their performance by means of contact angle measurements. Next, a second screening was realized by permeation tests in a stirred cell. Finally, to compare the stability of modified with unmodified support in a process of interest for chemical and/or biochemical industries, some permeation tests for resolution of DNB-DL-Leucine were realized in a re-circulation system. Results showed a better surface hydrophilization of chemically modified support and better stability of the sulphonated support. However, in operating conditions a little high stability of the unmodified support was obtained. [Italian] Nel presente lavoro sono stati realizzati degli studi di stabilita' di Membrane Liquide Supportate (SLMs) da impiegare in separazioni chirali. In particolare, obiettivo principale e' stato quello di determinare l'influenza che una modifica della superficie del supporto ha sulla stabilita' della SLM. Cosi', in un primo momento, e' stata ottimizzata le procedura di modifica del supporto, facendo una selezione tra vari composti (acido solforico, acido nitrico, acido cromico, sodio dodecil solfato (SDS), glicerolo, alcool oleico, glicole propilenico (PPG), siero di albumina bovina (BSA)) basata su misure dell'angolo di contatto. Successivamente, e' stata realizzata una seconda selezione mediante prove di permeazione in una cella agitata. Infine, con lo scopo di confrontare la stabilita' della SLM con supporto modificato rispetto

  14. Chemical Sensors Based on IR Spectroscopy and Surface-Modified Waveguides

    Science.gov (United States)

    Lopez, Gabriel P.; Niemczyk, Thomas

    1999-01-01

    Sol-gel processing techniques have been used to apply thin porous films to the surfaces of planar infrared (IR) waveguides to produce widely useful chemical sensors. The thin- film coating serves to diminish the concentration of water and increase the concentration of the analyte in the region probed by the evanescent IR wave. These porous films are composed of silica, and therefore, conventional silica surface modification techniques can be used to give the surface a specific functional character. The sol-gel film was surface-modified to make the film highly hydrophobic. These sensors were shown to be capable of detecting non-polar organic analytes, such as benzonitrile, in aqueous solution with detection limits in the ppb range. Further, these porous sol-gel structures allow the analytes to diffuse into and out of the films rapidly, thus reaching equilibrium in less than ten seconds. These sensors are unique because of the fact that their operation is based on the measurement of an IR absorption spectrum. Thus, these sensors are able to identify the analytes as well as measure concentration with high sensitivity. These developments have been documented in previous reports and publications. Recently, we have also targeted detection of the polar organic molecules acetone and isopropanol in aqueous solution. Polar organics are widely used in industrial and chemical processes, hence it is of interest to monitor their presence in effluents or decontamination process flows. Although large improvements in detection limits were expected with non-polar organic molecules in aqueous solutions using very hydrophobic porous sol-gel films on silicon attenuated total reflectance (Si ATR) waveguides, it was not as clear what the detection enhancements might be for polar organic molecules. This report describes the use of modified sol-gel-coated Si ATR sensors for trace detection and quantitation of small polar organic molecules in aqueous solutions. The detection of both acetone

  15. Modified chemical synthesis of porous α-Sm{sub 2}S{sub 3} thin films

    Energy Technology Data Exchange (ETDEWEB)

    Kumbhar, V.S.; Jagadale, A.D. [Thin Film Physics Laboratory, Department of Physics, Shivaji University, Kolhapur, (M.S.) 416004 (India); Gaikwad, N.S. [Rayat Shikshan Sanstha, Satara, (M.S.) 415 001 (India); Lokhande, C.D., E-mail: l_chandrakant@yahoo.com [Thin Film Physics Laboratory, Department of Physics, Shivaji University, Kolhapur, (M.S.) 416004 (India)

    2014-08-15

    Highlights: • A novel chemical route to prepare α-Sm{sub 2}S{sub 3} thin films. • A porous honeycomb like morphology of the α-Sm{sub 2}S{sub 3} thin film. • An application of α-Sm{sub 2}S{sub 3} thin film toward its supercapacitive behaviour. - Abstract: The paper reports synthesis of porous α-Sm{sub 2}S{sub 3} thin films using modified chemical synthesis, also known as successive ionic layer adsorption and reaction (SILAR) method. The X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), atomic force microscopy (AFM), wettability and ultraviolet–visible spectroscopy (UV–vis) techniques are used for the study of structural, elemental, morphological and optical properties of α-Sm{sub 2}S{sub 3} films. An orthorhombic crystal structure of α-Sm{sub 2}S{sub 3} is resulted from XRD study. The SEM and AFM observations showed highly porous α-Sm{sub 2}S{sub 3} film surface. An optical band gap of 2.50 eV is estimated from optical absorption spectrum. The porous α-Sm{sub 2}S{sub 3} thin film tuned for supercapacitive behaviour using cyclic voltammetry and galvanostatic charge discharge showed a specific capacitance and energy density of 294 Fg{sup –1} and 48.9 kW kg{sup –1}, respectively in 1 M LiClO{sub 4}–propylene carbonate electrolyte.

  16. The chemical and catalytic properties of nanocrystalline metal oxides prepared through modified sol-gel synthesis

    Science.gov (United States)

    Carnes, Corrie Leigh

    The goal of this research was to synthesize, characterize and study the chemical properties of nanocrystalline metal oxides. Nanocrystalline (NC) ZnO, CuO, NiO, Al2O3, and the binary Al2O 3/MgO and ZnO/CuO were prepared through modified sol gel methods. These NC metal oxides were studied in comparison to the commercial (CM) metal oxides. The samples were characterized by XRD, TGA, FTIR, BET, and TEM. The NC samples were all accompanied by a significant increase in surface area and decrease in crystallite size. Several chemical reactions were studied to compare the NC samples to the CM samples. One of the reactions involved a high temperature reaction between carbon tetrachloride and the oxide to form carbon dioxide and the corresponding metal chloride. A similar high temperature reaction was conducted between the metal oxide and hydrogen sulfide to form water and the corresponding metal sulfide. A room temperature gas phase adsorption was studied where SO2 was adsorbed onto the oxide. A liquid phase adsorption conducted at room temperature was the destructive adsorption of paraoxon (a toxic insecticide). In all reactions the NC samples exhibited greater activity, destroying or adsorbing a larger amount of the toxins compared to the CM samples. To better study surface area effects catalytic reactions were also studied. The catalysis of methanol was studied over the nanocrystalline ZnO, CuO, NiO, and ZnO/CuO samples in comparison to their commercial counterparts. In most cases the NC samples proved to be more active catalysts, having higher percent conversions and turnover numbers. A second catalytic reaction was also studied, this reaction was investigated to look at the support effects. The catalysis of cyclopropane to propane was studied over Pt and Co catalysts. These catalysts were supported onto NC and CM alumina by impregnation. By observing differences in the catalytic behavior, support effects have become apparent.

  17. Distribution of phosphorus and hydroxypropyl groups within granules of modified sweet potato starches as determined after chemical peeling

    NARCIS (Netherlands)

    Zhao, J.; Schols, H.A.; Chen Zenghong,; Jin, Z.; Buwalda, P.; Gruppen, H.

    2015-01-01

    The distributions of phosphorus and hydroxypropyl groups within granules of cross-linked and hydroxypropylated sweet potato starches were investigated. Chemical surface peeling of starch granules was performed after sieving of native and modified starches into large-size (diameter = 20 µm) and small

  18. Enhanced forward osmosis from chemically modified polybenzimidazole (PBI) nanofiltration hollow fiber membranes with a thin wall

    KAUST Repository

    Wang, Kai Yu

    2009-04-01

    To develop high-flux and high-rejection forward osmosis (FO) membranes for water reuses and seawater desalination, we have fabricated polybenzimidazole (PBI) nanofiltration (NF) hollow fiber membranes with a thin wall and a desired pore size via non-solvent induced phase inversion and chemically cross-linking modification. The cross-linking by p-xylylene dichloride can finely tune the mean pore size and enhance the salt selectivity. High water permeation flux and improved salt selectivity for water reuses were achieved by using the 2-h modified PBI NF membrane which has a narrow pore size distribution. Cross-linking at a longer time produces even a lower salt permeation flux potentially suitable for desalination but at the expense of permeation flux due to tightened pore sizes. It is found that draw solution concentration and membrane orientations are main factors determining the water permeation flux. In addition, effects of membrane morphology and operation conditions on water and salt transport through membrane have been investigated. © 2008 Elsevier Ltd. All rights reserved.

  19. Photoelectrochemical Properties of CuO Grown by Using a Modified Chemical Bath Deposition Method

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Jin-wook; Ryu, Hyukhyun [Inje University, Gimhae (Korea, Republic of); Lee, Won-Jae [Dong-Eui University, Busan (Korea, Republic of)

    2016-06-15

    In this study, cupric oxide (CuO) nanorods were grown on the fluorine-doped tin oxide (FTO) glass substrate using a modified-chemical bath deposition (M-CBD) method. We investigated the morphology, structural, optical and photoelectrochemical properties of the cupric oxide nanorods with various growth durations by using field-emission scanning-electron microscopy (FE-SEM), X-ray diffraction (XRD), UV-visible spectroscopy (UV-vis) and three-electrode potentiostat, respectively. In this work, we found that the morphologies, thickness, growth rate, crystallinities, grain sizes and optical bandgap were controllable on the growth duration, which affected photocurrent density and photo-stability. The highest growth rate of CuO nanorods was 126 nm/min. From the XRD measurement, we also confirmed that (020) directional growth affected the growth of the CuO nanorods. A maximum photocurrent density of-1.88 mA/cm² at -0.55 V (vs. SCE) and high photo-stability value about 40% was obtained with 10 minutes growth duration.

  20. Optimizing the lanthanum adsorption process onto chemically modified biomaterials using factorial and response surface design.

    Science.gov (United States)

    Gabor, Andreea; Davidescu, Corneliu Mircea; Negrea, Adina; Ciopec, Mihaela; Grozav, Ion; Negrea, Petru; Duteanu, Narcis

    2017-01-29

    The rare metals' potential to pollute air, water, soil, and especially groundwater has received lot of attention recently. One of the most common rare earth group elements, lanthanum, is used in many industrial branches, and due to its toxicity, it needs to be eliminated from all residual aqueous solutions. The goal of this study was to evaluate the control of the adsorption process for lanthanum removal from aqueous solutions, using cellulose, a known biomaterial with high adsorbent properties, cheap, and environment friendly. The cellulose was chemically modified by functionalization with sodium β-glycerophosphate. The experimental results obtained after factorial design indicate optimum adsorption parameters as pH 6, contact time 60 min, and temperature 298 K, when the equilibrium concentration of lanthanum was 250 mg L(-1), and the experimental adsorption capacity obtained was 31.58 mg g(-1). Further refinement of the optimization of the adsorption process by response surface design indicates that at pH 6 and the initial concentration of 256 mg L(-1), the adsorption capacity has maximum values between 30.87 and 36.73 mg g(-1).

  1. Removal of lead from aqueous solution with native and chemically modified corncobs.

    Science.gov (United States)

    Tan, Guangqun; Yuan, Hongyan; Liu, Yong; Xiao, Dan

    2010-02-15

    In this study, corncobs biomass was utilized as an adsorbent to remove Pb(II) from aqueous solution. The adsorption behavior of Pb(II) was studied under different conditions, including solution pH, contact time and metal concentration. Ground corncobs were modified with CH(3)OH and NaOH to investigate the effect of chemical modification on Pb(II) binding capacity. Results showed that Pb(II) binding on the biomass is pH-dependent and the kinetics can be well described by the Lagergren-second-order model. The maximum Pb(II) binding capacity q(max) calculated from Langmuir isotherm was 0.0783 mmol/g. After base hydrolysis of the biomass, Pb(II) binding capacity increased from 0.0783 to 0.2095 mmol/g (about 43.4 mg Pb/g). However, Pb(II) binding capacity on the esterified corncobs decreased greatly from 0.0783 to 0.0381 mmol/g. Fourier transform infrared spectroscopy (FTIR) analysis showed that hydroxyl and carboxylic (COO(-)) groups on the biomass play an important role in Pb(II) binding process. The X-ray photoelectron spectroscopy (XPS) data further indicated that lead is adsorbed as Pb(2+) and is attached to oxide groups on the biomass.

  2. Removal of heavy metals from aqueous phases using chemically modified waste Lyocell fiber.

    Science.gov (United States)

    Bediako, John Kwame; Wei, Wei; Kim, Sok; Yun, Yeoung-Sang

    2015-12-15

    In this study, an outstanding performance of chemically modified waste Lyocell for heavy metals treatment is reported. The sorbent, which was prepared by a simple and concise method, was able to bind heavy metals such as Pb(II), Cu(II) and Cd(II), with very high efficiencies. The binding mechanisms were studied through adsorption and standard characterization tests such as scanning electron microscopy, energy-dispersive spectroscopy, Fourier transform infrared spectroscopy, and X-ray diffraction analyses. Adsorption kinetics was very fast and attained equilibrium within 5 min in all metals studied. The maximum single metal uptakes were 531.29±0.28 mg/g, 505.64±0.21 mg/g, and 123.08±0.26 mg/g for Pb(II), Cd(II) and Cu(II), respectively. In ternary metal systems, Cu(II) selectivity was observed and the underlying factors were discussed. The sorbent by its nature, could be very effective in treating large volumes of wastewater with the contact of very little amount.

  3. Removal of methylene blue from aqueous solutions by chemically modified bamboo.

    Science.gov (United States)

    Guo, Jian-Zhong; Li, Bing; Liu, Li; Lv, Kangle

    2014-09-01

    Chemically modified bamboo (CMB) was utilized for removing methylene blue (MB) from aqueous media in the present study. The adsorbent was characterized by Fourier transform infrared (FTIR) spectra and elemental analysis, which confirms that carboxyl groups and diethylenetriamine were successfully introduced into the surface of bamboo. The effects of initial MB concentration (100-900mgL(-1)), contact time (15-315min), the pH of the solution (3-10), temperature (298-318K), adsorbent dosage (0.4-2.6gL(-1)) and salt concentration on the adsorption efficiency of CMB towards MB were investigated. It was found that the adsorption of MB in CMB fits Langmuir mode well, and the maximum adsorption capacity of CMB achieved 606mgg(-1) at 298K, which is much higher than those obtained from previously investigated bioadsorbents. The adsorption kinetics can be described by pseudo-second-order kinetic model, and the adsorption of MB on CMB was an exothermic process. The results of the present study suggest that CMB is an effective biosorbent for removal of organic pollutants from aqueous solutions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Chemically modified peptide scaffolds target the CFTR-associated ligand PDZ domain.

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    Jeanine F Amacher

    Full Text Available PDZ domains are protein-protein interaction modules that coordinate multiple signaling and trafficking pathways in the cell and that include active therapeutic targets for diseases such as cancer, cystic fibrosis, and addiction. Our previous work characterized a PDZ interaction that restricts the apical membrane half-life of the cystic fibrosis transmembrane conductance regulator (CFTR. Using iterative cycles of peptide-array and solution-binding analysis, we targeted the PDZ domain of the CFTR-Associated Ligand (CAL, and showed that an engineered peptide inhibitor rescues cell-surface expression of the most common CFTR disease mutation ΔF508. Here, we present a series of scaffolds containing chemically modifiable side chains at all non-motif positions along the CAL PDZ domain binding cleft. Concordant equilibrium dissociation constants were determined in parallel by fluorescence polarization, isothermal titration calorimetry, and surface plasmon resonance techniques, confirming robust affinity for each scaffold and revealing an enthalpically driven mode of inhibitor binding. Structural studies demonstrate a conserved binding mode for each peptide, opening the possibility of combinatorial modification. Finally, we diversified one of our peptide scaffolds with halogenated substituents that yielded modest increases in binding affinity. Overall, this work validates our approach and provides a stereochemical foundation for further CAL inhibitor design and screening.

  5. Chemically modified peptide scaffolds target the CFTR-associated ligand PDZ domain.

    Science.gov (United States)

    Amacher, Jeanine F; Zhao, Ruizhi; Spaller, Mark R; Madden, Dean R

    2014-01-01

    PDZ domains are protein-protein interaction modules that coordinate multiple signaling and trafficking pathways in the cell and that include active therapeutic targets for diseases such as cancer, cystic fibrosis, and addiction. Our previous work characterized a PDZ interaction that restricts the apical membrane half-life of the cystic fibrosis transmembrane conductance regulator (CFTR). Using iterative cycles of peptide-array and solution-binding analysis, we targeted the PDZ domain of the CFTR-Associated Ligand (CAL), and showed that an engineered peptide inhibitor rescues cell-surface expression of the most common CFTR disease mutation ΔF508. Here, we present a series of scaffolds containing chemically modifiable side chains at all non-motif positions along the CAL PDZ domain binding cleft. Concordant equilibrium dissociation constants were determined in parallel by fluorescence polarization, isothermal titration calorimetry, and surface plasmon resonance techniques, confirming robust affinity for each scaffold and revealing an enthalpically driven mode of inhibitor binding. Structural studies demonstrate a conserved binding mode for each peptide, opening the possibility of combinatorial modification. Finally, we diversified one of our peptide scaffolds with halogenated substituents that yielded modest increases in binding affinity. Overall, this work validates our approach and provides a stereochemical foundation for further CAL inhibitor design and screening.

  6. A Novel Chemically Modified Curcumin Reduces Severity of Experimental Periodontal Disease in Rats: Initial Observations

    Directory of Open Access Journals (Sweden)

    Muna S. Elburki

    2014-01-01

    Full Text Available Tetracycline-based matrix metalloproteinase- (MMP- inhibitors are currently approved for two inflammatory diseases, periodontitis and rosacea. The current study addresses the therapeutic potential of a novel pleiotropic MMP-inhibitor not based on an antibiotic. To induce experimental periodontitis, endotoxin (LPS was repeatedly injected into the gingiva of rats on one side of the maxilla; the contralateral (control side received saline injections. Two groups of rats were treated by daily oral intubation with a chemically modified curcumin, CMC 2.24, for two weeks; the control groups received vehicle alone. After sacrifice, gingiva, blood, and maxilla were collected, the jaws were defleshed, and periodontal (alveolar bone loss was quantified morphometrically and by μ-CT scan. The gingivae were pooled per experimental group, extracted, and analyzed for MMPs (gelatin zymography; western blot and for cytokines (e.g., IL-1β; ELISA; serum and plasma samples were analyzed for cytokines and MMP-8. The LPS-induced pathologically excessive bone loss was reduced to normal levels based on either morphometric (P=0.003 or μ-CT (P=0.008 analysis. A similar response was seen for MMPs and cytokines in the gingiva and blood. This initial study, on a novel triketonic zinc-binding CMC, indicates potential efficacy on inflammatory mediators and alveolar bone loss in experimental periodontitis and warrants future therapeutic and pharmacokinetic investigations.

  7. Chemically modified tetracyclines: Novel therapeutic agents in the management of chronic periodontitis

    Directory of Open Access Journals (Sweden)

    Rupali Agnihotri

    2012-01-01

    Full Text Available Chronic periodontitis is a complex infection initiated by gram-negative bacteria which destroy the supporting structures of the tooth. Recently, it has been recognized that it is the host response to bacterial infection which causes greater destruction of the connective tissue elements, periodontal ligament and alveolar bone in periodontitis. This has led to the development of various host modulating approaches to target cells and their destructive mediators involved in tissue degradation. Chemically modified tetracyclines (CMTs are derivatives of tetracycline group of drugs which lack antimicrobial action but have potent host modulating affects. They inhibit pathologically elevated matrix metal loproteinases, pro-inflammtory cytokines and other destructive mediators. Bone resorption is also suppressed due to their combined anti-proteinase and apoptotic affects on osteoblasts and osteoclasts, respectively. Development of resistant bacteria and gastrointestinal toxicity seen with parent tetracyclines is not produced by CMTs. Hence, CMTs are viewed as potential therapeutic agents in the management of chronic diseases like periodontitis that involve destruction of connective tissue and bone.

  8. Palladium-Catalyzed Modification of Unprotected Nucleosides, Nucleotides, and Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Kevin H. Shaughnessy

    2015-05-01

    Full Text Available Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

  9. Polymerase-Endonuclease Amplification Reaction (PEAR) for Large-Scale Enzymatic Production of Antisense Oligonucleotides

    Science.gov (United States)

    Wang, Xiaolong; Gou, Deming; Xu, Shuang-yong

    2010-01-01

    Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR), for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI) cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs. PMID:20062528

  10. Polymerase-endonuclease amplification reaction (PEAR for large-scale enzymatic production of antisense oligonucleotides.

    Directory of Open Access Journals (Sweden)

    Xiaolong Wang

    Full Text Available Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR, for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.

  11. Effects of Zn Content on Crystal Structure, Cytocompatibility, Antibacterial Activity, and Chemical Stability in Zn-Modified Calcium Silicate Coatings

    Science.gov (United States)

    Li, Kai; Yu, Jiangming; Xie, Youtao; Huang, Liping; Ye, Xiaojian; Zheng, Xuebin

    2013-08-01

    In our previous study, Zn-modified calcium silicate coatings possess not only excellent chemical stability but also well antibacterial activity. Still, effects of zinc content on these properties and cytocompatibility remain unclear. In this paper, two kinds of Zn-modified calcium silicate coatings (ZC0.3, ZC0.5) were fabricated on Ti-6Al-4V substrates via plasma spraying technology. X-ray diffraction results and transmission electron microscopy observations showed that the ZC0.5 coating was composed of pure hardystonite (Ca2ZnSi2O7) phase, while, besides Ca2ZnSi2O7 phase, the amorphous CaSiO3 phase was also detected in the ZC0.3 coating. Chemical stability in Tris-HCl buffer solution and antibacterial activity of the Zn-modified calcium silicate coatings increased with an increase in zinc content. In vitro cytocompatibility evaluation demonstrated that the proliferation and alkaline phosphatase activity and collagen type I (COLI) secretion of osteoblast-like MC3T3-E1 cells on Zn-modified coatings were significantly enhanced compared to the Zn-free coating and Ti-6Al-4V control, and no cytotoxicity appeared on Zn-modified coatings. The better antibacterial activity and the enhanced capability to promote MC3T3-E1 cells differentiation of Zn-modified coatings should be attributed to the slow and constant Zn2+ releasing from the coatings.

  12. Chemical ligation methods for the tagging of DNA-encoded chemical libraries.

    Science.gov (United States)

    Keefe, Anthony D; Clark, Matthew A; Hupp, Christopher D; Litovchick, Alexander; Zhang, Ying

    2015-06-01

    The generation of DNA-encoded chemical libraries requires the unimolecular association of multiple encoding oligonucleotides with encoded chemical entities during combinatorial synthesis processes. This has traditionally been achieved using enzymatic ligation. We discuss a range of chemical ligation methods that provide alternatives to enzymatic ligation. These chemical ligation methods include the generation of modified internucleotide linkages that support polymerase translocation and other modified linkages that while not supporting the translocation of polymerases can also be used to generate individual cDNA molecules containing encoded chemical information specifying individual library members. We also describe which of these approaches have been successfully utilized for the preparation of DNA-encoded chemical libraries and those that were subsequently used for the discovery of inhibitors.

  13. Fretting Wear Behavior of Medium Carbon Steel Modified by Low Temperature Gas Multi-component Thermo-chemical Treatment

    Institute of Scientific and Technical Information of China (English)

    LUO Jun; ZHENG Jianfeng; PENG Jinfang; HE Liping; ZHU Minhao

    2010-01-01

    The introduction of surface engineering is expected to be an effective strategy against fretting damage. A large number of studies show that the low gas multi-component (such as carbon, nitrogen, sulphur and oxygen, etc) thermo-chemical treatment(LTGMTT) can overcome the brittleness of nitriding process, and upgrade the surface hardness and improve the wear resistance and fatigue properties of the work-pieces significantly. However, there are few reports on the anti-fretting properties of the LTGMTT modified layer up to now, which limits the applications of fretting. So this paper discusses the fretting wear behavior of modified layer on the surface of LZ50 (0.48%C) steel prepared by low temperature gas multi-component thermo-chemical treatment (LTGMTT) technology. The fretting wear tests of the modified layer flat specimens and its substrate (LZ50 steel) against 52100 steel balls with diameter of 40 mm are carried out under normal load of 150 N and displacement amplitudes varied from 2 μm to 40 μm. Characterization of the modified layer and dynamic analyses in combination with microscopic examinations were performed through the means of scanning electron microscope(SEM), optical microscope(OM), X-ray diffraction(XRD) and surface profilometer. The experimental results showed that the modified layer with a total thickness of 60 μm was consisted of three parts, i.e., loose layer, compound layer and diffusion layer. Compared with the substrate, the range of the mixed fretting regime(MFR) of the LTGMTT modified layer diminished, and the slip regime(SR) of the modified layer shifted to the direction of smaller displacement amplitude. The coefficient of friction(COF) of the modified layer was lower than that of the substrate in the initial stage. For the modified layer, the damage in partial slip regime(PSR) was very slight. The fretting wear mechanism of the modified layer both in MFR and SR was abrasive wear and delamination. The modified layer presented better wear

  14. Liposome-coated lipoplex-based carrier for antisense oligonucleotides.

    Science.gov (United States)

    Wyrozumska, Paulina; Meissner, Justyna; Toporkiewicz, Monika; Szarawarska, Marta; Kuliczkowski, Kazimierz; Ugorski, Maciej; Walasek, Marta A; Sikorski, Aleksander F

    2015-01-01

    The chemical nature of genetic drugs (e.g. antisense oligonucleotides, siRNA, vectors) requires a suitable carrier system to protect them from enzymatic degradation without changing their properties and enable efficient delivery into target cells. Lipid vectors for nucleic acid delivery that have been widely investigated for years can be very effective. As the majority of attempts made in the field of cancer gene therapy have focused on solid tumors, while blood cancer cells have attracted less attention, the latter became the subject of our investigation. The lipid carrier proposed here is based on liposomes constructed by others but the lipid composition is original. A liposome-coated lipoplex (L-cL) consists of a core arising from complexation of positively charged lipid and negatively charged oligodeoxynucleotide (ODN) or plasmid DNA coated by a neutral or anionic lipid bilayer. Moreover, our lipid vector demonstrates size stability and is able to retain a high content of enclosed plasmid DNA or antisense oligodeoxynucleotides (asODNs). Observed transfection efficacies of the tested preparation using a plasmid coding for fluorescent protein were up to 60-85% of examined leukemia cells (Jurkat T and HL-60 lines) in the absence or the presence of serum. When BCL‑2 asODN was encapsulated in the L-cL, specific silencing of this gene product at both the mRNA and protein level and also a markedly decreased cell survival rate were observed in vitro. Moreover, biodistribution analysis in mice indicates prolonged circulation characteristic for PEG-modified liposomal carriers. Experiments on tumor-engrafted animals indicate substantial inhibition of tumor growth.

  15. Oligonucleotide-based biosensors for in vitro diagnostics and environmental hazard detection.

    Science.gov (United States)

    Jung, Il Young; Lee, Eun Hee; Suh, Ah Young; Lee, Seung Jin; Lee, Hyukjin

    2016-04-01

    Oligonucleotide-based biosensors have drawn much attention because of their broad applications in in vitro diagnostics and environmental hazard detection. They are particularly of interest to many researchers because of their high specificity as well as excellent sensitivity. Recently, oligonucleotide-based biosensors have been used to achieve not only genetic detection of targets but also the detection of small molecules, peptides, and proteins. This has further broadened the applications of these sensors in the medical and health care industry. In this review, we highlight various examples of oligonucleotide-based biosensors for the detection of diseases, drugs, and environmentally hazardous chemicals. Each example is provided with detailed schematics of the detection mechanism in addition to the supporting experimental results. Furthermore, future perspectives and new challenges in oligonucleotide-based biosensors are discussed.

  16. Direct determination of cadmium in Orujo spirit samples by electrothermal atomic absorption spectrometry: Comparative study of different chemical modifiers

    Energy Technology Data Exchange (ETDEWEB)

    Vilar Farinas, M. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Facultad de Ciencias, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo (Spain); Barciela Garcia, J. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Facultad de Ciencias, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo (Spain); Garcia Martin, S. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Facultad de Ciencias, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo (Spain); Pena Crecente, R. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Facultad de Ciencias, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo (Spain); Herrero Latorre, C. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Facultad de Ciencias, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo (Spain)]. E-mail: cherrero@lugo.usc.es

    2007-05-22

    In this work, several analytical methods are proposed for cadmium determination in Orujo spirit samples using electrothermal atomic absorption spectrometry (ETAAS). Permanent chemical modifiers thermally coated on the platforms inserted in pyrolytic graphite tubes (such as W, Ir, Ru, W-Ir and W-Ru) were comparatively studied in relation to common chemical modifier mixtures [Pd-Mg(NO{sub 3}){sub 2} and (NH{sub 4})H{sub 2}PO{sub 4}-Mg(NO{sub 3}){sub 2}] for cadmium stabilization. Different ETAAS Cd determination methods based on the indicated modifiers have been developed. In each case, pyrolysis and atomization temperatures, atomization shapes, characteristic masses and detection limits as well as other analytical characteristics have been determined. All the assayed modifiers (permanent and conventional) were capable of achieving the appropriate stabilization of the analyte, with the exception of Ru and W-Ru. Moreover, for all developed methods, recoveries (99-102%) and precision (R.S.D. lower than 10%) were acceptable. Taking into account the analytical performance (best detection limit LOD = 0.01 {mu}g L{sup -1}), the ETAAS method based on the use of W as a permanent modifier was selected for further direct Cd determinations in Orujo samples from Galicia (NW Spain). The chosen method was applied in the determination of the Cd content in 38 representative Galician samples. The cadmium concentrations ranged

  17. Targeting several CAG expansion diseases by a single antisense oligonucleotide.

    Directory of Open Access Journals (Sweden)

    Melvin M Evers

    Full Text Available To date there are 9 known diseases caused by an expanded polyglutamine repeat, with the most prevalent being Huntington's disease. Huntington's disease is a progressive autosomal dominant neurodegenerative disorder for which currently no therapy is available. It is caused by a CAG repeat expansion in the HTT gene, which results in an expansion of a glutamine stretch at the N-terminal end of the huntingtin protein. This polyglutamine expansion plays a central role in the disease and results in the accumulation of cytoplasmic and nuclear aggregates. Here, we make use of modified 2'-O-methyl phosphorothioate (CUGn triplet-repeat antisense oligonucleotides to effectively reduce mutant huntingtin transcript and protein levels in patient-derived Huntington's disease fibroblasts and lymphoblasts. The most effective antisense oligonucleotide, (CUG(7, also reduced mutant ataxin-1 and ataxin-3 mRNA levels in spinocerebellar ataxia 1 and 3, respectively, and atrophin-1 in dentatorubral-pallidoluysian atrophy patient derived fibroblasts. This antisense oligonucleotide is not only a promising therapeutic tool to reduce mutant huntingtin levels in Huntington's disease but our results in spinocerebellar ataxia and dentatorubral-pallidoluysian atrophy cells suggest that this could also be applicable to other polyglutamine expansion disorders as well.

  18. Oligonucleotide and Long Polymeric DNA Encoding

    Energy Technology Data Exchange (ETDEWEB)

    Miller, E; Mariella Jr., R P; Christian, A T; Gardner, S N; Williams, J M

    2003-11-24

    This report summarizes the work done at Lawrence Livermore National Laboratory for the Oligonucleotide and Long Polymeric DNA Encoding project, part of the Microelectronic Bioprocesses Program at DARPA. The goal of the project was to develop a process by which long (circa 10,000 base-pair) synthetic DNA molecules could be synthesized in a timely and economic manner. During construction of the long molecule, errors in DNA sequence occur during hybridization and/or the subsequent enzymatic process. The work done on this project has resulted in a novel synthesis scheme that we call the parallel pyramid synthesis protocol, the development of a suit of computational tools to minimize and quantify errors in the synthesized DNA sequence, and experimental proof of this technique. The modeling consists of three interrelated modules: the bioinformatics code which determines the specifics of parallel pyramid synthesis for a given chain of long DNA, the thermodynamics code which tracks the products of DNA hybridization and polymerase extension during the later steps in the process, and the kinetics model which examines the temporal and spatial processes during one thermocycle. Most importantly, we conducted the first successful syntheses of a gene using small starting oligomers (tetramers). The synthesized sequence, 813 base pairs long, contained a 725 base pair gene, modified green fluorescent protein (mGFP), which has been shown to be a functional gene by cloning into cells and observing its green fluorescent product.

  19. Adaptive resolution simulation of oligonucleotides

    Science.gov (United States)

    Netz, Paulo A.; Potestio, Raffaello; Kremer, Kurt

    2016-12-01

    Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.

  20. Porous silicon-cell penetrating peptide hybrid nanocarrier for intracellular delivery of oligonucleotides.

    Science.gov (United States)

    Rytkönen, Jussi; Arukuusk, Piret; Xu, Wujun; Kurrikoff, Kaido; Langel, Ulo; Lehto, Vesa-Pekka; Närvänen, Ale

    2014-02-01

    The largest obstacle to the use of oligonucleotides as therapeutic agents is the delivery of these large and negatively charged biomolecules through cell membranes into intracellular space. Mesoporous silicon (PSi) is widely recognized as a potential material for drug delivery purposes due to its several beneficial features like large surface area and pore volume, high loading capacity, biocompatibility, and biodegradability. In the present study, PSi nanoparticles stabilized by thermal oxidation or thermal carbonization and subsequently modified by grafting aminosilanes on the surface are utilized as an oligonucleotide carrier. Splice correcting oligonucleotides (SCOs), a model oligonucleotide drug, were loaded into the positively charged PSi nanoparticles with a loading degree as high as 14.3% (w/w). Rapid loading was achieved by electrostatic interactions, with the loading efficiencies reaching 100% within 5 min. The nanoparticles were shown to deliver and release SCOs, in its biologically active form, inside cells when formulated together with cell penetrating peptides (CPP). The biological effect was monitored with splice correction assay and confocal microscopy utilizing HeLa pLuc 705 cells. Furthermore, the use of PSi carrier platform in oligonucleotide delivery did not reduce the cell viability. Additionally, the SCO-CPP complexes formed in the pores of the carrier were stabilized against proteolytic digestion. The advantageous properties of protecting and releasing the cargo and the possibility to further functionalize the carrier surface make the hybrid nanoparticles a potential system for oligonucleotide delivery.

  1. Fragment-based solid-phase assembly of oligonucleotide conjugates with peptide and polyethylene glycol ligands.

    Science.gov (United States)

    Dirin, Mehrdad; Urban, Ernst; Noe, Christian R; Winkler, Johannes

    2016-10-04

    Ligand conjugation to oligonucleotides is an attractive strategy for enhancing the therapeutic potential of antisense and siRNA agents by inferring properties such as improved cellular uptake or better pharmacokinetic properties. Disulfide linkages enable dissociation of ligands and oligonucleotides in reducing environments found in endosomal compartments after cellular uptake. Solution-phase fragment coupling procedures for producing oligonucleotide conjugates are often tedious, produce moderate yields and reaction byproducts are frequently difficult to remove. We have developed an improved method for solid-phase coupling of ligands to oligonucleotides via disulfides directly after solid-phase synthesis. A 2'-thiol introduced using a modified nucleotide building block was orthogonally deprotected on the controlled pore glass solid support with N-butylphosphine. Oligolysine peptides and a short monodisperse ethylene glycol chain were successfully coupled to the deprotected thiol. Cleavage from the resin and full removal of oligonucleotide protection groups were achieved using methanolic ammonia. After standard desalting, and without further purification, homogenous conjugates were obtained as demonstrated by HPLC, gel electrophoresis, and mass spectrometry. The attachment of both amphiphilic and cationic ligands proves the versatility of the conjugation procedure. An antisense oligonucleotide conjugate with hexalysine showed pronounced gene silencing in a cell culture tumor model in the absence of a transfection reagent and the corresponding ethylene glycol conjugate resulted in down regulation of the target gene to nearly 50% after naked application. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  2. Electrochemical impedance spectroscopy for graphene surface modification and protein translocation through the chemically modified graphene nanopore

    Science.gov (United States)

    Tiwari, Purushottam; Shan, Yuping; Wang, Xuewen; Darici, Yesim; He, Jin

    2014-03-01

    The multilayer graphene surface has been modified using mercaptohexadecanoic acid (MHA) and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-750] (DPPE-PEG750). The surface modifications are evaluated using electrochemical impedance spectroscopy (EIS). EIS measurements show the better graphene surface passivation with DPPE-PEG750 than with MHA. After modification with ferritin, the MHA modified surface shows greater charge transfer resistance (Rct) change than DPPE-PEG750 modified surface. Based on these results the translocations of ferritin through modified graphene nanopore with diameter 5-20 nm are studied. The translocation is more successful through DPPE-PEG750 modified graphene nanopore. This concludes that that the attachment of ferritin to DPPE-PEG750 modified graphene nanopore is not significant compared to MHA modified pore for the ferritin translocation hindrance. These results nicely correlate with the EIS data for respective Rct change of ferritin modified surfaces. P. Tiwari would like to thank FIU School of Integrated Science & Humanity, College Arts & Sciences for the research assistantship.

  3. Streptavidin-coated gold nanoparticles: critical role of oligonucleotides on stability and fractal aggregation

    Directory of Open Access Journals (Sweden)

    Roberta D'Agata

    2017-01-01

    Full Text Available Gold nanoparticles (AuNPs exhibit unique properties that can be modulated through a tailored surface functionalization, enabling their targeted use in biochemical sensing and medical diagnostics. In particular, streptavidin-modified AuNPs are increasingly used for biosensing purposes. We report here a study of AuNPs surface-functionalized with streptavidin-biotinylated oligonucleotide, focussing on the role played by the oligonucleotide probes in the stabilization/destabilization of the functionalized nanoparticle dispersion. The behaviour of the modified AuNP dispersion as a consequence of the competitive displacement of the biotinylated oligonucleotide has been investigated and the critical role of displaced oligonucletides in triggering the quasi one-dimensional aggregation of nanoparticles is demonstrated for the first time. The thorough understanding of the fundamental properties of bioconjugated AuNPs is of great importance for the design of highly sensitive and reliable functionalized AuNP-based assays.

  4. Sex determination of bovine preimplantation embryos by oligonucleotide microarray.

    Science.gov (United States)

    Yang, Hua; Zhong, Fagang; Yang, Yonglin; Wang, Xinhua; Liu, Shouren; Zhu, Bin

    2013-06-01

    The aim has been to set up a rapid and accurate microarray assay using sandwich mode for sex determination of bovine preimplantation embryos. Twelve sequence-specific oligonucleotide capture probes used to discriminate 12 samples were spotted onto the aldehyde-modified glass slides by Arrayer. The 2 recognition probes used to identify coding regions of the sex-determining region of the Y chromosome gene (SRY) and β-casein (CSN2) reference gene were coupled with biotin. The assay was optimized by using genomic DNA extracted from blood samples of known sex individuals. Polymerase chain reaction (PCR) was used to amplify the fragments in the HMG box region of SRY gene and CSN2 gene with sequence-specific primers. The sex of samples was identified by detecting both the SRY and CSN2 genes simultaneously in 2 reaction cells of microarrays, with the male having SRY and CSN2 signals and the female only CSN2. The sex of 20 bovine preimplantation embryos was determined by oligonucleotide microarray. The protocol was run with a blind test that showed a 100% (82/82) specificity and accuracy in sexing of leukocytes. The bovine embryos were transferred into 20 bovine recipients, with a pregnant rate of 40% (8/20). Three calves were born at term, and 5 fetuses were miscarried. Their sexes were fully in accordance with the embryonic sex predetermination predicted by oligonucleotide microarray. This suggests that the oligonucleotide microarray method of SRY gene analysis can be used in early sex prediction of bovine embryos in breeding programs.

  5. Study of the adsorption and electroadsorption process of Cu (II) ions within thermally and chemically modified activated carbon.

    Science.gov (United States)

    Macías-García, A; Gómez Corzo, M; Alfaro Domínguez, M; Alexandre Franco, M; Martínez Naharro, J

    2017-04-15

    The aim of this work is to modify the porous texture and superficial groups of a commercial activated carbon through chemical and thermal treatment and subsequently study the kinetics of adsorption and electroadsorption of Cu (II) ion for these carbons. Samples of three activated carbons were used. These were a commercial activated carbon, commercial activated carbon modified thermically (C-N2-900) and finally commercial activated carbon modified chemically C-SO2-H2S-200. The activated carbons were characterized chemically and texturally and the electrical conductivity of them determined. Different kinetic models were applied. The kinetics of the adsorption and electroadsorption process of the Cu (II) ion fits a pseudo second order model and the most likely mechanism takes place in two stages. A first step through transfer of the metal mass through the boundary layer of the adsorbent and distribution of the Cu (II) on the external surface of the activated carbon and a second step that represents intraparticle diffusion and joining of the Cu (II) with the active centres of the activated carbon. Finally, the kinetics of the adsorption process are faster than the kinetics of the electroadsorption but the percentage of the Cu (II) ion retained is much higher in the electroadsorption process.

  6. Effect of surface chemical composition on the work function of silicon substrates modified by binary self-assembled monolayers.

    Science.gov (United States)

    Kuo, Che-Hung; Liu, Chi-Ping; Lee, Szu-Hsian; Chang, Hsun-Yun; Lin, Wei-Chun; You, Yun-Wen; Liao, Hua-Yang; Shyue, Jing-Jong

    2011-09-07

    It has been shown that the application of self-assembled monolayers (SAMs) to semiconductors or metals may enhance the efficiency of optoelectronic devices by changing the surface properties and tuning the work functions at their interfaces. In this work, binary SAMs with various ratios of 3-aminopropyltrimethoxysilane (APTMS) and 3-mercaptopropyltrimethoxysilane (MPTMS) were used to modify the surface of Si to fine-tune the work function of Si to an arbitrary energy level. As an electron-donor, amine SAM (from APTMS) produced outward dipole moments, which led to a lower work function. Conversely, electron-accepting thiol SAM (from MPTMS) increased the work function. It was found that the work function of Si changed linearly with the chemical composition and increased with the concentration of thiol SAMs. Because dipoles of opposite directions cancelled each other out, homogeneously mixing them leads to a net dipole moment (hence the additional surface potential) between the extremes defined by each dipole and changes linearly with the chemical composition. As a result, the work function changed linearly with the chemical composition. Furthermore, the amine SAM possessed a stronger dipole than the thiol SAM. Therefore, the SAMs modified with APTMS showed a greater work function shift than did the SAMs modified with MPTMS.

  7. Detection of Aeromonas hydrophila DNA oligonucleotide sequence using a biosensor design based on Ceria nanoparticles decorated reduced graphene oxide and Fast Fourier transform square wave voltammetry.

    Science.gov (United States)

    Jafari, Safiye; Faridbod, Farnoush; Norouzi, Parviz; Dezfuli, Amin Shiralizadeh; Ajloo, Davood; Mohammadipanah, Fatemeh; Ganjali, Mohammad Reza

    2015-10-01

    A new strategy was introduced for ssDNA immobilization on a modified glassy carbon electrode. The electrode surface was modified using polyaniline and chemically reduced graphene oxide decorated cerium oxide nanoparticles (CeO2NPs-RGO). A single-stranded DNA (ssDNA) probe was immobilized on the modified electrode surface. Fast Fourier transform square wave voltammetry (FFT-SWV) was applied as detection technique and [Ru(bpy)3](2+/3+) redox signal was used as electrochemical marker. The hybridization of ssDNA with its complementary target caused a dramatic decrease in [Ru(bpy)3](2+/3+) FFT-SW signal. The proposed electrochemical biosensor was able to detect Aeromonas hydrophila DNA oligonucleotide sequence encoding aerolysin protein. Under optimal conditions, the biosensor showed excellent selectivity toward complementary sequence in comparison with noncomplementary and two-base mismatch sequences. The dynamic linear range of this electrochemical DNA biosensor for detecting 20-mer oligonucleotide sequence of A. hydrophila was from 1 × 10(-15) to 1 × 10(-8) mol L(-1). The proposed biosensor was successfully applied for the detection of DNA extracted from A. hydrophila in fish pond water up to 0.01 μg mL(-1) with RSD of 5%. Besides, molecular docking was applied to consider the [Ru(bpy)3](2+/3+) interaction with ssDNA before and after hybridization.

  8. Splice-switching antisense oligonucleotides as therapeutic drugs

    OpenAIRE

    Havens, Mallory A.; Hastings, Michelle L.

    2016-01-01

    Splice-switching oligonucleotides (SSOs) are short, synthetic, antisense, modified nucleic acids that base-pair with a pre-mRNA and disrupt the normal splicing repertoire of the transcript by blocking the RNA–RNA base-pairing or protein–RNA binding interactions that occur between components of the splicing machinery and the pre-mRNA. Splicing of pre-mRNA is required for the proper expression of the vast majority of protein-coding genes, and thus, targeting the process offers a means to manipu...

  9. Conjugates of Phthalocyanines With Oligonucleotides as Reagents for Sensitized or Catalytic DNA Modification

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available Several conjugates of metallophthalocyanines with deoxyribooligonucleotides were synthesized to investigate sequence-specific modification of DNA by them. Oligonucleotide parts of these conjugates were responsible for the recognition of selected complementary sequences on the DNA target. Metallophthalocyanines were able to induce the DNA modification: phthalocyanines of Zn(II and Al(III were active as photosensitizers in the generation of singlet oxygen 1 O 2 , while phthalocyanine of Co(II promoted DNA oxidation by molecular oxygen through the catalysis of formation of reactive oxygen species ( ⋅ O 2 − , O 2 H 2 , OH. Irradiation of the reaction mixture containing either Zn(II- or Al(III-tetracarboxyphthalocyanine conjugates of oligonucleotide pd(TCTTCCCA with light of > 340 nm wavelength (Hg lamp or He/Ne laser resulted in the modification of the 22-nucleotide target d(TGAATGGGAAGAGGGTCAGGTT. A conjugate of Co(II-tetracarboxyphthalocyanine with the oligonucleotide was found to modify the DNA target in the presence of O 2 and 2-mercaptoethanol or in the presence of O 2 H 2 . Under both sensitized and catalyzed conditions, the nucleotides G 13 – G 15 were mainly modified, providing evidence that the reaction proceeded in the double-stranded oligonucleotide. These results suggest the possible use of phthalocyanine-oligonucleotide conjugates as novel artificial regulators of gene expression and therapeutic agents for treatment of cancer.

  10. Investigation of surface properties of physico-chemically modified natural fibres using inverse gas chromatography

    CSIR Research Space (South Africa)

    Cordeiro, N

    2011-01-01

    Full Text Available Inverse gas chromatography (IGC) is a suitable method to determine surface energy of natural fibres when compared to wetting techniques. In the present study, the surface properties of raw and modified lignocellulosic fibres have been investigated...

  11. Synthesis and Excellent Duplex Stability of Oligonucleotides Containing 2′-Amino-LNA Functionalized with Galactose Units

    Directory of Open Access Journals (Sweden)

    Rajesh Kumar

    2017-05-01

    Full Text Available A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2′-N-alkyne 2′-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.

  12. HIGHLY EFFECTIVE CHEMICAL MODIFIERS FOR PRODUCTION OF CONCRETES WITH PRE-SET PROPERTIES

    OpenAIRE

    2012-01-01

    The paper demonstrates the application of industrial by-products and recycled materials. Waterproofing admixtures improve the structure and the properties of the cement stone. Development and preparation of highly effective waterproofing modifiers of durable effect, as well as development of the process procedure parameters, including mixing, activation, heat treatment, etc. are to be implemented. The composition of waterproofing modifiers is to be fine-tuned to synergize the behaviour of var...

  13. Considerations for the Characterization and Interpretation of Results Related to Alternative Complement Activation in Monkeys Associated with Oligonucleotide-Based Therapeutics.

    Science.gov (United States)

    Henry, Scott P; Seguin, Rosanne; Cavagnaro, Joy; Berman, Cindy; Tepper, Jeff; Kornbrust, Douglas

    2016-08-01

    This article provides an overview of the discussions held by the Immunomodulatory Subcommittee of the Oligonucleotide Safety Working Group on complement activation induced by oligonucleotides, most notably the phosphorothioate-containing oligonucleotides. Alternative complement pathway activation in monkeys is a common effect of single-stranded phosphorothioate backbone oligonucleotides in toxicology studies. This article discusses the mechanism for activation, general investigational strategy, and the impact of various chemical modifications. The goal is to provide the best practice approach to characterizing this effect, understanding the implication of the species specificity, and the interpretation of clinical relevance.

  14. Injection site reactions after subcutaneous oligonucleotide therapy

    NARCIS (Netherlands)

    van Meer, L. (Leonie); M. Moerland (Matthijs); Gallagher, J. (Jolie); M.B.A. van Doorn (Martijn); E.P. Prens (Errol); A.F. Cohen; Rissmann, R. (Robert); J. Burggraaf (Jacobus)

    2016-01-01

    textabstractOligonucleotides (ONs) are short fragments of nucleic acids, currently being investigated as therapeutic agents. When administered subcutaneously (sc), ONs cause a specific local reaction originating around the injection site, such as erythema, itching, discomfort and pain, including

  15. HIGHLY EFFECTIVE CHEMICAL MODIFIERS FOR PRODUCTION OF CONCRETES WITH PRE-SET PROPERTIES

    Directory of Open Access Journals (Sweden)

    Tkach Evgeniya Vladimirovna

    2012-10-01

    Full Text Available The paper demonstrates the application of industrial by-products and recycled materials. Waterproofing admixtures improve the structure and the properties of the cement stone. Development and preparation of highly effective waterproofing modifiers of durable effect, as well as development of the process procedure parameters, including mixing, activation, heat treatment, etc. are to be implemented. The composition of waterproofing modifiers is to be fine-tuned to synergize the behaviour of various ingredients of cement systems to assure the substantial improvement of their strength, freeze- and corrosion resistance. Multi-functional waterproofing admixtures were used to produce highly effective modified concretes. The key idea of the new method of modifying cement-based building materials is that the waterproofing admixture concentration is to exceed 10% of the weight of the binding agent within the per-unit weight of the cement stone, given that its strength does not deteriorate. GKM-type modifier coupled with organo-mineral waterproofing admixture concentration agent GT-M may be recommended for mass use in the manufacturing of hydraulic concrete and reinforced concrete products. Overview of their practical implementation has proven that waterproofing modifier GKM-S, if coupled with waterproofing admixture concentration agent GT-M, improves the corrosion control inside the cement stone and makes it possible to manufacture durable concrete and reinforced concrete products that demonstrate pre-set physical and processing behaviour. Comprehensive concrete modification by modifier GKM-S and waterproofing admixture concentration agent GT-M may be regarded as one of the most ambitious methods of production of highly effective waterproof concretes.

  16. Cr(VI) adsorption from electroplating plating wastewater by chemically modified coir pith.

    Science.gov (United States)

    Suksabye, Parinda; Thiravetyan, Paitip

    2012-07-15

    Coir pith samples were chemically modified by grafting with acrylic acid for the removal of Cr(VI) from electroplating wastewater. The presence of acrylic acid on the coir pith surface was verified by a scanning electron microscope with an electron dispersive x-ray spectrometer (SEM/EDX), Fourier transform infrared spectroscopy (FTIR) and thermogravimetry (TG). The carbonyl groups (C==O) from the carboxylic acids (COOH) increased on the coir pith surface after grafting with acrylic acid. In addition, the thermal stability of the acrylic acid-grafted coir pith also improved. The optimum conditions for grafting the acrylic acid on the coir pith consisted of 2 M acrylic acid and 0.00125 M ceric ammonium nitrate (CAN, as an initiator). The maximum Cr(VI) removal (99.99 ± 0.07%) was obtained with the following conditions: a 1.3% (w/v) dosage of acrylic acid-grafted coir pith, a system pH of 2, a contact time of 22 h, a temperature of 30 °C, a particle size of <150 μm and an initial Cr(VI) of 1,171 mg l(-1). At system pH of 2, Cr(VI) in the HCrO(4)(-) form can be adsorbed with acrylic acid-grafted coir pith via an electrostatic attraction. The adsorption isotherm of 2 M acrylic acid-grafted coir pith exhibited a good fit with the Langmuir isotherm. The maximum Cr(VI) adsorption capacity of the 2 M acrylic acid-grafted coir pith was 196.00 mg Cr(VI) g(-1) adsorbent, whereas for coir pith without grafting, the maximum Cr(VI) removal was 165.00 mg Cr(VI) g(-1) adsorbent. The adsorption capacity of the acrylic acid-grafted coir pith for Cr(VI) was higher compared to the original coir pith. This result was due to the enhancement of the carbonyl groups on the coir pith surface that may have involved the mechanism of chromium adsorption. The X-ray absorption near edged structure (XANES) and desorption studies suggested that most of the Cr(III) that presented on the acrylic acid-grafted coir pith was due to the Cr(VI) being reduced to Cr(III) on the adsorbent surface. FTIR

  17. Chemical and rheological evaluation of ageing properties of SBS polymer modified bitumens

    Energy Technology Data Exchange (ETDEWEB)

    Lu, X.; Isacsson, U. [Royal Institute of Technology, Stockholm (Sweden). Division of Highway Engineering

    1998-07-01

    The ageing properties of Styrene-Butadiene-Styrene (SBS) polymer modified bitumens were evaluated using Dynamic Mechanical Analysis (DMA), Gel Permeation Chromatography (GPC) and Fourier Transform InfraRed (FTIR) spectroscopy. The binders were aged by means of the Thin Film Oven Test (TFOT) and the Rolling Thin Film Oven Test (RTFOT), respectively. It was observed that ageing resulted in degradation of the SBS polymer containing molecules and increase in bitumen molecular weight. The polymer was observed to resist formation of sulphoxides. Changes in the rheological properties of aged-modified binders were dependent on a combined effect of bitumen oxidation and polymer degradation, which varied with bitumen source/grade and polymer type/content. In all cases, the aged modified binders showed better rheological properties than aged base bitumens. The study also indicated that the ageing index obtained using DMA was largely influenced by temperature and frequency. This parameter may be applied for evaluating the base bitumens and modified binders with a low polymer content (3% in this study), but not for modified binders with a high (6%) polymer content. 18 refs., 9 figs., 4 tabs.

  18. A Modified Approach for Calculating Dressed Quark Propagator at Finite Chemical Potential

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Based on the rainbow approximation of Dyson-Schwinger equation and the assumption that the full inverse quark propagator at finite chemical potential is analytic in the neighborhood of μ = 0, it is proved that the dressed From the dressed quark propagator at finite chemical potential μ can be written as (g0-1)[μ]=iγ·(p~)A((p~2))+B((p~2))with (p~)μ=((p),p4+iμ).From the dressed quark propagator at finite chemical potential in Munczek model the bag constant of a baryon and the scalar quark condensate are evaluated. A comparison with previous results is given.

  19. Enzymatic electrochemical detection of epidemic-causing Vibrio cholerae with a disposable oligonucleotide-modified screen-printed bisensor coupled to a dry-reagent-based nucleic acid amplification assay.

    Science.gov (United States)

    Yu, Choo Yee; Ang, Geik Yong; Chan, Kok Gan; Banga Singh, Kirnpal Kaur; Chan, Yean Yean

    2015-08-15

    In this study, we developed a nucleic acid-sensing platform in which a simple, dry-reagent-based nucleic acid amplification assay is combined with a portable multiplex electrochemical genosensor. Preparation of an amplification reaction mix targeting multiple DNA regions of interest is greatly simplified because the lyophilized reagents need only be reconstituted with ultrapure water before the DNA sample is added. The presence of single or multiple target DNAs causes the corresponding single-stranded DNA (ssDNA) amplicons to be generated and tagged with a fluorescein label. The fluorescein-labeled ssDNA amplicons are then analyzed using capture probe-modified screen-printed gold electrode bisensors. Enzymatic amplification of the hybridization event is achieved through the catalytic production of electroactive α-naphthol by anti-fluorescein-conjugated alkaline phosphatase. The applicability of this platform as a diagnostic tool is demonstrated with the detection of toxigenic Vibrio cholerae serogroups O1 and O139, which are associated with cholera epidemics and pandemics. The platform showed excellent diagnostic sensitivity and specificity (100%) when challenged with 168 spiked stool samples. The limit of detection was low (10 colony-forming units/ml) for both toxigenic V. cholerae serogroups. A heat stability assay revealed that the dry-reagent amplification reaction mix was stable at temperatures of 4-56 °C, with an estimated shelf life of seven months. The findings of this study highlight the potential of combining a dry-reagent-based nucleic acid amplification assay with an electrochemical genosensor in a more convenient, sensitive, and sequence-specific detection strategy for multiple target nucleic acids.

  20. Magnetorheological finishing with chemically modified fluids for studying material removal of single-crystal ZnS

    Science.gov (United States)

    Salzman, S.; Romanofsky, H. J.; Clara, Y. I.; Giannechini, L. J.; West, Garrett J.; Lambropoulos, J. C.; Jacobs, S. D.

    2013-09-01

    Magnetorheological finishing (MRF) of polycrystalline, chemical-vapor-deposited (CVD) zinc sulfide (ZnS) and zinc selenide (ZnSe) can leave millimeter-size artifacts on the part surface. These pebble-like features come from the anisotropic mechanical and chemical properties of the ceramic material and from the CVD growth process itself. The resulting surface texture limits the use of MRF for polishing aspheric and other complex shapes using these important infrared (IR) ceramics. An investigation of the individual contributions of chemistry and mechanics to polishing of other polycrystalline ceramics has been employed in the past to overcome similar material anisotropy problems. The approach taken was to study the removal process for the different single-crystal orientations that comprise the ceramic, making adjustments to mechanics (polishing abrasive type and concentration) and polishing slurry chemistry (primarily pH) to equalize the removal rate for all crystal orientations. Polishing with the modified slurry was shown to prevent the development of surface texture. Here we present mechanical (microhardness testing) and chemical (acid etching) studies performed on the four single-crystal orientations of ZnS: 100, 110, 111, and 311. We found that the (111) plane is 35% to 55% harder and 30% to 40% more resistant to chemical etching than the other three planes. This relatively high degree of variation in these properties can help to explain the surface texture developed from MRF of the polycrystalline material. Theoretical calculations of microhardness, planar, and bond densities are presented and compared with the experimental data. Here surface characterization of these single-crystal orientations of ZnS for material removal and roughness with chemically modified MR fluids at various pH levels between pH 4 and pH 6 are presented for the first time.

  1. Single probe nucleic acid immobilization on chemically modified single protein by controlling ionic strength and pH.

    Science.gov (United States)

    Yamasaki, Ryujiroh; Ito, Masateru; Lee, BongKuk; Jung, HoSup; Lee, HeaYeon; Kawai, Tomoji

    2007-11-05

    In an effort toward determining the feasibility of single molecule analysis, we describe a case whereby the binding of one biotinylated DNA to one streptavidin molecule via electrostatic interactions was controlled by altering in pH 4.0-9.0 and 0.16 of the ion strength. The quantitative analysis of immobilized probe ssDNA was realized in real-time via a quartz crystal microbalance (QCM) and electrochemical (EC) measurement in the range 100 pM to 50 microM of probe oligonucleotide concentration. The variation amount of biotinylated ssDNA immobilized on the streptavidin-modified surface at pH 7.5 was about 0.16 pmol, giving a ratio of streptavidin to biotinylated ssDNA of about 1:1.1. On the other hand, at pH 4.9, it was immobilized about 0.29 pmol. From the shape of the Langmuir plot and QCM, the immobilization efficiency of biotinylated DNA via streptavidin at pH 4.9 was approximately twofold that at pH 7.5. In view points of the reaction velocity, it was increased with decreasing buffer solution pH, indicating a strong interaction of negatively charged probe DNA with the positively charged streptavidin. And also the EC response value of deltaI/I(streptavidin) for the immobilized biotinylated ssDNA in pH 4.9 was about 49%, while the corresponding value for the pH 7.5 was approximately 34%. As DNA molecules possess negative charges, electrostatic repulsion occurred between streptavidin and biotinylated ssDNA at pH 7.5. At pH 4.9, the attraction between the biotinylated ssDNA and streptavidin resulted in increased adsorption which has an isoelectric point of about 5.9. It was deduced that the binding of biotinylated ssDNA to one or two of the four binding sites of streptavidin can be controlled by adjusting the pH-controlled electrostatic interaction.

  2. Chemically Modified Starch; Allyl- and Epoxy-Starch Derivatives: Their Synthesis and Characterization

    NARCIS (Netherlands)

    Franssen, M.C.R.; Boeriu, C.

    2014-01-01

    Both native and modified starches, such as starch that is pregelatinized, extruded, acid-converted, cross-linked, and substituted, are widely used in industry. This chapter describes a mild two-step process for the synthesis of novel, highly reactive granular epoxy-starch derivatives. Via this metho

  3. Chemically Modified Starch; Allyl- and Epoxy-Starch Derivatives: Their Synthesis and Characterization

    NARCIS (Netherlands)

    Franssen, M.C.R.; Boeriu, C.

    2014-01-01

    Both native and modified starches, such as starch that is pregelatinized, extruded, acid-converted, cross-linked, and substituted, are widely used in industry. This chapter describes a mild two-step process for the synthesis of novel, highly reactive granular epoxy-starch derivatives. Via this metho

  4. Sulfur Fixation by Chemically Modified Red Mud Samples Containing Inorganic Additives: A Parametric Study

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2016-01-01

    Full Text Available Sulfur retention ability of Bayer red mud from alumina plant was investigated. Bayer red mud modified by fusel salt and waste mother liquor of sodium ferrocyanide as the main sulfur fixation agent and the calcium based natural mineral materials as servicing additives; the experimental results showed the following: (1 Through 10 wt% waste mother liquor of sodium ferrocyanide modifying Bayer red mud, sulfur fixation rate can increase by 13 wt%. (2 Magnesium oxide can obviously improve the sulfur fixation performance of Bayer red mud and up to a maximum sulfur fixation rate of 47 wt% at adding 1 wt% magnesium oxide. (3 Dolomite enhanced the sulfur fixation performances with the sulfur fixation rate of 68 wt% in optimized condition. (4 Vermiculite dust reduced sulfur dioxide during the fixed-sulfur process of modified Bayer red mud, and the desulphurization ration could reach up to a maximum 76 wt% at 950°C. (5 An advanced three-component sulfur fixation agent was investigated, in which the optimized mass ratio of modified Bayer red mud, dolomite, and vermiculite dust was 70 : 28 : 2 in order, and its sulfur fixation efficiency has reached to a maximum 87 wt% under its 20 wt% dosage in the coal.

  5. Chemically Modified Starch; Allyl- and Epoxy-Starch Derivatives: Their Synthesis and Characterization

    NARCIS (Netherlands)

    Franssen, M.C.R.; Boeriu, C.

    2014-01-01

    Both native and modified starches, such as starch that is pregelatinized, extruded, acid-converted, cross-linked, and substituted, are widely used in industry. This chapter describes a mild two-step process for the synthesis of novel, highly reactive granular epoxy-starch derivatives. Via this

  6. 新型纳米金荧光双标survivin反义寡核苷酸探针的合成及其对人恶性黑素瘤A375细胞的影响%Synthesis of the probe of survivin antisens oligonucleotide modified gold nanoparticles and its impact on A375 cells

    Institute of Scientific and Technical Information of China (English)

    李萍; 王梅; 肖生祥; 王冰; 霍佳

    2013-01-01

    目的 利用纳米金独特的生物和光学特性,合成一种新型纳米金荧光双标survivin反义寡核苷酸探针,观察其对人恶性黑素瘤A375细胞的影响.方法 用柠檬酸钠还原法制备纳米金,将巯基修饰后的survivin反义寡核苷酸结合在纳米金表面,合成纳米金survivin反义寡核苷酸探针;再结合互补的带荧光标记的报告序列,制成纳米金荧光双标survivin反义寡核苷酸探针;将制备的探针转染人恶性黑素瘤A375细胞,荧光显微镜观察细胞内荧光图像,MTT法及流式细胞仪检测A375细胞的增殖及凋亡情况.结果 制备的纳米金荧光双标survivin反义寡核苷酸探针转染A375细胞后,可观察到清晰的细胞内荧光图像,可以抑制A375细胞的增殖,与对照组比较差异有统计学意义(P<0.05),诱导细胞凋亡增多.结论 寡核苷酸功能化的纳米金颗粒可有效转染进人恶性黑素瘤A375细胞,通过反义封闭作用诱导人恶性黑素瘤A375细胞凋亡增多.%Objective To synthesize the probe of survivin antisense oligonucleotide modified gold nanoparticles by making use of the biological and optical characteristics of gold nanoparticles and to analyze its impact on A375 cells. Methods Citrate-stabilized gold nanoparticles were prepared using published procedures. Thiol-modified oligonucleotides were added to gold colloids to make nano-probes. Then the complementary reporter sequence was combined to prepare "nano-flare" probes. A375 cells were grown with media containing nano-flares probes. Fluorescent images were observed under the fluorescence microscope. Cell proliferation was measured by MTT and cell apoptosis was detected by Annexin V/PI double staining method. Results The nano-probes could inhibit A375 cell proliferation significantly (P<0.05) and induce cell apoptosis. Conclusion The nano-probes that can be stably synthesized can inhibit proliferation of A375 cells and induce their apoptosis.

  7. Biosorption of Cu (II onto chemically modified waste mycelium of Aspergillus awamori: Equilibrium, kinetics and modeling studies

    Directory of Open Access Journals (Sweden)

    ZDRAVKA VELKOVA

    2012-01-01

    Full Text Available The biosorption potential of chemically modified waste mycelium of industrial xylanase-producing strain Aspergillus awamori for Cu (II removal from aqueous solutions was evaluated. The influence of pH, contact time and initial Cu (II concentration on the removal efficiency was evaluated. Maximum biosorption capacity was reached by sodium hydroxide treated waste fungal mycelium at pH 5.0. The Langmuir adsorption equation matched very well the adsorption equilibrium data in the studied conditions. The process kinetic followed the pseudo-firs order model.

  8. Interpenetrating polymer networks based on polyol modified castor oil polyurethane and poly(2-hydroxyethylmethacrylate): Synthesis, chemical, mechanical and thermal properties

    Indian Academy of Sciences (India)

    K Prashantha; K Vasanth Kumar Pai; B S Sherigara; S Prasannakumar

    2001-10-01

    Interpenetrating polymer networks (IPNs) of glycerol modified castor oil polyurethane (GC–PU) and poly[2-hydroxyethylmethacrylate] (PHEMA) were synthesized using benzoyl peroxide as initiator and N,N-methylene bis acrylamide as crosslinker. GC–PU/PHEMA interpenetrating polymer networks were obtained by transfer moulding. These were characterized with respect to their resistance to chemical reagents and mechanical properties such as tensile strength, per cent elongation and shore A hardness. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) were undertaken for thermal characterization. The changes in NCO/OH ratio and GC–PU/PHEMA composition on the properties of the IPNs were studied.

  9. Use of modified chemical route for ZnSe nanocrystalline thin films growth: Study on surface morphology and physical properties

    Science.gov (United States)

    Kale, R. B.; Lokhande, C. D.; Mane, R. S.; Han, Sung-Hwan

    2006-06-01

    The zinc selenide thin films have been deposited using modified chemical bath deposition (M-CBD) method. Zinc acetate and sodium selenosulphate were used as Zn 2+ and Se 2- ion sources, respectively. The preparative parameters such as concentration, pH, number of deposition cycles have been optimized in order to deposit ZnSe thin films. The as-deposited ZnSe thin films are specularly reflective and faint yellowish in color. The as-deposited ZnSe films are annealed in an air atmosphere at 473 K for 2 h. The films are characterized using structural, morphological, compositional, optical and electrical properties.

  10. Repair of Thalassemic Human β -globin mRNA in Mammalian Cells by Antisense Oligonucleotides

    Science.gov (United States)

    Sierakowska, Halina; Sambade, Maria J.; Agrawal, Sudhir; Kole, Ryszard

    1996-11-01

    In one form of β -thalassemia, a genetic blood disorder, a mutation in intron 2 of the β -globin gene (IVS2-654) causes aberrant splicing of β -globin pre-mRNA and, consequently, β -globin deficiency. Treatment of mammalian cells stably expressing the IVS2-654 human β -globin gene with antisense oligonucleotides targeted at the aberrant splice sites restored correct splicing in a dose-dependent fashion, generating correct human β -globin mRNA and polypeptide. Both products persisted for up to 72 hr posttreatment. The oligonucleotides modified splicing by a true antisense mechanism without overt unspecific effects on cell growth and splicing of other pre-mRNAs. This novel approach in which antisense oligonucleotides are used to restore rather than to down-regulate the activity of the target gene is applicable to other splicing mutants and is of potential clinical interest.

  11. Removal of Chlorinated Chemicals in H2 Feedstock Using Modified Activated Carbon

    Directory of Open Access Journals (Sweden)

    Prapaporn Luekittisup

    2015-01-01

    Full Text Available Activated carbon (GAC was impregnated by sodium and used as adsorbent to remove chlorinated hydrocarbon (CHC gases contaminated in H2 feedstock. The adsorption was carried out in a continuous packed-bed column under the weight hourly space velocity range of 0.8–1.0 hr−1. The adsorption capacity was evaluated via the breakthrough curves. This modified GAC potentially adsorbed HCl and VCM of 0.0681 gHCl/gadsorbent and 0.0026 gVCM/gadsorbent, respectively. It showed higher adsorption capacity than SiO2 and Al2O3 balls for both organic and inorganic CHCs removal. In addition, the kinetic adsorption of chlorinated hydrocarbons on modified GAC fit well with Yoon-Nelson model.

  12. Determination of vanadium in mussels by electrothermal atomic absorption spectrometry without chemical modifiers

    Energy Technology Data Exchange (ETDEWEB)

    Saavedra, Y.; Fernandez, P. [Centro de Control do Medio Marino, Peirao de Vilaxoan s/n, Vilagarcia de Arousa, 36611 Pontevedra (Spain); Gonzalez, A. [Departamento de Quimica Analitica, Nutricion y Bromatologia, Facultad de Quimica, 15706, Santiago de Compostela (Spain)

    2004-05-01

    A method was developed for the quantitative determination of total vanadium concentration in mussels via electrothermal atomic absorption spectrometry (ETAAS). After the microwave digestion of the samples, a program using temperatures of 1600 C and 2600 C for ashing and atomization respectively, without any matrix modifiers, allowed us to obtain results that were satisfactory since they agreed closely with certified reference material values. The detection limit was 0.03 mg kg{sup -1} (dry weight), indicating that the method is suitable for the analysis of mussel samples. This determination was compared with matrix modifiers that have been reported previously. The method was applied to various cultivated and wild mussels from the Galician coast, yielding levels below 1 mg kg{sup -1} (wet weight). (orig.)

  13. Rheological behaviour of polymer-modified bituminous mastics : a comparative analysis between physical and chemical modification

    OpenAIRE

    Shivokhin, Maxim; García Morales, Moisés; Partal López, Pedro; Cuadri Vega, Antonio Abad; Gallegos Montes, Críspulo

    2012-01-01

    Mastic, a bitumen/filler blend which naturally forms when bitumen is mixed with aggregates is the actual product used to bind coarse mineral particles in the asphalt mixtures. As a result, the characterisation of mastics is essential to improve the understanding of the response and performance of asphalt concrete pavements. On the other hand, the lack of experimental data concerning the behaviour of mastics and, above all, polymer-modified mastics has been lately claimed. In that sense, this ...

  14. Rheological behaviour of polymer-modified bituminous mastics : a comparative analysis between physical and chemical modification

    OpenAIRE

    Shivokhin, Maxim; García Morales, Moisés; Partal López, Pedro; Cuadri Vega, Antonio Abad; Gallegos Montes, Críspulo

    2012-01-01

    Mastic, a bitumen/filler blend which naturally forms when bitumen is mixed with aggregates is the actual product used to bind coarse mineral particles in the asphalt mixtures. As a result, the characterisation of mastics is essential to improve the understanding of the response and performance of asphalt concrete pavements. On the other hand, the lack of experimental data concerning the behaviour of mastics and, above all, polymer-modified mastics has been lately claimed. In that sense, this ...

  15. Conjugation of mono and di-GalNAc sugars enhances the potency of antisense oligonucleotides via ASGR mediated delivery to hepatocytes.

    Science.gov (United States)

    Kinberger, Garth A; Prakash, Thazha P; Yu, Jinghua; Vasquez, Guillermo; Low, Audrey; Chappell, Alfred; Schmidt, Karsten; Murray, Heather M; Gaus, Hans; Swayze, Eric E; Seth, Punit P

    2016-08-01

    Antisense oligonucleotides (ASOs) conjugated to trivalent GalNAc ligands show 10-fold enhanced potency for suppressing gene targets expressed in hepatocytes. Trivalent GalNAc is a high affinity ligand for the asialoglycoprotein receptor (ASGR)-a C-type lectin expressed almost exclusively on hepatocytes in the liver. In this communication, we show that conjugation of two and even one GalNAc sugar to single stranded chemically modified ASOs can enhance potency 5-10 fold in mice. Evaluation of the mono- and di-GalNAc ASO conjugates in an ASGR binding assay suggested that chemical features of the ASO enhance binding to the receptor and provide a rationale for the enhanced potency.

  16. Influence of pyrolysis temperature on lead immobilization by chemically modified coconut fiber-derived biochars in aqueous environments.

    Science.gov (United States)

    Wu, Weidong; Li, Jianhong; Niazi, Nabeel Khan; Müller, Karin; Chu, Yingchao; Zhang, Lingling; Yuan, Guodong; Lu, Kouping; Song, Zhaoliang; Wang, Hailong

    2016-11-01

    Biochar has received widespread attention as an eco-friendly and efficient material for immobilization of toxic heavy metals in aqueous environments. In the present study, three types of coconut fiber-derived biochars were obtained by pyrolyzing at three temperatures, i.e., 300, 500, and 700 °C. In addition, nine types of biochars were prepared by chemical modification with ammonia, hydrogen peroxide, and nitric acid, respectively, which were used to investigate changes in physico-chemical properties by inter alia, Fourier transformation infrared spectrophotometry (FTIR), scanning electron microscope (SEM), and BET specific surface area analysis. Batch sorption experiments were carried out to determine the sorption capacity of the biochars for lead (Pb) in aqueous solutions. Results showed that the cation exchange capacity of biochar pyrolyzed at 300 °C and modified with nitric acid increased threefold compared to the control. Loosely corrugated carbon surface and uneven carbon surface of the biochar pyrolyzed at 300 °C were produced during ammonia and nitric acid modifications. Removal rate of Pb by the coconut biochar pyrolyzed at 300 °C and modified with ammonia was increased from 71.8 to 99.6 % compared to the untreated biochar in aqueous solutions containing 100 mg L(-1) Pb. However, chemical modification did not enhance adsorption of Pb of the biochars pyrolyzed at higher temperatures (e.g., 500 or 700 °C), indicating that resistance of biochars to chemical treatment increased with pyrolysis temperature.

  17. Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries.

    Science.gov (United States)

    Murgha, Yusuf; Beliveau, Brian; Semrau, Kassandra; Schwartz, Donald; Wu, Chao-Ting; Gulari, Erdogan; Rouillard, Jean-Marie

    2015-06-01

    Oligonucleotide microarrays allow the production of complex custom oligonucleotide libraries for nucleic acid detection-based applications such as fluorescence in situ hybridization (FISH). We have developed a PCR-free method to make single-stranded DNA (ssDNA) fluorescent probes through an intermediate RNA library. A double-stranded oligonucleotide library is amplified by transcription to create an RNA library. Next, dye- or hapten-conjugate primers are used to reverse transcribe the RNA to produce a dye-labeled cDNA library. Finally the RNA is hydrolyzed under alkaline conditions to obtain the single-stranded fluorescent probes library. Starting from unique oligonucleotide library constructs, we present two methods to produce single-stranded probe libraries. The two methods differ in the type of reverse transcription (RT) primer, the incorporation of fluorescent dye, and the purification of fluorescent probes. The first method employs dye-labeled reverse transcription primers to produce multiple differentially single-labeled probe subsets from one microarray library. The fluorescent probes are purified from excess primers by oligonucleotide-bead capture. The second method uses an RNA:DNA chimeric primer and amino-modified nucleotides to produce amino-allyl probes. The excess primers and RNA are hydrolyzed under alkaline conditions, followed by probe purification and labeling with amino-reactive dyes. The fluorescent probes created by the combination of transcription and reverse transcription can be used for FISH and to detect any RNA and DNA targets via hybridization.

  18. Surface modification of plasmonic nanostructured materials with thiolated oligonucleotides in 10 seconds using selective microwave heating

    Energy Technology Data Exchange (ETDEWEB)

    Abel, B.; Aslan, K. [Morgan State University, Department of Chemistry, 1700 East Cold Spring Lane, Baltimore, MD 21251 (United States)

    2012-11-15

    This study demonstrates the proof-of-principle of rapid surface modification of plasmonic nanostructured materials with oligonucleotides using low power microwave heating. Due to their interesting optical and electronic properties, silver nanoparticle films (SNFs, 2 nm thick) deposited onto glass slides were used as the model plasmonic nanostructured materials. Rapid surface modification of SNFs with oligonucleotides was carried out using two strategies (1) Strategy 1: for ss-oligonucleotides, surface hybridization and (2) Strategy 2: for ds-oligonucleotides, solution hybridization, where the samples were exposed to 10, 15, 30 and 60 seconds microwave heating. To assess the efficacy of our new rapid surface modification technique, identical experiments carried out without the microwave heating (i.e., conventional method), which requires 24 hours for the completion of the identical steps. It was found that SNFs can be modified with ss- and ds-oligonucleotides in 10 seconds, which typically requires several hours of incubation time for the chemisorption of thiol groups on to the planar metal surface using conventional techniques. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Novel Efficient Cell-Penetrating, Peptide-Mediated Strategy for Enhancing Telomerase Inhibitor Oligonucleotides.

    Science.gov (United States)

    Muñoz-Alarcón, Andrés; Eriksson, Jonas; Langel, Ülo

    2015-12-01

    At present, there are several therapeutic approaches for targeting telomerase in tumors. One in particular, currently undergoing clinical trials, is based on synthetic lipid-modified oligonucleotide antagonists aimed at inhibiting the ribonucleoprotein subunit of human telomerase. However, while enabling efficient uptake, the lipid modifications reduce the potency of the therapeutic oligonucleotides compared to nonmodified oligonucleotides. Moreover, lipid modification may increase oligonucleotide accumulation in the liver causing undesirable hepatotoxicity. Noncovalent complexation strategies for cell-penetrating peptide (CPP)-mediated delivery present an option to circumvent the need for potency-reducing modifications, while allowing for a highly efficient uptake, and could significantly improve the efficiency of telomerase-targeting cancer therapeutics. Delivery of a nonlipidated locked nucleic acid/2'-O-methyl mixmer significantly inhibits the telomerase activity in treated HeLa cells. The inhibitory effect was further improved through addition of a CPP. Furthermore, calculated IC50-values for the oligonucleotide delivered by CPPs into HeLa cells are more than 20 times lower than telomerase inhibitor Imetelstat, currently undergoing clinical trials. These results emphasize the potential of CPP-mediated delivery of future pharmaceuticals and provide means by which to enhance an already promising therapeutic strategy for cancer treatment.

  20. [Research progress in chemical communication among insect-resistant genetically modified plants, insect pests and natural enemies].

    Science.gov (United States)

    Liu, Qing-Song; Li, Yun-He; Chen, Xiu-Ping; Peng, Yu-Fa

    2014-08-01

    Semiochemicals released by plants or insects play an important role in the communication among plants, phytophagous insects and their natural enemies. They thus form a chemical information network which regulates intra- and inter-specific behaviors and sustains the composition and structure of plant and insect communities. The application of insect-resistant genetically modified (IRGM) crops may affect the chemical communication within and among the tritrophic levels, and thus cause disturbances to the biotic community structure and the stability of the farmland ecosystem. This has raised concerns about the environmental safety of IRGM crops and triggered research worldwide. In the current article we provided a brief summary of the chemical communication among plants, herbivores and natural enemies; analyzed the potential of IRGM crops to affect the chemical communication between plants and arthropods and the related mechanisms; and discussed the current research progress and the future prospects in this field. We hope that this will promote the research in this field by Chinese scientists and increase our understanding of the potential effects of growing of IRGM crops on the arthropod community structure.

  1. Chemically modified fatty acid methyl esters: their potential for use as lubrication fluids and surfactants

    Science.gov (United States)

    A review of recent developments in the synthesis and characterization of lubrication fluids and surfactants from methyl oleate. The synthesis of materials made using an epoxidation route is the focus. This versatile method of chemical modification of fatty acid methyl esters improves their oxidati...

  2. Chemical and physical properties of Paulownia elongata biochar modified with oxidants for horticultural applications

    Science.gov (United States)

    Treatment of biochar with oxidants such as acids and hydrogen peroxide has been shown to alter porosity, increase adsorption of chemicals, and introduce functional groups on the biochar surfaces, all of which are desirable for their use in horticultural applications. Biochar was produced from the py...

  3. An oligonucleotide hybridization approach to DNA sequencing.

    Science.gov (United States)

    Khrapko, K R; Lysov YuP; Khorlyn, A A; Shick, V V; Florentiev, V L; Mirzabekov, A D

    1989-10-09

    We have proposed a DNA sequencing method based on hybridization of a DNA fragment to be sequenced with the complete set of fixed-length oligonucleotides (e.g., 4(8) = 65,536 possible 8-mers) immobilized individually as dots of a 2-D matrix [(1989) Dokl. Akad. Nauk SSSR 303, 1508-1511]. It was shown that the list of hybridizing octanucleotides is sufficient for the computer-assisted reconstruction of the structures for 80% of random-sequence fragments up to 200 bases long, based on the analysis of the octanucleotide overlapping. Here a refinement of the method and some experimental data are presented. We have performed hybridizations with oligonucleotides immobilized on a glass plate, and obtained their dissociation curves down to heptanucleotides. Other approaches, e.g., an additional hybridization of short oligonucleotides which continuously extend duplexes formed between the fragment and immobilized oligonucleotides, should considerably increase either the probability of unambiguous reconstruction, or the length of reconstructed sequences, or decrease the size of immobilized oligonucleotides.

  4. Crystal engineering of energetic materials: co-crystals of Ethylenedinitramine (EDNA) with modified performance and improved chemical stability.

    Science.gov (United States)

    Aakeröy, Christer B; Wijethunga, Tharanga K; Desper, John

    2015-07-27

    In the area of energetic materials, co-crystallization is emerging as a new technology for modifying or enhancing the properties of existing energetic substances. Ethylenedinitramine (EDNA) is a known energetic material which requires attention partly due to its chemical instability originating with its two highly acidic protons. In order to stabilize EDNA, a co-crystallization approach targeting the acidic protons using a series of co-crystallizing agents with suitable hydrogen-bond acceptors was employed. Fifteen attempted co-crystallizations resulted in eight successful outcomes and six of these were crystallographically characterized and all showed evidence of hydrogen bonds to the intended protons. Calculated detonation properties and experimental thermal and impact data for the co-crystals were obtained and compared with those of pure EDNA. The co-crystal of EDNA and 1,2-bis(4-pyridyl)ethylene was recognized as a more thermally stable alternative to EDNA while the co-crystal of EDNA and pyrazine N,N'-dioxide showed comparable detonation strengths (and much improved chemical stability) compared with that of EDNA. The co-crystals EDNA:4,4'-bipyridine and EDNA:pyrazine N,N'-dioxide were found to be about 50 % less impact sensitive than EDNA, all of which illustrate how co-crystallizations can be utilized for successfully modifying specific aspects of energetic materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Oligonucleotide Aptamers: New Tools for Targeted Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Hongguang Sun

    2014-01-01

    Full Text Available Aptamers are a class of small nucleic acid ligands that are composed of RNA or single-stranded DNA oligonucleotides and have high specificity and affinity for their targets. Similar to antibodies, aptamers interact with their targets by recognizing a specific three-dimensional structure and are thus termed “chemical antibodies.” In contrast to protein antibodies, aptamers offer unique chemical and biological characteristics based on their oligonucleotide properties. Hence, they are more suitable for the development of novel clinical applications. Aptamer technology has been widely investigated in various biomedical fields for biomarker discovery, in vitro diagnosis, in vivo imaging, and targeted therapy. This review will discuss the potential applications of aptamer technology as a new tool for targeted cancer therapy with emphasis on the development of aptamers that are able to specifically target cell surface biomarkers. Additionally, we will describe several approaches for the use of aptamers in targeted therapeutics, including aptamer-drug conjugation, aptamer-nanoparticle conjugation, aptamer-mediated targeted gene therapy, aptamer-mediated immunotherapy, and aptamer-mediated biotherapy.

  6. Chemically Modified Chitosan Beads as Molecularly Imprinted Polymer Matrix for Adsorptive Separation of Proteins

    Institute of Scientific and Technical Information of China (English)

    Tian Ying GUO; Yong Qing XIA; Guang Jie HAO; Bang Hua ZHANG

    2004-01-01

    In a phosphate buffer, a hemoglobin (Hb)-imprinted polymer complex was prepared using maleic anhydride (MAH) modified chitosan beads as matrix, acrylamide (AM) as functional monomer, N,N-methylenebisacrylamide (MBA) as cross-linker and potassiumpersulfate (KPS)/sodium hydrogen sulfite (NaHSO3) as initiators. Langmuir analysis showed that an equal class of adsorption was formed in the molecular imprinting polymer (MIP), and the MIP has high adsorption capacity and selectivity for the imprinted molecule. The MIP can be reused and the recovery was approximately 100% at low concentration.

  7. Structure and Electrical Study of New Chemically Modified Poly(vinyl chloride

    Directory of Open Access Journals (Sweden)

    F. Ammari

    2015-01-01

    Full Text Available The aim of this work was to study the structural and electrical properties of a new polymer obtained by functionalization of a commercial poly(vinyl chloride (PVC (Mw = 48000 by grafting aminoalkyl and aminoaryl groups. Modified poly(vinyl chloride was prepared in two steps. The structural properties of the polymer were systematically investigated by varieties of techniques as differential scanning calorimetric (DSC, thermogravimetry analysis (TG, X-ray diffraction (XRD, and Fourier transform infrared (FTIR spectroscopy. The electrical properties of the polymer were studied by electrochemical impedance spectroscopy (EIS.

  8. Enhancing adsorption capacity of toxic malachite green dye through chemically modified breadnut peel: equilibrium, thermodynamics, kinetics and regeneration studies.

    Science.gov (United States)

    Chieng, Hei Ing; Lim, Linda B L; Priyantha, Namal

    2015-01-01

    Breadnut skin, in both its unmodified (KS) and base-modified (BM-KS) forms, was investigated for its potential use as a low-cost adsorbent for the removal of toxic dye, malachite green (MG). Characterization of the adsorbents was carried out using scanning electron microscope, X-ray fluorescence and Fourier transform infra-red spectroscopy. Batch adsorption experiments, carried out under optimized conditions, for the adsorption of MG were fitted using five isotherm models (Langmuir, Freundlich, Dubinin-Radushkevich, Temkin and Sips) and six error functions to determine the best-fit model. The adsorption capacity was greatly enhanced when breadnut skin was chemically modified with NaOH, leading to an adsorption capacity of 353.0 mg g(-1), that was far superior to most reported adsorbents for the removal of MG. Thermodynamics studies indicated that the adsorption of MG was spontaneous on KS and BM-KS, and the reactions were endothermic and exothermic, respectively. Kinetics studies showed that both followed the pseudo-second order. Regeneration experiments on BM-KS indicated that its adsorption capacity was still maintained at>90% even after five cycles. It can be concluded that NaOH-modified breadfruit skin has great potential to be utilized in real-life application as a low-cost adsorbent for the removal of MG in wastewater treatment.

  9. Thermogravimetric Analysis of Modified Hematite by Methane (CH{sub 4}) for Chemical-Looping Combustion: A Global Kinetics Mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Monazam, Esmail R; Breault, Ronald W; Siriwardane, Ranjani; Miller, Duane D

    2013-10-01

    Iron oxide (Fe{sub 2}O{sub 3}) or in its natural form (hematite) is a potential material to capture CO{sub 2} through the chemical-looping combustion (CLC) process. It is known that magnesium (Mg) is an effective methyl cleaving catalyst and as such it has been combined with hematite to assess any possible enhancement to the kinetic rate for the reduction of Fe{sub 2}O{sub 3} with methane. Therefore, in order to evaluate its effectiveness as a hematite additive, the behaviors of Mg-modified hematite samples (hematite –5% Mg(OH){sub 2}) have been analyzed with regard to assessing any enhancement to the kinetic rate process. The Mg-modified hematite was prepared by hydrothermal synthesis. The reactivity experiments were conducted in a thermogravimetric analyzer (TGA) using continuous stream of CH{sub 4} (5, 10, and 20%) at temperatures ranging from 700 to 825 {degrees}C over ten reduction cycles. The mass spectroscopy analysis of product gas indicated the presence of CO{sub 2}, H{sub 2}O, H{sub 2} and CO in the gaseous product. The kinetic data at reduction step obtained by isothermal experiments could be well fitted by two parallel rate equations. The modified hematite samples showed higher reactivity as compared to unmodified hematite samples during reduction at all investigated temperatures.

  10. Comparative repellent properties of certain chemicals against mosquitoes, house flies and cockroaches using modified techniques.

    Science.gov (United States)

    Vartak, P H; Tungikar, V B; Sharma, R N

    1994-09-01

    Several terpenoids were assessed for their repellent/toxic properties against mosquitoes (Aedes aegypti), house flies (Musca domestica) and cockroaches (Periplaneta americana). Impregnated wide mesh netting was used in the case of the Dipterans, while treated filtered paper was employed for the bioassays with cockroaches. Persistence of the repellent chemicals was studied. Doses ranged from 5-20 gm/M2 for the Dipterans and 25-100 mg per 4 x 4 cm filter paper for the cockroaches. Dimethyl phthalate (DMP) offered the maximum protection of the chemicals tested against mosquitoes but was not so effective against house flies and cockroaches. Citral and Eugenol were effective against all the three test insects. Other test compounds afforded varying degrees of protection. Application strategy and utility of the findings are discussed.

  11. Calcium phosphate formation from sea urchin - (brissus latecarinatus via modified mechano-chemical (ultrasonic conversion method

    Directory of Open Access Journals (Sweden)

    R. Samur

    2013-07-01

    Full Text Available This study aims to produce apatite structures, such as hydroxyapatite (HA and fluorapatite (FA, from precursor calcium phosphates of biological origin, namely from sea urchin, with mechano-chemical stirring and hot-plating conversion method. The produced materials were heat treated at 800 °C for 4 hours. X-ray diffraction and scanning electron microscopy (SEM studies were conducted. Calcium phosphate phases were developed. The SEM images showed the formation of micro to nano-powders. The experimental results suggest that sea urchin, Brissus latecarinatus skeleton could be an alternative source for the production of various mono or biphasic calcium phosphates with simple and economic mechano-chemical (ultrasonic conversion method.

  12. The optimal one dimensional periodic table: a modified Pettifor chemical scale from data mining

    Science.gov (United States)

    Glawe, Henning; Sanna, Antonio; Gross, E. K. U.; Marques, Miguel A. L.

    2016-09-01

    Starting from the experimental data contained in the inorganic crystal structure database, we use a statistical analysis to determine the likelihood that a chemical element A can be replaced by another B in a given structure. This information can be used to construct a matrix where each entry (A,B) is a measure of this likelihood. By ordering the rows and columns of this matrix in order to reduce its bandwidth, we construct a one-dimension ordering of the chemical elements, analogous to the famous Pettifor scale. The new scale shows large similarities with the one of Pettifor, but also striking differences, especially in what comes to the ordering of the non-metals.

  13. Calcium phosphate formation from sea urchin - (brissus latecarinatus) via modified mechano-chemical (ultrasonic) conversion method

    OpenAIRE

    R. Samur; Ozyegin, L.; D. Agaogullari; F. N. Oktar; Agathopoulos, S.; Kalkandelen, C.; I. Duman; B. Ben-Nissan

    2013-01-01

    This study aims to produce apatite structures, such as hydroxyapatite (HA) and fluorapatite (FA), from precursor calcium phosphates of biological origin, namely from sea urchin, with mechano-chemical stirring and hot-plating conversion method. The produced materials were heat treated at 800 °C for 4 hours. X-ray diffraction and scanning electron microscopy (SEM) studies were conducted. Calcium phosphate phases were developed. The SEM images showed the formation of micro to nano-powders. The e...

  14. Cellular RNA is chemically modified by exposure to air pollution mixtures.

    Science.gov (United States)

    Baldridge, Kevin C; Zavala, Jose; Surratt, Jason; Sexton, Kenneth G; Contreras, Lydia M

    2015-01-01

    RNAs are more susceptible to modifications than DNA, and chemical modifications in RNA have an effect on their structure and function. This study aimed to characterize chemical effects on total RNA in human A549 lung cells after exposure to elevated levels of major secondary air pollutants commonly found in urban locations, including ozone (O3), acrolein (ACR) and methacrolein (MACR). Enzyme-linked immunosorbent assays (ELISA) were used to measure levels of interleukin (IL)-8 in the growth media and 8-oxoguanine (8OG) levels in total cellular RNA, and lactate dehydrogenase (LDH) in the growth media was measured by a coupled enzymatic assay. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure levels of microRNA 10b (miR-10b). The study found that 1-h exposure to all tested pollutant mixtures consistently caused significant increases in the levels of 8OG in total RNA. In the case of 4 ppm O3 exposures, measured levels of IL-8, LDH and miR-10b each showed consistent trends between two independent trials, but varied among these three targets. After 1-h exposures to an ACR+MACR mixture, measured levels of IL-8, LDH and miR-10b showed variable results. For mixtures of O3+ACR+MACR, IL-8 measurements showed no change; miR-10b and LDH showed variable results. The results indicate that short-term high-concentration exposures to air pollution can cause RNA chemical modifications. Chemical modifications in RNAs could represent more consistent markers of cellular stress relative to other inflammation markers, such as IL-8 and LDH, and provide a new biomarker endpoint for mechanistic studies in toxicity of air pollution exposure.

  15. Unconventional assembly of bimetallic Au-Ni janus nanoparticles on chemically modified silica spheres.

    Science.gov (United States)

    Jia, Lei; Pei, Xiaowei; Zhou, Feng; Liu, Weimin

    2014-02-10

    This paper reports that Janus Au-Ni nanoparticles (JANNPs) can self-assemble onto silica spheres in a novel way, which is different from that of single-component isotropic nanoparticles. JANNPs modified with octadecylamine (ODA) assemble onto catechol-modified silica spheres (SiO2-OH) to form a very special core-loop complex structure and finally the core-loop assemblies link each other to form large assemblies through capillary force and the hydrophobic interaction of the alkyl chains of ODA. The nanocomposites disassemble in the presence of vanillin and oleic acid because of the breakage of the catechol-metal link. Vanillin-induced disassembly enables the JANNPs to reassemble into a core-loop structure upon ODA addition. The assembly of SiO2-OH and isotropic Ni or Fe3O4 particles generates traditional core-satellite structures. This unconventional self-assembly can be attributed to the synergistic effect of Janus specificity and capillary force, which is also confirmed by the assembly of thiol-terminated silica spheres (SH-SiO2) with anisotropic JANNPs, isotropic Au, and Ni nanoparticles. These results can guide the development of novel composite materials using Janus nanoparticles as the primary building blocks. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Calorimetric and Spectroscopic Analysis of the Thermal Stability of Short Duplex DNA-Containing Sugar and Base-Modified Nucleotides.

    Science.gov (United States)

    Fakhfakh, Kareem; Hughesman, Curtis B; Louise Creagh, A; Kao, Vincent; Haynes, Charles

    2016-01-01

    Base- and sugar-modified analogs of DNA and RNA are finding ever expanding use in medicine and biotechnology as tools to better tailor structured oligonucleotides by altering their thermal stability, nuclease resistance, base-pairing specificity, antisense activity, or cellular uptake. Proper deployment of these chemical modifications generally requires knowledge of how each affects base-pairing properties and thermal stabilities. Here, we describe in detail how differential scanning calorimetry and UV spectroscopy may be used to quantify the melting thermodynamics of short dsDNA containing chemically modified nucleosides in one or both strands. Insights are provided into why and how the presence of highly stable base pairs containing modified nucleosides can alter the nature of calorimetry or melting spectroscopy data, and how each experiment must therefore be conducted to ensure high-quality melting thermodynamics data are obtained. Strengths and weaknesses of the two methods when applied to chemically modified duplexes are also addressed.

  17. Delivery of antisense oligonucleotide into cells using synthetic peptide; Gosei pepuchido wo mochiita anchisensu origonukureochido no saibounai donyu

    Energy Technology Data Exchange (ETDEWEB)

    Niidome, Takuro [Nagasaki University, Nagasaki (Japan). Dept. of Applied Chemistry

    1999-12-16

    Much attention has been attracted to the antisense oligonucleotide as a novel nucleic acid medicine. However, many problems to be solved such as delivery system in vivo and permeation through cell membrane are pointed out. In this study, we found out that some cationic peptides were useful as an oligonucleotide-carrier molecule into cells. Furthermore, to develop a cell specific gene delivery system using the cationic peptide, we modified the peptides with several galactose residues. As a result, the modified peptides showed high transfer efficiencies into hepatoma cells, and then, it was clear that the internalization into cells was mediated by asialoglycoprotein receptor on hepatoma cell. (author)

  18. POLYPROPYLENE-MODIFIED KAOLINITE COMPOSITES: EFFECT OF CHEMICAL MODIFICATION ON MECHANICAL, THERMAL AND MORPHOLOGICAL PROPERTIES

    Directory of Open Access Journals (Sweden)

    O. Meziane

    2016-05-01

    Full Text Available The intercalation of kaolinite with an ammonium salt was performed. Untreated and treated kaolinite samples were examined by XRD. PP/kaolinite compounds were prepared by the melt intercalation method. The effects of modified clay on properties of the prepared composites were studied. The XRD results showed that the treatment with the ammonium salt caused the return to the initial state of the clay. TGA thermograms marked an increase in thermal degradation of the composites, while the DSC results showed the decrease of the crystallization temperature and the melting point in presence of clay in the matrix owing to the fact that the filler acts as reinforcing effect. The mechanical properties of the composites exhibited important variations, the morphology of the composites was further studied using SEM and showed poor dispersion of used nanoclay in PP matrix.

  19. Physico-chemical characteristics of nano-organo bentonite prepared using different organo-modifiers

    Directory of Open Access Journals (Sweden)

    A.M. Motawie

    2014-09-01

    Full Text Available Different types of nano-organo bentonite (NOB were prepared from the Egyptian Bentonite (EB. EB was characterized by energy dispersive X-ray EDX. It was purified from different impurities using a conventional method via the treatment with HCl and distilled water. The modification of the clay was carried out using different types of organo-modifiers namely; hexadecyl trimethyl ammonium bromide (HTAB, 3-aminopropyltriethoxysilane (Silane, octadecylamine (ODA, and dodecylamine (DDA. The cation exchange capacity (CEC was measured for pristine bentonite after and before modification. The NB was characterized by FTIR, XRD, TEM, and TGA techniques. The obtained results indicated that variation of the interlayer space gallery was effected by the type of the penetrator used.

  20. UV Spectral Analysis of the Chemical Modification and Photolysis of Acetylacetone Modified Alumina Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    Chengbin JING; Xiujian ZHAO; Haizheng TAO; Xina WANG; Aiyun LIU

    2004-01-01

    Acetylacetone was firstly introduced into the aqueous media with the presence of aluminum sec-butoxide and peptizator. It was confirmed that the UV (ultraviolet) absorption band of acetylacetone underwent 14 nm of red-shift due to the formation of the six-membered ring of the complex between alumina and acetylacetone in the aqueous solution. It was also found that the chemical modification can be dissociated by the UV irradiation with a wavelength shorter than 286 nm as a result of the excitation of π-π* transition in the complex.

  1. Modifying culture conditions in chemical library screening identifies alternative inhibitors of mycobacteria.

    Science.gov (United States)

    Miller, Christopher H; Nisa, Shahista; Dempsey, Sandi; Jack, Cameron; O'Toole, Ronan

    2009-12-01

    In this study, application of a dual absorbance/fluorescence assay to a chemical library screen identified several previously unknown inhibitors of mycobacteria. In addition, growth conditions had a significant effect on the activity profile of the library. Some inhibitors such as Se-methylselenocysteine were detected only when screening was performed under nutrient-limited culture conditions as opposed to nutrient-rich culture conditions. We propose that multiple culture condition library screening is required for complete inhibitory profiling and for maximal antimycobacterial compound detection.

  2. Study on Natural and Modified Bentonite Adsorption of Antibiotics%Guangzhou Chemical Industry

    Institute of Scientific and Technical Information of China (English)

    刘希

    2016-01-01

    To deal with the water polluted by antibiotics, adsorption experiments for adsorption behavior of oxytetracycline and tetracycline on bentonite/acid modified bentonite were carried out to investigate the effect of pH,activation temperature, dosing quantity and adsorption time. The results showed that two kind of antibiotics could beabsorbed effectively when theactivation temperature was 200 ℃, pH=6 , the dosing quantity was 1 gandadsorption time was 8 h. Asakind of environmental friendlyadsorbent for promotion, modified bentonite is better than natural bentonite.%针对制药工业产生的抗生素废水,研究了一定条件下膨润土/酸改性膨润土对土霉素( OTC)和四环素( TC)的吸附作用,综合考察了原土与改性膨润土在不同pH、活化温度、投加量以及吸附时间等条件下的吸附效率。结果表明:在活化温度为200℃、 pH=6、投加量为1 g、吸附时间为8 h时,可以有效地吸附两种抗生素,且酸改性膨润土比膨润土吸附效果更好,能够作为环境友好的抗生素吸附剂进行推广。

  3. Investigation of the biofouling properties of several algae on different textured chemical modified silicone surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Jihai [Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhao, Wenjie, E-mail: zhaowj@nimte.ac.cn [Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China); Peng, Shusen; Zeng, Zhixiang; Zhang, Xin [Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China); Wu, Xuedong, E-mail: xdwu@nimte.ac.cn [Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China); Xue, Qunji [Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China)

    2014-08-30

    Highlights: • Engineered pillars, pits and grooves spaced 3–12 μm apart were fabricated on siloxane modified acrylic resin films. • The effect of feature size, geometry, and wettability on the settlement of different algae was evaluated. • The feature size and geometry displayed a substantial correlation with the antifouling properties. • A comparatively physical fouling deterrent mechanism was analyzed. - Abstract: Engineered pillars, pits and grooves spaced 3, 6, 9 and 12 μm apart were fabricated on siloxane modified acrylic resin films. The effect of feature size, geometry, and wettability on the settlement of different algae was evaluated. These films showed various antifouling performances to Ulothrix, Closterium and Navicula. For Navicula (length: 10–12 μm), the feature size and geometry displayed a substantial correlation with the antifouling properties. The film with pillars spaced 3 μm reduced Navicula settlement by 73% compared to the control surface. For Closterium (length: 45–55 μm), their responses were governed by the same underlying thermodynamic principles as wettability, the largest reduction in Closterium, 81%, was obtained on the surface with grooves spaced 12 μm apart. For Ulothrix (length: 5–8 mm), the surface also showed the best antifouling performance, the reduction ratio of the settlement on the surface with grooves spaced 12 μm apart could even reach 92%. At last, physical fouling deterrent mechanisms for the films with various textures were analyzed in detail. The feature size and geometry display a substantial correlation with the antifouling properties when the size of fouling algae is close to the textures. With the increasing size for algae, antifouling performance was getting better on surface with pillars or grooves because the algae are bridged between two or more features other than stabilizing its entire mass on one single feature or able to settle between features.

  4. Nile tilapia skin collagen sponge modified with chemical cross-linkers as a biomedical hemostatic material.

    Science.gov (United States)

    Sun, Leilei; Li, Bafang; Jiang, Dandan; Hou, Hu

    2017-07-26

    Nile tilapia skin collagen sponges were fabricated by freeze-drying technology and modified with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide in the presence of N-hydroxysuccinimide (EDC/NHS), genipin+PBS, genipin+ethanol, tea polyphenol (TP), nordihydroguaiaretic acid (NDGA) and diphenyl phosphoryl azide (DPPA). Physicochemical and biological properties, micromorphology and compatibility before and after modification were investigated to evaluate collagen sponge as a hemostatic biomedical material. The mechanical property of collagen sponges strengthened after cross-linking. The elongation at break of cross-linked collagen sponges decreased except for EDC/NHS, which was close to that of non-crosslinked. The collagen sponge cross-linked with EDC/NHS exhibited the highest hygroscopicity in comparison with other cross-linkers. The resistance to collagenase biodegradation of collagen sponges after cross-linking strengthened significantly except for NDGA. Collagen sponges cross-linked with EDC/NHS, TP and NDGA maintained high porosity (97-98%), similar to non-crosslinked (98.42%). Collagen sponges could shorten the blood coagulation time. From the variations of the FTIR spectrum pattern and SEM, DPPA could change the secondary structure of collagen and destroy the spongy structure of collagen sponge, which was not suitable for the cross-linking of collagen sponge. Whereas, EDC/NHS was recognized as a perfect cross-linker owing to its excellent properties and porous microstructure. All fabricated collagen sponges were recognized to be biocompatible by the hemolysis assay in vitro. Therefore, collagen sponge modified with EDC/NHS could be used as a perfect biomedical hemostatic material. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Wrapping of a single bacterium with Functionalized - Chemically Modified Graphene (FCMG) sheets via highly specific protein-cell wall interaction

    Science.gov (United States)

    Mohanty, Nihar; Berry, Vikas

    2009-03-01

    Graphene has recently generated a lot of interest due to its unique structural and electrical properties. It's micro-scale area and sub-nano-scale thickness coupled with ballistic electronic transport at room temperature, low Johnston noise and low charge scattering, have made it a gold mine for novel applications. Since its discovery in 2004, there have been a plethora of studies on characterizing its unique physical, chemical and electrical properties of graphene as well as on integrating it with various physical/chemical systems to utilize these properties. But there have been limited or no studies on the integration of graphene with living microorganisms or mammalian cells. Here we describe the novel wrapping of a single live bacterium (Bacillus cereus) with a chemically modified graphene sheet functionalized with the protein Concanavalin-A (Con-A) via the highly specific Con-A - Teichoic acid interaction. We are investigating the structural and the electrical properties of these novel bacteria-FCMG ensembles. Further, we are also interested in characterizing this wrapping process in detail by studying the kinetics and the mechanism of action of bacterial-wrapping via 3D modelling. This is a first step towards the live-bio-nano-integration of graphene which would open up avenues for applications as diverse as bio-batteries using the Geobacter to recombinant enzyme compartmentalization.

  6. Evaluation of alkyne-modified isoprenoids as chemical reporters of protein prenylation.

    Science.gov (United States)

    DeGraw, Amanda J; Palsuledesai, Charuta; Ochocki, Joshua D; Dozier, Jonathan K; Lenevich, Stepan; Rashidian, Mohammad; Distefano, Mark D

    2010-12-01

    Protein prenyltransferases catalyze the attachment of C15 (farnesyl) and C20 (geranylgeranyl) groups to proteins at specific sequences localized at or near the C-termini of specific proteins. Determination of the specific protein prenyltransferase substrates affected by the inhibition of these enzymes is critical for enhancing knowledge of the mechanism of such potential drugs. Here, we investigate the utility of alkyne-containing isoprenoid analogs for chemical proteomics experiments by showing that these compounds readily penetrate mammalian cells in culture and become incorporated into proteins that are normally prenylated. Derivatization via Cu(I) catalyzed click reaction with a fluorescent azide reagent allows the proteins to be visualized and their relative levels to be analyzed. Simultaneous treatment of cells with these probes and inhibitors of prenylation reveals decreases in the levels of some but not all of the labeled proteins. Two-dimensional electrophoretic separation of these labeled proteins followed by mass spectrometric analysis allowed several labeled proteins to be unambiguously identified. Docking experiments and density functional theory calculations suggest that the substrate specificity of protein farnesyl transferase may vary depending on whether azide- or alkyne-based isoprenoid analogs is employed. These results demonstrate the utility of alkyne-containing analogs for chemical proteomic applications.

  7. Timing of leaf removal modifies chemical and phenolic composition of Sauvignon Blanc wine

    Directory of Open Access Journals (Sweden)

    Wurz Douglas André

    2017-01-01

    Full Text Available The objective of this work was to evaluate the effect of different defoliation times on the chemical and phenolic composition of Sauvignon Blanc wine in high altitude regions of Santa Catarina - Brazil. The experiment was conducted in the 2015 and 2016 seasons, in a vineyard located in the city of São Joaquim – Santa Catarina State. The defoliation was carried out during phenological stages: full bloom, berries pepper-corn size, pea-sized berries, veraison, 15 days after veraison and control without leaf removal. During harvest, severity of Botrytis cinerea was assessed by visual evaluation through a diagrammatic scale. For the wine samples from each season, total acidity (meq L−1, pH, total polyphenol content (mg L−1 of gallic acid and color (Abs 420nm were performed. For the wines of the 2015 harvest, phenolic compounds were analyzed: gallic acid, catechin, vanillic acid, P-coumaric acid and rutin. The chemical composition of Sauvignon Blanc wine was affected as a result of leaf removal timing, defoliation carried out in full bloom, berries pepper-corn size and pea-sized berries reduced total acidity and increased pH of the wines in both seasons. For wine color, in both seasons, it was found a greater yellow coloration in wines originated from grapes where the plants were not defoliated. The increase of yellow coloration is due to the oxidation of catechins and epicatechins, which is related to the increase of botrytis bunch rot. In the 2015 season there were no influence of leaf removal timing in total polyphenols, however, in the 2016, the defoliation performed in full bloom resulted in lower polyphenols contents. Wines from non-defoliated plants presented higher values of catechin, rutin, P-coumaric acid and gallic acid, related to yellow coloration of wines and greater susceptibility to darkening and oxidation. For vanillic acid, wines from non-defoliated plants have the lowest values, this compound is important in wine preservation

  8. Facile synthesis of graphene oxide-modified lithium hydroxide for low-temperature chemical heat storage

    Science.gov (United States)

    Yang, Xixian; Huang, Hongyu; Wang, Zhihui; Kubota, Mitsuhiro; He, Zhaohong; Kobayashi, Noriyuki

    2016-01-01

    LiOH·H2O nanoparticles supported on graphene oxide (GO) were facilely synthesized by a hydrothermal process. The mean diameter of nanoparticles on the integrated graphene sheet was about 5-10 nm showed by SEM and TEM results. XRD results suggested that the nanoparticles are in good agreement with the data of LiOH·H2O. The as-prepared sample showed a greatly enhanced thermal energy storage density and exhibit higher rate of heat release than pure lithium hydroxide, and thermal conductivity of composites increased due to the introduction of nano carbon. LiOH·H2O/GO nanocomposites are novel chemical heat storage materials for potential highly efficient energy system.

  9. Preparation and mechanism of calcium phosphate coatings on chemical modified carbon fibers by biomineralization

    Institute of Scientific and Technical Information of China (English)

    HUANG Su-ping; ZHOU Ke-chao; LI Zhi-you

    2008-01-01

    In order to prepare HA coatings on the carbon fibers, chemical modification and biomineralization processes were applied. The phase components, morphologies, and possible growth mechanism of calcium phosphate were studied by infrared spectroscopy(IR), X-ray diffractometry(XRD) and scanning electron microscopy(SEM). The results show that calcium phosphate coating on carbon fibers can be obtained by biomineralization. But the phase components and morphologies of calcium phosphate coatings are different due to different modification methods. Plate-like CaHPO4-2H2O (DCPD) crystals grow from one site of the active centre by HNO3 treatment. While on the para-aminobenzoic acid treated fibers, the coating is composed of nano-structural HA crystal homogeneously. This is because the -COOH functional groups of para-aminobenzoic acid graft on fibers, with negative charge and arranged structure, accelerating the HA crystal nucleation and crystallization on the carbon fibers.

  10. Improved actuation strain of PDMS-based DEA materials chemically modified with softening agents

    Science.gov (United States)

    Biedermann, Miriam; Blümke, Martin; Wegener, Michael; Krüger, Hartmut

    2015-04-01

    Dielectric elastomer actuators (DEAs) are smart materials that gained much in interest particularly in recent years. One active field of research is the improvement of their properties by modification of their structural framework. The object of this work is to improve the actuation properties of polydimethylsiloxane (PDMS)-based DEAs by covalent incorporation of mono-vinyl-terminated low-molecular PDMS chains into the PDMS network. These low-molecular units act as a kind of softener within the PDMS network. The loose chain ends interfere with the network formation and lower the network's density. PDMS films with up to 50wt% of low-molecular PDMS additives were manufactured and the chemical, mechanical, electrical, and electromechanical properties of these novel materials were investigated.

  11. The Compatibility of Hepatocytes with Chemically Modified Porous Silicon with Reference to In Vitro Biosensors

    Science.gov (United States)

    Alvarez, Sara D.; Derfus, Austin M.; Schwartz, Michael P.; Bhatia, Sangeeta N.; Sailor, Michael J.

    2008-01-01

    Porous Si is a nanostructured material that is of interest for molecular and cell-based biosensing, drug delivery, and tissue engineering applications. Surface chemistry is an important factor determining the stability of porous Si in aqueous media, its affinity for various biomolecular species, and its compatibility with tissues. In this study, the attachment and viability of a primary cell type to porous Si samples containing various surface chemistries is reported, and the ability of the porous Si films to retain their optical reflectivity properties relevant to molecular biosensing is assessed. Four chemical species grafted to the porous Si surface are studied: silicon oxide (via ozone oxidation), dodecyl (via hydrosilylation with dodecene), undecanoic acid (via hydrosilylation with undecylenic acid), and oligo(ethylene) glycol (via hydrosilylation with undecylenic acid followed by an oligo(ethylene) glycol coupling reaction). Fourier Transform Infrared (FTIR) spectroscopy and contact angle measurements are used to characterize the surface. Adhesion and short-term viability of primary rat hepatocytes on these surfaces, with and without pre-adsorption of collagen type I, are assessed using vital dyes (calcein-AM and ethidium homodimer I). Cell viability on undecanoic acid-terminated porous Si, oxide-terminated porous Si, and oxide-terminated flat (non-porous) Si are monitored by quantification of albumin production over the course of 8 days. The stability of porous Si thin films after 8 days in cell culture is probed by measuring the optical interferometric reflectance spectra. Results show that hepatocytes adhere better to surfaces coated with collagen, and that chemical modification does not exert a deleterious effect on primary rat hepatocytes. The hydrosilylation chemistry greatly improves the stability of porous Si in contact with cultured primary cells while allowing cell coverage levels comparable to standard culture preparations on tissue culture

  12. Electrochemical investigation of the surface-modifying roles of guanidine carbonate in chemical mechanical planarization of tantalum

    Energy Technology Data Exchange (ETDEWEB)

    Rock, S.E.; Crain, D.J.; Zheng, J.P. [Department of Physics, Clarkson University, Potsdam, NY 13699-5820 (United States); Pettit, C.M. [Department of Physics, Emporia State University, Emporia, KS 66801-5087 (United States); Roy, D., E-mail: samoy@clarkson.edu [Department of Physics, Clarkson University, Potsdam, NY 13699-5820 (United States)

    2011-10-03

    Highlights: {yields} This work contributes to the development of CMP slurries for Ta and Cu at low pressure. {yields} We present here a model of the chemical mechanism of the CMP of Ta and Cu using guanidine slurries. {yields} Removal of Ta occurs as structurally weak guanidinium-tantalic-acid surface complexes. {yields} The results will be useful for the CMP processing of interconnects with low-k dielectrics. {yields} We demonstrate the utility of electro-analytical techniques in the development of CMP slurries. - Abstract: The fabrication of interconnect structures for semiconductor devices requires low down-pressure chemical mechanical planarization (CMP) of Ta barrier layers. Guanidine carbonate (GC) serves as an effective surface-complexing agent for such CMP applications, where the rate of Ta removal can be chemically controlled through pH-tuned selectivity with respect to the removal of Cu lines. Electrochemical techniques are employed in this work to study the surface-modifying roles of GC that make this chemical an attractive complexing agent for Ta CMP. In addition, the effects of including H{sub 2}O{sub 2} (an oxidizer) and dodecyl benzene sulfonic acid (DBSA, a dissolution inhibitor for Cu) in GC-based CMP solutions are investigated to examine the selective CMP mechanisms of Ta and Cu in these solutions. The results suggest that the removal of Ta is supported in part by structurally weak guanidinium-tantalic-acid surface complexes formed on Ta/Ta{sub 2}O{sub 5}. The bicarbonate/carbonate anions of GC also facilitate Ta removal through the generation of ion-incorporated tantalum pentoxide. DBSA strongly affects the CMP chemistry of Cu, but exhibits relatively weaker effects on the surface activity of Ta, and thus plays a vital role in dictating the selectivity of Ta:Cu polish rates.

  13. Adsorption behavior of Cu(II) and Co(II) using chemically modified marine algae.

    Science.gov (United States)

    Foroutan, Rauf; Esmaeili, Hossein; Abbasi, Mohsen; Rezakazemi, Mashallah; Mesbah, Mohammad

    2017-08-28

    In this study, brown algae-modified biomass Padina sanctae crucis was used for copper (Cu(II)) and cobalt (Co(II)) heavy metal ions adsorption in synthetic wastewater. The effects of solution pH and adsorption efficiency for Cu(II) and Co(II) removal from aqueous solutions were studied. In order to study the kinetic behavior of adsorption, pseudo-first-order, pseudo-second-order kinetic models, liquid film penetration, and Ritchie second-order models were used. The results showed that the pseudo-second-order kinetic model was able to describe adsorbent behavior in comparison to the other models. Moreover, in order to study adsorbent equilibrium behavior, Langmuir and Freundlich isothermal models were used. Based on the Langmuir model, the adsorption capacity of Co(II) and Cu(II) was determined and their values were 13.73 and 13.996 mg/g, respectively. It was shown that both metal ions adsorption process is favorable and adsorption is physical. In this research, thermodynamic parameters were also studied in order to determine Gibbs free energy for both metal ions which were negative, indicating that metal ions adsorption process is spontaneous and the degree of self-adsorption increases as temperature increases.

  14. Chemical, Physical, and Mechanical Characterization of Isocyanate Cross-linked Amine-Modified Silica Aerogels

    Science.gov (United States)

    Katti, Atul; Shimpi, Nilesh; Roy, Samit; Lu, Hongbing; Fabrizio, Eve F.; Dass, Amala; Capadona, Lynn A.; Leventis, Nicholas

    2006-01-01

    We describe a new mechanically strong lightweight porous composite material obtained by encapsulating the skeletal framework of amine-modified silica aerogels with polyurea. The conformal polymer coating preserves the mesoporous structure of the underlying silica framework and the thermal conductivity remains low at 0.041 plus or minus 0.001 W m(sup -1 K(sup -1). The potential of the new cross-linked silica aerogels for load-carrying applications was determined through characterization of their mechanical behavior under compression, three-point bending, and dynamic mechanical analysis (DMA). A primary glass transition temperature of 130 C was identified through DMA. At room temperature, results indicate a hyperfoam behavior where in compression cross-linked aerogels are linearly elastic under small strains (less than 4%) and then exhibit yield behavior (until 40% strain), followed by densification and inelastic hardening. At room temperature the compressive Young's modulus and the Poisson's ratio were determined to be 129 plus or minus 8 MPa and 0.18, respectively, while the strain at ultimate failure is 77% and the average specific compressive stress at ultimate failure is 3.89 x 10(exp 5) N m kg(sup -1). The specific flexural strength is 2.16 x 10(exp 4) N m kg(sup -1). Effects on the compressive behavior of strain rate and low temperature were also evaluated.

  15. Applicability of Vacuum Impregnation to Modify Physico-Chemical, Sensory and Nutritive Characteristics of Plant Origin Products—A Review

    Directory of Open Access Journals (Sweden)

    Elżbieta Radziejewska-Kubzdela

    2014-09-01

    Full Text Available Vacuum impregnation is a non-destructive method of introducing a solution with a specific composition to the porous matrices of fruit and vegetables. Mass transfer in this process is a result of mechanically induced differences in pressure. Vacuum impregnation makes it possible to fill large volumes of intercellular spaces in tissues of fruit and vegetables, thus modifying physico-chemical properties and sensory attributes of products. This method may be used, e.g., to reduce pH and water activity of the product, change its thermal properties, improve texture, color, taste and aroma. Additionally, bioactive compounds may be introduced together with impregnating solutions, thus improving health-promoting properties of the product or facilitating production of functional food.

  16. Effect of chemically converted graphene as an electrode interfacial modifier on device-performances of inverted organic photovoltaic cells

    Science.gov (United States)

    Kang, Tae-Woon; Noh, Yong-Jin; Yun, Jin-Mun; Yang, Si-Young; Yang, Yong-Eon; Lee, Hae-Seong; Na, Seok-In

    2015-06-01

    This study examined the effects of chemically converted graphene (CCG) materials as a metal electrode interfacial modifier on device-performances of inverted organic photovoltaic cells (OPVs). As CCG materials for interfacial layers, a conventional graphene oxide (GO) and reduced graphene oxide (rGO) were prepared, and their functions on OPV-performances were compared. The inverted OPVs with CCG materials showed all improved cell-efficiencies compared with the OPVs with no metal/bulk-heterojunction (BHJ) interlayers. In particular, the inverted OPVs with reduction form of GO showed better device-performances than those with GO and better device-stability than poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS)-based inverted solar cells, showing that the rGO can be more desirable as a metal/BHJ interfacial material for fabricating inverted-configuration OPVs.

  17. Chemically modified amino porphyrin/TiO2 for the degradation of Acid Black 1 under day light illumination.

    Science.gov (United States)

    Krishnakumar, Balu; Balakrishna, Avula; Arranja, Cláudia T; Dias, Carlos M F; Sobral, Abilio J F N

    2017-04-05

    In this paper, for the first time, chemically modified 5,10,15,20-meso-tetra-(para-amino)-phenyl-porphyrin/TiO2 (TPAPP/TiO2) was prepared and used for the degradation of an azo dye Acid Black 1 (AB 1) under direct sunlight. Initially, TiO2 was prepared by sol-gel method. Before making a TPAPP/TiO2 composite, the surface modification of TiO2 was carried out with glycidoxypropyltrimethoxy silane (GPTMS) which acts as a coupling agent. This is an epoxy terminated silane and could easily bond to the amino group of TPAPP through epoxy cleavage. The formation of TPAPP/TiO2 was confirmed by different characterization techniques such as FT-IR, XRD, SEM and DRS. The photocatalytic activity of TiO2 was highly influenced by TPAPP. A mechanism was proposed for AB 1 degradation by TPAPP/TiO2 under sun light.

  18. Chemically modified amino porphyrin/TiO2 for the degradation of Acid Black 1 under day light illumination

    Science.gov (United States)

    Krishnakumar, Balu; Balakrishna, Avula; Arranja, Cláudia T.; Dias, Carlos M. F.; Sobral, Abilio J. F. N.

    2017-04-01

    In this paper, for the first time, chemically modified 5,10,15,20-meso-tetra-(para-amino)-phenyl-porphyrin/TiO2 (TPAPP/TiO2) was prepared and used for the degradation of an azo dye Acid Black 1 (AB 1) under direct sunlight. Initially, TiO2 was prepared by sol-gel method. Before making a TPAPP/TiO2 composite, the surface modification of TiO2 was carried out with glycidoxypropyltrimethoxy silane (GPTMS) which acts as a coupling agent. This is an epoxy terminated silane and could easily bond to the amino group of TPAPP through epoxy cleavage. The formation of TPAPP/TiO2 was confirmed by different characterization techniques such as FT-IR, XRD, SEM and DRS. The photocatalytic activity of TiO2 was highly influenced by TPAPP. A mechanism was proposed for AB 1 degradation by TPAPP/TiO2 under sun light.

  19. Raman spectra investigation of the defects of chemical vapor deposited multilayer graphene and modified by oxygen plasma treatment

    Science.gov (United States)

    Li, Zongyao; Xu, Yu; Cao, Bing; Qi, Lin; He, Shunyu; Wang, Chinhua; Zhang, Jicai; Wang, Jianfeng; Xu, Ke

    2016-11-01

    Graphene, a two dimensional material, can be modified its properties by defects engineering. Here, we present Raman spectra studies of the multilayer graphene (MLG) fabricated by low-pressure chemical vapor deposition over copper foil, and report that the defects of MLG can be controlled by adjusting methane concentration. Moreover, MLG can be changed from metallic to semiconductoring properties by using oxygen plasma treatment, and we investigate the defects evolution of the graphene after exposing to oxygen plasma by Raman spectra. Our results indicate that the amount of defects in graphene can be changed by regulating the methane concentration and oxygen plasma exposure times, but the primary type of defect in MLG is still boundary-like defect. It is valuable for understanding the physics of defects evolution through artificially generated defects, and such defect engineering will greatly open up the future application of the novel material.

  20. Applicability of Vacuum Impregnation to Modify Physico-Chemical, Sensory and Nutritive Characteristics of Plant Origin Products—A Review

    Science.gov (United States)

    Radziejewska-Kubzdela, Elżbieta; Biegańska-Marecik, Róża; Kidoń, Marcin

    2014-01-01

    Vacuum impregnation is a non-destructive method of introducing a solution with a specific composition to the porous matrices of fruit and vegetables. Mass transfer in this process is a result of mechanically induced differences in pressure. Vacuum impregnation makes it possible to fill large volumes of intercellular spaces in tissues of fruit and vegetables, thus modifying physico-chemical properties and sensory attributes of products. This method may be used, e.g., to reduce pH and water activity of the product, change its thermal properties, improve texture, color, taste and aroma. Additionally, bioactive compounds may be introduced together with impregnating solutions, thus improving health-promoting properties of the product or facilitating production of functional food. PMID:25244012

  1. The application of solid sorbents for the purification of aluminum contaminated chemicals used as modifiers in electrothermal atomic absorption spectrometry.

    Science.gov (United States)

    Bulska, E; Pyrzyńska, K

    1996-06-01

    Various microcolumns with solid sorbents (ion exchange resins, functionalised cellulose sorbents, chelating resins) have been tested with respect to their ability for the purification of aluminum contaminated chemicals used as modifiers in electrothermal atomic absorption spectrometry. The purification of NaNO(3), Mg(NO(3))(2), K(2)SO(4) and (NH(4))(2)HPO(4) has been the most effective with an almost 100% efficiency, when Spheron-Oxine was used as chelating resin. The sorption of aluminum from KOH solution has been found to be very high (around 90%) for all investigated sorbents. However, the best results have been obtained with anion-exchange resins. It has been difficult to purify concentrated mineral acids (HCl, H(2)SO(4)). A retention of aluminum above 80% has been achieved only when Cellex P, Chelex 100 or Amberlite XAD-2 have been used.

  2. Interaction of plasma-generated water cluster ions with chemically-modified Si surfaces investigated by infrared absorption spectroscopy

    Directory of Open Access Journals (Sweden)

    Ayumi Hirano-Iwata

    2016-03-01

    Full Text Available We have investigated the interaction of water cluster ions generated by discharge plasma, with chemically modified Si surfaces using infrared absorption spectroscopy in the multiple internal reflection geometry. We observe that water cluster ions readily adsorb on SiO2-covered Si surfaces to form water droplets. We demonstrate that positively- and negatively-charged cluster ions adsorb on the SiO2-covered Si surface in different manners, indicating ionic interaction of the water droplets with the negatively-charged SiO2 surface. Water droplets formed on the protein-coated surface rupture the amide bond of the proteins, suggesting the function of protein decomposition of water cluster ions.

  3. Interaction of plasma-generated water cluster ions with chemically-modified Si surfaces investigated by infrared absorption spectroscopy

    Science.gov (United States)

    Hirano-Iwata, Ayumi; Matsumura, Ryosuke; Ma, Teng; Kimura, Yasuo; Niwano, Michio; Nishikawa, Kazuo

    2016-03-01

    We have investigated the interaction of water cluster ions generated by discharge plasma, with chemically modified Si surfaces using infrared absorption spectroscopy in the multiple internal reflection geometry. We observe that water cluster ions readily adsorb on SiO2-covered Si surfaces to form water droplets. We demonstrate that positively- and negatively-charged cluster ions adsorb on the SiO2-covered Si surface in different manners, indicating ionic interaction of the water droplets with the negatively-charged SiO2 surface. Water droplets formed on the protein-coated surface rupture the amide bond of the proteins, suggesting the function of protein decomposition of water cluster ions.

  4. Methidium intercalator inserted into synthetic oligonucleotides.

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, E. N.; Smirnov, I. P.; Haff, L. A.; Tishchenko, E. I.; Mirzabekov, A. D.; Florentiev, V. L.; Center for Mechanistic Biology and Biotechnology; Engelhardt Inst. of Molecular Biology; PerSeptive BioSystems Inc.

    1996-01-01

    A new methidium intercalator phosphoramidite has been synthesized. Methidium incorporation into an oligonucleotide during the synthesis was confirmed by UV and MALDI TOF MS data. UV melting experiments showed enhanced stability of a duplex, containing internal methidium. Methidium phosphoramidite has been synthesized and used for insertion of intercalator into the deoxyoligonucleotides.

  5. Hsp90 protein interacts with phosphorothioate oligonucleotides containing hydrophobic 2'-modifications and enhances antisense activity.

    Science.gov (United States)

    Liang, Xue-Hai; Shen, Wen; Sun, Hong; Kinberger, Garth A; Prakash, Thazha P; Nichols, Joshua G; Crooke, Stanley T

    2016-05-05

    RNase H1-dependent antisense oligonucleotides (ASOs) are chemically modified to enhance pharmacological properties. Major modifications include phosphorothioate (PS) backbone and different 2'-modifications in 2-5 nucleotides at each end (wing) of an ASO. Chemical modifications can affect protein binding and understanding ASO-protein interactions is important for better drug design. Recently we identified many intracellular ASO-binding proteins and found that protein binding could affect ASO potency. Here, we analyzed the structure-activity-relationships of ASO-protein interactions and found 2'-modifications significantly affected protein binding, including La, P54nrb and NPM. PS-ASOs containing more hydrophobic 2'-modifications exhibit higher affinity for proteins in general, although certain proteins, e.g. Ku70/Ku80 and TCP1, are less affected by 2'-modifications. We found that Hsp90 protein binds PS-ASOs containing locked-nucleic-acid (LNA) or constrained-ethyl-bicyclic-nucleic-acid ((S)-cEt) modifications much more avidly than 2'-O-methoxyethyl (MOE). ASOs bind the mid-domain of Hsp90 protein. Hsp90 interacts with more hydrophobic 2' modifications, e.g. (S)-cEt or LNA, in the 5'-wing of the ASO. Reduction of Hsp90 protein decreased activity of PS-ASOs with 5'-LNA or 5'-cEt wings, but not with 5'-MOE wing. Together, our results indicate Hsp90 protein enhances the activity of PS/LNA or PS/(S)-cEt ASOs, and imply that altering protein binding of ASOs using different chemical modifications can improve therapeutic performance of PS-ASOs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Rehabilitation of irradiated patients with chemically modified and conventional SLA implants: five-year follow-up.

    Science.gov (United States)

    Nack, C; Raguse, J-D; Stricker, A; Nelson, K; Nahles, S

    2015-01-01

    The aim of this study is to evaluate the clinical and radiological parameters of standard SLA surface implants compared to chemically modified hydrophilic SLActive implants in irradiated patients after the initial 12-month loading period up to 5 years. Twenty patients with a mean age of 61·1 years were treated with dental implants after ablative surgery and radio-chemotherapy of oral cancer. All patients were non-smokers. The placement of 102 implants (50 SLA, 52 SLActive) was performed bilaterally according to a split-mouth design. Mean crestal bone changes were evaluated using standardised orthopantomographies and clinical parameters. Data were analysed using a Kaplan-Meier curve, Mann-Whitney U-test and two-factorial non-parametric analysis. The average observation period was 60 months. The amount of bone loss at the implant shoulder of SLA implants was mesial and distal 0·7 mm. The SLActive implants displayed a bone loss of mesial 0·6 mm as well as distal 0·7 mm after 5 years. Two SLA implants were lost before loading. One patient lost five implants due to recurrence of a tumour. The overall cumulative 12-month, 3-year and 5-year survival rate of SLA implants was 92%, 80% and 75·8% and of SLActive implants 94·2%, 78·8% and 74·4%, respectively. Eighteen implants were considered lost because the patients had died. Sandblasted acid-etched implants with or without a chemically modified surface can be used in irradiated patients with a high predictability of success. Lower implant survival rates in patients with irradiated oral cancer may be associated with systemic effects rather than peri-implantitis. © 2014 John Wiley & Sons Ltd.

  7. Chemical stability and osteogenic activity of plasma-sprayed boron-modified calcium silicate-based coatings.

    Science.gov (United States)

    Lu, Xiang; Li, Kai; Xie, Youtao; Huang, Liping; Zheng, Xuebin

    2016-11-01

    In recent years, CaSiO3 bio-ceramic coatings have attracted great attention because of their good bioactivity. However, their high degradation rates in physiological environment restrict their practical applications. In this work, boron-modified CaSiO3 ceramic (Ca11Si4B2O22, B-CS) coating was developed on Ti substrates by plasma-spraying technique attempting to obtain enhanced chemical stability and osteogenic activity. The B-CS coating possessed significantly increased chemical stability due to the introduction of boron and consequently the modified crystal structure, while maintaining good bioactivity. Scanning electron microscope and immunofluorescence studies showed that better cellular adhesion and extinctive filopodia-like processes were observed on the B-CS coating. Compared with the pure CaSiO3 (CS) coating, the B-CS coating promoted MC3T3-E1 cells attachment and proliferation. In addition, enhanced collagen I (COL-I) secretion, alkaline phosphatase activity, and extracellular matrix mineralization levels were detected from the B-CS coating. According to RT-PCR results, notable up-regulation expressions of mineralized tissue-related genes, such as runt-related transcription factor 2 (Runx2), bone sialoprotein and osteocalcin, and bone morphogenetic protein 7 (BMP-7) were observed on the B-CS coating compared with the CS coating. The above results suggested that Ca11Si4B2O22 coatings possess excellent osteogenic activity and might be a promising candidate for orthopedic applications.

  8. Chemically modified carbon paste ion-selective electrodes for determination of atorvastatin calcium in pharmaceutical preparations

    Directory of Open Access Journals (Sweden)

    Salwa Fares Rassi

    2017-06-01

    Full Text Available A simple, rapid and sensitive method for the determination of atorvastatin calcium in pharmaceutical preparations using two modified carbon paste electrodes was developed. One electrode (sensor A is based on ion-pair of atorvastatin with 5,6-diaminouracil hydrochloride (ATS-DAUH and the other (sensor B is based on atorvastatin with picric acid (ATS-PC. Among three different solvent mediators tested, dioctylphthalate (DOPH exhibited a proper behavior including Nernstian slopes of the calibration curve at 58.76 ± 0.8 and 57.48±1 mV per decade for sensors A and B. The response times were 10 and 12 s, detection limits 1.3 × 10−6 and 2.2 × 10−6 M; the concentration range 2.5 × 10−6-7.9 × 10−2 M and 3.0 × 10−6 to 7.9 × 10−2 M respectively. The present electrodes show good discrimination of atorvastatin calcium from several inorganic, organic ions, sugars and some common excipients. The sensors were applied for the determination of atorvastatin calcium in pharmaceutical preparations using standard addition and the calibration curve methods. The results obtained were satisfactory with excellent percentage recovery comparable and sometimes better than those obtained by other routine methods for the assay. The proposed potentiometric methods offer the advantages of simplicity, accuracy, automation feasibility and applicability to turbid and colored sample solutions.

  9. Efficient acetone-butanol-ethanol production (ABE) by Clostridium acetobutylicum XY16 immobilized on chemically modified sugarcane bagasse.

    Science.gov (United States)

    Kong, Xiangping; He, Aiyong; Zhao, Jie; Wu, Hao; Jiang, Min

    2015-07-01

    Sugarcane bagasse was chemically modified by polyethylenimine (PEI) and glutaraldehyde (GA) and then used as a support to immobilize Clostridium acetobutylicum XY16 in the process of butanol production. Compared with batch fermentation using unmodified sugarcane bagasse, 22.3 g/L total solvents were produced by cells immobilized on 4 g/L PEI treated sugarcane bagasse with high solvent productivity of 0.62 g/(L h) and glucose consumption rate of 1.67 g/(L h). Improvement of 14, 43, and 37 % in total solvent titer, solvent productivity and glucose consumption rate was observed, respectively. Enhanced solvent production of 25.14 g/L was obtained when using a high concentration of glucose of 80 g/L. Continuous fermentation was studied using PEI/GA modified sugarcane bagasse as immobilization support with a range of dilution which rates from 0.2 to 2.5 to find an optimal condition. The maximum solvent productivity of 11.32 g/(L h) was obtained at a high dilution rate of 2.0 h(-1).

  10. Factors affecting protein transfer into surfactant-isooctane solution: a case study of extraction behavior of chemically modified cytochrome c.

    Science.gov (United States)

    Ono, T; Goto, M

    1998-01-01

    The extraction mechanism of proteins by surfactant molecules in an organic solvent has been investigated using a chemically modified protein. We conducted guanidylation on lysine residues of cytochrome c by replacing their amino groups with homoarginine to enhance the protein-surfactant interaction. Results have shown that guanidylated cytochrome c readily forms a hydrophobic complex with dioleyl phosphoric acid (DOLPA) through hydrogen bonding between the phosphate moiety and the guanidinium groups. Although improved protein-surfactant interaction activated the formation of a hydrophobic complex at the interface, it could not improve the protein transfer in isooctane. It has been established that the protein extraction mechanism using surfactant molecules is mainly governed by two processes: formation of an interfacial complex at the oil-water interface and the subsequent solubilization of the complex into the organic phase. In addition, a kinetic study demonstrated that guanidylation of lysine accelerated the initial extraction rate of cytochrome c. This fact implies that the protein transferability from aqueous phase into organic phase depends on the protein-surfactant interaction which can be modified by protein surface engineering.

  11. Biocompatibility and surface structure of chemically modified immunoisolating alginate-PLL capsules.

    Science.gov (United States)

    Bünger, C M; Gerlach, C; Freier, T; Schmitz, K P; Pilz, M; Werner, C; Jonas, L; Schareck, W; Hopt, U T; de Vos, P

    2003-12-15

    Grafting of encapsulated living cells has the potential to cure a wide variety of diseases. Large-scale application of the technique, however, is hampered by insufficient biocompatibility of the capsules. A major factor in the biocompatibility of capsules is inadequate covering of the inflammatory poly-L-lysine (PLL) on the capsules' surface. In the present study, we investigate whether tissue responses against alginate-PLL capsules can be reduced by crosslinking the surface of the capsules with heparin or polyacrylic acid. Our transplant study in rats shows a tissue response composed of fibroblasts and macrophages on alginate-PLL-alginate and alginate-PLL-heparin capsules that was completely absent on alginate-PLL-polyacrylic acid capsules. Atomic force microscopy analyses of the capsules demonstrates that the improved biocompatibility of alginate-PLL-capsules by polyacrylic acid coating should not only be explained by a more adequate binding of PLL but also by the induction of a smoother surface. This study shows for the first time that biologic responses against capsules can be successfully deleted by chemically crosslinking biocompatible molecules on the surface of alginate-PLL capsules. Copyright 2003 Wiley Periodicals, Inc. J Biomed Mater Res 67A: 1219-1227, 2003

  12. Physisorption of DNA molecules on chemically modified single-walled carbon nanotubes with and without sonication.

    Science.gov (United States)

    Umemura, Kazuo; Ishibashi, Yu; Oura, Shusuke

    2016-09-01

    We investigated the physisorption phenomenon of single-stranded DNA (ssDNA) molecules onto two types of commercially available chemically functionalized single-walled carbon nanotubes (SWNTs) by atomic force microscopy (AFM) and agarose gel electrophoresis. We found that DNA molecules can adsorb on the water-soluble SWNT surfaces without sonication, although sonication treatment has been used for hybridization of DNA and SWNTs in many previous studies. Using our method, damage of DNA molecules by sonication can be avoided. On the other hand, the amount of DNA molecules adsorbed on SWNT surfaces increased when the samples were sonicated. This fact suggests that the sonication is effective not only at debundling of SWNTs, but also at assisting DNA adsorption. Furthermore, DNA adsorption was affected by the types of functionalized SWNTs. In the case of SWNTs functionalized with polyethylene glycol (PEG-SWNT), physisorption of ssDNA molecules was confirmed only by agarose-gel electrophoresis. In contrast, amino-terminated SWNTs (NH2-SWNTs) showed a change in the height distribution profile based on AFM observations. These results suggest that DNA molecules tended to adsorb to NH2-SWNT surfaces, although DNA molecules can also adsorb on PEG-SWNT surfaces. Our results revealed fundamental information for developing nanobiodevices using hybrids of DNA and SWNTs.

  13. Chemosensitization by antisense oligonucleotides targeting MDM2.

    Science.gov (United States)

    Bianco, Roberto; Ciardiello, Fortunato; Tortora, Giampaolo

    2005-02-01

    The MDM2 oncogene is overexpressed in many human cancers, including sarcomas, certain hematologic malignancies, and breast, colon and prostate cancers. The p53-MDM2 interaction pathway has been suggested as a novel target for cancer therapy. To that end, several strategies have been explored, including the use of small polypeptides targeted to the MDM2-p53 binding domain, anti-MDM2 antisense oligonucleotides, and natural agents. Different generations of anti-human-MDM2 oligonucleotides have been tested in in vitro and in vivo human cancer models, revealing specific inhibition of MDM2 expression and significant antitumor activity. Use of antisense oligos potentiated the effects of growth inhibition, p53 activation and p21 induction by several chemotherapeutic agents. Increased therapeutic effectiveness of chemotherapeutic drugs in human cancer cell lines carrying p53 mutations or deletions have shown the ability of MDM2 inhibitors to act as chemosensitizers in various types of tumors through both p53-dependent and p53-independent mechanisms. Inhibiting MDM2 appears to also have a role in radiation therapy for human cancer, regardless of p53 status, providing a rationale for the development of a new class of radiosensitizers. Moreover, MDM2 antisense oligonucleotides potentiate the effect of epidermal growth factor receptor (EGFR) inhibitors by affecting in vitro and in vivo proliferation, apoptosis and protein expression in hormone-refractory and hormone-dependent human prostate cancer cells. These data support the development, among other MDM2 inhibitors, of anti-MDM2 antisense oligonucleotides as a novel class of anticancer agents, and suggest a potentially relevant role for the oligonucleotides when integrated with conventional treatments and/or other signaling inhibitors in novel therapeutic strategies.

  14. Multiple depositions of Ag nanoparticles on chemically modified agarose films for surface-enhanced Raman spectroscopy

    Science.gov (United States)

    Zhai, Wen-Lei; Li, Da-Wei; Qu, Lu-Lu; Fossey, John S.; Long, Yi-Tao

    2011-12-01

    A facile and cost-effective approach for the preparation of a surface-enhanced Raman spectroscopy (SERS) substrate through constructing silver nanoparticle/3-aminopropyltriethoxysilane/agarose films (Ag NPs/APTES/Agar film) on various solid supports is described. The SERS performance of the substrate was systematically investigated, revealing a maximum SERS intensity with four layers of the Ag NP deposition. The enhancement factor of the developed substrate was calculated as 1.5 × 107 using rhodamine 6G (R6G) as the probe molecule, and the reproducibility of the SERS signals was established. A high throughput screening platform was designed, manufactured and implemented which utilised the ability to cast agarose to assemble arrays. Quantitative analysis of 4-aminobenzoic acid (4-ABA) and 4-aminothiophenol (4-ATP) was achieved over a ~0.5 nM-0.1 μM range.A facile and cost-effective approach for the preparation of a surface-enhanced Raman spectroscopy (SERS) substrate through constructing silver nanoparticle/3-aminopropyltriethoxysilane/agarose films (Ag NPs/APTES/Agar film) on various solid supports is described. The SERS performance of the substrate was systematically investigated, revealing a maximum SERS intensity with four layers of the Ag NP deposition. The enhancement factor of the developed substrate was calculated as 1.5 × 107 using rhodamine 6G (R6G) as the probe molecule, and the reproducibility of the SERS signals was established. A high throughput screening platform was designed, manufactured and implemented which utilised the ability to cast agarose to assemble arrays. Quantitative analysis of 4-aminobenzoic acid (4-ABA) and 4-aminothiophenol (4-ATP) was achieved over a ~0.5 nM-0.1 μM range. Electronic supplementary information (ESI) available: the chemical structure of agarose, the SEM characterization of the synthesised Ag NPs, the calculation of the EF, the stability of the SERS substrate. See DOI: 10.1039/c1nr10956a

  15. The effect of chemically modified alginates on macrophage phenotype and biomolecule transport.

    Science.gov (United States)

    Bygd, Hannah C; Bratlie, Kaitlin M

    2016-07-01

    Macrophage (MΦ) reprogramming has received significant attention in applications such as cancer therapeutics and tissue engineering where the host immune response to biomaterials is crucial in determining the success or failure of an implanted device. Polymeric systems can potentially be used to redirect infiltrating M1 MΦs toward a proangiogenic phenotype. This work exploits the concept of MΦ reprogramming in the engineering of materials for improving the longevity of tissue engineering scaffolds. We have investigated the effect of 13 different chemical modifications of alginate on MΦ phenotype. Markers of the M1 response-tumor necrosis factor-α (TNF-α) and inducible nitric oxide synthase-and the M2 response-arginase-were measured and used to determine the ability of the materials to alter MΦ phenotype. It was found that some modifications were able to reduce the pro-inflammatory response of M1 MΦs, others appeared to amplify the M2 phenotype, and the results for two materials suggested they were able to reprogram a MΦ population from M1 to M2. These findings were supplemented by studies done to examine the permselectivity of the materials. Diffusion of TNF-α was completely prevented through some of these materials, while up to 84% was found to diffuse through others. The diffusion of insulin through the materials was statistically consistent. These results suggest that the modification of these materials might alter mass transport in beneficial ways. The ability to control polarization of MΦ phenotypes with immunoprotective materials has the potential to augment the success of tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1707-1719, 2016.

  16. A chemically modified [alpha]-amylase with a molten-globule state has entropically driven enhanced thermal stability

    Energy Technology Data Exchange (ETDEWEB)

    Siddiqui, Khawar Sohail; Poljak, Anne; De Francisci, Davide; Guerriero, Gea; Pilak, Oliver; Burg, Dominic; Raftery, Mark J.; Parkin, Don M.; Trewhella, Jill; Cavicchioli, Ricardo (Sydney); (New South)

    2010-11-15

    The thermostability properties of TAA were investigated by chemically modifying carboxyl groups on the surface of the enzyme with AMEs. The TAA{sub MOD} exhibited a 200% improvement in starch-hydrolyzing productivity at 60 C. By studying the kinetic, thermodynamic and biophysical properties, we found that TAA{sub MOD} had formed a thermostable, MG state, in which the unfolding of the tertiary structure preceded that of the secondary structure by at least 20 C. The X-ray crystal structure of TAA{sub MOD} revealed no new permanent interactions (electrostatic or other) resulting from the modification. By deriving thermodynamic activation parameters of TAA{sub MOD}, we rationalised that thermostabilisation have been caused by a decrease in the entropy of the transition state, rather than being enthalpically driven. Far-UV CD shows that the origin of decreased entropy may have arisen from a higher helical content of TAA{sub MOD}. This study provides new insight into the intriguing properties of an MG state resulting from the chemical modification of TAA.

  17. Phase Stability of Ce-Modified La2Zr2O7 Coatings and Chemical Compatibility with YSZ

    Science.gov (United States)

    Wu, Qiong; Ji, Xiaojuan; Peng, Haoran; Ren, Xianjing; Yu, Yueguang

    2016-04-01

    Ce-modified La2Zr2O7 powders, i.e., La2Zr2O7 (LZ), La2(Zr0.7Ce0.3)2O7 (LZ7C3), and La2(Zr0.3Ce0.7)2O7 (LZ3C7), were used to produce thermal barrier coatings by atmospheric plasma spray process. The chemical compatibility of the CeO2-doped La2Zr2O7 with the traditional YSZ was investigated in LZ-YSZ powder mixtures and LZ-YSZ bilayer coatings by x-ray diffraction and scanning electron microscope. The powder mixtures and coatings were aged at 1200 and 1300 °C for 100 h. The results showed that LZ and LZ7C3 presented single pyrochlore structure after the heat treatments at both 1200 and 1300 °C. For LZ3C7, however, fluorite structure was observed at 1300 °C, indicating a poor phase stability of LZ3C7 at the elevated temperature. The results further showed that La2(Zr0.3Ce0.7)2O7 reacted with YSZ in the bilayer ceramic coatings due to the diffusion of cerium, zirconium, and yttrium. While for La2Zr2O7(LZ) and La2(Zr0.7Ce0.3)2O7, a better chemical compatibility with YSZ was shown.

  18. A genotype of modified vaccinia Ankara (MVA) that facilitates replication in suspension cultures in chemically defined medium.

    Science.gov (United States)

    Jordan, Ingo; Horn, Deborah; John, Katrin; Sandig, Volker

    2013-01-21

    While vectored vaccines, based on hyperattenuated viruses, may lead to new treatment options against infectious diseases and certain cancers, they are also complex products and sometimes difficult to provide in sufficient amount and purity. To facilitate vaccine programs utilizing host-restricted poxviruses, we established avian suspension cell lines (CR and CR.pIX) and developed a robust, chemically defined, culturing process for production of this class of vectors. For one prominent member, modified vaccinia Ankara (MVA), we now describe a new strain that appears to replicate to greater yields of infectious units, especially in the cell-free supernatant of cultures in chemically defined media. The new strain was obtained by repeated passaging in CR suspension cultures and, consistent with reports on the exceptional genetic stability of MVA, sequencing of 135 kb of the viral genomic DNA revealed that only three structural proteins (A3L, A9L and A34R) each carry a single amino acid exchange (H639Y, K75E and D86Y, respectively). Host restriction in a plaque-purified isolate of the new genotype appears to be maintained in cell culture. Processing towards an injectable vaccine preparation may be simplified with this strain as a complete lysate, containing the main burden of host cell contaminants, may not be required anymore to obtain adequate yields.

  19. Electron Transfer Reactivity Patterns at Chemically Modified Electrodes: Fundamentals and Application to the Optimization of Redox Recycling Amplification Systems

    Energy Technology Data Exchange (ETDEWEB)

    Bergren, Adam Johan [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    Electroanalytical chemistry is often utilized in chemical analysis and Fundamental studies. Important advances have been made in these areas since the advent of chemically modified electrodes: the coating of an electrode with a chemical film in order to impart desirable, and ideally, predictable properties. These procedures enable the exploitation of unique reactivity patterns. This dissertation presents studies that investigate novel reaction mechanisms at self-assembled monolayers on gold. In particular, a unique electrochemical current amplification scheme is detailed that relies on a selective electrode to enable a reactivity pattern that results in regeneration of the analyte (redox recycling). This regenerating reaction can occur up to 250 times for each analyte molecule, leading to a notable enhancement in the observed current. The requirements of electrode selectivity and the resulting amplification and detection limit improvements are described with respect to the heterogeneous and homogeneous electron transfer rates that characterize the system. These studies revealed that the heterogeneous electrolysis of the analyte should ideally be electrochemically reversible, while that for the regenerating agent should be held to a low level. Moreover, the homogeneous reaction that recycles the analyte should occur at a rapid rate. The physical selectivity mechanism is also detailed with respect to the properties of the electrode and redox probes utilized. It is shown that partitioning of the analyte into/onto the adlayer leads to the extraordinary selectivity of the alkanethiolate monolayer modified electrode. Collectively, these studies enable a thorough understanding of the complex electrode mechanism required for successful redox recycling amplification systems, Finally, in a separate (but related) study, the effect of the akyl chain length on the heterogeneous electron transfer behavior of solution-based redox probes is reported, where an odd-even oscillation

  20. Enhanced compatibility of chemically modified titanium surface with periodontal ligament cells

    Energy Technology Data Exchange (ETDEWEB)

    Kado, T.; Hidaka, T. [Division of Periodontology and Endodontology, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293 (Japan); Aita, H. [Division of Occlusion and Removable Prosthodontics, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293 (Japan); Endo, K. [Division of Biomaterials and Bioengineering, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293 (Japan); Furuichi, Y., E-mail: furuichi@hoku-iryo-u.ac.jp [Division of Periodontology and Endodontology, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293 (Japan)

    2012-12-01

    Highlights: Black-Right-Pointing-Pointer Cell-adhesive molecules were covalently immobilized on a Ti surface. Black-Right-Pointing-Pointer Immobilized cell-adhesive molecules maintained native function on the Ti surface. Black-Right-Pointing-Pointer Immobilized collagen enhanced adhesion of periodontal ligament cells to the Ti. - Abstract: A simple chemical modification method was developed to immobilize cell-adhesive molecules on a titanium surface to improve its compatibility with human periodontal ligament cells (HPDLCs).The polished titanium disk was immersed in 1% (v/v) p-vinylbenzoic acid solution for 2 h to introduce carboxyl groups onto the surface. After rinsing with distilled deionized water, the titanium disk was dipped into 1.47% 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide solution containing 0.1 mg/ml Gly-Arg-Gly-Asp-Ser (GRGDS), human plasma fibronectin (pFN), or type I collagen from calf skin (Col) to covalently immobilize the cell-adhesive molecules on the titanium surface via formation of peptide bonds. X-ray photoelectron spectroscopy analyses revealed that cell-adhesive molecules were successfully immobilized on the titanium surfaces. The Col-immobilized titanium surface revealed higher values regarding nano rough characteristics than the as-polished titanium surface under scanning probe microscopy. The number of HPDLCs attached to both the pFN- and Col-immobilized titanium surfaces was twice that attached to the as-polished titanium surfaces. The cells were larger with the cellular processes that stretched to a greater extent on the pFN- and Col-immobilized titanium surfaces than on the as-polished titanium surface (p < 0.05). HPDLCs on the Col-immobilized titanium surfaces showed more extensive expression of vinculin at the tips of cell projections and more contiguously along the cell outline than on the as-polished, GRGDS-immobilized and pFN-immobilized titanium surfaces. It was concluded that cell-adhesive molecules successfully

  1. Design Considerations for Array CGH to OligonucleotideArrays

    Energy Technology Data Exchange (ETDEWEB)

    Baldocchi, R.A.; Glynne, R.J.; Chin, K.; Kowbel, D.; Collins, C.; Mack, D.H.; Gray, J.W.

    2005-03-04

    Background: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. Methods: In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. Results: In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. Conclusion: Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.

  2. Mechanism of antisense oligonucleotide interaction with natural RNAs.

    Science.gov (United States)

    Serikov, R; Petyuk, V; Vorobijev, Y; Koval, V; Fedorova, O; Vlassov, V; Zenkova, M

    2011-08-01

    Oligonucleotides find several numbers of applications: as diagnostic probes, RT and PCR primers and antisense agents due to their ability of forming specific interactions with complementary nucleotide sequences within nucleic acids. These interactions are strongly affected by accessibility of the target sequence in the RNA structure. In the present work the mechanism of invasion of RNA structure by oligonucleotide was investigated using a model system: yeast tRNA(Phe) and oligonucleotides complementary to the 3'-part of this molecule. Kinetics of interaction of oligonucleotides with in vitro transcript of yeast tRNAPhe was studied using stopped-flow technique with fluorescence quenching detection, 5'-DABCYL labeled oligonucleotide was hybridized with 3'-fluorescein labeled tRNA(Phe). The results evidence for a four-step invasion process of the oligonucleotide-RNA complex formation. The process is initiated by formation of transition complexes with nucleotides in the T-loop and ACCA sequence. This complex formation is followed by RNA unfolding and formation of an extended heteroduplex with the oligonucleotide via strand displacement process. Computer modeling of oligonucleotide-tRNA(Phe) interaction revealed potential factors that could favor transition complexes formation and confirmed the proposed mechanism, showing the oligonucleotide to be a molecular "wedge". Our data evidence that oligonucleotide invasion into structured RNA is initiated by loop-single strand interactions, similar to the initial step of the antisense RNA-RNA interactions. The obtained results can be used for choosing efficient oligonucleotide probes.

  3. Oligonucleotide and Parylene Surface Coating of Polystyrene and ePTFE for Improved Endothelial Cell Attachment and Hemocompatibility

    Directory of Open Access Journals (Sweden)

    Martina Schleicher

    2012-01-01

    Full Text Available In vivo self-endothelialization by endothelial cell adhesion on cardiovascular implants is highly desirable. DNA-oligonucleotides are an intriguing coating material with nonimmunogenic characteristics and the feasibility of easy and rapid chemical fabrication. The objective of this study was the creation of cell adhesive DNA-oligonucleotide coatings on vascular implant surfaces. DNA-oligonucleotides immobilized by adsorption on parylene (poly(monoaminomethyl-para-xylene coated polystyrene and ePTFE were resistant to high shear stress (9.5 N/m2 and human blood serum for up to 96 h. Adhesion of murine endothelial progenitor cells, HUVECs and endothelial cells from human adult saphenous veins as well as viability over a period of 14 days of HUVECs on oligonucleotide coated samples under dynamic culture conditions was significantly enhanced (P<0.05. Oligonucleotide-coated surfaces revealed low thrombogenicity and excellent hemocompatibility after incubation with human blood. These properties suggest the suitability of immobilization of DNA-oligonucleotides for biofunctionalization of blood vessel substitutes for improved in vivo endothelialization.

  4. Electrochemical Detection of a Dengue-related Oligonucleotide Sequence Using Ferrocenium as a Hybridization Indicator

    OpenAIRE

    José Luiz de Lima-Filho; Duarte Miguel França dos Prazeres; ernando Rodrigues Ribeiro Teles

    2007-01-01

    A simple method for electrochemical detection of a synthetic 20-bp oligonucleotide sequence related with dengue virus genome was developed. A complimentary DNA probe sequence was electrostatically immobilized onto a glassy carbon electrode modified with chitosan. Electrochemical detection of hybridization between probe and target was performed by cyclic voltammetry, using ferrocene (Fc+) as a hybridization label. After hybridization, the peak current response of Fc+ oxidation increased around...

  5. Delivering Antisense Morpholino Oligonucleotides to Target Telomerase Splice Variants in Human Embryonic Stem Cells.

    Science.gov (United States)

    Radan, Lida; Hughes, Chris S; Teichroeb, Jonathan H; Postovit, Lynne-Marie; Betts, Dean H

    2016-01-01

    Morpholino oligonucleotides (MO) are an innovative tool that provides a means for examining and modifying gene expression outcomes by antisense interaction with targeted RNA transcripts. The site-specific nature of their binding facilitates focused modulation to alter splice variant expression patterns. Here we describe the steric-blocking of human telomerase reverse transcriptase (hTERT) Δα and Δβ splice variants using MO to examine cellular outcomes related to pluripotency and differentiation in human embryonic stem cells.

  6. Massive and selective delivery of lipid-coated cationic lipoplexes of oligonucleotides targeted in vivo to hepatic endothelial cells

    NARCIS (Netherlands)

    Bartsch, M; Weeke-Klimp, AH; Meijer, DKF; Scherphof, GL; Kamps, JAAM

    2002-01-01

    Purpose. Previously we reported on massive uptake of liposomes surface-modified with negatively charged aconitylated albumin (Aco-HSA) by liver sinusoidal endothelial cells (EC) in vivo. In the present work we applied this principle for the in vivo delivery of antisense oligonucleotides (ODN) to the

  7. [Transfection of hypertrophic cardiac myocytes in vitro with (99)Tc(m)-labeled antisense miR208b oligonucleotide].

    Science.gov (United States)

    Wang, Jing; Feng, Huijuan; Ou, Yangwei; Sun, Yungang; Wu, Juqing; Chen, Pan

    2015-08-01

    To test the efficiency of transfecting (99)Tc(m)-labeled anti-miR208b oligonucleotide into early hypertrophic cardiac myocytes in vitro. The anti-oligonucleotide targeting miR208b (AMO) was synthesized and modified with LNA followed by conjugation with N-hydroxysuccinimidyl S-acetyl-meraptoacetyl triglycine (NHS-MAG3) and radiolabeling with (99)Tc(m). NHS-MAG3-LNA-AMO and labeled AMO were purified with Sep-Pak C18 column chromatography, and the former was examined for UV absorption at the 260 nm using Gene Quant DNA/RNA calculator. The labeling efficiency, radiochemical purity, stability and molecular hybridization activity were analyzed. An angiotensin II-induced cell model of hypertrophic cardiac myocytes was transfected with (99)Tc(m)-NHS-MAG3-LNA-AMO via liposome, and the relative expression of miRNA208b and retention ratio of the labeled AMO in early hypertrophic cells were determined. The labeling efficiency and radiochemical purity of the labeled AMO after purification exceeded 84% and 86%, respectively. The radio- chemical purities of the labeled AMO incubated in serum and normal saline for 12 h were both higher than 80%, and the labeled AMO showed a capacity to hybridize with the target gene. In the hypertrophic model of cardiac myocytes, the retention ratio of labeled AMO at 6 h was higher than 20%. The (99)Tc(m)-labeled antisense probe can be efficiently transfected into hypertrophic cardiac myocytes in vitro, which provides an experimental basis for subsequent radionuclide imaging studies.

  8. Electrochemical study of hepta–oligonucleotides

    Directory of Open Access Journals (Sweden)

    Zdenka Balcarova

    2010-12-01

    Full Text Available The study deals with the description and characterization of twohepta–oligonucleotides (DNA and RNA forming special structures.We studied their electrochemical behaviour by means of cyclicvoltammetry (CV and elimination voltammetry with linear scan(EVLS in combination with adsorptive stripping (AdS technique.Differences in electrochemical behaviour of hepta–deoxyribonucleotide and its RNA analog were discussed with regardto their different structures in solutions and their melting points.

  9. Abundant oligonucleotides common to most bacteria.

    Directory of Open Access Journals (Sweden)

    Colin F Davenport

    Full Text Available BACKGROUND: Bacteria show a bias in their genomic oligonucleotide composition far beyond that dictated by G+C content. Patterns of over- and underrepresented oligonucleotides carry a phylogenetic signal and are thus diagnostic for individual species. Patterns of short oligomers have been investigated by multiple groups in large numbers of bacteria genomes. However, global distributions of the most highly overrepresented mid-sized oligomers have not been assessed across all prokaryotes to date. We surveyed overrepresented mid-length oligomers across all prokaryotes and normalised for base composition and embedded oligomers using zero and second order Markov models. PRINCIPAL FINDINGS: Here we report a presumably ancient set of oligomers conserved and overrepresented in nearly all branches of prokaryotic life, including Archaea. These oligomers are either adenine rich homopurines with one to three guanine nucleosides, or homopyridimines with one to four cytosine nucleosides. They do not show a consistent preference for coding or non-coding regions or aggregate in any coding frame, implying a role in DNA structure and as polypeptide binding sites. Structural parameters indicate these oligonucleotides to be an extreme and rigid form of B-DNA prone to forming triple stranded helices under common physiological conditions. Moreover, the narrow minor grooves of these structures are recognised by DNA binding and nucleoid associated proteins such as HU. CONCLUSION: Homopurine and homopyrimidine oligomers exhibit distinct and unusual structural features and are present at high copy number in nearly all prokaryotic lineages. This fact suggests a non-neutral role of these oligonucleotides for bacterial genome organization that has been maintained throughout evolution.

  10. Synthesis and hybridization properties of inverse oligonucleotides.

    OpenAIRE

    Marangoni, M.; Van Aerschot, Arthur; Augustijns, Patrick; Rozenski, Jef; Herdewijn , Piet

    1997-01-01

    The synthesis of adenine and thymine cyclopentylethyl nucleosides is presented. This novel constrained monomeric building block is very difficult to incorporate into oligonucleotides. It was introduced in 13mer oligodeoxynucleotide sequences at a single position using H-phosphonate chemistry. Phosphoramidite chemistry completely failed in this particular case. The H-phosphonate building blocks were obtained starting from the corresponding phosphoramidites. Stability of duplexes with RNA and D...

  11. Detection of Aeromonas hydrophila DNA oligonucleotide sequence using a biosensor design based on Ceria nanoparticles decorated reduced graphene oxide and Fast Fourier transform square wave voltammetry

    Energy Technology Data Exchange (ETDEWEB)

    Jafari, Safiye [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Faridbod, Farnoush, E-mail: faridbodf@khayam.ut.ac.ir [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Biosensor Research Center, Endocrinology & Metabolism Molecular and Cellular Research Institute, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Norouzi, Parviz [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Biosensor Research Center, Endocrinology & Metabolism Molecular and Cellular Research Institute, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Dezfuli, Amin Shiralizadeh [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Ajloo, Davood [School of Chemistry, Damghan University, Damghan (Iran, Islamic Republic of); Mohammadipanah, Fatemeh [Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran (Iran, Islamic Republic of); Ganjali, Mohammad Reza [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Biosensor Research Center, Endocrinology & Metabolism Molecular and Cellular Research Institute, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of)

    2015-10-01

    A new strategy was introduced for ssDNA immobilization on a modified glassy carbon electrode. The electrode surface was modified using polyaniline and chemically reduced graphene oxide decorated cerium oxide nanoparticles (CeO{sub 2}NPs-RGO). A single-stranded DNA (ssDNA) probe was immobilized on the modified electrode surface. Fast Fourier transform square wave voltammetry (FFT-SWV) was applied as detection technique and [Ru(bpy){sub 3}]{sup 2+/3+} redox signal was used as electrochemical marker. The hybridization of ssDNA with its complementary target caused a dramatic decrease in [Ru(bpy){sub 3}]{sup 2+/3+} FFT-SW signal. The proposed electrochemical biosensor was able to detect Aeromonas hydrophila DNA oligonucleotide sequence encoding aerolysin protein. Under optimal conditions, the biosensor showed excellent selectivity toward complementary sequence in comparison with noncomplementary and two-base mismatch sequences. The dynamic linear range of this electrochemical DNA biosensor for detecting 20-mer oligonucleotide sequence of A. hydrophila was from 1 × 10{sup −15} to 1 × 10{sup −8} mol L{sup −1}. The proposed biosensor was successfully applied for the detection of DNA extracted from A. hydrophila in fish pond water up to 0.01 μg mL{sup −1} with RSD of 5%. Besides, molecular docking was applied to consider the [Ru(bpy){sub 3}]{sup 2+/3+} interaction with ssDNA before and after hybridization. - Highlights: • New DNA biosensor is designed for sub-femtomolar detection of Aeromonas hydrophila DNA sequence. • Reduced graphene oxide decorated Ceria nanoparticles was used as a new immobilization platform. • Biosensor was successfully used to detect A. hydrophila DNA sequence in fish pond water.

  12. Cobalt as chemical modifier to improve chromium sensitivity and minimize matrix effects in tungsten coil atomic emission spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Sidnei G. [Group of Applied Instrumental Analysis, Department of Chemistry, Federal University of São Carlos, P.O. Box 676, São Carlos, SP 13560-970 (Brazil); Donati, George L., E-mail: georgedonati@yahoo.com.br [Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109 (United States); Santos, Luana N. [Group of Applied Instrumental Analysis, Department of Chemistry, Federal University of São Carlos, P.O. Box 676, São Carlos, SP 13560-970 (Brazil); Jones, Bradley T. [Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109 (United States); Nóbrega, Joaquim A. [Group of Applied Instrumental Analysis, Department of Chemistry, Federal University of São Carlos, P.O. Box 676, São Carlos, SP 13560-970 (Brazil)

    2013-05-30

    Graphical abstract: -- Highlights: •Charge transfer reactions increase the population of Cr{sup +}. •Chromium ions and electrons recombine to form excited-state Cr atoms. •A 10-fold improvement in LOD is observed for Cr emission measurements. •The two-step ionization/excitation mechanism improves sensitivity and accuracy. •High concentrations of Co also minimize matrix effects. -- Abstract: Cobalt is used as chemical modifier to improve sensitivity and minimize matrix effects in Cr determinations by tungsten coil atomic emission spectrometry (WCAES). The atomizer is a tungsten filament extracted from microscope light bulbs. A solid-state power supply and a handheld CCD-based spectrometer are also used in the instrumental setup. In the presence of 1000 mg L{sup −1} Co, WCAES limit of detection for Cr (λ = 425.4 nm) is calculated as 0.070 mg L{sup −1}; a 10-fold improvement compared to determinations without Co modifier. The mechanism involved in such signal enhancement is similar to the one observed in ICP OES and ICP-MS determinations of As and Se in the presence of C. Cobalt increases the population of Cr{sup +} by charge transfer reactions. In a second step, Cr{sup +}/e{sup −} recombination takes place, which results in a larger population of excited-state Cr atoms. This alternative excitation route is energetically more efficient than heat transfer from atomizer and gas phase to analyte atoms. A linear dynamic range of 0.25–10 mg L{sup −1} and repeatability of 3.8% (RSD, n = 10) for a 2.0 mg L{sup −1} Cr solution are obtained with this strategy. The modifier high concentration also contributes to improving accuracy due to a matrix-matching effect. The method was applied to a certified reference material of Dogfish Muscle (DORM-2) and no statistically significant difference was observed between determined and certified Cr values at a 95% confidence level. Spike experiments with bottled water samples resulted in recoveries between 93% and

  13. The effect of different annealing temperatures on tin and cadmium telluride phases obtained by a modified chemical route

    Energy Technology Data Exchange (ETDEWEB)

    Mesquita, Anderson Fuzer [Departamento de Química, CCE, Universidade Federal do Espírito Santo, Campus Goiabeiras, 29075-910 Vitória, Espírito Santo (Brazil); Porto, Arilza de Oliveira, E-mail: arilzaporto@yahoo.com.br [Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais (Brazil); Magela de Lima, Geraldo [Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais (Brazil); Paniago, Roberto [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais (Brazil); Ardisson, José Domingos [Centro de Desenvolvimento da Tecnologia Nuclear, CDTN/CNEN, Belo Horizonte, Minas Gerais (Brazil)

    2012-11-15

    Graphical abstract: Display Omitted Highlights: ► Synthesis of cadmium and tin telluride. ► Chemical route to obtain pure crystalline cadmium and tin telluride. ► Effect of the annealing temperature on the crystalline phases. ► Removal of tin oxide as side product through thermal treatment. -- Abstract: In this work tin and cadmium telluride were prepared by a modification of a chemical route reported in the literature to obtain metallacycles formed by oxidative addition of tin-tellurium bonds to platinum (II). Through this procedure it was possible to obtain tin and cadmium telluride. X-ray diffraction and X-ray photoelectron spectroscopy were used to identify the crystalline phases obtained as well as the presence of side products. In the case of tin telluride it was identified potassium chloride, metallic tellurium and tin oxide as contaminants. The tin oxidation states were also monitored by {sup 119}Sn Mössbauer spectroscopy. The annealing in hydrogen atmosphere was chosen as a strategy to reduce the tin oxide and promote its reaction with the excess of tellurium present in the medium. The evolution of this tin oxide phase was studied through the annealing of the sample at different temperatures. Cadmium telluride was obtained with high degree of purity (98.5% relative weight fraction) according to the Rietveld refinement of X-ray diffraction data. The modified procedure showed to be very effective to obtain amorphous tin and cadmium telluride and the annealing at 450 °C has proven to be useful to reduce the amount of oxide produced as side product.

  14. Influence of soft bitumens on the chemical and rheological properties of reclaimed polymer-modified binders from the "old" surface-layer asphalt

    NARCIS (Netherlands)

    Liu, G.; Nielsen, E.; Komacka, J.; Leegwater, G.; Ven, M. van de

    2015-01-01

    Reclaimed asphalt (RA) that contains polymer-modified bitumen (PMB) offers a potential premium material contribution for recycling. This study investigated the influence of soft virgin bitumens on the chemical and rheological properties of three reclaimed PMBs from different "old" surface-layer

  15. Effects of modified atmosphere and vacuum packaging on microbiological and chemical properties of rainbow trout (Oncorynchus mykiss) fillets.

    Science.gov (United States)

    Arashisar, Sükriye; Hisar, Olcay; Kaya, Mükerrem; Yanik, Telat

    2004-12-15

    Microbial (psychrotrophic, mesophilic aerobic bacteria and Enterobacteriacae counts), and chemical analysis [pH, total volatile bases nitrogen (TVB-N), lipid oxidation (Thiobarbituric acid reactive substance, TBARS)] of rainbow trout (Oncorynchus mykiss) fillets in air (control), vacuum and modified atmosphere packaging (MAP) with various gas mixtures conditions at 4+/-1 degrees C were determined. The gas mixtures evaluated were 100% CO2, 2.5% O2+7.5% N2+90% CO2 and 30% O2+30% N2+40% CO2. Psychrotrophic bacteria count was above 1 x 10(7) cfu/g on the 12th day in 100% CO2. However; mesophilic bacteria count was below 1 x 10(6) cfu/g at the end of the 14-day storage period. Enterobacteriaceae count was significantly lower in samples packaged with MAP. Lipid oxidation increased rapidly after 6 days of storage in the samples containing 30% O2. While minimum TBARS values were recorded in fillets containing 100% CO2 and vacuumed fillets, the lowest TVB-N values were obtained in fillets with 100% CO2.

  16. Effect of chemically modified silicas on the properties of hybrid gel electrolyte for Li-ion batteries

    Science.gov (United States)

    Walkowiak, Mariusz; Zalewska, Aldona; Jesionowski, Teofil; Waszak, Daniel; Czajka, Bogdan

    The aim of the presented work was to perform a preliminary study the physico-chemical properties of hybrid organic-inorganic gel electrolytes for Li-ion batteries based on the PVdF-HFP polymeric matrix and surface modified fumed silicas. Modifications were done by means of the so-called dry method using seven different silanes differing in the nature of the principal functional group: N-2-(aminoethyl)-3-amino propyltrimethoxysilane, 3-glycidoxypropyltrimetoxysilane, 3-mercaptopropyltrimetoxysilane, n-octyltriethoxysilane, 3-(chloropropyl)trimethoxysilane, 3-methacryloxypropyltrimetoxysilane, vinyltrimethoxysilane. The PVdF-HFP gels were prepared according to the so-called Bellcore process (two-step method). Impact of the silicas surface functionality on the degree of crystallinity of the polymeric membranes was studied using the differential scanning calorimetry technique. Applicability of the prepared gel electrolytes for the Li-ion technology was estimated on the basis of specific conductivity measurements. It was shown that modification of the silica surface by most of the silanes causes an increase in the gel specific conductivity by about two orders of magnitude as compared to gel with unmodified silica.

  17. Effect of chemically modified silicas on the properties of hybrid gel electrolyte for Li-ion batteries

    Energy Technology Data Exchange (ETDEWEB)

    Walkowiak, Mariusz; Waszak, Daniel; Czajka, Bogdan [Central Laboratory of Batteries and Cells, ul. Forteczna 12, 61-362 Poznan (Poland); Zalewska, Aldona [Warsaw University of Technology, Department of Chemistry, ul. Noakowskiego 3, 00-664 Warsaw (Poland); Jesionowski, Teofil [Poznan University of Technology, Institute of Chemical Technology and Engineering, Pl. Marii Sklodowskiej-Curie 2, 60-965 Poznan (Poland)

    2006-09-13

    The aim of the presented work was to perform a preliminary study the physico-chemical properties of hybrid organic-inorganic gel electrolytes for Li-ion batteries based on the PVdF-HFP polymeric matrix and surface modified fumed silicas. Modifications were done by means of the so-called dry method using seven different silanes differing in the nature of the principal functional group: N-2-(aminoethyl)-3-amino propyltrimethoxysilane, 3-glycidoxypropyltrimetoxysilane, 3-mercaptopropyltrimetoxysilane, n-octyltriethoxysilane, 3-(chloropropyl)trimethoxysilane, 3-methacryloxypropyltrimetoxysilane, vinyltrimethoxysilane. The PVdF-HFP gels were prepared according to the so-called Bellcore process (two-step method). Impact of the silicas surface functionality on the degree of crystallinity of the polymeric membranes was studied using the differential scanning calorimetry technique. Applicability of the prepared gel electrolytes for the Li-ion technology was estimated on the basis of specific conductivity measurements. It was shown that modification of the silica surface by most of the silanes causes an increase in the gel specific conductivity by about two orders of magnitude as compared to gel with unmodified silica. (author)

  18. Comparison of adsorption of Cd(II and Pb(II ions on pure and chemically modified fly ashes

    Directory of Open Access Journals (Sweden)

    Sočo Eleonora

    2016-06-01

    Full Text Available The study investigates chemical modifications of coal fly ash (FA treated with HCl or NH4HCO3 or NaOH or Na2edta, based on the research conducted to examine the behaviour of Cd(II and Pb(II ions adsorbed from water solution on treated fly ash. In laboratory tests, the equilibrium and kinetics were examined applying various temperatures (293 - 333 K and pH (2 - 11 values. The maximum Cd(II and Pb(II ions adsorption capacity obtained at 293 K, pH 9 and mixing time 2 h from the Langmuir model can be grouped in the following order: FA-NaOH > FA-NH4HCO3 > FA > FA-Na2edta > FA-HCl. The morphology of fly ash grains was examined via small-angle X-ray scattering (SAXS and images of scanning electron microscope (SEM. The adsorption kinetics data were well fitted by a pseudo-second-order rate model but showed a very poor fit for the pseudofirst order model. The intra-particle model also revealed that there are two separate stages in the sorption process, i.e. the external diffusion and the inter-particle diffusion. Thermodynamics parameters such as free energy, enthalpy and entropy were also determined. A laboratory test demonstrated that the modified coal fly ash worked well for the Cd(II and Pb(II ion uptake from polluted waters.

  19. Optical properties of carbon nanostructures produced by laser irradiation on chemically modified multi-walled carbon nanotubes

    Science.gov (United States)

    Santiago, Enrique Vigueras; López, Susana Hernández; Camacho López, Marco A.; Contreras, Delfino Reyes; Farías-Mancilla, Rurik; Flores-Gallardo, Sergio G.; Hernández-Escobar, Claudia A.; Zaragoza-Contreras, E. Armando

    2016-10-01

    This research focused on the nanosecond (Nd: YAG-1064 nm) laser pulse effect on the optical and morphological properties of chemically modified multi-walled carbon nanotubes (MWCNT). Two suspensions of MWCNT in tetrahydrofuran (THF) were prepared, one was submitted to laser pulses for 10 min while the other (blank) was only mechanically homogenized during the same time. Following the laser irradiation, the suspension acquired a yellow-amber color, in contrast to the black translucent appearance of the blank. UV-vis spectroscopy confirmed this observation, showing the blank a higher absorption. Additionally, photoluminescence measurements exhibited a broad blue-green emission band both in the blank and irradiated suspension when excited at 369 nm, showing the blank a lower intensity. However, a modification in the excitation wavelength produced a violet to green tuning in the irradiated suspension, which did not occur in the blank. Lastly, the electron microscopy analysis of the treated nanotubes showed the abundant formation of amorphous carbon, nanocages, and nanotube unzipping, exhibiting the intense surface modification produced by the laser pulse. Nanotube surface modification and the coexistence with the new carbon nanostructures were considered as the conductive conditions for optical properties modification.

  20. COL-3, a chemically modified tetracycline, inhibits lipopolysaccharide-induced microglia activation and cytokine expression in the brain.

    Directory of Open Access Journals (Sweden)

    Rawan Abdulhameed Edan

    Full Text Available Microglia activation results in release of proinflammatory molecules including cytokines, which contribute to neuronal damage in the central nervous system (CNS if not controlled. Tetracycline antibiotics such as minocycline inhibit microglial activation and cytokine expression during CNS inflammation. In the present study we found that administration of chemically modified tetracycline-3 (COL-3, inhibits lipopolysaccharide (LPS-induced microglial and p38 MAPK activation, as well as the increase in TNF-α, but not IL-1β expression, in the brains of BALB/c mice. COL-3 has been described to have no antibacterial activity. We observed that COL-3 had no activity against a Gram-negative bacteria, Escherichia coli; however surprisingly, COL-3 had antibacterial activity against a Gram-positive bacteria Staphylococcus aureus, with a minimum inhibitory concentration of 1 mg/ml. Our data show that COL-3 has some antibacterial activity against S. aureus, inhibits LPS-induced neuroinflammation, and displays potential as a therapeutic agent for treatment of conditions involving CNS inflammation.

  1. COL-3, a chemically modified tetracycline, inhibits lipopolysaccharide-induced microglia activation and cytokine expression in the brain.

    Science.gov (United States)

    Edan, Rawan Abdulhameed; Luqmani, Yunus A; Masocha, Willias

    2013-01-01

    Microglia activation results in release of proinflammatory molecules including cytokines, which contribute to neuronal damage in the central nervous system (CNS) if not controlled. Tetracycline antibiotics such as minocycline inhibit microglial activation and cytokine expression during CNS inflammation. In the present study we found that administration of chemically modified tetracycline-3 (COL-3), inhibits lipopolysaccharide (LPS)-induced microglial and p38 MAPK activation, as well as the increase in TNF-α, but not IL-1β expression, in the brains of BALB/c mice. COL-3 has been described to have no antibacterial activity. We observed that COL-3 had no activity against a Gram-negative bacteria, Escherichia coli; however surprisingly, COL-3 had antibacterial activity against a Gram-positive bacteria Staphylococcus aureus, with a minimum inhibitory concentration of 1 mg/ml. Our data show that COL-3 has some antibacterial activity against S. aureus, inhibits LPS-induced neuroinflammation, and displays potential as a therapeutic agent for treatment of conditions involving CNS inflammation.

  2. Tetracyclines and chemically modified tetracycline-3 (CMT-3) modulate cytokine secretion by lipopolysaccharide-stimulated whole blood.

    Science.gov (United States)

    Cazalis, Julia; Tanabe, Shin-ichi; Gagnon, Guy; Sorsa, Timo; Grenier, Daniel

    2009-04-01

    In addition to their bacteriostatic effect, tetracyclines, which are often used in the treatment of periodontitis, also present anti-inflammatory properties. In the present study, we investigated the effects of tetracycline (TC), doxycycline (doxy), and chemically modified tetracycline-3 (CMT-3) on the production of pro-inflammatory mediators and matrix metalloproteinases (MMPs) in an ex vivo human whole blood (WB) model stimulated with Porphyromonas gingivalis lipopolysaccharide (LPS). WB samples obtained from three periodontitis patients and six healthy subjects were stimulated with P. gingivalis LPS in the absence and presence of TC, doxy, or CMT-3. The secretion of interleukin-1beta (IL-1beta), interleukin-6 (IL-6), interleukin-8 (IL-8), MMP-8, and MMP-9 by the WB samples was determined using enzyme-linked immunosorbent assays. P. gingivalis LPS significantly increased the secretion of all cytokines and MMPs tested. While we observed inter-patient variations, TC, doxy, and CMT-3 caused reductions of LPS-induced cytokine secretion to various degrees. TC, doxy, and CMT-3 had no significant effect on MMP-8 and MMP-9 secretion by LPS-stimulated WB samples. In conclusion, we used a human WB model that takes into consideration relevant in vivo immune cell interactions in the presence of plasma proteins to show that TC, doxy, and CMT-3 can reduce the production of pro-inflammatory mediators. This property may contribute to the clinically proven benefits of these molecules in the treatment of periodontitis and other chronic inflammatory diseases.

  3. Compositionally and structurally modified SrTiO{sub 3} thin films prepared by chemical solution deposition

    Energy Technology Data Exchange (ETDEWEB)

    Spitzner, Dirk; Gutmann, Emanuel; Reibold, Marianne; Meyer, Dirk C. [Institut fuer Strukturphysik, Technische Universitaet Dresden (Germany); Mahltig, Boris [GMBU e.V., Arbeitsgruppe Funktionelle Schichten, Dresden (Germany)

    2009-07-01

    For electronic and architectural design of functional electroceramic devices, materials with a perovskite-type of structure play a major role. For high-k dielectric, sensing and thermal switching applications the introduction of Barium into SrTiO{sub 3}(STO) allows tuning the electrical properties by tuning the paraelectric-to-ferroelectric transition temperature. For thin film preparation a classic sol-gel route was modified by refluxing as well as solvothermal treatment of the as-synthesized sols. For treated sols the decomposition, phase evolution and transition behaviour differed and from X-ray diffraction (XRD) we observed a supression of foreign phases and a higher degree of compositional homogeneity. In this context also the homologous series of perovskite-related Ruddlesden-Popper (RP) phases promise an engineering of electrical properties by selecting a specific member. Exemplarily we realised the chemical solution deposition of epitaxial thin films of SrO(SrTiO{sub 3}){sub n} RP phases (n=1,2,3) on STO substrates. Structural characteristics of the films were analysed by means of XRD and HRTEM. An application as buffer layers exhibiting tuneable dielectric properties is conceivable.

  4. Glassy carbon electrode modified with a graphene oxide/poly(o-phenylenediamine) composite for the chemical detection of hydrogen peroxide

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Van Hoa [School of Chemical Engineering, Yeungnam University, Gyeongsan, Gyeongbuk 712-749 (Korea, Republic of); Department of Chemistry, Nha Trang University, 2 Nguyen Dinh Chieu, Nha Trang (Viet Nam); Tran, Trung Hieu [School of Chemical Engineering, Yeungnam University, Gyeongsan, Gyeongbuk 712-749 (Korea, Republic of); Shim, Jae-Jin, E-mail: jjshim@yu.ac.kr [School of Chemical Engineering, Yeungnam University, Gyeongsan, Gyeongbuk 712-749 (Korea, Republic of)

    2014-11-01

    Conducting poly(o-phenylenediamine) (POPD)/graphene oxide (GO) composites were prepared using a facile and efficient method involving the in-situ polymerization of OPD in the presence of GO in an aqueous medium. Copper sulfate was used as an oxidative initiator for the polymerization of OPD. Scanning electron microscopy and transmission electron microscopy images showed that POPD microfibrils were formed and distributed relatively uniformly with GO sheets in the obtained composites. X-ray diffraction results revealed the highly crystal structure of POPD. This composite exhibited good catalytic activity and stability. These results highlight the potential applications of POPD/GO composites as excellent electrochemical sensors. The composites were used to modify glass carbon electrodes for the chemical detection of hydrogen peroxide in aqueous media. - Highlights: • Graphene oxide/poly(o-phenylenediamine) composites were prepared efficiently. • POPD microfibrils were distributed relatively uniformly with GO sheets. • The composite exhibited good catalytic activity and stability for H{sub 2}O{sub 2} sensing.

  5. Improved properties of chemically modified graphene/poly(methyl methacrylate nanocomposites via a facile in-situ bulk polymerization

    Directory of Open Access Journals (Sweden)

    X. Y. Yuan

    2012-10-01

    Full Text Available The nanosheet of graphene was chemically modified by long alkyl chain for enhanced compatibility with polymer matrix and graphene/poly(methyl methacrylate (PMMA nanocomposites with homogeneous dispersion of the nanosheets and enhanced nanofiller-matrix interfacial interaction were fabricated via a facile in-situ bulk polymerization. The nanocomposites were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, Scanning electron microscopy and thermogravimetry. The results showed that the graphene nanosheets were fully exfoliated in PMMA matrix and the thermal and mechanical properties of the nanocomposites were significantly improved at low graphene loadings. Large shifts of 15°C in the glass transition temperature and 27°C improvement of onset thermal degradation temperature were achieved with graphene loading as low as 0.07 wt%. A 67% increase in tensile strength was also observed by the addition of only 0.5 wt% graphene. The method used in this study provided a novel route to other graphene-based polymers.

  6. Eletrodos quimicamente modificados aplicados à eletroanálise: uma breve abordagem Chemically modified electrodes applyes to electroanalysis: a brief presentation

    Directory of Open Access Journals (Sweden)

    Maria de Fátima Brito Souza

    1997-04-01

    Full Text Available Chemically modified electrodes (CMEs have been subject of considerable attention since its inception about 23 years ago. CMEs result of a deliberate immobilization of a modifier agent onto the electrode surface obtained through chemical reactions, chemisorption, composite formation or polymer coating. This immobilization seeks transfer the physicochemical properties of the modifier to the electrode surface and thus to dictate and control the behavior of the electrode/solution interface. In recent years the interest in CMEs has increased particularly to enhance the sensitivity and/or the selectivity of electroanalytical techniques. In general higher sensitivity and/or selectivity may be achieved by exploiting one or more of the following phenomena: electrocatalysis, preconcentration and interferents exclusion. This paper deals with the application of CMEs in electroanalysis, including a brief presentation of the more general procedures that have been employed for the modification of electrode surfaces.

  7. Design and development of thermolytic DNA oligonucleotide prodrugs.

    Science.gov (United States)

    Grajkowski, Andrzej; Pedras-Vasconcelos, Joao; Ausín, Cristina; Verthelyi, Daniela; Beaucage, Serge L

    2005-11-01

    Deoxyribonucleoside phosphoramidites functionalized with the thermolytic 2-(N-formyl-N-methyl)aminoethyl group for phosphorus protection (1a-d) have been prepared and employed in the solid-phase synthesis of CpG ODN fma1555. Given that this modified oligonucleotide can be converted to the immunomodulatory CpG ODN 1555 under neutral conditions at 37 degrees C, its biologic activity was demonstrated in vivo by studies showing that intraperitoneal administration of CpG ODN fma1555 in mice resulted in the activation of cytokine-secreting splenocytes. Furthermore, administration of CpG ODN fma1555 to mice that were challenged intradermally in the ear with live L. major metacyclic promastigotes, reduced the severity of Leishmania skin lesions over time to an extent similar to that obtained with CpG ODN 1555. In another infectious model experiment, CpG ODN fma1555 protected newborn mice from death (65% survival) when administered 3 days before infection with the aggressive Tacaribe (TCRV) virus. A comparable immunoprotection was obtained by treatment of TCRV-infected mice with CpG ODN 1555 administered on the same day of infection (45% survival). However, when TCRV-infected mice were treated with CpG ODN fma1555 on the day of infection, they died as a consequence of the relatively slow conversion of the oligonucleotide prodrug to the bioactive CpG ODN 1555. Co-administration of both CpG ODN 1555 and CpG ODN fma1555 to mice 3 days prior to TCRV infection or on the day of infection provided protection from death (45-65% survival) and thus widened the immunoprotection window against TCRV-infection.

  8. Template-Directed Ligation of Peptides to Oligonucleotides

    Science.gov (United States)

    Bruick, Richard K.; Dawson, Philip E.; Kent, Stephen BH; Usman, Nassim; Joyce, Gerald F.

    1996-01-01

    Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

  9. Sequence-specific targeting of RNA with an oligonucleotide-neomycin conjugate.

    Science.gov (United States)

    Charles, Irudayasamy; Xi, Hongjuan; Arya, Dev P

    2007-01-01

    The synthesis of neomycin covalently attached at the C5-position of 2'-deoxyuridine is reported. The synthesis outlined allows for incorporation of an aminoglycoside (neomycin) at any given site in an oligonucleotide (ODN) where a thymidine (or uridine) is present. Incorporation of this modified base into an oligonucleotide, which is complementary to a seven-bases-long alpha-sarcin loop RNA sequence, leads to enhanced duplex hybridization. The increase in Tm for this duplex (DeltaTm = 6 degrees C) suggests a favorable interaction of neomycin within the duplex groove. CD spectroscopy shows that the modified duplex adopts an A-type confirmation. ITC measurements indicate the additive effects of ODN and neomycin binding to the RNA target (Ka = 4.5 x 107 M-1). The enhanced stability of the hybrid duplex from this neomycin-ODN conjugate originates primarily from the enthalpic contribution of neomycin {DeltaDeltaHobs = -7.21 kcal/mol (DeltaHneomycin conjugated - DeltaH nonconjugated)} binding to the hybrid duplex. The short linker length allows for selective stabilization of the hybrid duplex over the hybrid triplex. The results described here open up new avenues in the design and synthesis of nucleo-aminoglycoside-conjugates (N-Ag-C) where the inclusion of any number of aminoglycoside (neomycin) molecules per oligonucleotide can be accomplished.

  10. Guanine-tethered antisense oligonucleotides as synthetic riboregulators.

    Science.gov (United States)

    Hagihara, Masaki

    2014-01-01

    Regulation of gene expression by short oligonucleotides (antisense oligonucleotides), which can modulate RNA structures and inhibit subsequent associations with the translation machinery, is a potential approach for gene therapy. This chapter describes an alternative antisense strategy using guanine-tethered antisense oligonucleotides (G-ASs) to introduce a DNA-RNA heteroquadruplex structure at a designated sequence on RNA targets. The feasibility of using G-ASs to modulate RNA conformation may allow control of RNA function by inducing biologically important quadruplex structures. This approach to manipulate quadruplex structures using G-ASs may expand the strategies for regulating RNA structures and the functions of short oligonucleotide riboregulators.

  11. A novel setup for the determination of absolute cross sections for low-energy electron induced strand breaks in oligonucleotides - The effect of the radiosensitizer 5-fluorouracil*

    Science.gov (United States)

    Rackwitz, Jenny; Ranković, Miloš Lj.; Milosavljević, Aleksandar R.; Bald, Ilko

    2017-02-01

    Low-energy electrons (LEEs) play an important role in DNA radiation damage. Here we present a method to quantify LEE induced strand breakage in well-defined oligonucleotide single strands in terms of absolute cross sections. An LEE irradiation setup covering electron energies Measurements are presented for 10.0 and 5.5 eV for different oligonucleotide targets. The determination of absolute strand break cross sections is performed by atomic force microscopy analysis. An accurate fluence determination ensures small margins of error of the determined absolute single strand break cross sections σ SSB . In this way, the influence of sequence modification with the radiosensitive 5-Fluorouracil (5FU) is studied using an absolute and relative data analysis. We demonstrate an increase in the strand break yields of 5FU containing oligonucleotides by a factor of 1.5 to 1.6 compared with non-modified oligonucleotide sequences when irradiated with 10 eV electrons.

  12. Antisense Oligonucleotides Internally Labeled with Peptides Show Improved Target Recognition and Stability to Enzymatic Degradation.

    Science.gov (United States)

    Taskova, Maria; Madsen, Charlotte S; Jensen, Knud J; Hansen, Lykke Haastrup; Vester, Birte; Astakhova, Kira

    2017-03-15

    Specific target binding and stability in diverse biological media is of crucial importance for applications of synthetic oligonucleotides as diagnostic and therapeutic tools. So far, these issues have been addressed by chemical modification of oligonucleotides and by conjugation with a peptide, most often at the terminal position of the oligonucleotide. Herein, we for the first time systematically investigate the influence of internally attached short peptides on the properties of antisense oligonucleotides. We report the synthesis and internal double labeling of 21-mer oligonucleotides that target the BRAF V600E oncogene, with a library of rationally designed peptides employing CuAAC "click" chemistry. The peptide sequence has an influence on the specificity and affinity of target DNA/RNA binding. We also investigated the impact of locked nucleic acids (LNAs) on the latter. Lysine residues improve binding of POCs to target DNA and RNA, whereas the distance to lysine correlates exclusively with a decrease in binding of mismatched RNA targets. Glycine and tyrosine residues affect target binding as well. Importantly, the resistance of POCs to enzymatic degradation is dramatically improved by the internal attachment of peptides but not by LNA alone. Independently of the peptide sequence, the conjugates are stable for up to 24 h in 90% human serum and duplexes of POCs with complementary DNA for up to 160 h in 90% human serum. Such excellent stability has not been previously reported for DNA and makes internally labeled POCs an exciting object of study, i.e., showing high target specificity and simultaneous stability in biological media.

  13. Efficient Synthesis and Biological Evaluation of 5'-GalNAc Conjugated Antisense Oligonucleotides.

    Science.gov (United States)

    Østergaard, Michael E; Yu, Jinghua; Kinberger, Garth A; Wan, W Brad; Migawa, Michael T; Vasquez, Guillermo; Schmidt, Karsten; Gaus, Hans J; Murray, Heather M; Low, Audrey; Swayze, Eric E; Prakash, Thazha P; Seth, Punit P

    2015-08-19

    Conjugation of triantennary N-acetyl galactosamine (GalNAc) to oligonucleotide therapeutics results in marked improvement in potency for reducing gene targets expressed in hepatocytes. In this report we describe a robust and efficient solution-phase conjugation strategy to attach triantennary GalNAc clusters (mol. wt. ∼2000) activated as PFP (pentafluorophenyl) esters onto 5'-hexylamino modified antisense oligonucleotides (5'-HA ASOs, mol. wt. ∼8000 Da). The conjugation reaction is efficient and was used to prepare GalNAc conjugated ASOs from milligram to multigram scale. The solution phase method avoids loading of GalNAc clusters onto solid-support for automated synthesis and will facilitate evaluation of GalNAc clusters for structure activity relationship (SAR) studies. Furthermore, we show that transfer of the GalNAc cluster from the 3'-end of an ASO to the 5'-end results in improved potency in cells and animals.

  14. Ultramild protein-mediated click chemistry creates efficient oligonucleotide probes for targeting and detecting nucleic acids

    DEFF Research Database (Denmark)

    Nåbo, Lina J.; Madsen, Charlotte Stahl; Jensen, Knud Jørgen

    2015-01-01

    results by electronic structure calculations. Functionalized oligonucleotides were prepared in good yields by protein-mediated CuAAC click reactions for the first time with a human copper-binding chaperon. The carbohydrate, peptide, and fluorescent derivatives display high binding affinity and selectivity...... targeting and detection properties. We focus in particular on the pH sensitivity of these new probes and their high target specificity. For the first time, human copper(I)-binding chaperon Cox17 was applied to effectively catalyze click labeling of oligonucleotides. This was performed under ultramild...... conditions with fluorophore, peptide, and carbohydrate azide derivatives. In thermal denaturation studies, the modified probes showed specific binding to complementary DNA and RNA targets. Finally, we demonstrated the pH sensitivity of the new rhodamine-based fluorescent probes in vitro and rationalize our...

  15. Synthesis of the Tellurium-Derivatized Phosphoramidites and their Incorporation into DNA Oligonucleotides

    Science.gov (United States)

    Jiang, Sibo; Sheng, Jia

    2015-01-01

    Introduction In this unit, an efficient method for the synthesis of 2’-tellerium modified phosphoramidite and its incorporation into oligonucleotide are presented. We choose 5’-O-DMTr-2,2’-anhydro-uridine and -thymidine nucleosides (S.1, S.2) as starting materials due to their easy preparation. The 5’-O-DMTr-2,2’-anhydro-uridine and -thymidine can be converted to corresponding the 2’-tellerium-derivatized nucleosides by treating with the telluride nucleophiles. Subsequently, the 2’-Te-nucleosides can be transformed into 3’-phosphoramidites, which are the building blocks for DNA/RNA synthesis. The DNA synthesis, purification and applications of oligonucleotides containing 2’-Te-U or 2’-Te-T are described in this protocol. PMID:22147418

  16. A Standardized Chemically Modified Curcuma longa Extract Modulates IRAK-MAPK Signaling in Inflammation and Potentiates Cytotoxicity

    Directory of Open Access Journals (Sweden)

    Minakshi Rana

    2016-07-01

    Full Text Available The TLR/IL-1R pathway is a critical signaling module that is misregulated in pathologies like inflammation and cancer. Extracts from turmeric (Curcuma longa L. enriched in curcumin and carbonyls like turmerones have been shown to exert potent anti-inflammatory effects. The present study evaluated the anti-inflammatory activity, cytotoxic effect and the underlying mechanism of a novel chemically modified, non-carbonyl compound enriched Curcuma longa L. (C. longa extract (CMCE. CMCE (1 or 10 µg/mL; 14 h significantly decreased LPS (50-100 ng/mL induced TNF-α and IL-1β production in THP-1 cells, human, and mouse whole blood as measured by ELISA. LPS-induced IRAK1, MAPK activation, TLR4 expression, TLR4-MyD88 interaction and IκBα degradation were significantly reduced in CMCE pre-treated THP-1 cells as assessed by Western blotting. CMCE (30, 100 and 300 mg/kg; 10 days p.o. pre-treated and LPS (10 mg/kg challenged Swiss mice exhibited attenuated plasma TNF-α, IL-1β, nitrite, aortic iNOS expression and vascular dysfunction. In a PI permeability assay, cell lines derived from acute myeloid leukemia were most sensitive to the cytotoxic effects of CMCE. Analysis of Sub-G1 phase, Annexin V-PI positivity, loss of mitochondrial membrane potential, increased caspase-3 and PARP-1 activation confirmed CMCE induced apoptosis in HL-60 cells. IRAK inhibition also sensitized HL-60 cells to CMCE induced cytotoxicity. The present study defines the mechanism underlying the action of CMCE and suggests a therapeutic potential for its use in sepsis and leukemia.

  17. A Standardized Chemically Modified Curcuma longa Extract Modulates IRAK-MAPK Signaling in Inflammation and Potentiates Cytotoxicity.

    Science.gov (United States)

    Rana, Minakshi; Maurya, Preeti; Reddy, Sukka S; Singh, Vishal; Ahmad, Hafsa; Dwivedi, Anil K; Dikshit, Madhu; Barthwal, Manoj K

    2016-01-01

    The TLR/IL-1R pathway is a critical signaling module that is misregulated in pathologies like inflammation and cancer. Extracts from turmeric (Curcuma longa L.) enriched in curcumin and carbonyls like turmerones have been shown to exert potent anti-inflammatory effects. The present study evaluated the anti-inflammatory activity, cytotoxic effect and the underlying mechanism of a novel chemically modified, non-carbonyl compound enriched Curcuma longa L. (C. longa) extract (CMCE). CMCE (1 or 10 μg/mL; 14 h) significantly decreased LPS (50-100 ng/mL) induced TNF-α and IL-1β production in THP-1 cells, human, and mouse whole blood as measured by ELISA. LPS-induced IRAK1, MAPK activation, TLR4 expression, TLR4-MyD88 interaction, and IκBα degradation were significantly reduced in CMCE pre-treated THP-1 cells as assessed by Western blotting. CMCE (30, 100, and 300 mg/kg; 10 days p.o.) pre-treated and LPS (10 mg/kg) challenged Swiss mice exhibited attenuated plasma TNF-α, IL-1β, nitrite, aortic iNOS expression, and vascular dysfunction. In a PI permeability assay, cell lines derived from acute myeloid leukemia were most sensitive to the cytotoxic effects of CMCE. Analysis of Sub-G1 phase, Annexin V-PI positivity, loss of mitochondrial membrane potential, increased caspase-3, and PARP-1 activation confirmed CMCE induced apoptosis in HL-60 cells. IRAK inhibition also sensitized HL-60 cells to CMCE induced cytotoxicity. The present study defines the mechanism underlying the action of CMCE and suggests a therapeutic potential for its use in sepsis and leukemia.

  18. Investigation of chemical modifiers for sulfur determination in diesel fuel samples by high-resolution continuum source graphite furnace molecular absorption spectrometry using direct analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huber, Charles S. [Instituto Federal Sul-rio-grandense, Câmpus Pelotas, Pelotas, RS (Brazil); Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Vale, Maria Goreti R. [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Welz, Bernhard [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Universidade Federal de Santa Catarina, Departamento de Química, Florianópolis, SC (Brazil); Andrade, Jailson B. [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Dessuy, Morgana B., E-mail: mbdessuy@ufrgs.br [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil)

    2015-06-01

    High-resolution continuum source graphite furnace molecular absorption spectrometry has been applied for sulfur determination in diesel fuel. The sharp rotational lines of the carbon monosulfide molecule (formed during the vaporization step) were used to measure the absorbance. The analytical line at 258.056 nm was monitored using the sum of three pixels. Different chemical modifiers were investigated and the mixture of palladium and magnesium was used as chemical modifier in combination with iridium as permanent modifier. L-Cysteine was chosen as sulfur standard and the calibration was done against aqueous standard solutions. The proposed method was applied for the analyses of four diesel samples: two S10 samples and two S500 samples. The trueness of the method was checked with a certified reference material (CRM) of sulfur in diesel fuel (NIST 2724b). Accurate results, for samples and CRM, were achieved after a dilution with propan-1-ol. The following figures of merit were obtained: characteristic mass of 17 ± 3 ng, limit of detection and limit of quantification of 1.4 mg kg{sup −1} and 4.7 mg kg{sup −1}, respectively. - Highlights: • Ir, Ru and Zr were investigated as permanent modifiers. • Ca, Mg, Pd and Pd/Mg were investigated as modifiers in solution. • Indirect determination of sulfur monitoring the molecular absorbance of the CS • Direct analysis of diesel samples using a dilution in propan-1-ol.

  19. Lipid Oligonucleotide Conjugates as Responsive Material

    Science.gov (United States)

    2012-09-28

    U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS Amphiphiles, oligonucleotides, lipids...peer-reviewed journals: (c) Presentations 1. Philippe Barthélémy, « Hybrid Lipids for Biomedical Applications », Targeting and Triggering Basic Research ...Steadel C. ; Pierre, N. ; Barthélémy, P. : Oligonucléotides amphiphile : Journée Scientifique de l’IFR 66, Talence, le 2 décembre 2008, France 29. Taib

  20. Activation of the ERK1/2 Signaling Pathway during the Osteogenic Differentiation of Mesenchymal Stem Cells Cultured on Substrates Modified with Various Chemical Groups

    Directory of Open Access Journals (Sweden)

    Bing Bai

    2013-01-01

    Full Text Available The current study examined the influence of culture substrates modified with the functional groups –OH, –COOH, –NH2, and –CH3 using SAMs technology, in conjunction with TAAB control, on the osteogenic differentiation of rabbit BMSCs. The CCK-8 assay revealed that BMSCs exhibited substrate-dependent cell viability. The cells plated on –NH2- and –OH-modified substrates were well spread and homogeneous, but those on the –COOH- and –CH3-modified substrates showed more rounded phenotype. The mRNA expression of BMSCs revealed that –NH2-modified substrate promoted the mRNA expression and osteogenic differentiation of the BMSCs. The contribution of ERK1/2 signaling pathway to the osteogenic differentiation of BMSCs cultured on the –NH2-modified substrate was investigated in vitro. The –NH2-modified substrate promoted the expression of integrins; the activation of FAK and ERK1/2. Inhibition of ERK1/2 activation by PD98059, a specific inhibitor of the ERK signaling pathway, blocked ERK1/2 activation in a dose-dependent manner, as revealed for expression of Cbfα-1 and ALP. Blockade of ERK1/2 phosphorylation in BMSCs by PD98059 suppressed osteogenic differentiation on chemical surfaces. These findings indicate a potential role for ERK in the osteogenic differentiation of BMSCs on surfaces modified by specific chemical functional groups, indicating that the microenvironment affects the differentiation of BMSCs. This observation has important implications for bone tissue engineering.

  1. Self-Assembly into Nanoparticles Is Essential for Receptor Mediated Uptake of Therapeutic Antisense Oligonucleotides.

    Science.gov (United States)

    Ezzat, Kariem; Aoki, Yoshitsugu; Koo, Taeyoung; McClorey, Graham; Benner, Leif; Coenen-Stass, Anna; O'Donovan, Liz; Lehto, Taavi; Garcia-Guerra, Antonio; Nordin, Joel; Saleh, Amer F; Behlke, Mark; Morris, John; Goyenvalle, Aurelie; Dugovic, Branislav; Leumann, Christian; Gordon, Siamon; Gait, Michael J; El-Andaloussi, Samir; Wood, Matthew J A

    2015-07-08

    Antisense oligonucleotides (ASOs) have the potential to revolutionize medicine due to their ability to manipulate gene function for therapeutic purposes. ASOs are chemically modified and/or incorporated within nanoparticles to enhance their stability and cellular uptake, however, a major challenge is the poor understanding of their uptake mechanisms, which would facilitate improved ASO designs with enhanced activity and reduced toxicity. Here, we study the uptake mechanism of three therapeutically relevant ASOs (peptide-conjugated phosphorodiamidate morpholino (PPMO), 2'Omethyl phosphorothioate (2'OMe), and phosphorothioated tricyclo DNA (tcDNA) that have been optimized to induce exon skipping in models of Duchenne muscular dystrophy (DMD). We show that PPMO and tcDNA have high propensity to spontaneously self-assemble into nanoparticles. PPMO forms micelles of defined size and their net charge (zeta potential) is dependent on the medium and concentration. In biomimetic conditions and at low concentrations, PPMO obtains net negative charge and its uptake is mediated by class A scavenger receptor subtypes (SCARAs) as shown by competitive inhibition and RNAi silencing experiments in vitro. In vivo, the activity of PPMO was significantly decreased in SCARA1 knockout mice compared to wild-type animals. Additionally, we show that SCARA1 is involved in the uptake of tcDNA and 2'OMe as shown by competitive inhibition and colocalization experiments. Surface plasmon resonance binding analysis to SCARA1 demonstrated that PPMO and tcDNA have higher binding profiles to the receptor compared to 2'OMe. These results demonstrate receptor-mediated uptake for a range of therapeutic ASO chemistries, a mechanism that is dependent on their self-assembly into nanoparticles.

  2. Antisense Oligonucleotide Therapy in Diabetic Retinopathy

    Science.gov (United States)

    Hnik, Peter; Boyer, David S.; Grillone, Lisa R.; Clement, John G.; Henry, Scott P.; Green, Ellen A.

    2009-01-01

    Diabetic retinopathy is one of the leading causes of blindness in the United States and other parts of the world. Historically, laser photocoagulation and vitrectomy surgery have been used for the treatment of diabetic retinopathy, including diabetic macular edema. Both procedures have proven to be useful under certain conditions but have their limitations. New pathways and processes that promote diabetic retinopathy have been identified, and several new therapeutic approaches are under investigation. These new therapies may be beneficial in the treatment of diabetic retinopathy and include antivascular endothelial growth factor agents, corticosteroids, and therapies that may potentially target a number of additional diabetic retinopathy-related factors and processes, including antisense oligonucleotides. Second-generation antisense oligonucleotides, such as iCo-007, may offer a significant advantage in the treatment of diabetic retinopathy by downregulating the signal pathways of multiple growth factors that seem to play a critical role in the process of ocular angiogenesis and vascular leakage. Benefits of such molecules are expected to include the specificity of the kinase target and an extended half-life, resulting in less frequent intravitreal drug administration, resistance to molecule degradation, and a good safety profile. PMID:20144342

  3. Template switching between PNA and RNA oligonucleotides

    Science.gov (United States)

    Bohler, C.; Nielsen, P. E.; Orgel, L. E.; Miller, S. L. (Principal Investigator)

    1995-01-01

    The origin of the RNA world is not easily understood, as effective prebiotic syntheses of the components of RNA, the beta-ribofuranoside-5'-phosphates, are hard to envisage. Recognition of this difficulty has led to the proposal that other genetic systems, the components of which are more easily formed, may have preceded RNA. This raises the question of how transitions between one genetic system and another could occur. Peptide nucleic acid (PNA) resembles RNA in its ability to form double-helical complexes stabilized by Watson-Crick hydrogen bonding between adenine and thymine and between cytosine and guanine, but has a backbone that is held together by amide rather than by phosphodiester bonds. Oligonucleotides bases on RNA are known to act as templates that catalyse the non-enzymatic synthesis of their complements from activated mononucleotides, we now show that RNA oligonucleotides facilitate the synthesis of complementary PNA strands and vice versa. This suggests that a transition between different genetic systems can occur without loss of information.

  4. An imputation approach for oligonucleotide microarrays.

    Directory of Open Access Journals (Sweden)

    Ming Li

    Full Text Available Oligonucleotide microarrays are commonly adopted for detecting and qualifying the abundance of molecules in biological samples. Analysis of microarray data starts with recording and interpreting hybridization signals from CEL images. However, many CEL images may be blemished by noises from various sources, observed as "bright spots", "dark clouds", and "shadowy circles", etc. It is crucial that these image defects are correctly identified and properly processed. Existing approaches mainly focus on detecting defect areas and removing affected intensities. In this article, we propose to use a mixed effect model for imputing the affected intensities. The proposed imputation procedure is a single-array-based approach which does not require any biological replicate or between-array normalization. We further examine its performance by using Affymetrix high-density SNP arrays. The results show that this imputation procedure significantly reduces genotyping error rates. We also discuss the necessary adjustments for its potential extension to other oligonucleotide microarrays, such as gene expression profiling. The R source code for the implementation of approach is freely available upon request.

  5. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Wernersson, Rasmus; Knudsen, Steen

    2003-01-01

    Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer with an ......Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer...

  6. Oligonucleotides Containing Aminated 2′-Amino-LNA Nucleotides

    DEFF Research Database (Denmark)

    Lou, Chenguang; Samuelsen, Simone V.; Christensen, Niels Johan

    2017-01-01

    Mono- and diaminated 2′-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity, and significant nuclease resistance. Molecular modeling suggested...... that structural stabilization occurs via intrastrand electrostatic attraction between the protonated amino groups of the aminated 2′-amino-LNA monomers and the host oligonucleotide backbone....

  7. Voltage-gated calcium channel and antisense oligonucleotides thereto

    Science.gov (United States)

    Hruska, Keith A. (Inventor); Friedman, Peter A. (Inventor); Barry, Elizabeth L. R. (Inventor); Duncan, Randall L. (Inventor)

    1998-01-01

    An antisense oligonucleotide of 10 to 35 nucleotides in length that can hybridize with a region of the .alpha..sub.1 subunit of the SA-Cat channel gene DNA or mRNA is provided, together with pharmaceutical compositions containing and methods utilizing such antisense oligonucleotide.

  8. CHEMICALS

    CERN Document Server

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  9. Heated oligonucleotide ligation assay (HOLA): an affordable single nucleotide polymorphism assay.

    Science.gov (United States)

    Black, W C; Gorrochotegui-Escalante, N; Duteau, N M

    2006-03-01

    Most single nucleotide polymorphism (SNP) detection requires expensive equipment and reagents. The oligonucleotide ligation assay (OLA) is an inexpensive SNP assay that detects ligation between a biotinylated "allele-specific detector" and a 3' fluorescein-labeled "reporter" oligonucleotide. No ligation occurs unless the 3' detector nucleotide is complementary to the SNP nucleotide. The original OLA used chemical denaturation and neutralization. Heated OLA (HOLA) instead uses a thermal stable ligase and cycles of denaturing and hybridization for ligation and SNP detection. The cost per genotype is approximately US$1.25 with two-allele SNPs or approximately US$1.75 with three-allele SNPs. We illustrate the development of HOLA for SNP detection in the Early Trypsin and Abundant Trypsin loci in the mosquito Aedes aegypti (L.) and at the a-glycerophosphate dehydrogenase locus in the mosquito Anopheles gambiae s.s.

  10. Extracellular biosynthesis of gadolinium oxide (Gd2O3) nanoparticles, their biodistribution and bioconjugation with the chemically modified anticancer drug taxol

    OpenAIRE

    Khan, Shadab Ali; Gambhir, Sanjay; Ahmad, Absar

    2014-01-01

    As a part of our programme to develop nanobioconjugates for the treatment of cancer, we first synthesized extracellular, protein-capped, highly stable and well-dispersed gadolinium oxide (Gd2O3) nanoparticles by using thermophilic fungus Humicola sp. The biodistribution of the nanoparticles in rats was checked by radiolabelling with Tc-99m. Finally, these nanoparticles were bioconjugated with the chemically modified anticancer drug taxol with the aim of characterizing the role of this bioconj...

  11. Chemically-enzymatic synthesis of photosensitive DNA.

    Science.gov (United States)

    Westphal, Kinga; Zdrowowicz, Magdalena; Zylicz-Stachula, Agnieszka; Rak, Janusz

    2017-02-01

    The sensitizing propensity of radio-/photosensitizing nucleoside depends on DNA sequence surrounding a sensitizer. Therefore, in order to compare sensitizers with regard to their ability to induce a DNA damage one has to study the sequence dependence of damage yield. However, chemical synthesis of oligonucleotides labeled with sensitizing nucleosides is hindered due to the fact that a limited number of such nucleoside phosphoramidites are accessible. Here, we report on a chemically-enzymatic method, employing a DNA polymerase and ligase, that enables a modified nucleoside, in the form of its 5'-triphosphate, to be incorporated into DNA fragment in a pre-determined site. Using such a protocol two double-stranded DNA fragments - a long one, 75 base pairs (bp), and a short one, 30bp in length - were pin-point labeled with 5-bromodeoxyuridine. Four DNA polymerases together with DHPLC for the inspection of reaction progress were used to optimize the process under consideration. As an ultimate test showing that the product possessing an assumed nucleotide sequence was actually obtained, we irradiated the synthesized oligonucleotide with UVB photons and analyzed its photoreactivity with the LC-MS method. Our results prove that a general approach enabling precise labeling of DNA with any nucleoside modification processed by DNA polymerase and ligase has been worked out.

  12. Preparation, Biodegradation of Coconut Oil Driven Chemically Modified Bovine Serum Albumin Microparticles of Encapsulated Cicer arietinum Amylase and Study of Their Application in Washing Detergents

    Directory of Open Access Journals (Sweden)

    Kirti Rani

    2014-10-01

    Full Text Available In present work, Cicer arietinum amylase was encapsulated by emulsification through covalent coupling by glutaraldehyde into chemically modified bovine serum albumin. Biodegradation of coconut oil driven emulsified bovine serum albumin encapsulated Cicer arietinum amylase was carried out by the alkaline protease for its controlled and sustained release of encapsulated enzyme from prepared microparticles of encapsulated Cicer arietinum amylase and its stability increased up to 6 months as compared to free enzyme. Its biodegradation was carried out by the using different concentration of alkaline protease (5U, 10U, 15U, 20U, 25U, 30U, 35U, 40U. Further, this coconut oil driven chemically modified bovine serum albumin microparticles of encapsulated Cicer arietinum amylase with alkaline protease were used with detergents for washing of stained cloths which have rust, gel pen ink, grease and chocolate strains. These chosen strains are very commonly present on uniforms of school going children which are very tough upon drying, hence, not to be easily vanish with well known brand detergents upon in one wash. But, the mixture solution of coconut oil driven chemically modified bovine serum albumin microparticles of encapsulated Cicer arietinum amylase along with alkaline protease were used with detergents powder for washing of these dry tough strains (rust, gel pen ink, grease and chocolate strains leads to vanishing these strains very fast with absolute clear results were found as compared to results of washing of stained cloths with detergents only.

  13. Effect of chemically modified Vulcan XC-72R on the performance of air-breathing cathode in a single-chamber microbial fuel cell.

    Science.gov (United States)

    Duteanu, N; Erable, B; Senthil Kumar, S M; Ghangrekar, M M; Scott, K

    2010-07-01

    The catalytic activity of modified carbon powder (Vulcan XC-72R) for oxygen reduction reaction (ORR) in an air-breathing cathode of a microbial fuel cell (MFC) has been investigated. Chemical modification was carried out by using various chemicals, namely 5% nitric acid, 0.2N phosphoric acid, 0.2N potassium hydroxide and 10% hydrogen peroxide. Electrochemical study was performed for ORR of these modified carbon materials in the buffer solution pH range of 6-7.5 in the anodic compartment. Although, these treatments influenced the surface properties of the carbon material, as evident from the SEM-EDX analysis, treatment with H(2)PO(4), KOH, and H(2)O(2) did not show significant activity during the electrochemical test. The HNO(3) treated Vulcan demonstrated significant ORR activity and when used in the single-chamber MFC cathode, current densities (1115mA/m(2), at 5.6mV) greater than those for a Pt-supported un-treated carbon cathode were achieved. However, the power density for the latter was higher. Such chemically modified carbon material can be a cheaper alternative for expensive platinum catalyst used in MFC cathode construction.

  14. A novel modification of real-time AS-qPCR by using locked nucleic acid-modified oligonucleotide probe as wild type allele amplification blockers for quantitative detection of the JAK2 V617F mutation%评价AS-LNA-qPCR法检测JAK2 V617F突变率的临床应用价值

    Institute of Scientific and Technical Information of China (English)

    邵冬华; 梁国威; 何美琳; 曹清芸

    2013-01-01

    Objective To develop a novel real-time PCR for sensitively quantitative detection of JAK2 V617F allele burden in peripheral blood.Methods Based on the real-time allele-specific PCR (AS-qPCR),the locked nucleic acid (LNA)-modified oligonucleotide probe was used for selectively blocking amplification of wild-type alleles in AS-qPCR,and then a novel AS-LNA-qPCR method was established.The percentages of sample JAK2 V617F alleles were directly calculated by its threshold cycle (Ct) values according to the standard curve which generated by JAK2 V617F alleles with its Ct values.We validated intra-and inter-assay variability for quantifying JAK2 V617F.We also assayed 623 apparent healthy donors by our method to validate its clinical application value.Results The quantitative lower limit of this method for JAK2 V617F was 0.01%,and the intra-and inter-assay average variability for quantifying percentage of JAK2 V617F in total DNA was 6.3% and 8.6%,respectively.Nineteen JAK2 V617F-positive individuals were identified using AS-LNA-qPCR in blood of 623 apparently healthy donors,and the range of percentages of JAK2 V617F alleles were 0.01%-5.49%.Conclusion The AS-LNA-qPCR with highly sensitive and reproducible quantification of JAK2 V617F mutant burden can be used clinically for diagnosis as well as evaluation of disease prognosis and efficacy of therapy in patients with myeloproliferative neoplasms.%目的 建立一种定量检测外周血细胞酪氨酸激酶2(JAK2)基因V617F突变率的等位基因特异性实时荧光定量PCR(AS-qPCR)方法.方法 在AS-qPCR基础上,引入1条锁核酸(LNA)修饰的寡核苷酸探针,用以选择性抑制AS-qPCR中突变引物对野生等位基因的非特异性扩增,定量检测JAK2 V617F突变率,称之为AS-LNA-qPCR法.通过AS-LNA-qPCR法测定样本的循环阈值(Ct值),根据AS-LNA-qPCR法检测不同JAK2 V617F突变率标准品的Ct值,绘制标准曲线,根据标准曲线直接获得检测样本中JAK2 V617F突变率.

  15. Target gene knockdown by 2',4'-BNA/LNA antisense oligonucleotides in zebrafish.

    Science.gov (United States)

    Itoh, Motoyuki; Nakaura, Mizuki; Imanishi, Takeshi; Obika, Satoshi

    2014-06-01

    Gene knockdowns using oligonucleotide-based approaches are useful for studying gene function in both in vitro cell culture systems and in vivo animal models. We evaluated the efficacy of 2',4'-bridged nucleic acids (BNA)-modified antisense oligonucleotides (AONs) for gene knockdown in zebrafish. We used the tcf7l1a gene as a model for testing the knockdown efficacy of 2',4'-BNA AONs and examined how the target sites/affinity and RNase H induction activity of 2',4'-BNA AONs affect knockdown efficacy. We found that tcf7l1a gene function was knocked down by 2',4'-BNA AONs that target the start codon and induce RNase H activity. Although nonspecific p53-mediated developmental defects were observed at higher doses, the effective dose of the 2',4'-BNA AONs for tcf7l1a is much lower than that of morpholino oligonucleotides. Our data thus show a potential application for 2',4'-BNA AONs in the downregulation of specific genes in zebrafish.

  16. Detection of Glucose with Atomic Absorption Spectroscopy by Using Oligonucleotide Functionalized Gold Nanoparticle.

    Science.gov (United States)

    Zhang, Hong; Yan, Honglian; Ling, Liansheng

    2016-06-01

    A novel method for the detection of glucose was established with atomic absorption spectroscopy by using the label of gold nanoparticle (AuNP). Silver-coated glass assembled with oligonucleotide 5'-SH-T12-AGA CAA GAG AGG-3' (Oligo 1) was acted as separation probe, oligonucleotide 5'-CAA CAG AGA ACG-T12-SH-3' modified gold nanoparticle (AuNP-Oligo 2) was acted as signal-reporting probe. Oligonucleotide 5'-CGT TCT CTG TTG CCT CTC TTG TCT-3' (Oligo 3) could hybridize with Oligo 1 on the surface of silver-coated glass and AuNP-Oligo 2, and free AuNP-Oligo 2 could be removed by rinsing with buffer. Hence the concentration of Oligo 3 was transformed into the concentration of gold element. In addition, Oligo 3 could be cleaved into DNA fragments by glucose, glucose oxidase and Fe(2+)-EDTA through Fenton reaction. Thereby the concentration of glucose could be transformed to the absorbance of gold element. Under the optimum conditions, the integrated absorbance decreased proportionally to the concentration of glucose over the range from 50.0 μM to 1.0 mM with a detection limit of 40.0 μM. Moreover, satisfactory result was obtained when the assay was used to determinate glucose in human serum.

  17. Antineoplastic effect of decoy oligonucleotide derived from MGMT enhancer.

    Directory of Open Access Journals (Sweden)

    Tamar Canello

    Full Text Available Silencing of O(6-methylguanine-DNA-methyltransferase (MGMT in tumors, mainly through promoter methylation, correlates with a better therapeutic response and with increased survival. Therefore, it is conceivable to consider MGMT as a potential therapeutic target for the treatment of cancers. Our previous results demonstrated the pivotal role of NF-kappaB in MGMT expression, mediated mainly through p65/NF-kappaB homodimers. Here we show that the non-canonical NF-KappaB motif (MGMT-kappaB1 within MGMT enhancer is probably the major inducer of MGMT expression following NF-kappaB activation. Thus, in an attempt to attenuate the transcription activity of MGMT in tumors we designed locked nucleic acids (LNA modified decoy oligonucleotides corresponding to the specific sequence of MGMT-kappaB1 (MGMT-kB1-LODN. Following confirmation of the ability of MGMT-kB1-LODN to interfere with the binding of p65/NF-kappaB to the NF-KappaB motif within MGMT enhancer, the efficacy of the decoy was studied in-vitro and in-vivo. The results of these experiments show that the decoy MGMT-kB1-LODN have a substantial antineoplastic effect when used either in combination with temozolomide or as monotherapy. Our results suggest that MGMT-kB1-LODN may provide a novel strategy for cancer therapy.

  18. Antineoplastic effect of decoy oligonucleotide derived from MGMT enhancer.

    Science.gov (United States)

    Canello, Tamar; Ovadia, Haim; Refael, Miri; Zrihan, Daniel; Siegal, Tali; Lavon, Iris

    2014-01-01

    Silencing of O(6)-methylguanine-DNA-methyltransferase (MGMT) in tumors, mainly through promoter methylation, correlates with a better therapeutic response and with increased survival. Therefore, it is conceivable to consider MGMT as a potential therapeutic target for the treatment of cancers. Our previous results demonstrated the pivotal role of NF-kappaB in MGMT expression, mediated mainly through p65/NF-kappaB homodimers. Here we show that the non-canonical NF-KappaB motif (MGMT-kappaB1) within MGMT enhancer is probably the major inducer of MGMT expression following NF-kappaB activation. Thus, in an attempt to attenuate the transcription activity of MGMT in tumors we designed locked nucleic acids (LNA) modified decoy oligonucleotides corresponding to the specific sequence of MGMT-kappaB1 (MGMT-kB1-LODN). Following confirmation of the ability of MGMT-kB1-LODN to interfere with the binding of p65/NF-kappaB to the NF-KappaB motif within MGMT enhancer, the efficacy of the decoy was studied in-vitro and in-vivo. The results of these experiments show that the decoy MGMT-kB1-LODN have a substantial antineoplastic effect when used either in combination with temozolomide or as monotherapy. Our results suggest that MGMT-kB1-LODN may provide a novel strategy for cancer therapy.

  19. Kinetic Hairpin Oligonucleotide Blockers for Selective Amplification of Rare Mutations

    Science.gov (United States)

    Jia, Yanwei; Sanchez, J. Aquiles; Wangh, Lawrence J.

    2014-01-01

    Detection of rare mutant alleles in an excess of wild type alleles is increasingly important in cancer diagnosis. Several methods for selective amplification of a mutant allele via the polymerase chain reaction (PCR) have been reported, but each of these methods has its own limitations. A common problem is that Taq DNA polymerase errors early during amplification generate false positive mutations which also accumulate exponentially. In this paper, we described a novel method using hairpin oligonucleotide blockers that can selectively inhibit the amplification of wild type DNA during LATE-PCR amplification. LATE-PCR generates double-stranded DNA exponentially followed by linear amplification of single-stranded DNA. The efficiency of the blocker is optimized by adjusting the LATE-PCR temperature cycling profile. We also demonstrate that it is possible to minimize false positive signals caused by Taq DNA polymerase errors by using a mismatched excess primer plus a modified PCR profile to preferentially enrich for mutant target sequences prior to the start of the exponential phase of LATE-PCR amplification. In combination these procedures permit amplification of specific KRAS mutations in the presence of more than 10,000 fold excess of wild type DNA without false positive signals. PMID:25082368

  20. Direct oligonucleotide-photosensitizer conjugates for photochemical delivery of antisense oligonucleotides.

    Science.gov (United States)

    Yuan, Ahu; Laing, Brian; Hu, Yiqiao; Ming, Xin

    2015-04-18

    Activation of photosensitizers in endosomes enables release of therapeutic macromolecules into the cytosol of the target cells for pharmacological actions. In this study, we demonstrate that direct conjugation of photosensitizers to oligonucleotides (ONs) allows spatial and temporal co-localization of the two modalities in the target cells, and thus leads to superior functional delivery of ONs. Further, light-activated delivery of an anticancer ON caused cancer cell killing via modulation of an oncogene and photodynamic therapy.

  1. Preparation and application of triple helix forming oligonucleotides and single strand oligonucleotide donors for gene correction.

    Science.gov (United States)

    Alam, Rowshon; Thazhathveetil, Arun Kalliat; Li, Hong; Seidman, Michael M

    2014-01-01

    Strategies for site-specific modulation of genomic sequences in mammalian cells require two components. One must be capable of recognizing and activating a specific target sequence in vivo, driving that site into an exploitable repair pathway. Information is transferred to the site via participation in the pathway by the second component, a donor nucleic acid, resulting in a permanent change in the target sequence. We have developed biologically active triple helix forming oligonucleotides (TFOs) as site-specific gene targeting reagents. These TFOs, linked to DNA reactive compounds (such as a cross-linking agent), activate pathways that can engage informational donors. We have used the combination of a psoralen-TFO and single strand oligonucleotide donors to generate novel cell lines with directed sequence changes at the target site. Here we describe the synthesis and purification of bioactive psoralen-linked TFOs, their co-introduction into mammalian cells with donor nucleic acids, and the identification of cells with sequence conversion of the target site. We have emphasized details in the synthesis and purification of the oligonucleotides that are essential for preparation of reagents with optimal activity.

  2. Heterogeneous oligonucleotide-hybridization assay based on hot electron-induced electrochemiluminescence of a rhodamine label at oxide-coated aluminum and silicon electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Spehar-Deleze, Anna-Maria [Laboratory of Sensors, Actuators and Microsystems, Institute of Microtechnology, University of Neuchatel, Rue Jaquet-Droz 1, CH-2007 Neuchatel (Switzerland) and Laboratory of Inorganic and Analytical Chemistry, Helsinki University of Technology, Kemistintie 1, FIN-02015 HUT (Finland)]. E-mail: anna-maria.spehar@unine.ch; Suomi, Johanna [Laboratory of Inorganic and Analytical Chemistry, Helsinki University of Technology, Kemistintie 1, FIN-02015 HUT (Finland); Jiang Qinghong [Laboratory of Inorganic and Analytical Chemistry, Helsinki University of Technology, Kemistintie 1, FIN-02015 HUT (Finland); Rooij, Nico de [Laboratory of Sensors, Actuators and Microsystems, Institute of Microtechnology, University of Neuchatel, Rue Jaquet-Droz 1, CH-2007 Neuchatel (Switzerland); Koudelka-Hep, Milena [Laboratory of Sensors, Actuators and Microsystems, Institute of Microtechnology, University of Neuchatel, Rue Jaquet-Droz 1, CH-2007 Neuchatel (Switzerland); Kulmala, Sakari [Laboratory of Inorganic and Analytical Chemistry, Helsinki University of Technology, Kemistintie 1, FIN-02015 HUT (Finland)

    2006-07-28

    This paper describes a heterogeneous oligonucleotide-hybridization assay based on hot electron-induced electrochemiluminescence (HECL) of a rhodamine label. Thin oxide-film coated aluminum and silicon electrodes were modified with an aminosilane layer and derivatized with short, 15-mer oligonucleotides via diisothiocyanate coupling. Target oligonucleotides were conjugated with tetramethylrhodamine (TAMRA) dye at their amino modified 5' end and hybridization was detected using HECL of TAMRA. Preliminary results indicate sensitivity down to picomolar level and low nonspecific adsorption. The sensitivity was better on oxide-coated silicon compared to oxide-coated aluminum electrodes and two-base pair mismatched hybrids were successfully discriminated. The experimental results presented here might be useful for the design of disposable electrochemiluminescent DNA biosensors.

  3. INFLUENCE OF PACKAGING MATERIAL AND STORAGE TIME ON PHYSICAL, CHEMICAL AND MICROBIOLOGICAL PROPERTIES OF SET YOGURT: A COMPARATIVE STUDY BETWEEN MODIFIED BIODEGRADABLE POLY(LACTIC ACID AND POLYPROPYLENE

    Directory of Open Access Journals (Sweden)

    NAWADON PETCHWATTANA

    2016-10-01

    Full Text Available The current paper investigates the influence of storage time and type of polymeric packaging material on the chemical, physical and microbiological properties of set yogurt. Firstly, poly(lactic acid (PLA was modified by using a core-shell rubber (CSR and an acrylic processing aid (PA to produce PLA with high toughness and good processability. Secondly, an appropriate PLA/PA/CSR composition was selected and fabricated to yogurt cup. The yogurt was stored in both modified PLA and polypropylene (PP packages to observe some physical, chemical and biological changes. Finally, the biodegradation test was made on both packages and compared with that cellulose. Experimental results revealed that adding 5wt% CSR gave PLA/PA as tough as PP. Types of packaging material and storage time did not change the color of yogurt. The number of lactic acid bacteria grew significantly after they had been incubated for 6 days. The bacterial viability decreased dramatically due to the increased acidity and the decreased pH. A positive impact on the viability of bacterial growth was found when yogurt was stored in modified PLA package. This made yogurt had more health benefits than stored in PP package. The biodegradation test results indicated that the modified PLA degraded at a rapid rate. It achieved approximately 50% biodegradation within 40 days which was comparable to the time required to degrade the cellulose, whereas PP was non-biodegradable over the period studied. In summary, substitution conventional PP by a novel modified PLA seems to be a better way for both the health and the environment benefits.

  4. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    Science.gov (United States)

    Nolan, John P.; White, P. Scott

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  5. [Effects of Different Modifier Concentrations on Lead-Zinc Tolerance, Subcellular Distribution and Chemical Forms for Four Kinds of Woody Plants].

    Science.gov (United States)

    Chen, Yong-hua; Zhang, Fu-yun; Wu, Xiao-fu; Liang, Xi; Yuan, Si-wen

    2015-10-01

    Four kinds of lead-zinc tolerant woody plants: Nerium oleander, Koelreuteria paniculata, Paulownia and Boehmeria were used as materials to estimate their enrichment and transferable capacity of lead (Pb) and zinc (Zn) and analyze the subcellular distribution and chemical speciation of Zn and Ph in different parts of plants, under different modifier concentrations (CK group: 100% lead-zinc slag plus a small amount of phosphate fertilizer, improved one: 85% of lead-zinc slag ± 10% peat ± 5% bacterial manure plus a small amount of phosphate fertilizer, improved two: 75% lead-zinc slag ± 20% peat ± 5% bacterial manure ± a small amount of phosphate). Results showed that: (1) The content of Pb, Zn in matrix after planting four kinds of plants was lower than before, no significant difference between improved one and improved two of Nerium oleander and Boehmeria was found, but improved two was better than improved one of Paulownia, while improved one was better than improved two of Koelreuteria paniculata; Four plants had relatively low aboveground enrichment coefficient of Pb and Zn, but had a high transfer coefficient, showed that the appropriate modifier concentration was able to improve the Pb and Zn enrichment and transfer ability of plants. (2) In subcellular distribution, most of Pb and Zn were distributed in plant cell wall components and soluble components while the distribution in cell organelles such as mitochondria, chloroplasts and nucleus component were less. Compared with CK group, two improved group made soluble components of the cell walls of Pb fixation and retention of zinc role in the enhancement. (3) As for the chemical forms of Pb and Zn in plants, the main chemical forms of Pb were hydrochloric acid, sodium chloride and ethanol extractable forms, while other chemical form contents were few, the main chemical forms of Zn were different based on plant type. Compared with CK group, the proportion of the active Pb chemical form in different plant

  6. Information Limited Oligonucleotide Amplification Assay for Affinity-Based, Parallel Detection Studies.

    Directory of Open Access Journals (Sweden)

    Harish Bokkasam

    Full Text Available Molecular communication systems encounter similar constraints as telecommunications. In either case, channel crosstalk at the receiver end will result in information loss that statistical analysis cannot compensate. This is because in any communication channel there is a physical limit to the amount of information that can be transmitted. We present a novel and simple modified end amplification (MEA technique to generate reduced and defined amounts of specific information in form of short fragments from an oligonucleotide source that also contains unrelated and redundant information. Our method can be a valuable tool to investigate information overflow and channel capacity in biomolecular recognition systems.

  7. Postsynthetic modification of oligonucleotides with imidazophenazine dye and its effect on duplex stability.

    Science.gov (United States)

    Dubey, Larysa; Ryazanova, Olga; Zozulya, Victor; Fedoryak, Dmytro; Dubey, Igor

    2011-01-01

    Carboxyalkyl derivative of the intercalating agent imidazo[4,5-b]phenazine was used for the postsynthetic oligonucleotide modification. Model pentadecathymidylate-imidazophenazine conjugate was prepared from 5'-aminoalkyl-modified (dT)(15) by using phosphonium coupling reagent BOP in the presence of 1-hydroxybenzotriazole. Spectral-fluorescent properties of the conjugate were studied. The attachment of the dye was found to increase the thermal stability of (dT)(15) duplex with poly(dA) by more than 4°C, probably by the intercalation mechanism.

  8. Carboranyl Nucleosides & Oligonucleotides for Neutron Capture Therapy Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Schinazi, Raymond F.

    2004-12-01

    -methyl)phosphonate (CBMP) internucleotide group. Unmodified phosphodiester linkages were formed using a standard {beta}-cyanoethyl cycle and automated DNA synthesizer. Modified CBMP internucleotide linkage was produced using the phosphotriester method and 5'-O-monomethoxytritylthymidine 3'-O-[(o-carboran-1-yl-methyl)phosphonate] monomer. Several dodecathymidylic acids bearing modification at 3'- or 5'-end, or in the middle of oligonucleotide chain were synthesized. The resulting oligomers are being characterized by reverse phase high-pressure liquid chromatography (RP-HPLC), electrospray ionization mass spectrometry (ESIMS), ultraviolet spectroscopy (UV), and circular dichroism (CD). In collaboration with Cornell University, we employed a secondary ion mass spectrometry (SIMS) based subcellular isotopic imaging technique of ion microscopy for evaluating 4 carboranyl nucleosides. Nucleosides synthesized by our group, including CDU, HMCDU, CTU, and CFAU were tested for their boron delivery to the nuclear and cytoplasmic compartments of U251 human and F98 rat glioma cells. Quantitative SIMS analysis of boron was performed in cryogenically prepared cells. For all drugs, the cell cytoplasm revealed significantly higher boron than the nucleus. However, the boron partitioning between the cell nucleus and the nutrient medium indicated 6.4-10.6 times higher boron in the nucleus. The results suggested that these novel carboranyl nucleosides should provide efficient BNCT agents that accumulate in malignant cells and the need for further evaluations in vitro and in animal models.

  9. Enzymatically hydrolysed, acetylated and dually modified corn starch: physico-chemical, rheological and nutritional properties and effects on cake quality.

    Science.gov (United States)

    Sahnoun, Mouna; Ismail, Nouha; Kammoun, Radhouane

    2016-01-01

    Corn starch was treated by enzymatic hydrolysis with Aspergillus oryzae S2 α-amylase, acetylation with vinyl acetate, and dual modification. The dual modified starch displayed a higher substitution degree than the acetylated starch and lower reducing sugar content than the hydrolysed starch. The results revealed that the cooling viscosity and amylose content of those products decrease (P cake formulations at 5 and 10 % concentrations on a wheat flour basis and compared to native starch. The results revealed that when applied at 5 % concentrations, the modified starches reduced the hardness, cohesion, adhesion and chewiness of baked cakes and enhanced their elasticity, volume, height, crust color, and appearance as compared to native starch. These effects were more pronounced for the cake incorporating the dually modified starch.

  10. Immunostimulatory oligonucleotide, CpG-like motif exists in Lactobacillus delbrueckii ssp. bulgaricus NIAI B6.

    Science.gov (United States)

    Kitazawa, Haruki; Watanabe, Hiroshi; Shimosato, Takeshi; Kawai, Yasushi; Itoh, Takatoshi; Saito, Tadao

    2003-08-15

    The present study was conducted to find an immunostimulatory oligonucleotide derived from yogurt starter cultures. The chromosomal DNA was purified from nine strains of Lactobacillus delbrueckii ssp. bulgaricus and six strains of Streptococcus thermophilus. An immunostimulatory ability of the DNA was examined in a proliferation of peyer's patch and splenic B cells. Only the DNA from L. bulgaricus NIAI B6 induced a significant proliferation of both cells. When the DNA was cloned and amplified using PCR, the mitogenic activities to B cells were significantly increased by 13 of 135 DNA clones. Ten homologous nucleotide sequences were found as possible oligonucleotide sequences of mitogens, and were then chemically synthesized (sOL-LB1 to sOL-LB10). One CpG-like motif (sOL-LB7; 5'-CGGCACGCTCACGATTCTTG-3') was identified as an immunostimulatory oligonucleotide, but it did not contain palindromic CpG structure known as a B cell-specific mitogen. The sOL-LB7 substantially bound to B cells and increased the CD69 positive cells in peyer's patch cells. This study demonstrated that L. bulgaricus NIAI B6 was a good candidate of a starter culture for the production of new functional foods, "Bio-Defense Foods".

  11. Optical Characterization of Oligonucleotide DNA Influenced by Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Seyedeh Maryam Banihashemian

    2013-09-01

    Full Text Available UV-VIS spectroscopic analysis of oligonucleotide DNA exposed to different magnetic fields was performed in order to investigate the relationship between DNA extinction coefficients and optical parameters according to magnetic-field strength. The results with the oligonucleotides adenine-thymine 100 mer (AT-100 DNA and cytosine-guanine 100 mer (CG-100 DNA indicate that the magnetic field influences DNA molar extinction coefficients and refractive indexes. The imaginary parts of the refractive index and molar extinction coefficients of the AT-100 and CG-100 DNA decreased after exposure to a magnetic field of 750 mT due to cleavage of the DNA oligonucleotides into smaller segments.

  12. Respirable antisense oligonucleotides: a new drug class for respiratory disease

    Directory of Open Access Journals (Sweden)

    Tanaka Makoto

    2000-12-01

    Full Text Available Abstract Respirable antisense oligonucleotides (RASONs, which attenuate specific disease-associated mRNAs, represent a new class of respiratory therapeutics with considerable potential. RASONs overcome previous obstacles that have impeded the development of antisense therapeutics targeting diseases in other organ systems. RASONs are delivered directly to the target tissue via inhalation; their uptake seems to be enhanced by cationic properties inherent in pulmonary surfactant, and, because of the markedly different target properties of mRNA and proteins, they can have very long durations of effect compared with traditional drugs targeting the protein of the same gene. RASONs contain chemical modifications that decrease their degradation by cellular nucleases. However, total insensitivity to nucleases is probably not an optimal design criterion for RASONs, because moderate nuclease sensitivity can prevent their systemic delivery, decreasing the potential for systemic toxicity. EPI-2010 is a 21-mer phosphorothioate RASON that attenuates bronchoconstriction, inflammation and surfactant depletion in preclinical models of human asthma, has a duration of effect of seven days, and seems to undergo minimal systemic delivery.

  13. Enzymic synthesis of oligonucleotides containing methylphosphonate internucleotide linkages.

    Science.gov (United States)

    Higuchi, H; Endo, T; Kaji, A

    1990-09-18

    Thymidine 5'-O-(pyrophosphoryl methylphosphonate) (dTTP alpha CH3) has been chemically synthesized by condensation of thymidine 5'-O-(methylphosphonate) with pyrophosphate. This novel nucleotide, which contained an alpha-phosphorus atom as methylphosphonate, was used as a substrate of terminal deoxynucleotidyltransferase (TDTase) in the presence of oligonucleotide (5'-GCTGTATCGTCAAGGCACTC-3') as an initiator. The reaction products were separated into two components by reverse-phase high-performance liquid chromatography (RP-HPLC). These products were, after purification, digested with nuclease P1 and alkaline phosphatase followed by separation of digested products by RP-HPLC. The result showed the presence of one of the isomers of 2'-deoxycytidyl-3'-methylphosphonyl-5'-thymidine (dCpCH3T) and 2'-deoxycytidyl-3'-methylphosphonyl-5'-thymidyl-3'-methyl phosphonyl-5'-thymidin e (dCpCH3TpCH3T), respectively. Fast atom bombardment mass spectrometry of these products further supported identification of the dinucleotide and the trinucleotide. These results indicated that dTTP alpha CH3 was used as a substrate of TDTase, resulting in methylphosphonate linkages. Produced oligomers were resistant to hydrolysis by snake venom phosphodiesterase I.

  14. Targeted delivery of chemically modified anti-miR-221 to hepatocellular carcinoma with negatively charged liposomes

    Directory of Open Access Journals (Sweden)

    Zhang W

    2015-07-01

    Full Text Available Wendian Zhang,1 Fangqi Peng,1 Taotao Zhou,1 Yifei Huang,2 Li Zhang,3 Peng Ye,4 Miao Lu,1 Guang Yang,5 Yongkang Gai,1 Tan Yang,1 Xiang Ma,1 Guangya Xiang1 1School of Pharmacy, Tongji Medical College, 2Department of Pharmacy, 3Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 4Department of Pharmacy, Wuhan University, Renmin Hospital, 5School of Medicine, Jianghan University, Wuhan, People’s Republic of China Abstract: Hepatocellular carcinoma (HCC is one of the leading causes of cancer-related death. Gene therapy was established as a new strategy for treating HCC. To explore the potential delivery system to support the gene therapy of HCC, negatively charged liposomal delivery system was used to deliver miR-221 antisense oligonucleotide (anti-miR-221 to the transferrin (Tf receptor over expressed HepG2 cells. The liposome exhibited a mean particle size of 122.5 nm, zeta potential of -15.74 mV, anti-miR-221 encapsulation efficiency of 70%, and excellent colloidal stability at 4°C. Anti-miR-221-encapsulated Tf-targeted liposome demonstrated a 15-fold higher delivery efficiency compared to nontargeted liposome in HepG2 cells in vitro. Anti-miR-221 Tf-targeted liposome effectively delivered anti-miR-221 to HepG2 cells, upregulated miR-221 target genes PTEN, P27kip1, and TIMP3, and exhibited greater silencing efficiency over nontargeted anti-miR-221 liposome. After intravenous injection into HepG2 tumor-bearing xenografted mice with Cy3-labeled anti-miR-221 Tf-targeted liposome, Cy3-anti-miR-221 was successfully delivered to the tumor site and increased the expressions of PTEN, P27kip1, and TIMP3. Our results demonstrate that the Tf-targeted negatively charged liposome could be a potential therapeutic modality in the gene therapy of human HCC. Keywords: transferrin, gene, HCC, target delivery system, anionic liposome 

  15. Fatigue behavior of Ti–6Al–4V alloy in saline solution with the surface modified at a micro- and nanoscale by chemical treatment

    Energy Technology Data Exchange (ETDEWEB)

    Claros, Cesar Adolfo Escobar; Oliveira, Diego Pedreira; Campanelli, Leonardo Contri; Pereira da Silva, Paulo Sergio Carvalho; Bolfarini, Claudemiro

    2016-10-01

    This work evaluated the influence of the surface modification using acid etching combined with alkaline treatment on the fatigue strength of Ti–6Al–4V ELI alloy. The topography developed by chemical surface treatments (CST) was examined by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Increased roughness and effective surface area were investigated and compared with the Ti–6Al–4V samples without modification. Surface composition was analyzed by energy dispersive X-ray spectroscopy (EDS). Axial fatigue resistance of polished and modified surfaces was determined by stepwise load increase tests and staircase test method. Light microscopy and SEM were employed to examine the fracture surface of the tested specimens. According to the results, a similar fatigue behavior was found and a negligible difference in the fatigue crack nucleation was observed for the Ti–6Al–4V with CST in comparison to the samples without treatment. - Highlights: • Fatigue behavior of Ti–6Al–4V with the surface modified by chemical treatments • The topography developed did not induce differences in the fatigue resistance. • Untreated and chemically treated surfaces presented fractographic similarities.

  16. Intrinsically Labeled Fluorescent Oligonucleotide Probes on Quantum Dots for Transduction of Nucleic Acid Hybridization.

    Science.gov (United States)

    Shahmuradyan, Anna; Krull, Ulrich J

    2016-03-15

    Quantum dots (QDs) have been widely used in chemical and biosensing due to their unique photoelectrical properties and are well suited as donors in fluorescence resonance energy transfer (FRET). Selective hybridization interactions of oligonucleotides on QDs have been determined by FRET. Typically, the QD-FRET constructs have made use of labeled targets or have implemented labeled sandwich format assays to introduce dyes in proximity to the QDs for the FRET process. The intention of this new work is to explore a method to incorporate the acceptor dye into the probe molecule. Thiazole orange (TO) derivatives are fluorescent intercalating dyes that have been used for detection of double-stranded nucleic acids. One such dye system has been reported in which single-stranded oligonucleotide probes were doubly labeled with adjacent thiazole orange derivatives. In the absence of the fully complementary (FC) oligonucleotide target, the dyes form an H-aggregate, which results in quenching of fluorescence emission due to excitonic interactions between the dyes. The hybridization of the FC target to the probe provides for dissociation of the aggregate as the dyes intercalate into the double stranded duplex, resulting in increased fluorescence. This work reports investigation of the dependence of the ratiometric signal on the type of linkage used to conjugate the dyes to the probe, the location of the dye along the length of the probe, and the distance between adjacent dye molecules. The limit of detection for 34mer and 90mer targets was found to be identical and was 10 nM (2 pmol), similar to analogous QD-FRET using labeled oligonucleotide target. The detection system could discriminate a one base pair mismatch (1BPM) target and was functional without substantial compromise of the signal in 75% serum. The 1BPM was found to reduce background signal, indicating that the structure of the mismatch affected the environment of the intercalating dyes.

  17. A STUDY COMPARING CHEMICAL PEELING USING MODIFIED JESSNER'S SOLUTION AND 15%TRICHLOROACETIC ACID VERSUS 15% TRICHLOROACETIC ACID IN THE TREATMENT OF MELASMA

    Science.gov (United States)

    Safoury, Omar Soliman; Zaki, Nagla Mohamed; El Nabarawy, Eman Ahmad; Farag, Eman Abas

    2009-01-01

    Background: Melasma is a symmetric progressive hyperpigmentation of the facial skin that occurs in all races but has a predilection for darker skin phenotypes. Depigmenting agents, laser and chemical peeling as classic Jessner's solution, modified Jessner's solution and trichloroacetic acid have been used alone and in combination in the treatment of melasma. Objectives: The aim of the study was to compare the therapeutic effect of combined 15% Trichloroacetic acid (TCA) and modified Jessner's solution with 15% TCA on melasma. Materials and Methods: Twenty married females with melasma (epidermal type), with a mean age of 38.25 years, were included in this study. All were of skin type III or IV. Fifteen percent TCA was applied to the whole face, with the exception of the left malar area to which combined TCA 15% and modified Jessner's solution was applied. Results: Our results revealed statistically highly significant difference between MASI Score (Melasma Area and Severity Index) between the right malar area and the left malar area. Conclusion: Modified Jessner's solution proved to be useful as an adjuvant treatment with TCA in the treatment of melasma, improving the results and minimizing postinflammatory hyperpigmentation. PMID:20049268

  18. A study comparing chemical peeling using modified jessner′s solution and 15% trichloroacetic acid versus 15% trichloroacetic acid in the treatment of melasma

    Directory of Open Access Journals (Sweden)

    Safoury Omar

    2009-01-01

    Full Text Available Background: Melasma is a symmetric progressive hyperpigmentation of the facial skin that occurs in all races but has a predilection for darker skin phenotypes. Depigmenting agents, laser and chemical peeling as classic Jessner′s solution, modified Jessner′s solution and trichloroacetic acid have been used alone and in combination in the treatment of melasma. Objectives: The aim of the study was to compare the therapeutic effect of combined 15% Trichloroacetic acid (TCA and modified Jessner′s solution with 15% TCA on melasma. Materials and Methods: Twenty married females with melasma (epidermal type, with a mean age of 38.25 years, were included in this study. All were of skin type III or IV. Fifteen percent TCA was applied to the whole face, with the exception of the left malar area to which combined TCA 15% and modified Jessner′s solution was applied. Results: Our results revealed statistically highly significant difference between MASI Score (Melasma Area and Severity Index between the right malar area and the left malar area. Conclusion: Modified Jessner′s solution proved to be useful as an adjuvant treatment with TCA in the treatment of melasma, improving the results and minimizing postinflammatory hyperpigmentation.

  19. Comparison of Fe-Al-modified natural materials by an electrochemical method and chemical precipitation for the adsorption of F- and As(V).

    Science.gov (United States)

    Vázquez Mejía, G; Martínez-Miranda, V; Fall, C; Linares-Hernández, I; Solache-Ríos, M

    2016-01-01

    The adsorption of fluoride and arsenic ions by modified natural materials may have an impact on the removal of F- and As(V) from waters. In this work, a zeolitic material and pozzolan (commonly known as pumicite) were modified with aluminium an iron by an electrochemical method and chemical precipitation, respectively. The adsorbents were characterized by X-ray diffraction, scanning electron microscopy with energy X-ray disperse spectroscopy analysis and the point of zero charge (pHzpc). F- and As(V) adsorption properties of both materials were investigated. Adsorption kinetic data were best fitted to pseudo-second-order model and equilibrium data to the Langmuir isotherm model. The highest F- and As(V) sorption capacities were obtained for modified zeolitic (0.866 mg/g) and pozzolan (3.35 mg/g) materials, respectively, with initial F- or As(V) concentrations of 10 mg/L. It was found that the unmodified materials did not show either adsorption of F- ions or As(V), which indicated that Al and Fe in the adsorbents are responsible for the adsorption of these ions. In general, both modified materials show similar capacities for the adsorption of F- and As(V).

  20. Surface Structure and Photocatalytic Properties of Bi2WO6 Nanolatelets Modified by Molybdena Islands from Chemical Vapor Deposition

    NARCIS (Netherlands)

    Dittmer, A.; Menze, J.; Mei, B.T.; Strunk, J.; Luftman, H.S.; Gutkowski, R.; Wachs, I.E.; Schuhmann, W.; Muhler, M.

    2016-01-01

    We report on a novel route of preparing molybdena-modified bismuth tungstates and their successful application in the photocatalytic oxygen evolution reaction and the oxidation of glycerol. Hierarchically assembled monocrystalline Bi2WO6 nanoplatelets with a specific surface area of 10 m2/g were obt

  1. Rheological and chemical evaluation on the ageing properties of SBS polymer modified bitumen: From the laboratory to the field

    NARCIS (Netherlands)

    Liu, G.; Nielsen, E.; Komacka, J.; Greet, L.; Ven, M.V.D.

    2014-01-01

    This study investigated the ageing properties of the styrene-butadiene- styrene polymer modified bitumen (SBS PMB) from the laboratory to the field. The virgin SBS PMB had been kept for 23 years and its field-aged binder was extracted from the reclaimed stone matrix asphalt (SMA) after the 22-year s

  2. Rheological and chemical evaluation on the ageing properties of SBS polymer modified bitumen: From the laboratory to the field

    NARCIS (Netherlands)

    Liu, G.; Nielsen, E.; Komacka, J.; Greet, L.; Ven, M.V.D.

    2014-01-01

    This study investigated the ageing properties of the styrene-butadiene- styrene polymer modified bitumen (SBS PMB) from the laboratory to the field. The virgin SBS PMB had been kept for 23 years and its field-aged binder was extracted from the reclaimed stone matrix asphalt (SMA) after the 22-year

  3. Surface Structure and Photocatalytic Properties of Bi2WO6 Nanolatelets Modified by Molybdena Islands from Chemical Vapor Deposition

    NARCIS (Netherlands)

    Dittmer, A.; Menze, J.; Mei, Bastian Timo; Strunk, J.; Luftman, H.S.; Gutkowski, R.; Wachs, I.E.; Schuhmann, W.; Muhler, M.

    2016-01-01

    We report on a novel route of preparing molybdena-modified bismuth tungstates and their successful application in the photocatalytic oxygen evolution reaction and the oxidation of glycerol. Hierarchically assembled monocrystalline Bi2WO6 nanoplatelets with a specific surface area of 10 m2/g were

  4. Rheological and chemical evaluation on the ageing properties of SBS polymer modified bitumen: From the laboratory to the field

    NARCIS (Netherlands)

    Liu, G.; Nielsen, E.; Komacka, J.; Greet, L.; Ven, M.V.D.

    2014-01-01

    This study investigated the ageing properties of the styrene-butadiene- styrene polymer modified bitumen (SBS PMB) from the laboratory to the field. The virgin SBS PMB had been kept for 23 years and its field-aged binder was extracted from the reclaimed stone matrix asphalt (SMA) after the 22-year s

  5. Chemically modified polymeric resins for separation of cations, organic acids, and small polar moleculea by high performance liquid chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Morris, John B. [Iowa State Univ., Ames, IA (United States)

    1993-07-01

    This thesis is divided into 4 parts: a review, ion chromatography of metal cations on carboxylic resins, separation of hydrophilic organic acids and small polar compounds on macroporous resin columns, and use of eluent modifiers for liquid chromatographic separation of carboxylic acids using conductivity detection.

  6. Enzymatically hydrolysed, acetylated and dually modified corn starch: physico-chemical, rheological and nutritional properties and effects on cake quality

    OpenAIRE

    Sahnoun, Mouna; Ismail, Nouha; Kammoun, Radhouane

    2015-01-01

    Corn starch was treated by enzymatic hydrolysis with Aspergillus oryzae S2 α-amylase, acetylation with vinyl acetate, and dual modification. The dual modified starch displayed a higher substitution degree than the acetylated starch and lower reducing sugar content than the hydrolysed starch. The results revealed that the cooling viscosity and amylose content of those products decrease (P 

  7. Conventional SLA and chemically modified SLA implants in patients with poorly controlled type 2 diabetes mellitus--a randomized controlled trial.

    Science.gov (United States)

    Khandelwal, Namita; Oates, Thomas W; Vargas, Adriana; Alexander, Peggy P; Schoolfield, John D; Alex McMahan, C

    2013-01-01

    The objective of this study was to evaluate the potential for a chemically modified Sand blasted, Large grit, Acid etched (SLA) surface, compared with a conventional SLA surface, to enhance implant healing and integration in poorly controlled diabetic patients, a group previously demonstrated to have compromises and delays in implant stabilization during the metabolically active healing period following implant placement. The study enrolled 24 patients with type 2 diabetes, baseline HbA1c levels between 7.5-11.4%, and a minimum of two posterior mandibular tooth sites at least 4 months following extraction and appropriate for implant placement. Each patient, at a randomly selected site, received an implant with the conventional SLA surface; at the second site, the patient received an implant with the chemically modified SLA (modSLA) surface. Thus, 48 study implants were placed. Implant stability was assessed using Resonance Frequency Analysis (RFA). Readings were taken from the buccal and proximal directions for each implant. Implant stability (ISQ) was assessed at the time of surgical placement (baseline) and 2, 3, 4, 6, 8, 10, 12, and 16 weeks following implant placement. No significant differences in implant stability were observed between conventional SLA implants and modSLA implants, and the time courses of implant stabilization following implant placement were similar for the two implant types. Baseline ISQ and minimum ISQ was slightly higher in subjects with higher HbA1c levels, but were similar during 12-16 weeks following implant placement. Forty-seven (98%) of the 48 implants were determined to be successfully osseointegrated and continued to restoration. Implant stabilization was similar for the conventional SLA and chemically modified SLA implants in type 2 diabetic patients with relatively poor glycemic control. Furthermore, this study demonstrated clinically successful implant placement even in poorly controlled diabetic patients. © 2011 John Wiley

  8. Chemical Modification of Cyclodextrin and Amylose by Click Reaction and Its Application to the Synthesis of Poly-alkylamine-Modified Antibacterial Sugars.

    Science.gov (United States)

    Yamamura, Hatsuo

    2017-01-01

    Cyclodextrin (CD) can be chemically modified into desired and sophisticated functional molecules. However, poly-modification often produces complicated mixtures, resulting in a low yield of the desired product. As the most promising procedure to solve such problems and to achieve poly-modification of the CD molecule, we present here the Huisgen 1,3-dipolar cycloaddition, known as a click reaction. This review will describe the results of our microwave-assisted click reaction for the poly-modification of CD and amylose molecules, and its application to the study of synthetic membrane active antibacterial derivatives.

  9. One-pot chemical synthesis of small ubiquitin-like modifier protein-peptide conjugates using bis(2-sulfanylethyl)amido peptide latent thioester surrogates.

    Science.gov (United States)

    Boll, Emmanuelle; Drobecq, Hervé; Ollivier, Nathalie; Blanpain, Annick; Raibaut, Laurent; Desmet, Rémi; Vicogne, Jérôme; Melnyk, Oleg

    2015-02-01

    Small ubiquitin-like modifier (SUMO) post-translational modification (PTM) of proteins has a crucial role in the regulation of important cellular processes. This protocol describes the chemical synthesis of functional SUMO-peptide conjugates. The two crucial stages of this protocol are the solid-phase synthesis of peptide segments derivatized by thioester or bis(2-sulfanylethyl)amido (SEA) latent thioester functionalities and the one-pot assembly of the SUMO-peptide conjugate by a sequential native chemical ligation (NCL)/SEA native peptide ligation reaction sequence. This protocol also enables the isolation of a SUMO SEA latent thioester, which can be attached to a target peptide or protein in a subsequent step. It is compatible with 9-fluorenylmethoxycarbonyl (Fmoc) chemistry, and it gives access to homogeneous, reversible and functional SUMO conjugates that are not easily produced using living systems. The synthesis of SUMO-peptide conjugates on a milligram scale takes 20 working days.

  10. Towards combined electrochemistry and surface-enhanced resonance Raman of heme proteins: Improvement of diffusion electrochemistry of cytochrome c at silver electrodes chemically modified with 4-mercaptopyridine.

    Science.gov (United States)

    Millo, Diego; Ranieri, Antonio; Koot, Wynanda; Gooijer, Cees; van der Zwan, Gert

    2006-08-01

    To date, a successful combination of surface-enhanced resonance Raman spectroscopy (SERRS) and electrochemistry to study heme proteins is inhibited by the problems raised by the prerequisite to use silver as electrode metal. This paper indicates an approach to overcome these problems. It describes a quick and reproducible procedure to prepare silver electrodes chemically modified with 4-mercaptopyridine suitable to perform diffusion electrochemistry of cytochrome c (cyt c). The method involves the employment of a mechanical and a chemical treatment and avoids the use of alumina slurries and any electrochemical pretreatment. Cyclic voltammetry (CV) was used to test the electrochemical response of cyt c, and the CV signals were found identical with those obtained on gold electrodes under the same experimental conditions. Compared to previous literature, a significant improvement of the CV signal of cyt c at silver electrodes was achieved. Preliminary results show that this treatment can be also successfully employed for the preparation of SERRS-active electrodes.

  11. A Modified Model for Flexibility Analysis in Chemical Engineering Processes%化工过程中柔性分析的改进模型

    Institute of Scientific and Technical Information of China (English)

    张蕾; 何小荣; 徐强

    2004-01-01

    This paper discussed an extended model for flexibility analysis of chemical process. Under uncertainty, probability density function is used to describe uncertain parameters instead of hyper-rectangle, and chanceconstrained programming is a feasible way to deal with the violation of constraints. Because the feasible region of control variables would change along with uncertain parameters, its smallest acceptable size threshold is presented to ensure the controllability condition. By synthesizing the considerations mentioned above, a modified model can describe the flexibility analysis problem more exactly. Then a hybrid algorithm, which integrates stochastic simulation and genetic algorithm, is applied to solve this model and maximize the flexibility region. Both numerical and chemical process examples are presented to demonstrate the effectiveness of the method.

  12. Integrated Safety Assessment of 2'-O-Methoxyethyl Chimeric Antisense Oligonucleotides in NonHuman Primates and Healthy Human Volunteers.

    Science.gov (United States)

    Crooke, Stanley T; Baker, Brenda F; Kwoh, T Jesse; Cheng, Wei; Schulz, Dan J; Xia, Shuting; Salgado, Nelson; Bui, Huynh-Hoa; Hart, Christopher E; Burel, Sebastien A; Younis, Husam S; Geary, Richard S; Henry, Scott P; Bhanot, Sanjay

    2016-10-01

    The common chemical and biological properties of antisense oligonucleotides provide the opportunity to identify and characterize chemical class effects across species. The chemical class that has proven to be the most versatile and best characterized is the 2'-O-methoxyethyl chimeric antisense oligonucleotides. In this report we present an integrated safety assessment of data obtained from controlled dose-ranging studies in nonhuman primates (macaques) and healthy human volunteers for 12 unique 2'-O-methoxyethyl chimeric antisense oligonucleotides. Safety was assessed by the incidence of safety signals in standardized laboratory tests for kidney and liver function, hematology, and complement activation; as well as by the mean test results as a function of dose level over time. At high doses a number of toxicities were observed in nonhuman primates. However, no class safety effects were identified in healthy human volunteers from this integrated data analysis. Effects on complement in nonhuman primates were not observed in humans. Nonhuman primates predicted safe doses in humans, but over predicted risk of complement activation and effects on platelets. Although limited to a single chemical class, comparisons from this analysis are considered valid and accurate based on the carefully controlled setting for the specified study populations and within the total exposures studied.

  13. RNA Interference-Guided Targeting of Hepatitis C Virus Replication with Antisense Locked Nucleic Acid-Based Oligonucleotides Containing 8-oxo-dG Modifications.

    Science.gov (United States)

    Mutso, Margit; Nikonov, Andrei; Pihlak, Arno; Žusinaite, Eva; Viru, Liane; Selyutina, Anastasia; Reintamm, Tõnu; Kelve, Merike; Saarma, Mart; Karelson, Mati; Merits, Andres

    2015-01-01

    The inhibitory potency of an antisense oligonucleotide depends critically on its design and the accessibility of its target site. Here, we used an RNA interference-guided approach to select antisense oligonucleotide target sites in the coding region of the highly structured hepatitis C virus (HCV) RNA genome. We modified the conventional design of an antisense oligonucleotide containing locked nucleic acid (LNA) residues at its termini (LNA/DNA gapmer) by inserting 8-oxo-2'-deoxyguanosine (8-oxo-dG) residues into the central DNA region. Obtained compounds, designed with the aim to analyze the effects of 8-oxo-dG modifications on the antisense oligonucleotides, displayed a unique set of properties. Compared to conventional LNA/DNA gapmers, the melting temperatures of the duplexes formed by modified LNA/DNA gapmers and DNA or RNA targets were reduced by approximately 1.6-3.3°C per modification. Comparative transfection studies showed that small interfering RNA was the most potent HCV RNA replication inhibitor (effective concentration 50 (EC50): 0.13 nM), whereas isosequential standard and modified LNA/DNA gapmers were approximately 50-fold less efficient (EC50: 5.5 and 7.1 nM, respectively). However, the presence of 8-oxo-dG residues led to a more complete suppression of HCV replication in transfected cells. These modifications did not affect the efficiency of RNase H cleavage of antisense oligonucleotide:RNA duplexes but did alter specificity, triggering the appearance of multiple cleavage products. Moreover, the incorporation of 8-oxo-dG residues increased the stability of antisense oligonucleotides of different configurations in human serum.

  14. RNA Interference-Guided Targeting of Hepatitis C Virus Replication with Antisense Locked Nucleic Acid-Based Oligonucleotides Containing 8-oxo-dG Modifications.

    Directory of Open Access Journals (Sweden)

    Margit Mutso

    Full Text Available The inhibitory potency of an antisense oligonucleotide depends critically on its design and the accessibility of its target site. Here, we used an RNA interference-guided approach to select antisense oligonucleotide target sites in the coding region of the highly structured hepatitis C virus (HCV RNA genome. We modified the conventional design of an antisense oligonucleotide containing locked nucleic acid (LNA residues at its termini (LNA/DNA gapmer by inserting 8-oxo-2'-deoxyguanosine (8-oxo-dG residues into the central DNA region. Obtained compounds, designed with the aim to analyze the effects of 8-oxo-dG modifications on the antisense oligonucleotides, displayed a unique set of properties. Compared to conventional LNA/DNA gapmers, the melting temperatures of the duplexes formed by modified LNA/DNA gapmers and DNA or RNA targets were reduced by approximately 1.6-3.3°C per modification. Comparative transfection studies showed that small interfering RNA was the most potent HCV RNA replication inhibitor (effective concentration 50 (EC50: 0.13 nM, whereas isosequential standard and modified LNA/DNA gapmers were approximately 50-fold less efficient (EC50: 5.5 and 7.1 nM, respectively. However, the presence of 8-oxo-dG residues led to a more complete suppression of HCV replication in transfected cells. These modifications did not affect the efficiency of RNase H cleavage of antisense oligonucleotide:RNA duplexes but did alter specificity, triggering the appearance of multiple cleavage products. Moreover, the incorporation of 8-oxo-dG residues increased the stability of antisense oligonucleotides of different configurations in human serum.

  15. Hole hopping rates in single strand oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Borrelli, Raffaele [Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, TO (Italy); Capobianco, Amedeo [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy); Peluso, Andrea, E-mail: apeluso@unisa.it [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy)

    2014-08-31

    Highlights: • DNA hole transfer rates have been computed. • Delocalized adenine domains significantly affect hole transfer rates in DNA. • Franck–Condon weighted density of state from DFT normal modes. • DNA application in molecular electronics. - Abstract: The rates of hole transfer between guanine and adenine in single strand DNA have been evaluated by using Fermi’s golden rule and Kubo’s generating function approach for the Franck–Condon weighted density of states. The whole sets of the normal modes and vibrational frequencies of the two nucleobases, obtained at DFT/B3LYP level of calculation, have been considered in computations. The results show that in single strand the pyramidalization/planarization mode of the amino groups of both nucleobases plays the major role. At room temperature, the Franck–Condon density of states extends over a wide range of hole site energy difference, 0–1 eV, giving some hints about the design of oligonucleotides of potential technological interest.

  16. Development of a virus concentration method using lanthanum-based chemical flocculation coupled with modified membrane filtration procedures.

    Science.gov (United States)

    Zhang, Yanyan; Riley, Lela K; Lin, Mengshi; Purdy, Gregory A; Hu, Zhiqiang

    2013-06-01

    Direct membrane filtration is often used to concentrate viruses in water but it may suffer from severe membrane fouling and clogging. Here, a lanthanum-based flocculation method coupled with modified membrane filtration procedures was developed and evaluated to detect viruses in large volume (40 L) water samples. The lanthanum-based flocculation method could easily reduce the water sample volume by a factor of 40. Additional volume reduction was achieved by a two-step membrane filtration approach. First, selected membrane filters (including 1MDS electropositive filters and nitrocellulose electronegative filters-Millipore HATF filters) were used to reduce water sample volume further and compare their efficiencies in virus recovery. The Mg²⁺-modified HATF membrane performed better on MS2 retention with an average virus recovery of 83.4% (±4.5% [standard deviation]). After HATF membrane filtration and elution, centrifugal ultrafiltration through a 30 kDa cut-off membrane resulted in an overall concentration factor of 20,000. Results from the infectivity assay showed that the MS2 recovery efficiencies from the NanoCeram- and 1MDS-based direct filtration and the lanthanum-based concentration coupled with the modified filtration procedure were 10.1% (±1.0%), 3.3% (±0.1%), and 17.5% (±1.1%), respectively. Results from the PCR analysis showed that the virus recoveries of the lanthanum-based method were 20.6% (±2.9%) and 19.5% (±3.4%) for MS2 and adenovirus, respectively, while no adenovirus could be detected through the NanoCeram- and 1MDS-based direct filtration. The lanthanum-based concentration method coupled with modified membrane filtration procedures is therefore a promising method for detecting waterborne viruses.

  17. Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel.

    Directory of Open Access Journals (Sweden)

    Weizhong Tang

    Full Text Available To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA, (dC, (dG and (dT to silver staining could be ranged as (dA > (dG > (dC > (dT from high to low. It was unexpected that oligo (dT was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt. The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution.

  18. Advance in researches on chemically modified starch used in food%变性淀粉在食品中的应用研究进展

    Institute of Scientific and Technical Information of China (English)

    张静静; 梁艳; 宫丽华; 崔波

    2014-01-01

    Starch has become a kind of important industrial raw material as renewable natural resources . Because many inherent qualities of the original starch( infusibility in cold water,instability of paste liquid in acid,heat and shearing action)limit its industrial application.So people developed modified technology according to the starch structure and physical and chemical properties ,named modified starch .With many good properties of the modified starch ,its application in food industry is becoming more and more widely at home and abroad.This paper introduces preparation methods of modified starch,domain,and prospects the development of modified starch.%淀粉作为一种可再生的天然资源,已成为重要的工业原料。由于原淀粉的许多固有性质(冷水不溶性,糊液在酸、热、剪切作用下不稳定)限定了淀粉的工业应用,人们根据淀粉的结构和理化性质开发了淀粉的变性技术,即变性淀粉。随着变性淀粉诸多优良性质的显现,其在国内外食品行业的应用也越来越广泛。本文介绍了变性淀粉的制备方法及应用领域,并对变性淀粉的发展做了展望。

  19. Co-Administration of an Excipient Oligonucleotide Helps Delineate Pathways of Productive and Nonproductive Uptake of Phosphorothioate Antisense Oligonucleotides in the Liver.

    Science.gov (United States)

    Donner, Aaron J; Wancewicz, Edward V; Murray, Heather M; Greenlee, Sarah; Post, Noah; Bell, Melanie; Lima, Walt F; Swayze, Eric E; Seth, Punit P

    2017-08-01

    Phosphorothioate (PS) modified antisense oligonucleotides (ASOs) have progressed rapidly in the clinic for treating a variety of disease indications. We previously demonstrated that the activity of PS ASOs in the liver can be enhanced by co-infusion of an excipient oligonucleotide (EON). It was posited that the EON saturates a nonproductive uptake pathway(s) thereby permitting accumulation of the PS ASO in a productive tissue compartment. In this report, we measured PS ASO activity following administration by bolus, infusion or co-fusion with EON within hepatocytes and nonparenchymal cells (NPCs), of the liver. This revealed that while ASOs accumulate preferentially in NPCs, they are intrinsically more active in hepatocytes. Furthermore, we show that the EON enhances ASO potency when infused up to 72 h before or after administration of the active ASO suggesting that the EON can saturate and displace the ASO from nonproductive to productive compartments. Physical presence of the EON in tissues was required for optimal potentiation suggesting that there is a dynamic distribution of the ASO and EON between the compartments. Lastly, using a candidate approach, we confirmed Stabilin-2 as a molecular pathway for ASO uptake in sinusoidal endothelial cells and the ASGR as a pathway for ASO uptake into hepatocytes in the liver.

  20. Effects of a Modified Through-Mask Drinking System (MDS) on Fluid Intake During Exercise in Chemical Protective Gear

    Science.gov (United States)

    1989-10-12

    in chemical protective gear. METHODS Test Subiects: Eighteen (18) unacclimated male volunteers were recruited from the military population at USARIEM...hydration status, a pretest urine sample was analyzed for specific gravity ( refractometry ) and no significant difference was observed between the two

  1. Targeting of single stranded oligonucleotides through metal-induced cyclization of short complementary strands : Targeting of single stranded oligonucleotides

    OpenAIRE

    Freville, Fabrice; Richard, Tristan; Bathany, Katell; Moreau, Serge

    2006-01-01

    International audience; A new strategy to cyclize a short synthetic oligonucleotide on a DNA or a RNA target strand is described. This one relies on a metal-mediated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2':6',2”-terpyridine moieties at their 3' and 5' ends. Cyclization following metal addition (Zn2+, Fe2+) was demonstrated using UV monitored thermal denaturation experiments, mass spectrometry analysis and gel shift assays. NMR experiments were used t...

  2. Study of the roles of chemical modifiers in determining boron using graphite furnace atomic absorption spectrometry and optimization of the temperature profile during atomization.

    Science.gov (United States)

    Yamamoto, Yuhei; Shirasaki, Toshihiro; Yonetani, Akira; Imai, Shoji

    2015-01-01

    The measurement conditions for determining boron using graphite furnace-atomic absorption spectrometry (GF-AAS) were investigated. Differences in the boron absorbance profiles were found using three different commercially available GF-AAS instruments when the graphite atomizers in them were not tuned. The boron absorbances found with and without adjusting the graphite atomizers suggested that achieving an adequate absorbance for the determination of boron requires a sharp temperature profile that overshoots the target temperature during the atomization process. Chemical modifiers that could improve the boron absorbance without the need for using coating agents were tested. Calcium carbonate improved the boron absorbance but did not suppress variability in the peak height. Improvement of boron absorbance was comparatively less using iron nitrate or copper nitrate than using calcium carbonate, but variability in the peak height was clearly suppressed using iron nitrate or copper nitrate. The limit of detection was 0.0026 mg L(-1) when iron nitrate was used. It appears that iron nitrate is a useful new chemical modifier for the quick and simple determination of boron using GF-AAS.

  3. Use of sodium tungstate as a permanent chemical modifier for slurry sampling electrothermal atomic absorption spectrometric determination of indium in soils

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Garcia, Ignacio; Rivas, Ricardo E.; Hernandez-Cordoba, Manuel [University of Murcia, Department of Analytical Chemistry, Faculty of Chemistry, Murcia (Spain)

    2008-06-15

    A number of chemical modifiers have been assessed for the direct determination of indium in soils using electrothermal atomic absorption spectrometry and slurry sampling. The best results were obtained when the graphite atomizer was impregnated with sodium tungstate, which acts as a permanent chemical modifier. Slurries were prepared by suspending 100 mg sample in a solution containing 1% (v/v) concentrated nitric acid and 10% (v/v) concentrated hydrofluoric acid and then 15-{mu}L aliquots were directly introduced into the atomizer. Standard indium solutions prepared in the suspension medium in the range 4-80 {mu}g L{sup -1} indium were used for calibration. The relative standard deviation for ten consecutive measurements of a 40 {mu}g L{sup -1} indium solution was 2.8%. The limit of detection in soils was 0.1 {mu}g g{sup -1}. The reliability of the procedures was confirmed by analysing two standard reference materials and by using an alternative procedure. (orig.)

  4. Reversing Antisense Oligonucleotide Activity with a Sense Oligonucleotide Antidote: Proof of Concept Targeting Prothrombin.

    Science.gov (United States)

    Crosby, Jeff R; Zhao, Chenguang; Zhang, Hong; MacLeod, A Robert; Guo, Shuling; Monia, Brett P

    2015-12-01

    The tissue half-life of second-generation antisense oligonucleotide drugs (ASOs) is generally longer than traditional small molecule therapeutics. Thus, a strategy to reverse the activity of antisense drugs is warranted in certain settings. In this study, we describe a strategy employing the administration of a complementary sense oligonucleotide antidote (SOA). As a model system we have chosen to target the coagulation factor and antithrombotic drug target, prothrombin, to assess the feasibility of this approach. ASO targeting mouse prothrombin specifically suppressed >90% hepatic prothrombin mRNA levels and circulating prothrombin protein in mice. These effects were dose- and time-dependent, and as expected produced predictable increases in anticoagulation activity [prothrombin time/activated partial thromboplastin time (PT/aPTT)]. Treatment with prothrombin SOAs resulted in a dose-dependent reversal of ASO activity, as measured by a return in prothrombin mRNA levels and thrombin activity, and normalization of aPTT and PT. The antithrombotic activity of prothrombin ASOs was demonstrated in a FeCl3-induced thrombosis mouse model, and as predicted for this target, the doses required for antithrombotic activity were also associated with increased bleeding. Treatment with SOA was able to prevent prothrombin ASO-induced bleeding in a dose-dependent manner. These studies demonstrate for the first time the utility of SOAs to selectively and specifically reverse the intracellular effects of an antisense therapy.

  5. Application of chemical modified starch in adhesives%经化学改性后淀粉在胶粘剂中的应用

    Institute of Scientific and Technical Information of China (English)

    姜青松; 黄庆东; 李广源; 韦志福; 李军生; 胡孝勇

    2015-01-01

    The starch adhesives is a kind of environment friendly and renewable biomass products, which have broad application prospects. Starch has the disadvantages of low bond strength, poor water resistance, slow drying rate, etc,. and needs to be modified. In this paper, using the oxidation, esterification, crosslinking and grafting as the chemical methods to modify starch, the applications of the modified starch in adhesives and their development trend were reviewed.%淀粉胶粘剂是一种环保型、可再生型生物质产品,具有广阔应用前景。淀粉具有粘接强度低、耐水性差、干燥速度慢等缺点,需对其进行化学改性。本文综述了淀粉经氧化、酯化、交联化、接枝化等化学手段改性后在胶粘剂中的应用以及发展趋势。

  6. Electrochemical properties of the hexacyanoferrate(II)–ruthenium(III) complex immobilized on silica gel surface chemically modified with zirconium(IV) oxide

    Energy Technology Data Exchange (ETDEWEB)

    Panice, Lucimara B.; Oliveira, Elisangela A. de; Filho, Ricardo A.D. Molin; Oliveira, Daniela P. de [Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, 87020-900 Maringá, PR (Brazil); Lazarin, Angélica M., E-mail: amlazarin2@uem.br [Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, 87020-900 Maringá, PR (Brazil); Andreotti, Elza I.S.; Sernaglia, Rosana L. [Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, 87020-900 Maringá, PR (Brazil); Gushikem, Yoshitaka [Instituto de Química, Universidade Estadual de Campinas, Caixa Postal 6154, 13084-971 Campinas, São Paulo (Brazil)

    2014-10-15

    Highlights: • The cyano-bridged mixed valence ruthenium composite material was synthesized. • This newly synthesized compound was incorporated into a carbon paste electrode. • The electrode did not show significant changes in response after six months of use. • The modified electrode is very stable and reproducible. • The electrode sensor was successfully applied for ascorbic acid determination. - Abstract: The chemically modified silica gel with zirconium(IV) oxide was used to immobilize the [Fe(CN){sub 6}]{sup 4−} complex ion initially. The reaction of this material with [Ru(edta)H{sub 2}O]{sup −} complex ion formed the immobilized cyano-bridged mixed valence ruthenium complex, (≡Zr){sub 5}[(edta)RuNCFe(CN){sub 5}]. This material was incorporated into a carbon paste electrode and, its electrochemical properties were investigated. However, for an ascorbic acid solution, an enhancement of the anodic peak current was detected due to electrocatalytic oxidation. The electrode presented the same response for at least 150 successive measurements, with a good repeatability. The modified electrode is very stable and reproducible. The sensor was applied for ascorbic acid determination in pharmaceutical preparation with success.

  7. A sensitive method to detect the hepatitis B virus mutations by using solid phase PCR on oligonucleotide array

    Institute of Scientific and Technical Information of China (English)

    YAN QIN LU; JIN XIANG HAN; ZHONG LIN SHEN; CHUAN XI WANG

    2006-01-01

    A sensitive method based on solid phase PCR on oligonucleotide array was established to detect two point mutations 1896G-A and 1901G-A in hepatitis B virus (HBV) DNA, in which 6 probes including these two point mutations were immobilized on modified glass slides through 5' terminal linker,while the 3' terminal was made to be free. The mutated loci were designed to locate on the last nucleotides of 3' terminal respectively, and the positive control probes lacked the last nucleotide of 3' terminal in comparison with the probes used for detection. Probes fixed on oligonucleotide array were also the solid phase amplification primers. One pair of liquid primers was used to amplify the short template product from whole HBV DNA. Using target DNA as template, the solid primers were extended under the action of Taq DNA polymerase and incorporated with Cy-3dCTP as marker. During the thermal cycling reaction,probes served as solid phase amplification primers and amplification products bound to the oligonucleotide array, which could be visualized by incorporation with fluorescent dyes. After amplification, the oligonucleotide array was washed, performed with laser scanning, and then used for quantitative analysis to obtain the information for mutations. The hybridization results were compared with DNA sequencing. It was demonstrated that in case of sample A, the ratios of fluorescence intensities in wide type and in the muin these two loci. These results correlated to those obtained from DNA sequencing analysis in which the fluorescence intensity ratios in wide type and in the mutated types of 1996G-A and 1901D-A mutations in using solid phase PCR based on oligonucleotide array appears to be a sensitive and promising way to detect mutations with low-density.

  8. Immobilization of oligonucleotide probes on silicon surfaces using biotin–streptavidin system examined with microscopic and spectroscopic techniques

    Energy Technology Data Exchange (ETDEWEB)

    Awsiuk, K., E-mail: kamil.awsiuk@uj.edu.pl [M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, Kraków 30-059 (Poland); Rysz, J. [M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, Kraków 30-059 (Poland); Petrou, P. [Institute of Nuclear and Radiological Sciences and Technology, Energy and Safety, NCSR “Demokritos”, End Patriarchou Gregoriou Str., Aghia Paraskevi 15310 (Greece); Budkowski, A. [M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, Kraków 30-059 (Poland); Bernasik, A. [Faculty of Physics and Applied Computer Science, AGH-University of Science and Technology, Al. Mickiewicza 30, Kraków 30-059 (Poland); Kakabakos, S. [Institute of Nuclear and Radiological Sciences and Technology, Energy and Safety, NCSR “Demokritos”, End Patriarchou Gregoriou Str., Aghia Paraskevi 15310 (Greece); Marzec, M.M. [Faculty of Physics and Applied Computer Science, AGH-University of Science and Technology, Al. Mickiewicza 30, Kraków 30-059 (Poland); Raptis, I. [Institute for Advanced Materials, Physicochemical Processes, Nanotechnology and Microsystems, NCSR “Demokritos”, End Patriarchou Gregoriou Str., Aghia Paraskevi 15310 (Greece)

    2014-01-30

    To immobilize effectively oligonucleotide probes on SiO{sub 2} modified with (3-aminopropyl)triethoxysilane, four procedures based on streptavidin–biotin system are compared with Atomic Force Microscopy, Angle-Resolved X-ray Photoelectron Spectroscopy and Time-of-Flight Secondary Ion Mass Spectrometry. The first approach involves: adsorption of biotinylated Bovine Serum Albumin, blocking free surface sites with BSA, binding of streptavidin and biotinylated oligonucleotide (b-oligo). Final steps are exchanged in the second procedure with immobilization of preformed streptavidin–b-oligo conjugate. The third approach consists of streptavidin adsorption, blocking with BSA and b-oligo binding. Finally, streptavidin–b-oligo conjugate is immobilized directly within the fourth method. Surface coverage with biomolecules, determined from ARXPS, accords with average AFM height, and is anti-correlated with the intensity of Si+ ions. Higher biomolecular coverage was achieved during the last steps of the first (2.45(±0.38) mg/m{sup 2}) and second (1.31(±0.22) mg/m{sup 2}) approach, as compared to lower surface density resulting from the third (0.58(±0.20) mg/m{sup 2}) and fourth (0.41(±0.11) mg/m{sup 2}) method. Phosphorus atomic concentration indicates effectiveness of oligonucleotide immobilization. Secondary ions intensities, characteristic for oligonucleotides, streptavidin, BSA, and proteins, allow additional insight into overlayer composition. These measurements verify the ARXPS results and show the superiority of the first two immobilization approaches in terms of streptavidin and oligonucleotide density achieved onto the surface.

  9. A human in vitro whole blood assay to predict the systemic cytokine response to therapeutic oligonucleotides including siRNA.

    Directory of Open Access Journals (Sweden)

    Christoph Coch

    Full Text Available Therapeutic oligonucleotides including siRNA and immunostimulatory ligands of Toll-like receptors (TLR or RIG-I like helicases (RLH are a promising novel class of drugs. They are in clinical development for a broad spectrum of applications, e.g. as adjuvants in vaccines and for the immunotherapy of cancer. Species-specific immune activation leading to cytokine release is characteristic for therapeutic oligonucleotides either as an unwanted side effect or intended pharmacology. Reliable in vitro tests designed for therapeutic oligonucleotides are therefore urgently needed in order to predict clinical efficacy and to prevent unexpected harmful effects in clinical development. To serve this purpose, we here established a human whole blood assay (WBA that is fast and easy to perform. Its response to synthetic TLR ligands (R848: TLR7/8, LPS: TLR4 was on a comparable threshold to the more time consuming peripheral blood mononuclear cell (PBMC based assay. By contrast, the type I IFN profile provoked by intravenous CpG-DNA (TLR9 ligand in humans in vivo was more precisely replicated in the WBA than in stimulated PBMC. Since Heparin and EDTA, but not Hirudin, displaced oligonucleotides from their delivery agent, only Hirudin qualified as the anticoagulant to be used in the WBA. The Hirudin WBA exhibited a similar capacity as the PBMC assay to distinguish between TLR7-activating and modified non-stimulatory siRNA sequences. RNA-based immunoactivating TLR7/8- and RIG-I-ligands induced substantial amounts of IFN-α in the Hirudin-WBA dependent on delivery agent used. In conclusion, we present a human Hirudin WBA to determine therapeutic oligonucleotide-induced cytokine release during preclinical development that can readily be performed and offers a close reflection of human cytokine response in vivo.

  10. Improvement of the activation of lipase from Candida rugosa following physical and chemical immobilization on modified mesoporous silica.

    Science.gov (United States)

    Wang, Chunfeng; Li, Yanjing; Zhou, Guowei; Jiang, Xiaojie; Xu, Yunqiang; Bu, Zhaosheng

    2014-12-01

    Lipase from Candida rugosa (CRL) was chemically and physically immobilized onto four types of rod-shaped mesoporous silica (RSMS). RSMS prepared using surfactant P123 and poly(ethylene glycol) as co-templates was functionalized with (3-aminopropyl)triethoxysilane (APTES) to obtain P-RSMS by post-synthesis grafting. Tetraethoxysilane was hydrothermally co-condensed with APTES to obtain C-RSMS. A two-step process using APTES and glutaraldehyde was also performed to obtain G-RSMS. The effects of modification methods (including post-synthesis grafting and co-condensation) and glutaraldehyde on the mesoscopic order, interplanar spacing d100, cell parameter a0, mesoporous structure, and wall thickness of RSMS were studied in detail. Results showed that all samples were mesoporous materials with 2D mesostructures (p6mm). Pore size and d100 decreased, whereas the wall thickness increased after different modifications. CRL was used as a model enzyme to determine the effect of physical and chemical adsorption on loading amount and enzymatic activity. The possible mechanism of CRL immobilization on G-RSMS by chemical adsorption was systematically investigated. The chemical immobilization of CRL on G-RSMS increased the loading amount, hydrolytic activity, thermal stability, and reusability. Moreover, immobilized CRL was employed to catalyze the resolution of 2-octanol by esterification with caprylic acid. The enantiomeric excess of 2-octanol was 45.8% when the reaction was catalyzed by G-RSMS-CRL and decreased to about 38%-39% using the physically immobilized CRL, after 48 h of reaction in hexane. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Relative embryotoxicity of two classes of chemicals in a modified zebrafish embryotoxicity test and comparison with their in vivo potencies.

    Science.gov (United States)

    Hermsen, Sanne A B; van den Brandhof, Evert-Jan; van der Ven, Leo T M; Piersma, Aldert H

    2011-04-01

    The zebrafish embryotoxicity test (ZET) is a fast and simple method to study chemical toxicity after exposure of the complete vertebrate embryo during embryogenesis in ovo. We developed a novel quantitative evaluation method to assess the development of the zebrafish embryo based on specific endpoints in time, the general morphology score (GMS) system. For teratogenic effects a separate scoring list was developed. The relative effects of eight glycol ethers and six 1,2,4-triazole anti-fungals were evaluated in this system and results were compared with in vivo developmental toxicity potencies. Methoxyacetic acid and ethoxyacetic acid appeared as the most potent glycol ether metabolites, inducing growth retardation and malformations. Other glycol ethers showed no developmental toxicity. Flusilazole appeared the most potent triazole, followed by hexaconazole, cyproconazole, triadimefon, myclobutanil and triticonazole, respectively. In general, the potency ranking of the compounds within their class in the ZET was comparable to their in vivo ranking. In conclusion, the ZET with the GMS system appears an efficient and useful test system for screening embryotoxic properties of chemicals within the classes of compounds tested. This alternative test method may also be useful for the detection of embryotoxic properties of other classes of chemicals.

  12. Electrochemical behavior of folic acid at calixarene based chemically modified electrodes and its determination by adsorptive stripping voltammetry

    Energy Technology Data Exchange (ETDEWEB)

    Vaze, Vishwanath D. [Department of Chemistry, University of Mumbai, Vidyanagari, Santacruz (East), Mumbai 400098 (India); Srivastava, Ashwini K. [Department of Chemistry, University of Mumbai, Vidyanagari, Santacruz (East), Mumbai 400098 (India)], E-mail: aksrivastava@chem.mu.ac.in

    2007-12-31

    Voltammetric behavior of folic acid at plain carbon paste electrode and electrode modified with calixarenes has been studied. Two peaks for irreversible oxidation were observed. Out of the three calixarenes chosen for modification of the electrodes, p-tert-butyl-calix[6]arene modified electrode (CME-6) was found to have better sensitivity for folic acid. Chronocoulometric and differential pulse voltammetric studies reveal that folic acid can assemble at CME-6 to form a monolayer whose electron transfer rate is 0.00273 s{sup -1} with 2-electron/2-proton transfer for the peak at +0.71 V against SCE. An adsorption equilibrium constant of 5 x 10{sup 3} l/mol for maximum surface coverage of 2.89 x 10{sup -10} mol/cm{sup 2} was obtained. The current is found to be rectilinear with concentration by differential pulse voltammetry. However, linearity in the lower range of concentration 8.79 x 10{sup -12} M to 1.93 x 10{sup -9} M with correlation coefficient of 0.9920 was achieved by adsorptive stripping voltammetry. The limit of detection obtained was found to be 1.24 x 10{sup -12} M. This method was used for the determination of folic acid in a variety of samples, viz. serum, asparagus, spinach, oranges and multivitamin preparations.

  13. Antisense oligonucleotides for the treatment of dyslipidaemia.

    Science.gov (United States)

    Visser, Maartje E; Witztum, Joseph L; Stroes, Erik S G; Kastelein, John J P

    2012-06-01

    Antisense oligonucleotides (ASOs) are short synthetic analogues of natural nucleic acids designed to specifically bind to a target messenger RNA (mRNA) by Watson-Crick hybridization, inducing selective degradation of the mRNA or prohibiting translation of the selected mRNA into protein. Antisense technology has the ability to inhibit unique targets with high specificity and can be used to inhibit synthesis of a wide range of proteins that could influence lipoprotein levels and other targets. A number of different classes of antisense agents are under development. To date, mipomersen, a 2'-O-methoxyethyl phosphorothioate 20-mer ASO, is the most advanced ASO in clinical development. It is a second-generation ASO developed to inhibit the synthesis of apolipoprotein B (apoB)-100 in the liver. In Phase 3 clinical trials, mipomersen has been shown to significantly reduce plasma low-density lipoprotein cholesterol (LDL-c) as well as other atherogenic apoB containing lipoproteins such as lipoprotein (a) [Lp(a)] and small-dense LDL particles. Although concerns have been raised because of an increase in intrahepatic triglyceride content, preliminary data from long-term studies suggest that with continued treatment, liver fat levels tend to stabilize or decline. Further studies are needed to evaluate potential clinical relevance of these changes. Proprotein convertase subtilisin/kexin-9 (PCSK9) is another promising novel target for lowering LDL-c by ASOs. Both second-generation ASOs and ASOs using locked nucleic acid technology have been developed to inhibit PCSK9 and are under clinical development. Other targets currently being addressed include apoC-III and apo(a) or Lp(a). By directly inhibiting the synthesis of specific proteins, ASO technology offers a promising new approach to influence the metabolism of lipids and to control lipoprotein levels. Its application to a wide variety of potential targets can be expected if these agents prove to be clinically safe and

  14. Synthesis, hybridization and fluorescence properties of a 2'-C-pyrene-triazole modified arabino-uridine nucleotide

    DEFF Research Database (Denmark)

    Kumar, Pawan; Sharma, Pawan K.; Nielsen, Poul

    2017-01-01

    A new pyrene-modified nucleotide monomer is introduced, wherein pyrene is attached to the 2'-position of arabino-uridine through a triazolemethyl linker. When the monomer is introduced into oligonucleotides, very stable DNA duplexes and three way junctions are obtained. An oligonucleotide featuri...

  15. Cleavage and protection of locked nucleic acid-modified DNA by restriction endonucleases

    DEFF Research Database (Denmark)

    Crouzier, Lucile; Dubois, Camille; Wengel, Jesper;

    2012-01-01

    Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far. We herein for the first time report cleavage by restriction endonuclease of LNA-modified DNA oligonucleotides. The experiments revealed that RsaI is an efficient enzyme capable of recognizing and cleaving...... LNA-modified DNA oligonucleotides. Furthermore, introduction of LNA nucleotides protects against cleavage by the restriction endonucleases PvuII, PstI, SacI, KpnI and EcoRI....

  16. Monitoring of labeled antisense oligonucleotides within living cells by using a multifrequency phase/modulation approach for fluorescence lifetime measurements

    Science.gov (United States)

    Kocisova, E.; Sureau, F.; Praus, P.; Rosenberg, I.; Stepanek, J.; Turpin, P.-Y.

    2003-06-01

    A multifrequency phase/modulation method has been developed for our UV confocal laser microspectrofluorimeter (modulation frequency 1-200 MHz) for fluorescence lifetime measurements. This technique enables excited state lifetimes of mixed fluorescent components to be resolved and the fluorescence spectral contribution of each species to be determined without using any model spectra. This approach is very efficient for analyzing intracellular multicomponent fluorescence signals. Our effort is focused on the elucidation of the intracellular behavior of synthetic modified oligonucleotides - potential drugs for antisense and/or antigene strategies of curing viral and malignant diseases. A novel type single stranded dT 15 oligomer analogue containing isopolar, non-isosteric, phosphonate-based internucleotide linkages (3'-O-P-CH 2-O-5'), labeled with tetramethylrhodamine dye at the 3'-end, has been utilized. This method, along with fluorescence micro-imaging, was used to monitor uptake, distribution and stability of our modified oligonucleotide inside living cells. Binding to Escort™ vector leads to an homogeneous intracellular distribution of fluorescent labeled oligonucleotide, including nucleus staining, while point distribution only is achieved for its free form.

  17. Chemically modified polymeric resins for solid-phase extraction and group separation prior to analysis by liquid or gas chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, L.W.

    1993-07-01

    Polystyrene divinylbenzene was modified by acetyl, sulfonic acid, and quaternary ammonium groups. A resin functionalized with an acetyl group was impregnated in a PTFE membrane and used to extract and concentrate phenolic compounds from aqueous samples. The acetyl group created a surface easily wetted, making it an efficient adsorbent for polar compounds in water. The membrane stabilized the resin bed. Partially sulfonated high surface area resins are used to extract and group separate an aqueous mixture of neutral and basic organics; the bases are adsorbed electrostatically to the sulfonic acid groups, while the neutraons are adsorbed hydrophobically. A two-step elution is then used to separate the two fractions. A partially functionalized anion exchange resin is used to separate organic acids and phenols from neutrals in a similar way. Carboxylic acids are analyzed by HPLC and phenols by GC.

  18. Novel epoxy-silicone thermolytic transparent packaging adhesives chemical modified by ZnO nanowires for HB LEDs

    Energy Technology Data Exchange (ETDEWEB)

    He Ying, E-mail: yinghe@staff.shu.edu.c [Shanghai University, Department of Polymer Materials, School of Materials Science and Engineering (China); Wang Junan [Shanghai University, Institute of Materials, School of Materials Science and Engineering (China); Pei Changlong; Song Jizhong; Zhu Di; Chen Jie [Shanghai University, Department of Polymer Materials, School of Materials Science and Engineering (China)

    2010-10-15

    A novel high transparent thermolytic epoxy-silicone for high-brightness light-emitting diode (HB-LED) is introduced, which was synthesized by polymerization using silicone matrix via diglycidyl ether bisphenol-A epoxy resin (DGEBA) as reinforcing agent, and filling ZnO nanowires to modify thermal conductivity and control refractive index of the hybrid material. The interactions of ZnO nanowires with polymers are mediated by the ligands attached to the nanoparticles. Thus, the ligands markedly influence the properties of ZnO nanowires/epoxy-silicone composites. The refractive indices of the prepared hybrid adhesives can be tuned by the ZnO nanowires from 1.4711 to 1.5605. Light transmittance can be increased by 20% from 80 to 95%. The thermal conductivity of the transparent packaging adhesives is 0.89-0.90 W/mK.

  19. Novel epoxy-silicone thermolytic transparent packaging adhesives chemical modified by ZnO nanowires for HB LEDs

    Science.gov (United States)

    He, Ying; Wang, Jun-An; Pei, Chang-Long; Song, Ji-Zhong; Zhu, Di; Chen, Jie

    2010-10-01

    A novel high transparent thermolytic epoxy-silicone for high-brightness light-emitting diode (HB-LED) is introduced, which was synthesized by polymerization using silicone matrix via diglycidyl ether bisphenol-A epoxy resin (DGEBA) as reinforcing agent, and filling ZnO nanowires to modify thermal conductivity and control refractive index of the hybrid material. The interactions of ZnO nanowires with polymers are mediated by the ligands attached to the nanoparticles. Thus, the ligands markedly influence the properties of ZnO nanowires/epoxy-silicone composites. The refractive indices of the prepared hybrid adhesives can be tuned by the ZnO nanowires from 1.4711 to 1.5605. Light transmittance can be increased by 20% from 80 to 95%. The thermal conductivity of the transparent packaging adhesives is 0.89-0.90 W/mK.

  20. Nano-hydroxyapatite colloid suspension coated on chemically modified porous silicon by cathodic bias: a suitable surface for cell culture

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez, Alejandra [Escuela de Quimica, Universidad de Costa Rica, 2060 (Costa Rica); Centro de Electroquimica y Energia Quimica de la Universidad de Costa Rica (CELEQ), Universidad de Costa Rica, 2060 (Costa Rica); Gonzalez, Jerson [Escuela de Quimica, Universidad de Costa Rica, 2060 (Costa Rica); Garcia-Pineres, Alfonso [Escuela de Quimica, Universidad de Costa Rica, 2060 (Costa Rica); Centro de Investigacion en Biologia Celular y Molecular (CIBCM), Universidad de Costa Rica, 2060 (Costa Rica); Montero, Mavis L. [Escuela de Quimica, Universidad de Costa Rica, 2060 (Costa Rica); Centro de Electroquimica y Energia Quimica de la Universidad de Costa Rica (CELEQ), Universidad de Costa Rica, 2060 (Costa Rica); Centro de Ciencia e Ingenieria en Materiales (CICIMA), Universidad de Costa Rica, 2060 (Costa Rica)

    2011-06-15

    The properties of porous silicon make it an interesting material for biological applications. However, porous silicon is not an appropriate surface for cell growth. Surface modification is an alternative that could afford a bioactive material. In this work, we report a method to yield materials by modification of the porous silicon surface with hydroxyapatite of nanometric dimensions, produced using an electrochemical process and coated on macroporous silicon substrates by cathodic bias. The chemical nature of the calcium phosphate deposited on the substrates after the experimental process and the amount of cell growth on these surfaces were characterized. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)