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Sample records for nucleic acid-based electrical

  1. Developing nucleic acid-based electrical detection systems

    OpenAIRE

    Gabig-Ciminska Magdalena

    2006-01-01

    Abstract Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and r...

  2. Developing nucleic acid-based electrical detection systems

    OpenAIRE

    Gabig-Ciminska Magdalena

    2006-01-01

    Abstract Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and r...

  3. Developing nucleic acid-based electrical detection systems

    Directory of Open Access Journals (Sweden)

    Gabig-Ciminska Magdalena

    2006-03-01

    Full Text Available Abstract Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and requirements for an ideal detector suitable for nucleic acid analysis include high sensitivity and high specificity protocol that can be completed in a relatively short time offering at the same time low detection limit. Moreover, systems that can be miniaturized and automated present a significant advantage over conventional technology, especially if detection is needed in the field. Electrical system technology for nucleic acid-based detection is an enabling mode for making miniaturized to micro- and nanometer scale bio-monitoring devices via the fusion of modern micro- and nanofabrication technology and molecular biotechnology. The electrical biosensors that rely on the conversion of the Watson-Crick base-pair recognition event into a useful electrical signal are advancing rapidly, and recently are receiving much attention as a valuable tool for microbial pathogen detection. Pathogens may pose a serious threat to humans, animal and plants, thus their detection and analysis is a significant element of public health. Although different conventional methods for detection of pathogenic microorganisms and their toxins exist and are currently being applied, improvements of molecular-based detection methodologies have changed these traditional detection techniques and introduced a new era of rapid, miniaturized and automated electrical chip detection technologies into pathogen identification sector. In this review some developments and current directions in

  4. Nucleic acid based logical systems.

    Science.gov (United States)

    Han, Da; Kang, Huaizhi; Zhang, Tao; Wu, Cuichen; Zhou, Cuisong; You, Mingxu; Chen, Zhuo; Zhang, Xiaobing; Tan, Weihong

    2014-05-12

    Researchers increasingly visualize a significant role for artificial biochemical logical systems in biological engineering, much like digital logic circuits in electrical engineering. Those logical systems could be utilized as a type of servomechanism to control nanodevices in vitro, monitor chemical reactions in situ, or regulate gene expression in vivo. Nucleic acids (NA), as carriers of genetic information with well-regulated and predictable structures, are promising materials for the design and engineering of biochemical circuits. A number of logical devices based on nucleic acids (NA) have been designed to handle various processes for technological or biotechnological purposes. This article focuses on the most recent and important developments in NA-based logical devices and their evolution from in vitro, through cellular, even towards in vivo biological applications.

  5. Nucleic Acid-Based Nanoconstructs

    Science.gov (United States)

    Focuses on the design, synthesis, characterization, and development of spherical nucleic acid constructs as effective nanotherapeutic, single-entity agents for the treatment of glioblastoma multiforme and prostate cancers.

  6. Nucleic Acid--Based Nanodevices in Biological Imaging

    Science.gov (United States)

    Chakraborty, Kasturi; Veetil, Aneesh T.

    2017-01-01

    The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid--based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid--based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand. PMID:27294440

  7. Nucleic Acid-Based Nanodevices in Biological Imaging.

    Science.gov (United States)

    Chakraborty, Kasturi; Veetil, Aneesh T; Jaffrey, Samie R; Krishnan, Yamuna

    2016-06-02

    The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.

  8. A locked nucleic Acid-based nanocrawler

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Pasternak, Karol; Campbell, Meghan A

    2013-01-01

    Herein we introduce a novel fluorescent LNA/DNA machine, a nanocrawler, which reversibly moves along a directionally polar complementary road controlled by affinity-enhancing locked nucleic acid (LNA) monomers and additional regulatory strands. Polyaromatic hydrocarbon (PAH) dyes attached to 2......'-amino-LNA monomers are incorporated at four stations of the system, enabling simple detection of the position of the nanocrawler via a step-specific color signal. The sensing is provided by highly sensitive, chemically stable, and photostable PAH LNA interstrand communication systems, including pyrene...

  9. Boronic acid-based autoligation of nucleic acids

    DEFF Research Database (Denmark)

    Barbeyron, R.; Vasseur, J.-J.; Smietana, M.;

    2013-01-01

    Abstract: The development of synthetic systems displaying dynamic and adaptive characteristics is a formidable challenge with wide applications from biotechnology to therapeutics. Recently, we described a dynamic and programmable nucleic acid-based system relying on the formation of reversible...... boronate internucleosidic linkages. The DNA- or RNA-templated system comprises a 5′-ended boronic acid probe connecting a 3′-ended ribonucleosidic oligonucleotide partner. To explore the dominant factors that control the reversible linkage, we synthesized a series of 3′-end modified ribonucleotidic strands...

  10. Advances in nucleic acid-based diagnostics of bacterial infections

    DEFF Research Database (Denmark)

    Barken, Kim Bundvig; Haagensen, Janus Anders Juul; Tolker-Nielsen, Tim

    2007-01-01

    and slow growing microorgansims. The widespread use of antibiotics has resulted in an increased number of cases with resistant microorganisms such as methicillin-resistant Staphylococcus aureus, vancomycin resistant enterococci, and multidrug-resistant Mycobacterium tuberculosis. Rapid detection...... of multiparameter assays where several pathogens and antibiotic resistance genes can be detected simultaneously.......Methods for rapid detection of infectious bacteria and antimicrobial-resistant pathogens have evolved significantly over the last decade. Many of the new procedures are nucleic acid-based and replace conventional diagnostic methods like culturing which is time consuming especially with fastidious...

  11. Nucleic Acid-Based Therapy Approaches for Huntington's Disease

    Directory of Open Access Journals (Sweden)

    Tatyana Vagner

    2012-01-01

    Full Text Available Huntington's disease (HD is caused by a dominant mutation that results in an unstable expansion of a CAG repeat in the huntingtin gene leading to a toxic gain of function in huntingtin protein which causes massive neurodegeneration mainly in the striatum and clinical symptoms associated with the disease. Since the mutation has multiple effects in the cell and the precise mechanism of the disease remains to be elucidated, gene therapy approaches have been developed that intervene in different aspects of the condition. These approaches include increasing expression of growth factors, decreasing levels of mutant huntingtin, and restoring cell metabolism and transcriptional balance. The aim of this paper is to outline the nucleic acid-based therapeutic strategies that have been tested to date.

  12. Solution influence on biomolecular equilibria - Nucleic acid base associations

    Science.gov (United States)

    Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.

    1984-01-01

    Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

  13. [Development of Nucleic Acid-Based Adjuvant for Cancer Immunotherapy].

    Science.gov (United States)

    Kobiyama, Kouji; Ishii, Ken J

    2015-09-01

    Since the discovery of the human T cell-defined tumor antigen, the cancer immunotherapy field has rapidly progressed, with the research and development of cancer immunotherapy, including cancer vaccines, being conducted actively. However, the disadvantages of most cancer vaccines include relatively weak immunogenicity and immune escape or exhaustion. Adjuvants with innate immunostimulatory activities have been used to overcome these issues, and these agents have been shown to enhance the immunogenicity of cancer vaccines and to act as mono-therapeutic anti-tumor agents. CpG ODN, an agonist for TLR9, is one of the promising nucleic acid-based adjuvants, and it is a potent inducer of innate immune effector functions. CpG ODN suppresses tumor growth in the absence of tumor antigens and peptide administration. Therefore, CpG ODN is expected to be useful as a cancer vaccine adjuvant as well as a cancer immunotherapy agent. In this review, we discuss the potential therapeutic applications and mechanisms of CpG ODN for cancer immunotherapy.

  14. Biomedical Applications of Quantum Dots, Nucleic Acid-Based Aptamers, and Nanostructures in Biosensors.

    Science.gov (United States)

    Meshik, Xenia; Farid, Sidra; Choi, Min; Lan, Yi; Mukherjee, Souvik; Datta, Debopam; Dutta, Mitra; Stroscio, Michael A

    2015-01-01

    This review is a survey of the biomedical applications of semiconductor quantum dots, nucleic acid-based aptamers, and nanosensors as molecular biosensors. It focuses on the detection of analytes in biomedical applications using (1) advances in molecular beacons incorporating semiconductor quantum dots and nanoscale quenching elements; (2) aptamer-based nanosensors on a variety of platforms, including graphene; (3) Raman scattering and surface-enhanced Raman scattering (SERS) using nanostructures for enhanced SERS spectra of biomolecules, including aptamers; and (4) the electrical and optical properties of nanostructures incorporated into molecular beacons and aptamer-based nanosensors. Research done at the University of Illinois at Chicago (UIC) is highlighted throughout since it emphasizes the specific approaches taken by the bioengineering department at UIC.

  15. Spherical Nucleic Acids as Intracellular Agents for Nucleic Acid Based Therapeutics

    Science.gov (United States)

    Hao, Liangliang

    Recent functional discoveries on the noncoding sequences of human genome and transcriptome could lead to revolutionary treatment modalities because the noncoding RNAs (ncRNAs) can be applied as therapeutic agents to manipulate disease-causing genes. To date few nucleic acid-based therapeutics have been translated into the clinic due to challenges in the delivery of the oligonucleotide agents in an effective, cell specific, and non-toxic fashion. Unmodified oligonucleotide agents are destroyed rapidly in biological fluids by enzymatic degradation and have difficulty crossing the plasma membrane without the aid of transfection reagents, which often cause inflammatory, cytotoxic, or immunogenic side effects. Spherical nucleic acids (SNAs), nanoparticles consisting of densely organized and highly oriented oligonucleotides, pose one possible solution to circumventing these problems in both the antisense and RNA interference (RNAi) pathways. The unique three dimensional architecture of SNAs protects the bioactive oligonucleotides from unspecific degradation during delivery and supports their targeting of class A scavenger receptors and endocytosis via a lipid-raft-dependent, caveolae-mediated pathway. Owing to their unique structure, SNAs are able to cross cell membranes and regulate target genes expression as a single entity, without triggering the cellular innate immune response. Herein, my thesis has focused on understanding the interactions between SNAs and cellular components and developing SNA-based nanostructures to improve therapeutic capabilities. Specifically, I developed a novel SNA-based, nanoscale agent for delivery of therapeutic oligonucleotides to manipulate microRNAs (miRNAs), the endogenous post-transcriptional gene regulators. I investigated the role of SNAs involving miRNAs in anti-cancer or anti-inflammation responses in cells and in in vivo murine disease models via systemic injection. Furthermore, I explored using different strategies to construct

  16. Nucleic Acid-Based Approaches for Detection of Viral Hepatitis

    OpenAIRE

    BEHZADI, Payam; Ranjbar, Reza; Alavian, Seyed Moayed

    2014-01-01

    Context: To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections. Results: Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensit...

  17. Nucleic Acid-based Detection of Bacterial Pathogens Using Integrated Microfluidic Platform Systems

    Directory of Open Access Journals (Sweden)

    Carl A. Batt

    2009-05-01

    Full Text Available The advent of nucleic acid-based pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques, driving the development of portable, integrated biosensors. The miniaturization and automation of integrated detection systems presents a significant advantage for rapid, portable field-based testing. In this review, we highlight current developments and directions in nucleic acid-based micro total analysis systems for the detection of bacterial pathogens. Recent progress in the miniaturization of microfluidic processing steps for cell capture, DNA extraction and purification, polymerase chain reaction, and product detection are detailed. Discussions include strategies and challenges for implementation of an integrated portable platform.

  18. Nucleic acid-based aptamers: applications, development and clinical trials.

    Science.gov (United States)

    Kanwar, Jagat R; Roy, Kislay; Maremanda, Nihal G; Subramanian, Krishnakumar; Veedu, Rakesh N; Bawa, Raj; Kanwar, Rupinder K

    2015-01-01

    Short single-stranded oligonucleotides called aptamers, often termed as chemical antibodies, have been developed as powerful alternatives to traditional antibodies with respect to their obvious advantages like high specificity and affinity, longer shelf-life, easier manufacturing protocol, freedom to introduce chemical modifications for further improvement, etc. Reiterative selection process of aptamers over 10-15 cycles starting from a large initial pool of random nucleotide sequences renders them with high binding affinity, thereby making them extremely specific for their targets. Aptamer-based detection systems are well investigated and likely to displace primitive detection systems. Aptamer chimeras (combination of aptamers with another aptamer or biomacromolecule or chemical moiety) have the potential activity of both the parent molecules, and thus hold the capability to perform diverse functions at the same time. Owing to their extremely high specificity and lack of immunogenicity or pathogenicity, a number of other aptamers have recently entered clinical trials and have garnered favorable attention from pharmaceutical companies. Promising results from the clinical trials provide new hope to change the conventional style of therapy. Aptamers have attained high therapeutic relevance in a short time as compared to synthetic drugs and/or other modes of therapy. This review follows the various trends in aptamer technology including production, selection, modifications and success in clinical fields. It focusses largely on the various applications of aptamers which mainly depend upon their selection procedures. The review also sheds light on various modifications and chimerizations that have been implemented in order to improve the stability and functioning of the aptamers, including introduction of locked nucleic acids (LNAs). The application of various aptamers in detection systems has been discussed elaborately in order to stress on their role as efficient

  19. Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems

    DEFF Research Database (Denmark)

    Börjesson, Karl; Preus, Søren; El-Sagheer, Afaf

    2009-01-01

    distances covering up to more than one turn of the DNA duplex. Importantly, we show that the rigid stacking of the two base analogs, and consequently excellent control of their exact positions and orientations, results in a high control of the orientation factor and hence very distinct FRET changes...... as the number of bases separating tCO and tC(nitro) is varied. A set of DNA strands containing the FRET-pair at wisely chosen locations will, thus, make it possible to accurately distinguish distance- from orientation-changes using FRET. In combination with the good nucleobase analog properties, this points...... toward detailed studies of the inherent dynamics of nucleic acid structures. Moreover, the placement of FRET-pair chromophores inside the base stack will be a great advantage in studies where other (biomacro)molecules interact with the nucleic acid. Lastly, our study gives possibly the first truly solid...

  20. Nucleic acid-based methods for the early detection of sepsis in heart transplant recipients

    Directory of Open Access Journals (Sweden)

    Sarvesh Pal Singh

    2016-01-01

    Full Text Available Nucleic acid-based tests (NABTs were developed to decrease the time required to identify microorganism in the pathological specimens. The commercially available NABTs are of two types – one those can be applied to positive cultures grown in blood culture bottles and other those can be applied directly to blood samples. The latter tests are polymerase chain reaction (PCR-based assays which can amplify the existing load of microorganism nucleic acids many a times like a culture in a blood culture bottle. Both tests then identify the pathogenic organisms with the use of specific nucleic acid probes. These tests have proven useful in management of heart transplant sepsis management.

  1. Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium.

    Science.gov (United States)

    Mianzhi, Yao; Shah, Nagendra P

    2017-03-24

    Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.

  2. A Prebiotic Chemistry Experiment on the Adsorption of Nucleic Acids Bases onto a Natural Zeolite

    Science.gov (United States)

    Anizelli, Pedro R.; Baú, João Paulo T.; Gomes, Frederico P.; da Costa, Antonio Carlos S.; Carneiro, Cristine E. A.; Zaia, Cássia Thaïs B. V.; Zaia, Dimas A. M.

    2015-09-01

    There are currently few mechanisms that can explain how nucleic acid bases were synthesized, concentrated from dilute solutions, and/or protected against degradation by UV radiation or hydrolysis on the prebiotic Earth. A natural zeolite exhibited the potential to adsorb adenine, cytosine, thymine, and uracil over a range of pH, with greater adsorption of adenine and cytosine at acidic pH. Adsorption of all nucleic acid bases was decreased in artificial seawater compared to water, likely due to cation complexation. Furthermore, adsorption of adenine appeared to protect natural zeolite from thermal degradation. The C=O groups from thymine, cytosine and uracil appeared to assist the dissolution of the mineral while the NH2 group from adenine had no effect. As shown by FT-IR spectroscopy, adenine interacted with a natural zeolite through the NH2 group, and cytosine through the C=O group. A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters.

  3. A Prebiotic Chemistry Experiment on the Adsorption of Nucleic Acids Bases onto a Natural Zeolite.

    Science.gov (United States)

    Anizelli, Pedro R; Baú, João Paulo T; Gomes, Frederico P; da Costa, Antonio Carlos S; Carneiro, Cristine E A; Zaia, Cássia Thaïs B V; Zaia, Dimas A M

    2015-09-01

    There are currently few mechanisms that can explain how nucleic acid bases were synthesized, concentrated from dilute solutions, and/or protected against degradation by UV radiation or hydrolysis on the prebiotic Earth. A natural zeolite exhibited the potential to adsorb adenine, cytosine, thymine, and uracil over a range of pH, with greater adsorption of adenine and cytosine at acidic pH. Adsorption of all nucleic acid bases was decreased in artificial seawater compared to water, likely due to cation complexation. Furthermore, adsorption of adenine appeared to protect natural zeolite from thermal degradation. The C=O groups from thymine, cytosine and uracil appeared to assist the dissolution of the mineral while the NH2 group from adenine had no effect. As shown by FT-IR spectroscopy, adenine interacted with a natural zeolite through the NH2 group, and cytosine through the C=O group. A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters.

  4. Treatment of allergic asthma by targeting transcription factors using nucleic-acid based technologies.

    Science.gov (United States)

    Sel, Serdar; Henke, Wolfgang; Dietrich, Alexander; Herz, Udo; Renz, Harald

    2006-01-01

    There is considerable evidence that T-helper 2 (Th2) cells play a central role in the pathogenesis of allergic diseases such as bronchial asthma, hay fever or food allergy. The differentiation of naïve T cells into Th2 cells producing a specific pattern of cytokines is tightly controlled and regulated by transcription factors. Thus down-regulation of mRNA-levels of a single transcription factor leads to a "knock-down" of several mediators simultaneously, representing an advantage compared to earlier approaches involving down-regulation of one intercellular inflammatory mediator, which is unlikely to influence all pathophysiological aspects of the disease. We review the impact of specific and master transcription factors involved in Th2 cell commitment and evaluate approaches for the down-regulation of these proteins by degradation of their mRNA using nucleic-acid based technologies including antisense oligonucleotides, ribozymes, DNAzymes, decoys oligonucleotides and RNA interference.

  5. Interactions of Nucleic Acid Bases with Temozolomide. Stacked, Perpendicular, and Coplanar Heterodimers.

    Science.gov (United States)

    Kasende, Okuma Emile; Nziko, Vincent de Paul N; Scheiner, Steve

    2016-09-01

    Temozolomide (TMZ) was paired with each of the five nucleic acid bases, and the potential energy surface searched for all minima, in the context of dispersion-corrected density functional theory and MP2 methods. Three types of arrangements were observed, with competitive stabilities. Coplanar H-bonding structures, reminiscent of Watson-Crick base pairs were typically the lowest in energy, albeit by a small amount. Also very stable were perpendicular arrangements that included one or more H-bonds. The two monomers were stacked approximately parallel to one another in the third category, some of which contained weak and distorted H-bonds. Dispersion was found to be a dominating attractive force, largest for the stacked structures, and smallest for the coplanar dimers.

  6. Gas-phase hydration thermochemistry of sodiated and potassiated nucleic acid bases.

    Science.gov (United States)

    Wincel, Henryk

    2012-09-01

    Hydration reactions of sodiated and potassiated nucleic acid bases (uracil, thymine, cytosine, and adenine) produced by electrospray have been studied in a gas phase using the pulsed ion-beam high-pressure mass spectrometer. The thermochemical properties, ΔH(o)(n), ΔS(o)(n), and ΔG(o)(n), for the hydrated systems were obtained from hydration equilibrium measurement. The structural aspects of the hydrated complexes are discussed in conjunction with available literature data. The correlation between water binding energies in the hydrated complexes and the corresponding metal ion affinities of nucleobases suggests that a significant (if not dominant) amount of the canonical structure of cytosine undergoes tautomerization during electrospray ionization, and the thermochemical values for cationized cytosine probably correspond to a mixture of tautomeric complexes.

  7. The relationship between odd- and branched-chain fatty acids and microbial nucleic acid bases in rumen.

    Science.gov (United States)

    Liu, Keyuan; Hao, Xiaoyan; Li, Yang; Luo, Guobin; Zhang, Yonggen; Xin, Hangshu

    2017-06-26

    This study aims to identify the relationship between odd- and branched-chain fatty acids (OBCFAs) and microbial nucleic acid base in the rumen, and to establish a model to accurately predict microbial protein flow by using OBCFA. To develop the regression equations, data on the rumen contents of individual cows was obtained from 2 feeding experiments. In the first experiment, 3 rumen-fistulated dry dairy cows arranged in a 3×3 Latin square were fed diets of differing forage to concentration ratios (F:C). The second experiment consisted of 9 lactating Holstein dairy cows of similar body weights at the same fetal time. For each milk stage, 3 cows with similar milk production were selected. The rumen contents were sampled at 4 time points of every two hours after morning feeding 6 h, and then to analyse the concentrations of OBCFA and microbial nucleic acid bases in the rumen samples. The ruminal bacteria nucleic acid bases were significantly influenced by feeding diets of differing forge to concentration ratios and milk stages of dairy (P acids, especially odd-chain fatty acids and C15:0 isomers, strongly correlated with the microbial nucleic acid bases in the rumen (P acid bases which established by ruminal OBCFAs contents showed a good a good predictive capacity, as indicated by reasonably low SEs and high R-squared values. This finding suggests that the rumen OBCFA composition could be used as an internal marker of rumen microbial matter.

  8. Medical Devices; Immunology and Microbiology Devices; Classification of Gastrointestinal Microorganism Multiplex Nucleic Acid-Based Assay. Final order.

    Science.gov (United States)

    2015-11-02

    The Food and Drug Administration (FDA) is classifying a gastrointestinal microorganism multiplex nucleic acid-based assay into class II (special controls). The Agency is classifying the device into class II (special controls) in order to provide a reasonable assurance of safety and effectiveness of the device.

  9. Recent developments in nucleic acid based techniques for use in rumen manipulation

    Directory of Open Access Journals (Sweden)

    Christopher McSweeney

    2009-07-01

    Full Text Available Nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation are now being employed regularly in ruminant nutrition studies. Conventional culture-based methods for enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi have been superseded and are now used mainly to obtain pure isolates of novel organisms and reference strains that are required for the development and validation of the nucleic acid approaches. These reference strains are also essential for physiological studies of the lifestyle of the organisms as well as sources of genomic DNA and RNA that can be analysed for functional gene activity. The foundation of the molecular ecology techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. The use of this marker gene in assays involving the use of single nucleic acid probes or primer sets is rapidly evolving to high throughput approaches such as microarray analysis and new generation sequencing technologies. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The focus of nucleic acid research is now shifting to the functional analysis of the ecosystem which involves the measurement of functional genes and their expression in the predominant or specific members of the rumen microbial community. Functional gene studies are less developed than 16S rDNA-based analysis of community structure. Also for gene expression studies there are inherent problems involved in extracting high quality RNA from digesta, and priming cDNA synthesis from bacterial mRNA. This paper reviews nucleic acid based molecular methods which have recently been developed for studying the structure and function of rumen microbial

  10. Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases.

    Science.gov (United States)

    Psciuk, Brian T; Lord, Richard L; Munk, Barbara H; Schlegel, H Bernhard

    2012-12-11

    The oxidation potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine, thymine, uracil, xanthine, and 8-oxoguanine were computed using B3LYP and CBS-QB3 with the SMD solvation model. Acid-base and tautomeric equilibria present in aqueous solution were accounted for by combining standard redox potentials with calculated pKa and tautomerization energies to produce an ensemble averaged pH dependent potential. Gas phase free energies were computed using B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) and CBS-QB3. Solvation free energies were computed at the SMD/B3LYP/6-31+G(d,p) level of theory. Compared to experimental results, calculations with the CBS-QB3 level of theory have a mean absolute error (MAE) of ca. 1 kcal/mol for the gas phase proton affinity/gas phase basicity and an MAE of ca. 0.04 eV for the adiabatic/vertical ionization potentials. The B3LYP calculations have a MAE of ∼2 kcal/mol for the proton affinity/gas phase basicity data but systematically underestimated ionization potentials by 0.14-0.21 eV. Solvent cavities for charged solute species were rescaled uniformly by fitting computed pKa data to experimentally measured pKa values. After solvent cavity scaling, the MAEs for computed pKa's compared to experimental results are 0.7 for B3LYP and 0.9 for CBS-QB3. In acetonitrile, the computed E°(XH(+•)/XH) redox potentials are systematically lower than experimentally measured potentials by 0.21 V for CBS-QB3 and 0.33 V for B3LYP. However, the redox potentials relative to adenine are in very good agreement with experimental results, with MAEs of 0.10 V for CBS-QB3 and 0.07 V for B3LYP. In aqueous solution, B3LYP and CBS-QB3 have MAEs of 0.21 and 0.19 V for E7(X(•),H(+)/XH). Replacing the methyl substituent with ribose changes the calculated E7 potentials by 0.1-0.2 V. The calculated difference between the guanine and adenine oxidation potentials is too large compared to experimental results, but the calculated difference between

  11. A survey of advancements in nucleic acid-based logic gates and computing for applications in biotechnology and biomedicine.

    Science.gov (United States)

    Wu, Cuichen; Wan, Shuo; Hou, Weijia; Zhang, Liqin; Xu, Jiehua; Cui, Cheng; Wang, Yanyue; Hu, Jun; Tan, Weihong

    2015-03-04

    Nucleic acid-based logic devices were first introduced in 1994. Since then, science has seen the emergence of new logic systems for mimicking mathematical functions, diagnosing disease and even imitating biological systems. The unique features of nucleic acids, such as facile and high-throughput synthesis, Watson-Crick complementary base pairing, and predictable structures, together with the aid of programming design, have led to the widespread applications of nucleic acids (NA) for logic gate and computing in biotechnology and biomedicine. In this feature article, the development of in vitro NA logic systems will be discussed, as well as the expansion of such systems using various input molecules for potential cellular, or even in vivo, applications.

  12. Inulin Derivatives Obtained Via Enhanced Microwave Synthesis for Nucleic Acid Based Drug Delivery.

    Science.gov (United States)

    Sardo, Carla; Craparo, Emanuela Fabiola; Fiorica, Calogero; Giammona, Gaetano; Cavallaro, Gennara

    2015-01-01

    A new class of therapeutic agents with a high potential for the treatment of different socially relevant human diseases is represented by Nucleic Acid Based Drugs (NABD), including small interfering RNAs (siRNA), decoy oligodeoxynucleotides (decoy ODN) and antisense oligonucleotides (ASOs). Although NABD can be engineered to be specifically directed against virtually any target, their susceptibility to nuclease degradation and the difficulty of delivery into target tissues severely limit their use in clinical practice and require the development of an appropriate nanostructured delivery system. For delivery of NABD, Inulin (Inu), a natural, water soluble and biocompatible polysaccharide, was derivatized by Spermine (Spm), a flexible molecule with four amine groups that, having pKa values in the range between 8-11, is mainly in the protonated form at pH 7.4. The synthesis of related copolymers (Inu-Spm) was performed by a two step reaction, using a method termed Enhanced Microwave Synthesis (EMS) which has the advantage, compared to conventional microwave reaction, that high amount of energy can be applied to the reaction system, by administering microwave irradiation and simultaneously controlling the temperature in the reaction vessel with cooled air. The synthesized inulin derivatives were characterized by FT-IR spectra and (1)H-NMR. INU-Spm derivatives with a degree of derivatization of about 14 % mol/mol were obtained. These polycations were tested to evaluate their ability to form non covalent complexes with genetic material (polyplexes). Agarose gel retardation assays showed that the obtained copolymers are able to electrostatically interact with DNA duplex to form polyplexes at different c/p weight ratios. Moreover, light scattering studies, performed to analyze size and z-potential of polyplexes, evidenced that copolymers are able to interact with genetic material leading to the formation of nanoscaled systems. In addition, biocompatibility of polyplexes

  13. Application of locked nucleic acid-based probes in fluorescence in situ hybridization

    DEFF Research Database (Denmark)

    Fontenete, Sílvia; Carvalho, Daniel R; Guimarães, Nuno

    2016-01-01

    Fluorescence in situ hybridization (FISH) employing nucleic acid mimics as probes is becoming an emerging molecular tool in the microbiology area for the detection and visualization of microorganisms. However, the impact that locked nucleic acid (LNA) and 2′-O-methyl (2′-OMe) RNA modifications have...... on the probe that is targeting microorganisms is unknown. In this study, the melting and hybridization efficiency properties of 18 different probes in regards to their use in FISH for the detection of the 16S rRNA of Helicobacter pylori were compared. For the same sequence and target, probe length and the type...

  14. 77 FR 16126 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis

    Science.gov (United States)

    2012-03-19

    ... Food and Drug Administration 21 CFR Part 866 Microbiology Devices; Reclassification of Nucleic Acid... the Microbiology Devices Panel of the Medical Devices Advisory Committee (Microbiology Devices Panel.... VI. Risks to Health After considering the information discussed by the Microbiology Devices Panel...

  15. Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications.

    Science.gov (United States)

    Li, Juan; Mo, Liuting; Lu, Chun-Hua; Fu, Ting; Yang, Huang-Hao; Tan, Weihong

    2016-03-07

    Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of the DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.

  16. Small-Nucleic-Acid-Based Therapeutic Strategy Targeting the Transcription Factors Regulating the Vascular Inflammation, Remodeling and Fibrosis in Atherosclerosis

    Directory of Open Access Journals (Sweden)

    Sung Won Youn

    2015-05-01

    Full Text Available Atherosclerosis arises when injury to the arterial wall induces an inflammatory cascade that is sustained by a complex network of cytokines, together with accumulation of lipids and fibrous material. Inflammatory cascades involve leukocyte adherence and chemotaxis, which are coordinated by the local secretion of adhesion molecules, chemotactic factors, and cytokines. Transcription factors are critical to the integration of the various steps of the cascade response to mediators of vascular injury, and are induced in a stimulus-dependent and cell-type-specific manner. Several small-nucleic-acid-based therapeutic strategies have recently been developed to target transcription factors: antisense oligodeoxynucleotides, RNA interference, microRNA, and decoy oligodeoxynucleotides. The aim of this review was to provide an overview of these particular targeted therapeutic strategies, toward regulation of the vascular inflammation, remodeling and fibrosis associated with atherosclerosis.

  17. Physisorption of Nucleic Acid Bases on Boron Nitride Nanotubes: A new class of Hybrid Nano-Bio Materials

    CERN Document Server

    Mukhopadhyay, Saikat; Scheicher, Ralph H; Pandey, Ravindra; Karna, Shashi P

    2009-01-01

    We investigate the adsorption of the nucleic acid bases, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) on the outer wall of a high curvature semiconducting single-walled boron nitride nanotube (BNNT) by first principles density functional theory calculations. The calculated binding energy shows the order: G>A~C~T~U implying that the interaction strength of the (high-curvature) BNNT with the nucleobases, G being an exception, is nearly the same. A higher binding energy for the G-BNNT conjugate appears to result from a stronger hybridization of the molecular orbitals of G and BNNT, since the charge transfer involved in the physisorption process is insignificant. A smaller energy gap predicted for the G-BNNT conjugate relative to that of the pristine BNNT may be useful in application of this class of biofunctional materials to the design of the next generation sensing devices.

  18. Adsorption of nucleic acid bases and amino acids on single-walled carbon and boron nitride nanotubes: a first-principles study.

    Science.gov (United States)

    Zheng, Jiaxin; Song, Wei; Wang, Lu; Lu, Jing; Luo, Guangfu; Zhou, Jing; Qin, Rui; Li, Hong; Gao, Zhengxiang; Lai, Lin; Li, Guangping; Mei, Wai Ning

    2009-11-01

    We study the adsorptions of nucleic acid bases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) and four amino acids phenylalanine, tyrosine, tryptophan, alanine on the single-walled carbon nanotubes (SWCNTs) and boron nitride nanotubes (SWBNNTs) by using density functional theory. We find that the aromatic content plays a critical role in the adsorption. The adsorptions of nucleic acid bases and amino acids on the (7, 7) SWBNNT are stronger than those on the (7, 7) SWCNT. Oxidative treatment of SWCNTs favors the adsorption of biomolecules on nanotubes.

  19. Comparative Molecular Mechanics and Quantum Mechanics Study of Microhydration of Nucleic Acid Bases

    CERN Document Server

    Lino, J; Deriabina, A; Velasco, M; Poltev, V

    2013-01-01

    DNA is the most important biological molecule, and its hydration contributes essentially to the structure and functions of the double helix. We analyze the microhydration of the individual bases of nucleic acids and their methyl derivatives using methods of molecular mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values ...

  20. Target-responsive structural switching for nucleic acid-based sensors.

    Science.gov (United States)

    Li, Di; Song, Shiping; Fan, Chunhai

    2010-05-18

    Interest in the development of sensitive, selective, rapid, and cost-effective biosensors for biomedical analysis, environmental monitoring, and the detection of bioterrorism agents is rapidly increasing. A classic biosensor directly transduces ligand-target binding events into a measurable physical readout. More recently, researchers have proposed novel biosensing strategies that couple ligand-induced structural switching of biomolecules with advanced optical and electronic transducers. This approach has proven to be a highly general platform for the development of new biosensors. In this Account, we describe a series of electrochemical and optical nucleic acid sensors that use target-responsive DNA structures. By employing surface-confined DNA structures with appropriate redox labels, we can monitor target-induced structural switching of DNA or aptamer-specific small molecule probes by measuring electrochemical currents that are directly associated with the distance between the redox label and the electrode surface. We have also demonstrated significant improvements in sensing performance through optimization of the DNA self-assembly process at electrode surfaces or the introduction of nanomaterial-based signal amplification. Alternatively, gold nanoparticles interact differently with folded and unfolded DNA structures, which provides a visual method for detecting target-induced structural switching based on the plasmonic change of gold nanoparticles. This novel method using gold nanoparticles has proven particularly suitable for the detection of a range of small-molecule targets (e.g., cocaine) and environmentally toxic metal ions (e.g., Hg(2+)). Rational sequence design of DNA aptamers improves the sensitivity and increases the reaction kinetics. Recently, we have also designed microfluidic devices that allow rapid and portable mercury detection with the naked eye. This Account focuses on the use of bulk and nanoscale gold and DNA/aptamer molecules. We expect

  1. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, Mark T.

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, and analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: 1) to assess the potential terrorist threat to U.S. agricultural crops, 2) to determine whether suitable assays exist to monitor that threat, and 3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  2. Plant Flavone Apigenin Binds to Nucleic Acid Bases and Reduces Oxidative DNA Damage in Prostate Epithelial Cells

    Science.gov (United States)

    Bhaskaran, Natarajan; Gupta, Sanjay

    2014-01-01

    Oxidative stress has been linked to prostate carcinogenesis as human prostate tissue is vulnerable to oxidative DNA damage. Apigenin, a dietary plant flavone, possesses anti-proliferative and anticancer effects; however, its antioxidant properties have not been fully elucidated. We investigated sub-cellular distribution of apigenin, it’s binding to DNA and protective effects against H2O2-induced DNA damage using transformed human prostate epithelial RWPE-1 cells and prostate cancer LNCaP, PC-3 and DU145 cells. Exposure of cells to apigenin exhibited higher accumulation in RWPE-1 and LNCaP cells, compared to PC-3 and DU145 cells. The kinetics of apigenin uptake in LNCaP cells was estimated with a Km value of 5 µmole/L and Vmax of 190 pmoles/million cells/h. Sub-cellular fractionation demonstrated that nuclear matrix retains the highest concentration of apigenin (45.3%), followed by cytosol (23.9%), nuclear membranes (17.9%) and microsomes (12.9%), respectively. Spectroscopic analysis of apigenin with calf-thymus DNA exhibited intercalation as the dominant binding mode to DNA duplex. Apigenin exposure resulted in significant genoprotective effects in H2O2-stressed RWPE-1 cells by reduction in reactive oxygen species levels. In addition, apigenin exposure suppressed the formation of 8-hydroxy-2′ deoxyguanosine and protected exposed cells from apoptosis. Our studies demonstrate that apigenin is readily taken up by normal prostatic epithelial cells and prostate cancer cells, and is incorporated into their nuclei, where its intercalation with nucleic acid bases may account for its antioxidant and chemopreventive activities. PMID:24614817

  3. Comparison of three nucleic acid-based tests for detecting Anaplasma marginale and Anaplasma centrale in cattle

    Directory of Open Access Journals (Sweden)

    Mamohale E. Chaisi

    2017-01-01

    Full Text Available Several nucleic acid-based assays have been developed for detecting Anaplasma marginale and Anaplasma centrale in vectors and hosts, making the choice of method to use in endemic areas difficult. We evaluated the ability of the reverse line blot (RLB hybridisation assay, two nested polymerase chain reaction (nPCR assays and a duplex real-time quantitative polymerase chain reaction (qPCR assay to detect A. marginale and A. centrale infections in cattle (n = 66 in South Africa. The lowest detection limits for A. marginale plasmid DNA were 2500 copies by the RLB assay, 250 copies by the nPCR and qPCR assays and 2500, 250 and 25 copies of A. centrale plasmid DNA by the RLB, nPCR and qPCR assays respectively. The qPCR assay detected more A. marginale- and A. centrale-positive samples than the other assays, either as single or mixed infections. Although the results of the qPCR and nPCR tests were in agreement for the majority (38 of A. marginale-positive samples, 13 samples tested negative for A. marginale using nPCR but positive using qPCR. To explain this discrepancy, the target sequence region of the nPCR assay was evaluated by cloning and sequencing the msp1β gene from selected field samples. The results indicated sequence variation in the internal forward primer (AM100 area amongst the South African A. marginale msp1β sequences, resulting in false negatives. We propose the use of the duplex qPCR assay in future studies as it is more sensitive and offers the benefits of quantification and multiplex detection of both Anaplasma spp.

  4. CHEMOTHERAPEUTIC POLYMERS ⅩⅩⅢ SYNTHESIS AND ANTITUMOR ACTIVITY OF POLYPHOSPHATES CONTAINING BOTH NUCLEIC ACID BASE AND PHOSPHONOACETIC ACID ETHYL ESTER

    Institute of Scientific and Technical Information of China (English)

    ZHUO Renxi; LIU Zhenghua; LI Li

    1989-01-01

    Eight new polyphosphates containing both nucleic acid base and phosphonoacetic acid ethyl ester were synthesized by the polycondensation of P, P- dichloride of phosphonoacetic acid ethyl ester with 1, 3-dihydroxyalkyl - 5 - fluorouracil, 1,3 - dihydroxyalkyl - uracil and 1, 3 - dihydroxyalkylthymine. These polyphosphates were tested against Ehrlich Ascites Carcinoma in mice. Polymer Ⅱa and Ⅱc exhibited excellent antitumor activity. Ⅱc also showed lower toxicity.

  5. [Genotoxic modification of nucleic acid bases and biological consequences of it. Review and prospects of experimental and computational investigations

    Science.gov (United States)

    Poltev, V. I.; Bruskov, V. I.; Shuliupina, N. V.; Rein, R.; Shibata, M.; Ornstein, R.; Miller, J.

    1993-01-01

    The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.

  6. Isoelectric Point, Electric Charge, and Nomenclature of the Acid-Base Residues of Proteins

    Science.gov (United States)

    Maldonado, Andres A.; Ribeiro, Joao M.; Sillero, Antonio

    2010-01-01

    The main object of this work is to present the pedagogical usefulness of the theoretical methods, developed in this laboratory, for the determination of the isoelectric point (pI) and the net electric charge of proteins together with some comments on the naming of the acid-base residues of proteins. (Contains 8 figures and 4 tables.)

  7. Isoelectric Point, Electric Charge, and Nomenclature of the Acid-Base Residues of Proteins

    Science.gov (United States)

    Maldonado, Andres A.; Ribeiro, Joao M.; Sillero, Antonio

    2010-01-01

    The main object of this work is to present the pedagogical usefulness of the theoretical methods, developed in this laboratory, for the determination of the isoelectric point (pI) and the net electric charge of proteins together with some comments on the naming of the acid-base residues of proteins. (Contains 8 figures and 4 tables.)

  8. Transport Selectivity of a Diethylene Glycol Dimethacrylate-Based Thymine-imprinted Polymeric Membrane over a Cellulose Support for Nucleic Acid Bases

    Institute of Scientific and Technical Information of China (English)

    QU Xiang-Jin; CHEN Chang-Bao; ZHOU Jie; WU Chun-Hui

    2007-01-01

    The binding mechanism between 9-vinyladenine and pyrimidine base thymine in methanol was studied with UV-visible spectrophotometric method. Based on this study, using thymine as a template molecule, 9-vinyladenine as a novel functional monomer and diethylene glycol dimethacrylate as a new cross-linker, a specific diethylene glycol dimethacrylate-based molecularly imprinted polymeric membrane was prepared over a cellulose support.Then, the resultantly polymeric membrane morphologies were visualized with scanning electron microscopy and its permselectivity was examined using thymine, uracil, cytosine, adenine and guanine as substrates. This result showed that the imprinting polymeric membrane prepared with diethylene glycol dimethacrylate exhibited higher transport capacity for the template molecule thymine and its optimal analog uracil than other nucleic acid bases. The membrane also took on higher permselectivity than the imprinted membrane made with ethylene glycol dimethacrylate as a cross-linker. When a mixture including five nucleic acid bases thymine, uracil, cytosine, adenine and guanine passed through the diethylene glycol dimethacrylate-based thymine-imprinted polymeric membrane,recognition of the membrane for the template molecule thymine and its optimal analog uracil was demonstrated. It was predicted that the molecularly imprinted membrane prepared with diethylene glycol dimethacrylate as cross-linker might be applicable to thymine assay of absolute hydrolysates of DNA or uracil assay of absolute hydrolysates of RNA in biological samples because of its high selectivity for the template molecule thymine and its optimal analog uracil.

  9. Mean-field interactions between nucleic-acid-base dipoles can drive the formation of the double helix

    Science.gov (United States)

    He, Yi; Maciejczyk, Maciej; Ołdziej, Stanisław; Scheraga, Harold A.; Liwo, Adam

    2013-01-01

    A proposed coarse-grained model of nucleic acids demonstrates that average interactions between base dipoles, together with chain connectivity and excluded-volume interactions, are sufficient to form double-helical structures of DNA and RNA molecules. Additionally, local interactions determine helix handedness and direction of strand packing. This result, and earlier research on reduced protein models, suggest that mean-field multipole-multipole interactions are the principal factors responsible for the formation of regular structure of biomolecules. PMID:23496746

  10. The effects of borate minerals on the synthesis of nucleic acid bases, amino acids and biogenic carboxylic acids from formamide.

    Science.gov (United States)

    Saladino, Raffaele; Barontini, Maurizio; Cossetti, Cristina; Di Mauro, Ernesto; Crestini, Claudia

    2011-08-01

    The thermal condensation of formamide in the presence of mineral borates is reported. The products afforded are precursors of nucleic acids, amino acids derivatives and carboxylic acids. The efficiency and the selectivity of the reaction was studied in relation to the elemental composition of the 18 minerals analyzed. The possibility of synthesizing at the same time building blocks of both genetic and metabolic apparatuses, along with the production of amino acids, highlights the interest of the formamide/borate system in prebiotic chemistry.

  11. 13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases.

    Science.gov (United States)

    Fiala, Radovan; Sklenár, Vladimír

    2007-10-01

    The paper presents a set of two-dimensional experiments that utilize direct (13)C detection to provide proton-carbon, carbon-carbon and carbon-nitrogen correlations in the bases of nucleic acids. The set includes a (13)C-detected proton-carbon correlation experiment for the measurement of (13)C-(13)C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the (13)C-(13)C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a (13)C-detected (13)C-(15)N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon-carbon couplings and/or carbon decoupling in the direct dimension, while the S(3)E procedure is preferred in the indirect dimension of the carbon-nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of (13)C and (15)N chemical shifts and carbon-carbon and carbon-nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.

  12. Investigating the Co-Adsorption Behavior of Nucleic-Acid Base (Thymine and Cytosine) and Melamine at Liquid/Solid Interface

    Science.gov (United States)

    Zhao, Huiling; Li, Yinli; Chen, Dong; Liu, Bo

    2016-12-01

    The co-adsorption behavior of nucleic-acid base (thymine; cytosine) and melamine was investigated by scanning tunneling microscopy (STM) technique at liquid/solid (1-octanol/graphite) interface. STM characterization results indicate that phase separation happened after dropping the mixed solution of thymine-melamine onto highly oriented pyrolytic graphite (HOPG) surface, while the hetero-component cluster-like structure was observed when cytosine-melamine binary assembly system is used. From the viewpoints of non-covalent interactions calculated by using density functional theory (DFT) method, the formation mechanisms of these assembled structures were explored in detail. This work will supply a methodology to design the supramolecular assembled structures and the hetero-component materials composed by biological and chemical compound.

  13. Resolution-optimized NMR measurement of (1)D(CH), (1)D(CC) and (2)D(CH) residual dipolar couplings in nucleic acid bases.

    Science.gov (United States)

    Boisbouvier, Jérôme; Bryce, David L; O'neil-Cabello, Erin; Nikonowicz, Edward P; Bax, Ad

    2004-11-01

    New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond (2)D(CH) couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in (13)C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear (1)H-(1)H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven (1)H-(13)C and (13)C-(13)C couplings are measured for pyrimidines (U and C), including (1)D(C5H5), (1)D(C6H6), (2)D(C5H6), (2)D(C6H5), (1)D(C5C4), (1)D(C5C6), and (2)D(C4H5). For adenine, four base couplings ((1)D(C2H2), (1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy ((1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than +/-3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one- and two-bond J couplings cluster very tightly for each type of nucleotide.

  14. A new unnatural base pair system between fluorophore and quencher base analogues for nucleic acid-based imaging technology.

    Science.gov (United States)

    Kimoto, Michiko; Mitsui, Tsuneo; Yamashige, Rie; Sato, Akira; Yokoyama, Shigeyuki; Hirao, Ichiro

    2010-11-03

    In the development of orthogonal extra base pairs for expanding the genetic alphabet, we created novel, unnatural base pairs between fluorophore and quencher nucleobase analogues. We found that the nucleobase analogue, 2-nitropyrrole (denoted by Pn), and its 4-substitutions, such as 2-nitro-4-propynylpyrrole (Px) and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (NH(2)-hx-Px), act as fluorescence quenchers. The Pn and Px bases specifically pair with their pairing partner, 7-(2,2'-bithien-5-yl)imidazo[4,5-b]pyridine (Dss), which is strongly fluorescent. Thus, these unnatural Dss-Pn and Dss-Px base pairs function as reporter-quencher base pairs, and are complementarily incorporated into DNA by polymerase reactions as a third base pair in combination with the natural A-T and G-C pairs. Due to the static contact quenching, the Pn and Px quencher bases significantly decreased the fluorescence intensity of Dss by the unnatural base pairings in DNA duplexes. In addition, the Dss-Px pair exhibited high efficiency and selectivity in PCR amplification. Thus, this new unnatural base pair system would be suitable for detection methods of target nucleic acid sequences, and here we demonstrated the applications of the Dss-Pn and Dss-Px pairs as molecular beacons and in real-time PCR. The genetic alphabet expansion system with the replicable, unnatural fluorophore-quencher base pair will be a useful tool for sensing and diagnostic applications, as well as an imaging tool for basic research.

  15. Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care

    Science.gov (United States)

    2016-01-01

    We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone’s motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging. PMID:26898247

  16. Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care.

    Science.gov (United States)

    Priye, Aashish; Wong, Season; Bi, Yuanpeng; Carpio, Miguel; Chang, Jamison; Coen, Mauricio; Cope, Danielle; Harris, Jacob; Johnson, James; Keller, Alexandra; Lim, Richard; Lu, Stanley; Millard, Alex; Pangelinan, Adriano; Patel, Neal; Smith, Luke; Chan, Kamfai; Ugaz, Victor M

    2016-05-03

    We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone's motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging.

  17. Medical devices; immunology and microbiology devices; classification of nucleic acid-based devices for the detection of Mycobacterium tuberculosis complex and the genetic mutations associated with antibiotic resistance. Final order.

    Science.gov (United States)

    2014-10-22

    The Food and Drug Administration (FDA) is classifying nucleic acid-based in vitro diagnostic devices for the detection of Mycobacterium tuberculosis complex (MTB-complex) and the genetic mutations associated with MTB-complex antibiotic resistance in respiratory specimens devices into class II (special controls). The Agency is classifying the device into class II (special controls) because special controls, in addition to general controls, will provide a reasonable assurance of safety and effectiveness of the device.

  18. Extraction of total nucleic acid based on silica-coated magnetic particles for RT-qPCR detection of plant RNA virus/viroid.

    Science.gov (United States)

    Sun, Ning; Deng, Congliang; Zhao, Xiaoli; Zhou, Qi; Ge, Guanglu; Liu, Yi; Yan, Wenlong; Xia, Qiang

    2014-02-01

    In this study, a nucleic acid extraction method based on silica-coated magnetic particles (SMPs) and RT-qPCR assay was developed to detect Arabis mosaic virus (ArMV), Lily symptomless virus (LSV), Hop stunt viroid (HSVd) and grape yellow speckle viroid 1 (GYSVd-1). The amplification sequences of RT-qPCR were reversely transcribed in vitro as RNA standard templates. The standard curves covered six or seven orders of magnitude with a detection limit of 100 copies per each assay. Extraction efficiency of the SMPs method was evaluated by recovering spiked ssRNAs from plant samples and compared to two commercial kits (TRIzol and RNeasy Plant mini kit). Results showed that the recovery rate of SMPs method was comparable to the commercial kits when spiked ssRNAs were extracted from lily leaves, whereas it was two or three times higher than commercial kits when spiked ssRNAs were extracted from grapevine leaves. SMPs method was also used to extract viral nucleic acid from15 ArMV-positive lily leaf samples and 15 LSV-positive lily leaf samples. SMPs method did not show statistically significant difference from other methods on detecting ArMV, but LSV. The SMPs method has the same level of virus load as the TRIzol, and its mean virus load of was 0.5log10 lower than the RNeasy Plant mini kit. Nucleic acid was extracted from 19 grapevine-leaf samples with SMPs and the two commercial kits and subsequently screened for HSVd and GYSVd-1 by RT-qPCR. Regardless of HSVd or GYSVd-1, SMPs method outperforms other methods on both positive rate and the viroid load. In conclusion, SMPs method was able to efficiently extract the nucleic acid of RNA viruses or viroids, especially grapevine viroids, from lily-leaf or grapevine-leaf samples for RT-qPCR detection.

  19. Label-free and sensitive fluorescence detection of nucleic acid, based on combination of a graphene oxid /SYBR green I dye platform and polymerase assisted signal amplification

    Science.gov (United States)

    Zhu, Xiao; Xing, Da

    2012-12-01

    A new label-free isothermal fluorescence amplification detection for nucleic acid has been developed. In this paper, we first developed a novel sensitive and specific detection platform with an unmodified hairpin probe (HP) combination of the graphene oxid (GO)/ SYBR green I dye (SG), which was relied on the selective principle of adsorption and the high quenching efficiency of GO. Then for the application of this new strategy, we used Mirco RNA-21 (Mir-21) as the target to evaluate this working principle of our design. When the target was hybridizing with the HP and inducing its conformation of change, an efficient isothermal circular strand-displacement polymerization reaction was activating to assist the first signal amplification. In this format, the formed complex conformation of DNA would interact with its high affinity dye, then detached from the surface of GO after incubating with the platform of GO/intercalating dye. This reaction would accompany with obvious fluorescence recovery, and accomplish farther signal enhancement by a mass of intercalating dye inserting into the minor groove of the long duplex replication product. By taking advantage of the multiple amplification of signal, this method exerted substantial enhancement in sensitivity and could be used for rapid and selective detection of Mir-21 with attomole range. It is expected that this cost-effective GO based sensor might hold considerable potential to apply in bioanalysis studies.

  20. Nucleic acid-based polymers effective against hepatitis B Virus infection in patients don’t harbor immunostimulatory properties in primary isolated liver cells

    Science.gov (United States)

    Real, Catherine Isabell; Werner, Melanie; Paul, Andreas; Gerken, Guido; Schlaak, Joerg Friedrich; Vaillant, Andrew; Broering, Ruth

    2017-01-01

    Nucleic acid polymers (NAPs) block the release of subviral particles from hepatocytes, a mechanism consistent with their antiviral activity against hepatitis B virus (HBV) in patients. Analysis of immunostimulatory properties of NAPs were conducted with several NAP species: REP 2006, the prototypic degenerate NAP [dN]40, containing TLR9-stimulatory CpG; REP 2055 a clinically active NAP with a sequence [dAdC]20 devoid of CpG content; REP 2139 (also clinically active) and REP 2165 (REP 2055 analogues further rendered immunologically inactive by replacing cytidine with 5-methylcytidine and incorporating 2′-O methylation of riboses). These analyses revealed pro-inflammatory responses in human peripheral blood mononuclear cells with REP 2006 and with REP 2139 and REP 2165 only at high dose but displayed no significant antiviral activity. In primary isolated human hepatocytes and liver sinusoidal endothelial cells no significant inflammatory or antiviral responses were detected for any NAPs. In human Kupffer cells pro-inflammatory activity was observed with REP 2006 and REP 2055, whereas a weak but significant induction of interferon genes was only observed with REP 2006 at the highest concentration. We therefore hypothesize that the antiviral activity of NAPs optimized to treat HBV infection in patients cannot be explained by direct induction of innate antiviral responses. PMID:28272460

  1. 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.

  2. 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.

  3. Effect of maleic anhydride-aniline derivative buffer layer on the properties of flexible substrate heterostructures: Indium tin oxide/nucleic acid base/metal

    Energy Technology Data Exchange (ETDEWEB)

    Stanculescu, A., E-mail: sanca@infim.ro [National Institute of Materials Physics, 105 bis Atomistilor Street, P.O. Box MG-7, 077125, Bucharest-Magurele (Romania); Socol, M. [National Institute of Materials Physics, 105 bis Atomistilor Street, P.O. Box MG-7, 077125, Bucharest-Magurele (Romania); Socol, G.; Mihailescu, I.N. [National Institute for Laser, Plasma and Radiation Physics, P.O. Box MG-36, 077125, Bucharest-Magurele (Romania); Girtan, M. [Laboratoire de Photonique d' Angers, Universite d' Angers, 2, Bd. Lavoisier, 49045, Angers (France); Preda, N. [National Institute of Materials Physics, 105 bis Atomistilor Street, P.O. Box MG-7, 077125, Bucharest-Magurele (Romania); Albu, A.-M. [Department of Polymer Science, University ' Politehnica' of Bucharest, Bucharest (Romania); Stanculescu, F. [University of Bucharest, Faculty of Physics, Str. Atomistilor nr.405, P.O. Box MG-11, Bucharest-Magurele, 077125 (Romania)

    2011-12-01

    This paper presents some investigations on the properties of guanine (G) and cytosine (C) based heterostructures deposited on flexible substrates. The effects of two types of maleic anhydride-aniline derivatives (maleic anhydride-cyano aniline or maleic anhydride-2,4 dinitroaniline) buffer layer, deposited between indium tin oxide and (G) or (C) layer, on the optical and electrical properties of the heterostructures have been identified. The heterostructures containing a film of maleic anhydride-2,4 dinitroaniline have shown a good transparency and low photoluminescence in visible range. This buffer layer has determined an increase in the conductance only in the heterostructures based on (G) and (C) deposited on biaxially-oriented polyethylene terephthalate substrate.

  4. The use of the GSAM approach for the structural investigation of low-lying isomers of molecular clusters from density-functional-theory-based potential energy surfaces: the structures of microhydrated nucleic acid bases.

    Science.gov (United States)

    Thicoipe, Sandrine; Carbonniere, Philippe; Pouchan, Claude

    2013-08-15

    This study presents structural properties of microhydrated nucleic acid bases (NABs) - uracil (U), thymine (T), guanine (G), adenine (A), and cytosine (C) - investigated by theoretical computations at the B3LYP level of theory. To obtain the different representations of these microhydrated species, we applied the GSAM procedure: the most stable conformers labeled X,nH2O (X = U, T, G, A and n = 1...5) for which the Boltzmann population is higher than 2% at 298K are calculated at the B3LYP and B3LYP-D levels of theory. At the B3LYP level, our calculated geometries are compared with those obtained in the literature. New physically relevant isomers are found with the GSAM algorithm, especially for the tetra- and pentahydrated species. The use of DFT-D functional does not strongly modify the relative energies of the isomers for the monohydrated species. When the number of water molecules increases, the results become extremely sensitive to the consideration of dispersion contributions.

  5. 富勒醇/镱(Ⅲ)体系共振光散射法测定核酸%Determination of Nucleic Acids Based on Resonance Light Scattering Technique of Fullerol/Ytterbium(Ⅲ) System

    Institute of Scientific and Technical Information of China (English)

    赵广超; 马娟; 魏先文

    2007-01-01

    A sensitive method for the determination of nucleic acids based on the enhancement of resonance light scattering (RLS) of fullerol/ytterbium(Ⅲ) system has been developed. The fullerol showed a weak RLS spectrum in aqueous solution, but its intensity could be enhanced significantly in the presence of ytterbium(Ⅲ) to form a stable RLS system. Moreover, the RLS signal of fullerol/ytterbium(Ⅲ) system could be enhanced further by fish sperm DNA (fs DNA) and the enhanced RLS intensity was proportional to the concentration of fs DNA in the range of 0-20.0 μg/mL with a limit of detection of 13.3 ng/mL under the optimum conditions. The synthetic samples were analyzed with satisfactory results.%基于核酸对富勒醇/镱Ⅲ体系共振光散射强度的增强作用,建立了一种新的测定核酸的分析方法.富勒醇的水溶液表现出弱的共振光散射性质,但是当三价镱离子存在时,它的共振光散射强度显著增强,形成了一种稳定的富勒醇/镱Ⅲ共振光散射体系.鱼精DNA的加入使得该体系的共振光散射强度进一步增强.在优化条件下,0-20.0μg/mL浓度范围内,共振光散射强度的增强值与鱼精DNA的浓度呈线性关系,检出限可达13.3 ng/mL.该法用于合成样品的分析,结果令人满意.

  6. 老龄冠心病患者的核酸基与蛋白多肽分析及诊疗%Analysis and Diagnosis of Nucleic Acid Based and Protein Peptide in Aged Patients with Coronary Heart Disease

    Institute of Scientific and Technical Information of China (English)

    陈龙皓; 严金龙

    2015-01-01

    Objective:In aged patients with coronary heart disease (CHD) nucleic acid and protein polypeptide has different characteristics, prevention of coronary heart disease. To achieve the effective diagnosis and treatment of aged patients with coronary heart disease (CHD). Methods:To a specialized hospital of 33 cases of senile patients with coronary heart disease for subjects and for patients with clinical follow-up observation and biochemical index test, in aged patients with coronary heart disease in vivo nucleic acid bases and protein peptide feature. Effect on coronary heart disease of TSH suppression. In the polymerization of high density lipoprotein cholesterol, contrast rate was 3 ml/s, the Valsalva test, the kinase glo lu-minescent kinase assay kit determination of protein lipid body phospholipid and protein content, using SPSS12.0 software was used for statistical analysis and treatment scheme. Results:the carbon carbon triple bond series transformation, when free radicals is added to the reaction system caused agent (AIBN, 10 mol%), formation of optical coherence tomography (OCT), combined with auxiliary examination found evidence of myocardial ischemia and coronary occlusion, coronary angi-ography was performed, statistical analysis and treatment for aged patients with coronary heart disease. By adjusting the dif-ferent time protein polypeptide and nucleic acid bases. Conclusion:Check up method in aged patients with coronary heart disease (CHD) including routine electrocardiogram (ECG) and electrocardiogram stress test, nuclide myocardial imaging, and screening of high-risk patients with coronary artery disease, using the method of stable coronary artery disease and acute coronary artery syndrome has significant curative effect and preventive.%目的:老龄冠心病患者体内的核酸基与蛋白多肽具有差异性特征,通过对该类核酸基与蛋白多肽差异性特征进行分析,了解并干预危险因素,进行冠心病预防,实现对老龄

  7. Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

    Energy Technology Data Exchange (ETDEWEB)

    Morgado, Claudio A.; Jurecka, Petr; Svozil, Daniel; Hobza, Pavel; Sponer, Jiri

    2009-06-09

    We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantummechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the shortrange repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFTSAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geometries with close interatomic contacts and clashes, the repulsion effects are rather severely exaggerated. The discrepancy reported here should not affect the overall stability of MD simulations and qualitative applications of the force field. However, it may affect the description of subtle

  8. A simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings.

    Directory of Open Access Journals (Sweden)

    Paul LaBarre

    Full Text Available BACKGROUND: Molecular assays targeted to nucleic acid (NA markers are becoming increasingly important to medical diagnostics. However, these are typically confined to wealthy, developed countries; or, to the national reference laboratories of developing-world countries. There are many infectious diseases that are endemic in low-resource settings (LRS where the lack of simple, instrument-free, NA diagnostic tests is a critical barrier to timely treatment. One of the primary barriers to the practicality and availability of NA assays in LRS has been the complexity and power requirements of polymerase chain reaction (PCR instrumentation (another is sample preparation. METHODOLOGY/PRINCIPAL FINDINGS: In this article, we investigate the hypothesis that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays. We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison. Versions of the prototype for several different isothermal techniques are presented. CONCLUSIONS/SIGNIFICANCE: We demonstrate that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays, and that the results of those assays are not significantly different from ones incubated in parallel in commercially available PCR instruments. These results clearly suggest the potential of the non-instrumented nucleic acid amplification (NINA heater for molecular diagnostics in LRS. When combined with other innovations in development that eliminate power requirements for sample preparation, cold reagent storage, and readout, the NINA heater will comprise part of a kit that should enable electricity-free NA testing for many important analytes.

  9. Isothermal Amplification of Nucleic Acids.

    Science.gov (United States)

    Zhao, Yongxi; Chen, Feng; Li, Qian; Wang, Lihua; Fan, Chunhai

    2015-11-25

    Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.

  10. Standardized Procedures for Use of Nucleic Acid-Based Tools

    Science.gov (United States)

    2008-08-01

    FISH flow cytometry - fluorescence in situ hybridization GMO genetically modified organisms H. pylori Helicobacter pylori HIV Human Immunodeficiency...for calibration of a method to detect genetically modified organisms ( GMO ) in soy products. Other sources of CRM include those used in the Forensic...could provide benefits in terms of assessing biomass losses throughout shipping, storage, and processing. • The use of lyophilized surrogates would

  11. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    Science.gov (United States)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  12. Detection of Nucleic Acid Bases by Surface Enhanced Raman Scattering Technique Based on in-situ Photo-reduced Silver Colloids%基于在位光还原银胶法的表面增强拉曼散射技术检测核酸碱基

    Institute of Scientific and Technical Information of China (English)

    吴雷; 李海超; 赵海峰; 孙宇; 许浩然; 吕明; 杨春花; 李文钊; 李正强

    2011-01-01

    The formation of colloids induced by laser irradiation was proved by the means of Raman scattering, UV-Vis spectrum and transmission electron microscopy (TEM). The Raman signal of nucleic acid bases was slightly enlarged due to the surface-enhanced Raman scattering activity brought by the aggregation of silver atoms. Furthermore, the experiment results showed that the Raman spec-tra with high signal to noise ratio and with good repeatability could be obtained by this method and the Raman spectra of nucleic acid bases obtained were similar to those obtained in Lee-Meisel silver colloid and on silver membrane surface. Although there were some new peaks and shifts in our Raman study, the classical characteristic peaks could also be found and used to identify different species. Due to its simple operation, SERS (Surface Enhanced Raman Scattering) of colloids prepared by photo-reduced silver nitrate was of great application value in the in situ detection of small molecules.%在环状有机物存在的条件下,Ag+经激光诱导可发生光还原反应,形成Ag原子聚集的银胶体.本研究通过拉曼散射光谱、紫外-可见光谱和扫描电镜证明,核酸碱基和Ag+混合溶液经过激光诱导可以生成银胶体颗粒.随着银胶体的生成,核酸碱基的拉曼光谱信号因为表面增强拉曼散射效应而得到明显增强.实验表明,本方法不但可以获得高信噪比的拉曼光谱谱图,而且获得的胞嘧啶、尿嘧啶、胸腺嘧啶、腺嘌呤和鸟嘌呤的增强拉曼光谱与Lee-Meisel银胶和银膜表面两种体系下获得的表面增强拉曼光谱具有相似性.同时,腺嚓吟和鸟嘌呤又出现了一些因Ag+作用而产生的新位移谱带,但是仍然可以作为指征碱基类别的特征峰归属.利用Ag+光还原的方法在位获得银溶胶增强拉曼光谱信号,具有银胶制备操作简单、峰位特征等优点,在核酸碱基的低浓度在位检测方面具有应用前景.

  13. Integrated sample-to-detection chip for nucleic acid test assays.

    Science.gov (United States)

    Prakash, R; Pabbaraju, K; Wong, S; Tellier, R; Kaler, K V I S

    2016-06-01

    Nucleic acid based diagnostic techniques are routinely used for the detection of infectious agents. Most of these assays rely on nucleic acid extraction platforms for the extraction and purification of nucleic acids and a separate real-time PCR platform for quantitative nucleic acid amplification tests (NATs). Several microfluidic lab on chip (LOC) technologies have been developed, where mechanical and chemical methods are used for the extraction and purification of nucleic acids. Microfluidic technologies have also been effectively utilized for chip based real-time PCR assays. However, there are few examples of microfluidic systems which have successfully integrated these two key processes. In this study, we have implemented an electro-actuation based LOC micro-device that leverages multi-frequency actuation of samples and reagents droplets for chip based nucleic acid extraction and real-time, reverse transcription (RT) PCR (qRT-PCR) amplification from clinical samples. Our prototype micro-device combines chemical lysis with electric field assisted isolation of nucleic acid in a four channel parallel processing scheme. Furthermore, a four channel parallel qRT-PCR amplification and detection assay is integrated to deliver the sample-to-detection NAT chip. The NAT chip combines dielectrophoresis and electrostatic/electrowetting actuation methods with resistive micro-heaters and temperature sensors to perform chip based integrated NATs. The two chip modules have been validated using different panels of clinical samples and their performance compared with standard platforms. This study has established that our integrated NAT chip system has a sensitivity and specificity comparable to that of the standard platforms while providing up to 10 fold reduction in sample/reagent volumes.

  14. Acid-Base Homeostasis.

    Science.gov (United States)

    Hamm, L Lee; Nakhoul, Nazih; Hering-Smith, Kathleen S

    2015-12-07

    Acid-base homeostasis and pH regulation are critical for both normal physiology and cell metabolism and function. The importance of this regulation is evidenced by a variety of physiologic derangements that occur when plasma pH is either high or low. The kidneys have the predominant role in regulating the systemic bicarbonate concentration and hence, the metabolic component of acid-base balance. This function of the kidneys has two components: reabsorption of virtually all of the filtered HCO3(-) and production of new bicarbonate to replace that consumed by normal or pathologic acids. This production or generation of new HCO3(-) is done by net acid excretion. Under normal conditions, approximately one-third to one-half of net acid excretion by the kidneys is in the form of titratable acid. The other one-half to two-thirds is the excretion of ammonium. The capacity to excrete ammonium under conditions of acid loads is quantitatively much greater than the capacity to increase titratable acid. Multiple, often redundant pathways and processes exist to regulate these renal functions. Derangements in acid-base homeostasis, however, are common in clinical medicine and can often be related to the systems involved in acid-base transport in the kidneys.

  15. New nucleic acid testing devices to diagnose infectious diseases in resource-limited settings.

    Science.gov (United States)

    Maffert, P; Reverchon, S; Nasser, W; Rozand, C; Abaibou, H

    2017-06-01

    Point-of-care diagnosis based on nucleic acid testing aims to incorporate all the analytical steps, from sample preparation to nucleic acid amplification and detection, in a single device. This device needs to provide a low-cost, robust, sensitive, specific, and easily readable analysis. Microfluidics has great potential for handling small volumes of fluids on a single platform. Microfluidic technology has recently been applied to paper, which is already used in low-cost lateral flow tests. Nucleic acid extraction from a biological specimen usually requires cell filtration and lysis on specific membranes, while affinity matrices, such as chitosan or polydiacetylene, are well suited to concentrating nucleic acids for subsequent amplification. Access to electricity is often difficult in resource-limited areas, so the amplification step needs to be equipment-free. Consequently, the reaction has to be isothermal to alleviate the need for a thermocycler. LAMP, NASBA, HDA, and RPA are examples of the technologies available. Nucleic acid detection techniques are currently based on fluorescence, colorimetry, or chemiluminescence. For point-of-care diagnostics, the results should be readable with the naked eye. Nowadays, interpretation and communication of results to health professionals could rely on a smartphone, used as a telemedicine device. The major challenge of creating an "all-in-one" diagnostic test involves the design of an optimal solution and a sequence for each analytical step, as well as combining the execution of all these steps on a single device. This review provides an overview of available materials and technologies which seem to be adapted to point-of-care nucleic acid-based diagnosis, in low-resource areas.

  16. Electrical and electrochemical characterization of nano-sized LiFePO4 cathode materials synthesized by a lauric acid-based sol--gel method

    Science.gov (United States)

    Bazzi, Khadije; Dixit, Ambesh; Naik, Ratna; Naik, Vaman; Vaishnava, Prem; Nazri, Abbas; Nazri, Mariam

    2011-04-01

    We synthesized pure LiFePO4 and C-LiFePO4 nanoparticles by sol-gel technique. Carbon coating was accomplished by including Lauric acid in the sol-gel precursor solution. Three C-LiFePO4 samples of particle sizes 29, 27, 23 nm, were prepared by varying lauric acid concentration in the precursor solution. All the samples were characterized by X-ray diffraction, Raman, conductivity, and electrochemical measurements. The micro-Raman measurements showed two major bands at 1350 and 1590 cm-1 respectively (ID/IG) and the electronic conductivity were found to depend strongly on the amount of surfactant coverage. The 23 nm particle size sample showed minimum (D/G) band ratio and the maximum electrical conductivity among the three samples. The measured value of the capacity for 23 nm sized sample, ˜ 170 mAh/g, approached the theoretical capacity limit value for LiFePO4

  17. [The effect of electrical and acoustic stimulation in early ontogeny on the characteristics of higher nervous activity and on the nucleic acid content of the tissues in chum salmon fry].

    Science.gov (United States)

    Tikhomirov, A M; Vitvitskaia, L V

    1991-01-01

    Stimulation of salmon larvae by electric current led further to unstable character of reactions in the open field. Acoustic stimulation both by tonal and musical signals favourably influenced the behaviour in the open field and the ability to elaborate conditioned reflexes. Changes of the content of nucleic acids were not found in the brain tissue but were found in the muscles, where they correlated with the growth speed and motor activity of the experimental fishes. The obtained data show the possibility of elaboration of applied methods of the control of CNS development and behaviour of young fishes at fishing plants.

  18. Nanomaterials for delivery of nucleic acid to the central nervous system (CNS)

    DEFF Research Database (Denmark)

    Wang, Danyang; Wu, Lin-Ping

    2017-01-01

    Billions of dollars have been invested in the therapeutic application of nucleic acid-based agents in humans in recent years. There are inspirable data from ongoing clinical trial for different diseases. However, in order to widely apply nucleic acid in prevention, diagnosis and treatment of age...... system (CNS) and summary several types of nanomaterials which can be potentially used in the brain delivery nucleic acid....

  19. Nucleic Acid Immunity.

    Science.gov (United States)

    Hartmann, G

    2017-01-01

    Organisms throughout biology need to maintain the integrity of their genome. From bacteria to vertebrates, life has established sophisticated mechanisms to detect and eliminate foreign genetic material or to restrict its function and replication. Tremendous progress has been made in the understanding of these mechanisms which keep foreign or unwanted nucleic acids from viruses or phages in check. Mechanisms reach from restriction-modification systems and CRISPR/Cas in bacteria and archaea to RNA interference and immune sensing of nucleic acids, altogether integral parts of a system which is now appreciated as nucleic acid immunity. With inherited receptors and acquired sequence information, nucleic acid immunity comprises innate and adaptive components. Effector functions include diverse nuclease systems, intrinsic activities to directly restrict the function of foreign nucleic acids (e.g., PKR, ADAR1, IFIT1), and extrinsic pathways to alert the immune system and to elicit cytotoxic immune responses. These effects act in concert to restrict viral replication and to eliminate virus-infected cells. The principles of nucleic acid immunity are highly relevant for human disease. Besides its essential contribution to antiviral defense and restriction of endogenous retroelements, dysregulation of nucleic acid immunity can also lead to erroneous detection and response to self nucleic acids then causing sterile inflammation and autoimmunity. Even mechanisms of nucleic acid immunity which are not established in vertebrates are relevant for human disease when they are present in pathogens such as bacteria, parasites, or helminths or in pathogen-transmitting organisms such as insects. This review aims to provide an overview of the diverse mechanisms of nucleic acid immunity which mostly have been looked at separately in the past and to integrate them under the framework nucleic acid immunity as a basic principle of life, the understanding of which has great potential to

  20. Peptide Nucleic Acids (PNA)

    DEFF Research Database (Denmark)

    2002-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  1. Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  2. Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2003-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  3. Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2004-01-01

    A novel class of compounds known as peptide nucleic acids, bind complementary DNA and RNA strands, and generally do so more strongly than the corresponding DNA or RNA strands while exhibiting increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from...

  4. Peptide Nucleic Acid Synthons

    DEFF Research Database (Denmark)

    2004-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  5. Nucleic acid amplification using microfluidic systems.

    Science.gov (United States)

    Chang, Chen-Min; Chang, Wen-Hsin; Wang, Chih-Hung; Wang, Jung-Hao; Mai, John D; Lee, Gwo-Bin

    2013-04-07

    In the post-human-genome-project era, the development of molecular diagnostic techniques has advanced the frontiers of biomedical research. Nucleic-acid-based technology (NAT) plays an especially important role in molecular diagnosis. However, most research and clinical protocols still rely on the manual analysis of individual samples by skilled technicians which is a time-consuming and labor-intensive process. Recently, with advances in microfluidic designs, integrated micro total-analysis-systems have emerged to overcome the limitations of traditional detection assays. These microfluidic systems have the capability to rapidly perform experiments in parallel and with a high-throughput which allows a NAT analysis to be completed in a few hours or even a few minutes. These features have a significant beneficial influence on many aspects of traditional biological or biochemical research and this new technology is promising for improving molecular diagnosis. Thus, in the foreseeable future, microfluidic systems developed for molecular diagnosis using NAT will become an important tool in clinical diagnosis. One of the critical issues for NAT is nucleic acid amplification. In this review article, recent advances in nucleic acid amplification techniques using microfluidic systems will be reviewed. Different approaches for fast amplification of nucleic acids for molecular diagnosis will be highlighted.

  6. PHYSIOLOGY OF ACID BASE BALANCE

    Directory of Open Access Journals (Sweden)

    Awati

    2014-12-01

    Full Text Available Acid-base, electrolyte, and metabolic disturbances are common in the intensive care unit. Almost all critically ill patients often suffer from compound acid-base and electrolyte disorders. Successful evaluation and management of such patients requires recognition of common patterns (e.g., metabolic acidosis and the ability to dissect one disorder from another. The intensivists needs to identify and correct these condition with the easiest available tools as they are the associated with multiorgan failure. Understanding the elements of normal physiology in these areas is very important so as to diagnose the pathological condition and take adequate measures as early as possible. Arterial blood gas analysis is one such tool for early detection of acid base disorder. Physiology of acid base is complex and here is the attempt to simplify it in our day to day application for the benefit of critically ill patients.

  7. Neutron Nucleic Acid Crystallography.

    Science.gov (United States)

    Chatake, Toshiyuki

    2016-01-01

    The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

  8. Bipolar Membranes for Acid Base Flow Batteries

    Science.gov (United States)

    Anthamatten, Mitchell; Roddecha, Supacharee; Jorne, Jacob; Coughlan, Anna

    2011-03-01

    Rechargeable batteries can provide grid-scale electricity storage to match power generation with consumption and promote renewable energy sources. Flow batteries offer modular and flexible design, low cost per kWh and high efficiencies. A novel flow battery concept will be presented based on acid-base neutralization where protons (H+) and hydroxyl (OH-) ions react electrochemically to produce water. The large free energy of this highly reversible reaction can be stored chemically, and, upon discharge, can be harvested as usable electricity. The acid-base flow battery concept avoids the use of a sluggish oxygen electrode and utilizes the highly reversible hydrogen electrode, thus eliminating the need for expensive noble metal catalysts. The proposed flow battery is a hybrid of a battery and a fuel cell---hydrogen gas storing chemical energy is produced at one electrode and is immediately consumed at the other electrode. The two electrodes are exposed to low and high pH solutions, and these solutions are separated by a hybrid membrane containing a hybrid cation and anion exchange membrane (CEM/AEM). Membrane design will be discussed, along with ion-transport data for synthesized membranes.

  9. Calorimetry of Nucleic Acids.

    Science.gov (United States)

    Rozners, Eriks; Pilch, Daniel S; Egli, Martin

    2015-12-01

    This unit describes the application of calorimetry to characterize the thermodynamics of nucleic acids, specifically, the two major calorimetric methodologies that are currently employed: differential scanning (DSC) and isothermal titration calorimetry (ITC). DSC is used to study thermally induced order-disorder transitions in nucleic acids. A DSC instrument measures, as a function of temperature (T), the excess heat capacity (C(p)(ex)) of a nucleic acid solution relative to the same amount of buffer solution. From a single curve of C(p)(ex) versus T, one can derive the following information: the transition enthalpy (ΔH), entropy (ΔS), free energy (ΔG), and heat capacity (ΔCp); the state of the transition (two-state versus multistate); and the average size of the molecule that melts as a single thermodynamic entity (e.g., the duplex). ITC is used to study the hybridization of nucleic acid molecules at constant temperature. In an ITC experiment, small aliquots of a titrant nucleic acid solution (strand 1) are added to an analyte nucleic acid solution (strand 2), and the released heat is monitored. ITC yields the stoichiometry of the association reaction (n), the enthalpy of association (ΔH), the equilibrium association constant (K), and thus the free energy of association (ΔG). Once ΔH and ΔG are known, ΔS can also be derived. Repetition of the ITC experiment at a number of different temperatures yields the ΔCp for the association reaction from the temperature dependence of ΔH.

  10. Locked nucleic acid

    DEFF Research Database (Denmark)

    Jepsen, Jan Stenvang; Sørensen, Mads D; Wengel, Jesper

    2004-01-01

    Locked nucleic acid (LNA) is a class of nucleic acid analogs possessing very high affinity and excellent specificity toward complementary DNA and RNA, and LNA oligonucleotides have been applied as antisense molecules both in vitro and in vivo. In this review, we briefly describe the basic...... physiochemical properties of LNA and some of the difficulties that may be encountered when applying LNA technology. The central part of the review focuses on the use of LNA molecules in regulation of gene expression, including delivery to cells, stability, unspecific effects, toxicity, pharmacokinetics...

  11. Nucleic Acid Engineering: RNA Following the Trail of DNA.

    Science.gov (United States)

    Kim, Hyejin; Park, Yongkuk; Kim, Jieun; Jeong, Jaepil; Han, Sangwoo; Lee, Jae Sung; Lee, Jong Bum

    2016-02-01

    The self-assembly feature of the naturally occurring biopolymer, DNA, has fascinated researchers in the fields of materials science and bioengineering. With the improved understanding of the chemical and structural nature of DNA, DNA-based constructs have been designed and fabricated from two-dimensional arbitrary shapes to reconfigurable three-dimensional nanodevices. Although DNA has been used successfully as a building block in a finely organized and controlled manner, its applications need to be explored. Hence, with the myriad of biological functions, RNA has recently attracted considerable attention to further the application of nucleic acid-based structures. This Review categorizes different approaches of engineering nucleic acid-based structures and introduces the concepts, principles, and applications of each technique, focusing on how DNA engineering is applied as a guide to RNA engineering.

  12. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

    OpenAIRE

    Mauk, Michael G.; Changchun Liu; Jinzhao Song; Bau, Haim H.

    2015-01-01

    Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (poly...

  13. Delivery Systems for In Vivo use of Nucleic Acid Drugs

    Directory of Open Access Journals (Sweden)

    Resende R.R

    2007-01-01

    Full Text Available The notorious biotechnological advance of the last few decades has allowed the development of experimental methods for understanding molecular mechanisms of genes and new therapeutic approaches. Gene therapy is maturing into a viable, practical method with the potential to cure a variety of human illnesses. Some nucleic-acid-based drugs are now available for controlling the progression of genetic diseases by inhibiting gene expression or the activity of their gene products. New therapeutic strategies employ a wide range of molecular tools such as bacterial plasmids containing transgenic inserts, RNA interference aptamers. A nucleic-acid based constitution confers a lower immunogenic potential and as result of the high stringency selection of large molecular variety, these drugs have high affi nity and selectivity for their targets. However, nucleic acids have poor biostability thus requiring chemical modifications and delivery systems to maintain their activity and ease their cellular internalization. This review discusses some of the mechanisms of action and the application of therapies based on nucleic acids such as aptamers and RNA interference as well as platforms for cellular uptake and intracellular delivery of therapeutic oligonucleotides and their trade-offs.

  14. A sensitive SERS assay for detecting proteins and nucleic acids using a triple-helix molecular switch for cascade signal amplification.

    Science.gov (United States)

    Ye, Sujuan; Wu, Yanying; Zhang, Wen; Li, Na; Tang, Bo

    2014-08-25

    A novel surface-enhanced Raman scattering (SERS) detection system is developed for proteins and nucleic acids based on a triple-helix molecular switch for multiple cycle signal amplification, achieving high sensitivity, universality, rapid analysis, and high selectivity.

  15. Nucleic Acid Vaccines

    Institute of Scientific and Technical Information of China (English)

    LU Shan

    2004-01-01

    @@ Anew method of immunization was discovered in the early 1990s. Several research groups independently demonstrated that direct inoculation of DNA plasmids coding for a specific protein antigen could elicit immune responses against that antigen[1-4].Since in theory the mRNA molecules also have the potential to be translated into the protein antigen, this vaccination approach was officially named by WHO as the nucleic acid vaccination even though the term DNA vaccine has been used more commonly in the literature. This novel approach is considered the fourth generation of vaccines after live attenuated vaccines, killed or inactivated vaccines and recombinant protein based subunit vaccines.

  16. Molten fatty acid based microemulsions.

    Science.gov (United States)

    Noirjean, Cecile; Testard, Fabienne; Dejugnat, Christophe; Jestin, Jacques; Carriere, David

    2016-06-21

    We show that ternary mixtures of water (polar phase), myristic acid (MA, apolar phase) and cetyltrimethylammonium bromide (CTAB, cationic surfactant) studied above the melting point of myristic acid allow the preparation of microemulsions without adding a salt or a co-surfactant. The combination of SANS, SAXS/WAXS, DSC, and phase diagram determination allows a complete characterization of the structures and interactions between components in the molten fatty acid based microemulsions. For the different structures characterized (microemulsion, lamellar or hexagonal phases), a similar thermal behaviour is observed for all ternary MA/CTAB/water monophasic samples and for binary MA/CTAB mixtures without water: crystalline myristic acid melts at 52 °C, and a thermal transition at 70 °C is assigned to the breaking of hydrogen bounds inside the mixed myristic acid/CTAB complex (being the surfactant film in the ternary system). Water determines the film curvature, hence the structures observed at high temperature, but does not influence the thermal behaviour of the ternary system. Myristic acid is partitioned in two "species" that behave independently: pure myristic acid and myristic acid associated with CTAB to form an equimolar complex that plays the role of the surfactant film. We therefore show that myristic acid plays the role of a solvent (oil) and a co-surfactant allowing the fine tuning of the structure of oil and water mixtures. This solvosurfactant behaviour of long chain fatty acid opens the way for new formulations with a complex structure without the addition of any extra compound.

  17. Carbon nanotubes and nucleic acids: tools and targets

    Science.gov (United States)

    Onoa, Bibiana; Zheng, Ming; Dresselhaus, Mildred S.; Diner, Bruce A.

    2006-05-01

    Nucleic acids, with their intrinsic structural properties as well as their high specificity, are playing an important role in the rapid development of nano-technologies. In turn, these new technologies and their efficient performance enable fast and precise methods for detection of nucleic acids, improving the diagnosis of diseases and identification of pathogens. We discuss the use of nucleic acids to disperse and sort single walled carbon nanotubes (SWNTs), and carbon nanotube-based field effect transistors (CNT-FETs) to electrically detect specific nucleic acid sequences. Both DNA and RNA are efficient agents for dispersion and separation of SWNTs by diameter and chirality. Fractions enriched in a narrow band gap distribution of DNA:SWNT hybrids do not alter the electronic performance of field effect transistors. A CNT-FET fulfills the requirements for a nanosensing device that can greatly exceed the existing technologies. Electrical detection of specific nucleic acid sequence could potentially overcome the current limitations of optical detection, by increasing sensitivity and speed, while reducing sample manipulation, size, and cost.

  18. ADVANCEMENT OF NUCLEIC ACID-BASED TOOLS FOR MONITORING IN SITU REDUCTIVE DECHLORINATION

    Energy Technology Data Exchange (ETDEWEB)

    Vangelas, K; ELIZABETH EDWARDS, E; FRANK LOFFLER, F; Brian02 Looney, B

    2006-11-17

    Regulatory protocols generally recognize that destructive processes are the most effective mechanisms that support natural attenuation of chlorinated solvents. In many cases, these destructive processes will be biological processes and, for chlorinated compounds, will often be reductive processes that occur under anaerobic conditions. The existing EPA guidance (EPA, 1998) provides a list of parameters that provide indirect evidence of reductive dechlorination processes. In an effort to gather direct evidence of these processes, scientists have identified key microorganisms and are currently developing tools to measure the abundance and activity of these organisms in subsurface systems. Drs. Edwards and Luffler are two recognized leaders in this field. The research described herein continues their development efforts to provide a suite of tools to enable direct measures of biological processes related to the reductive dechlorination of TCE and PCE. This study investigated the strengths and weaknesses of the 16S rRNA gene-based approach to characterizing the natural attenuation capabilities in samples. The results suggested that an approach based solely on 16S rRNA may not provide sufficient information to document the natural attenuation capabilities in a system because it does not distinguish between strains of organisms that have different biodegradation capabilities. The results of the investigations provided evidence that tools focusing on relevant enzymes for functionally desired characteristics may be useful adjuncts to the 16SrRNA methods.

  19. Exploring the Potential of Nucleic Acid Bases in Organic Light Emitting Diodes

    Science.gov (United States)

    2014-01-01

    201403532 www.advmat.de www.MaterialsViews.com of the HOMO–LUMO levels of the various NBs as HBL/ETL within the energy level diagram of the overall device...T. Ishikawa , D. Nishioka , T. Ushikubo , N. Kobayashi , Appl. Phys. Lett. 2010 , 97 , 193301 . [36] M. J. Cho , U. R. Lee , Y. S

  20. Bioavailability of xenobiotics in unsaturated soils – implications for nucleic acid based stable isotope probing

    Science.gov (United States)

    The use of stable isotopes to label phylogenetically informative biomolecules (phospholipid fatty acids, DNA, or RNA), typically referred to as stable isotope probing (SIP) has the potential of providing definitive evidence that a detected population is active in a specific process, if that process ...

  1. Interaction of Mg-Rich Montmorillonite with Nucleic Acid Bases and Sugar

    Institute of Scientific and Technical Information of China (English)

    H. HASHIZUME

    2005-01-01

    @@ 1Introduction Because of their ability to adsorb, concentrate and catalyze the polymerization of organic molecules, clay minerals might have played a key role in the molecular origins of life[1]. RNA is one of the most important biopolymers in the early earth (RNA world) since protein and DNA appear to have derived later from RNA[2].

  2. Synthesis and evaluation of peptide and nucleic acid based Toll-like receptor ligands

    NARCIS (Netherlands)

    Weterings, Josephus Johannes

    2008-01-01

    Toll-like receptors (TLRs) are receptors that continuously scour their direct surroundings for pathogen associated molecular patterns (PAMPs) of bacterial, viral or fungal origin. TLRs can be found at cells that play a role in the immune system. Binding of the TLR with its corresponding ligand

  3. 78 FR 36698 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis

    Science.gov (United States)

    2013-06-19

    ... HUMAN SERVICES Food and Drug Administration 21 CFR Part 866 Microbiology Devices; Reclassification of... subsequently convened a meeting of the Microbiology Devices Panel of the Medical Devices Advisory Committee on... notification requirements. VI. Risks to Health After considering the information discussed by the Microbiology...

  4. Exploring the Potential of Nucleic Acid Bases in Organic Light Emitting Diodes.

    Science.gov (United States)

    Gomez, Eliot F; Venkatraman, Vishak; Grote, James G; Steckl, Andrew J

    2015-12-01

    Naturally occurring biomolecules have increasingly found applications in organic electronics as a low cost, performance-enhancing, environmentally safe alternative. Previous devices, which incorporated DNA in organic light emitting diodes (OLEDs), resulted in significant improvements in performance. In this work, nucleobases (NBs), constituents of DNA and RNA polymers, are investigated for integration into OLEDs. NB small molecules form excellent thin films by low-temperature evaporation, enabling seamless integration into vacuum deposited OLED fabrication. Thin film properties of adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) are investigated. Next, their incorporation as electron-blocking (EBL) and hole-blocking layers (HBL) in phosphorescent OLEDs is explored. NBs affect OLED performance through charge transport control, following their electron affinity trend: G < A < C < T < U. G and A have lower electron affinity (1.8-2.2 eV), blocking electrons but allowing hole transport. C, T, and U have higher electron affinities (2.6-3.0 eV), transporting electrons and blocking hole transport. A-EBL-based OLEDs achieve current and external quantum efficiencies of 52 cd A(-1) and 14.3%, a ca. 50% performance increase over the baseline device with conventional EBL. The combination of enhanced performance, wide diversity of material properties, simplicity of use, and reduced cost indicate the promise of nucleobases for future OLED development.

  5. Use of Nucleic Acid-Based Tools for Monitoring Biostimulation and Bioaugmentation

    Science.gov (United States)

    2011-01-01

    groundwater samples from an aquifer . The sampling and handling procedures described herein have been validated for Dhc assessment at chlorinated...Under methanogenic conditions, ethene is sometimes reduced to ethane. VC, ethene and ethane can be mineralized to carbon dioxide under both micro...not rare in subsurface environments and aquifers and cis-DCE plumes likely reflect the activity of such microorganisms. Dehalococcoides

  6. Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals

    OpenAIRE

    Hideo Hashizume

    2015-01-01

    Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate ...

  7. Adsorption of nucleic Acid bases, ribose, and phosphate by some clay minerals.

    Science.gov (United States)

    Hashizume, Hideo

    2015-01-01

    Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate how clays might catalyze the formation of nucleosides, nucleotides and polynucleotides in the "RNA world". The adsorption of purines, pyrimidines and nucleosides from aqueous solution to clay minerals is affected by suspension pH. With montmorillonite, adsorption is also influenced by the nature of the exchangeable cations. Here, we review the interactions of some clay minerals with RNA components.

  8. Nucleic Acid-Based Biosensors for the Detection of DNA Damage

    Science.gov (United States)

    Monitoring the environment for the presence of toxic compounds is not only required for cleanup of previously contaminated land and water, but is important for preventing future contamination and managing risks to human health and the environment. Identification and measurement o...

  9. Nucleic acid-based approaches to investigate microbial-related cheese quality defects.

    Science.gov (United States)

    O'Sullivan, Daniel J; Giblin, Linda; McSweeney, Paul L H; Sheehan, Jeremiah J; Cotter, Paul D

    2013-01-01

    The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.

  10. Nucleic acid-based approaches to investigate microbial-related cheese quality defects

    Directory of Open Access Journals (Sweden)

    Daniel eO Sullivan

    2013-01-01

    Full Text Available AbstractThe microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways, in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.

  11. Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals

    Directory of Open Access Journals (Sweden)

    Hideo Hashizume

    2015-02-01

    Full Text Available Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate how clays might catalyze the formation of nucleosides, nucleotides and polynucleotides in the “RNA world”. The adsorption of purines, pyrimidines and nucleosides from aqueous solution to clay minerals is affected by suspension pH. With montmorillonite, adsorption is also influenced by the nature of the exchangeable cations. Here, we review the interactions of some clay minerals with RNA components.

  12. Modeling DNA hydration: comparison of calculated and experimental hydration properties of nuclic acid bases.

    Science.gov (United States)

    Poltev, V I; Malenkov, G G; Gonzalez, E J; Teplukhin, A V; Rein, R; Shibata, M; Miller, J H

    1996-02-01

    Hydration properties of individual nucleic acid bases were calculated and compared with the available experimental data. Three sets of classical potential functions (PF) used in simulations of nucleic acid hydration were juxtaposed: (i) the PF developed by Poltev and Malenkov (PM), (ii) the PF of Weiner and Kollman (WK), which together with Jorgensen's TIP3P water model are widely used in the AMBER program, and (iii) OPLS (optimized potentials for liquid simulations) developed by Jorgensen (J). The global minima of interaction energy of single water molecules with all the natural nucleic acid bases correspond to the formation of two water-base hydrogen bonds (water bridging of two hydrophilic atoms of the base). The energy values of these minima calculated via PM potentials are in somewhat better conformity with mass-spectrometric data than the values calculated via WK PF. OPLS gave much weaker water-base interactions for all compounds considered, thus these PF were not used in further computations. Monte Carlo simulations of the hydration of 9-methyladenine, 1-methyluracil and 1-methylthymine were performed in systems with 400 water molecules and periodic boundary conditions. Results of simulations with PM potentials give better agreement with experimental data on hydration energies than WK PF. Computations with PM PF of the hydration energy of keto and enol tautomers of 9-methylguanine can account for the shift in the tautomeric equilibrium of guanine in aqueous media to a dominance of the keto form in spite of nearly equal intrinsic stability of keto and enol tautomers. The results of guanine hydration computations are discussed in relation to mechanisms of base mispairing errors in nucleic acid biosynthesis. The data presented in this paper along with previous results on simulation of hydration shell structures in DNA duplex grooves provide ample evidence for the advantages of PM PF in studies of nucleic-acid hydration.

  13. The Conjugate Acid-Base Chart.

    Science.gov (United States)

    Treptow, Richard S.

    1986-01-01

    Discusses the difficulties that beginning chemistry students have in understanding acid-base chemistry. Describes the use of conjugate acid-base charts in helping students visualize the conjugate relationship. Addresses chart construction, metal ions, buffers and pH titrations, and the organic functional groups and nonaqueous solvents. (TW)

  14. The Kidney and Acid-Base Regulation

    Science.gov (United States)

    Koeppen, Bruce M.

    2009-01-01

    Since the topic of the role of the kidneys in the regulation of acid base balance was last reviewed from a teaching perspective (Koeppen BM. Renal regulation of acid-base balance. Adv Physiol Educ 20: 132-141, 1998), our understanding of the specific membrane transporters involved in H+, HCO , and NH transport, and especially how these…

  15. The Kidney and Acid-Base Regulation

    Science.gov (United States)

    Koeppen, Bruce M.

    2009-01-01

    Since the topic of the role of the kidneys in the regulation of acid base balance was last reviewed from a teaching perspective (Koeppen BM. Renal regulation of acid-base balance. Adv Physiol Educ 20: 132-141, 1998), our understanding of the specific membrane transporters involved in H+, HCO , and NH transport, and especially how these…

  16. Nucleic Acid Aptamers Against Proteases

    DEFF Research Database (Denmark)

    Dupont, D M; Andersen, L M; Bøtkjær, Kenneth Alrø

    2011-01-01

    Proteases are potential or realized therapeutic targets in a wide variety of pathological conditions. Moreover, proteases are classical subjects for studies of enzymatic and regulatory mechanisms. We here review the literature on nucleic acid aptamers selected with proteases as targets. Designing...... strategies and of new principles for regulating the activity of the inhibitory action of aptamers of general interest to researchers working with nucleic acid aptamers...

  17. Acid-base disorders: learning the basics.

    Science.gov (United States)

    Ayers, Phil; Dixon, Carman; Mays, Andrew

    2015-02-01

    Nutrition support practitioners should be confident in their ability to recognize and treat various metabolic and respiratory disorders encountered in daily practice. A clinician's comprehension of the underlying physiologic processes and/or exogenous causes that occur during acid-base disorders is essential when making therapeutic decisions regarding fluids, parenteral nutrition, and electrolyte management. This invited review will discuss basic metabolic and respiratory disorders while briefly addressing mixed acid-base disorders. © 2014 American Society for Parenteral and Enteral Nutrition.

  18. Anions in Nucleic Acid Crystallography.

    Science.gov (United States)

    D'Ascenzo, Luigi; Auffinger, Pascal

    2016-01-01

    Nucleic acid crystallization buffers contain a large variety of chemicals fitting specific needs. Among them, anions are often solely considered for pH-regulating purposes and as cationic co-salts while their ability to directly bind to nucleic acid structures is rarely taken into account. Here we review current knowledge related to the use of anions in crystallization buffers along with data on their biological prevalence. Chloride ions are frequently identified in crystal structures but display low cytosolic concentrations. Hence, they are thought to be distant from nucleic acid structures in the cell. Sulfate ions are also frequently identified in crystal structures but their localization in the cell remains elusive. Nevertheless, the characterization of the binding properties of these ions is essential for better interpreting the solvent structure in crystals and consequently, avoiding mislabeling of electron densities. Furthermore, understanding the binding properties of these anions should help to get clues related to their potential effects in crowded cellular environments.

  19. Histidine-Containing Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2000-01-01

    Peptide nucleic acids containing histidine moieties are provided. These compounds have applications including diagnostics, research and potential therapeutics.......Peptide nucleic acids containing histidine moieties are provided. These compounds have applications including diagnostics, research and potential therapeutics....

  20. Application of living free radical polymerization for nucleic acid delivery.

    Science.gov (United States)

    Chu, David S H; Schellinger, Joan G; Shi, Julie; Convertine, Anthony J; Stayton, Patrick S; Pun, Suzie H

    2012-07-17

    Therapeutic gene delivery can alter protein function either through the replacement of nonfunctional genes to restore cellular health or through RNA interference (RNAi) to mask mutated and harmful genes. Researchers have investigated a range of nucleic acid-based therapeutics as potential treatments for hereditary, acquired, and infectious diseases. Candidate drugs include plasmids that induce gene expression and small, interfering RNAs (siRNAs) that silence target genes. Because of their self-assembly with nucleic acids into virus-sized nanoparticles and high transfection efficiency in vitro, cationic polymers have been extensively studied for nucleic acid delivery applications, but toxicity and particle stability have limited the clinical applications of these systems. The advent of living free radical polymerization has improved the quality, control, and reproducibility of these synthesized materials. This process yields well-defined, narrowly disperse materials with designed architectures and molecular weights. As a result, researchers can study the effects of polymer architecture and molecular weight on transfection efficiency and cytotoxicity, which will improve the design of next-generation vectors. In this Account, we review findings from structure-function studies that have elucidated key design motifs necessary for the development of effective nucleic acid vectors. Researchers have used robust methods such as atom transfer radical polymerization (ATRP), reverse addition-fragmentation chain transfer polymerization (RAFT), and ring-opening metastasis polymerization (ROMP) to engineer materials that enhance extracellular stability and cellular specificity and decrease toxicity. In addition, we discuss polymers that are biodegradable, form supramolecular structures, target specific cells, or facilitate endosomal release. Finally, we describe promising materials with a range of in vivo applications from pulmonary gene delivery to DNA vaccines.

  1. Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing

    Directory of Open Access Journals (Sweden)

    Ti-Hsuan Ku

    2015-07-01

    Full Text Available Detection of small molecules or proteins of living cells provides an exceptional opportunity to study genetic variations and functions, cellular behaviors, and various diseases including cancer and microbial infections. Our aim in this review is to give an overview of selected research activities related to nucleic acid-based aptamer techniques that have been reported in the past two decades. Limitations of aptamers and possible approaches to overcome these limitations are also discussed.

  2. Magnetic nanoparticles-based extraction and verification of nucleic acids from different sources.

    Science.gov (United States)

    Ma, Chao; Li, Chuanyan; Wang, Fang; Ma, Ningning; Li, Xiaolong; Li, Zhiyang; Deng, Yan; Wang, Zhifei; Xi, Zhijiang; Tang, Yongjun; Hel, Nongyue

    2013-04-01

    In many molecule biology and genetic technology studies, the amount of available DNA can be one of the important criteria for selecting the samples from different sources. Compared with those genomic DNA methods using organic solvents or other traditional commercial kits, the method based on magnetic nanoparticles (MNPs) and adsorption technology has many remarkable advantages like being time-saving and cost effective without the laborious centrifugation or precipitation steps, and more importantly it has the great potential and especially suitable for automated DNA extraction and up-scaling. In this paper, the extraction efficiency of genomic nucleic acids based on magnetic nanoparticles from four different sources including bacteria, yeast, human blood and virus samples are compared and verified. After measurement and verification of the extracted genomic nucleic acids, it was shown that all these genomic nucleic acids extracted using the MNPs method can be of high yield and be available for next molecule biological steps.

  3. Acid-base balance in heart failure.

    Science.gov (United States)

    Frangiosa, A; De Santo, L S; Anastasio, P; De Santo, N G

    2006-01-01

    In end-stage heart failure, various acid-base disorders can be discovered due to the renal loss of hydrogen ions and hydrogen ion movements into cells, the reduction of the effective circulating volume, hypoxemia and renal failure. This justifies the occurrence of metabolic alkalosis, metabolic acidosis, respiratory alkalosis, as well as respiratory acidosis alone or in combination. Several studies have been published on the acid-base state in heart failure. In a 1951 study, Squires et al analyzed the distribution of body fluid in congestive heart failure by taking into consideration the abnormalities in serum electrolyte concentration and in acid-base equilibrium. A recent study by Milionis et al, analyzed 86 patients with congestive heart failure receiving conventional treatment; the majority of these patients exhibited hypokalemia, hyponatremia, hypocalcemia and hypophosphatemia. Disorders in acid-base balance were noted in 37.2% of patients. In a recent study, 70 patients with severe congestive heart failure before heart transplantation showed high-normal pH, slightly reduced pCO 2 and a slight loss of hydrogen ions. After heart transplantation, stability of blood pH and hydrogen ion concentrations was found. In contrast, bicarbonate and pCO 2 increased significantly. The data led us to formulate the diagnosis of a mixed acid-base disorder that includes respiratory alkalosis and metabolic alkalosis before heart transplantation. In heart failure, the presence of acid-base imbalance associated with the activation of mechanisms that lead to salt and water retention reveals evidence concerning the pivotal role of the kidney in determining the outcome of these patients.

  4. Hypokalemic paralysis and acid-base balance

    Directory of Open Access Journals (Sweden)

    Ivo Casagranda

    2006-10-01

    Full Text Available Three cases of hypokalemic paralysis are reported, presenting to the Emergency Department. The first is a patient with a hypokalemic periodic paralysis with a normal acid-base status, the second is a case of hypokalemic flaccid paralysis of all extremities with a normal anion gap metabolic acidosis, the last is a patient with a hypokalemic distal paralysis of right upper arm with metabolic alkalosis. Afterwards some pathophysiologic principles and the clinical aspects of hypokalemia are discussed and an appropriate approach to do in Emergency Department, to identify the hypokalemic paralysis etiologies in the Emergency Department, is presented, beginning from the evaluation of acid-base status.

  5. Glycine/Glycolic acid based copolymers

    NARCIS (Netherlands)

    in 't Veld, P.J.A.; in 't Veld, Peter J.A.; Shen, Zheng-Rong; Shen, Z.; Takens, Gijsbert A.J.; Takens, G.A.J.; Dijkstra, Pieter J.; Feijen, Jan

    1994-01-01

    Glycine/glycolic acid based biodegradable copolymers have been prepared by ring-opening homopolymerization of morpholine-2,5-dione, and ring-opening copolymerization of morpholine-2,5-dione and glycolide. The homopolymerization of morpholine-2,5-dione was carried out in the melt at 200°C for 3 min

  6. Jigsaw Cooperative Learning: Acid-Base Theories

    Science.gov (United States)

    Tarhan, Leman; Sesen, Burcin Acar

    2012-01-01

    This study focused on investigating the effectiveness of jigsaw cooperative learning instruction on first-year undergraduates' understanding of acid-base theories. Undergraduates' opinions about jigsaw cooperative learning instruction were also investigated. The participants of this study were 38 first-year undergraduates in chemistry education…

  7. The Magic Sign: Acids, Bases, and Indicators.

    Science.gov (United States)

    Phillips, Donald B.

    1986-01-01

    Presents an approach that is used to introduce elementary and junior high students to a series of activities that will provide concrete experiences with acids, bases, and indicators. Provides instructions and listings of needed solutions and materials for developing this "magic sign" device. Includes background information and several…

  8. Jigsaw Cooperative Learning: Acid-Base Theories

    Science.gov (United States)

    Tarhan, Leman; Sesen, Burcin Acar

    2012-01-01

    This study focused on investigating the effectiveness of jigsaw cooperative learning instruction on first-year undergraduates' understanding of acid-base theories. Undergraduates' opinions about jigsaw cooperative learning instruction were also investigated. The participants of this study were 38 first-year undergraduates in chemistry education…

  9. Glycine/Glycolic acid based copolymers

    NARCIS (Netherlands)

    Veld, in 't Peter J.A.; Shen, Zheng-Rong; Takens, Gijsbert A.J.; Dijkstra, Pieter J.; Feijen, Jan

    1994-01-01

    Glycine/glycolic acid based biodegradable copolymers have been prepared by ring-opening homopolymerization of morpholine-2,5-dione, and ring-opening copolymerization of morpholine-2,5-dione and glycolide. The homopolymerization of morpholine-2,5-dione was carried out in the melt at 200°C for 3 min u

  10. Nucleic acid detection using MNAzymes.

    Science.gov (United States)

    Gerasimova, Yulia V; Kolpashchikov, Dmitry M

    2010-02-26

    Deoxyribozymes are promising biotechnological tools. In a recent JACS article, Mokany et al. reported on the design of multi-component deoxyribozyme (MNAzyme) sensors based on 10-23 and 8-17 DNA enzymes. The sensors can detect down to 5 pM of a specific nucleic acid. The versatility of MNAzyme platform allows the design of catalytic cascades for signal amplification. This work is a step forward to PCR-free molecular diagnostics.

  11. Whole body acid-base modeling revisited.

    Science.gov (United States)

    Ring, Troels; Nielsen, Søren

    2017-04-01

    The textbook account of whole body acid-base balance in terms of endogenous acid production, renal net acid excretion, and gastrointestinal alkali absorption, which is the only comprehensive model around, has never been applied in clinical practice or been formally validated. To improve understanding of acid-base modeling, we managed to write up this conventional model as an expression solely on urine chemistry. Renal net acid excretion and endogenous acid production were already formulated in terms of urine chemistry, and we could from the literature also see gastrointestinal alkali absorption in terms of urine excretions. With a few assumptions it was possible to see that this expression of net acid balance was arithmetically identical to minus urine charge, whereby under the development of acidosis, urine was predicted to acquire a net negative charge. The literature already mentions unexplained negative urine charges so we scrutinized a series of seminal papers and confirmed empirically the theoretical prediction that observed urine charge did acquire negative charge as acidosis developed. Hence, we can conclude that the conventional model is problematic since it predicts what is physiologically impossible. Therefore, we need a new model for whole body acid-base balance, which does not have impossible implications. Furthermore, new experimental studies are needed to account for charge imbalance in urine under development of acidosis.

  12. Multiplexed microfluidic approach for nucleic acid enrichment

    Energy Technology Data Exchange (ETDEWEB)

    VanderNoot, Victoria A.; Langevin, Stanley Alan; Bent, Zachary; Renzi, Ronald F.; Ferko, Scott M.; Van De Vreugde, James L.; Lane, Todd; Patel, Kamlesh; Branda, Steven

    2016-04-26

    A system for enhancing a nucleic acid sample may include a one pump, a denaturing chamber; a microfluidic hydroxyapatite chromatography device configured for performing hydroxyapatite chromatography on the nucleic acid sample, a sample collector, and tubing connecting the pump with the denaturing chamber, the hydroxyapatite chromatography device and the sample collector such that the pump may be used to move the nucleic acid sample from the denaturing chamber to the hydroxyapatite chromatography device and then to the sample collector.

  13. Double stranded nucleic acid biochips

    Energy Technology Data Exchange (ETDEWEB)

    Chernov, Boris; Golova, Julia

    2006-05-23

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  14. Cleaving Double-Stranded DNA with Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    1997-01-01

    Peptide nucleic acids and analogues of peptide nucleic acids are used to form duplex, triplex, and other structures with nucleic acids and to modify nucleic acids. The peptide nucleic acids and analogues thereof also are used to modulate protein activity through, for example, transcription arrest...

  15. Double-Stranded Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2001-01-01

    A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  16. An introduction to peptide nucleic acid

    DEFF Research Database (Denmark)

    Nielsen, P E; Egholm, M

    1999-01-01

    Peptide Nucleic Acid (PNA) is a powerful new biomolecular tool with a wide range of important applications. PNA mimics the behaviour of DNA and binds complementary nucleic acid strands. The unique chemical, physical and biological properties of PNA have been exploited to produce powerful...

  17. Teaching Acid/Base Physiology in the Laboratory

    Science.gov (United States)

    Friis, Ulla G.; Plovsing, Ronni; Hansen, Klaus; Laursen, Bent G.; Wallstedt, Birgitta

    2010-01-01

    Acid/base homeostasis is one of the most difficult subdisciplines of physiology for medical students to master. A different approach, where theory and practice are linked, might help students develop a deeper understanding of acid/base homeostasis. We therefore set out to develop a laboratory exercise in acid/base physiology that would provide…

  18. Investigating Students' Reasoning about Acid-Base Reactions

    Science.gov (United States)

    Cooper, Melanie M.; Kouyoumdjian, Hovig; Underwood, Sonia M.

    2016-01-01

    Acid-base chemistry is central to a wide range of reactions. If students are able to understand how and why acid-base reactions occur, it should provide a basis for reasoning about a host of other reactions. Here, we report the development of a method to characterize student reasoning about acid-base reactions based on their description of…

  19. Using Willie's Acid-Base Box for Blood Gas Analysis

    Science.gov (United States)

    Dietz, John R.

    2011-01-01

    In this article, the author describes a method developed by Dr. William T. Lipscomb for teaching blood gas analysis of acid-base status and provides three examples using Willie's acid-base box. Willie's acid-base box is constructed using three of the parameters of standard arterial blood gas analysis: (1) pH; (2) bicarbonate; and (3) CO[subscript…

  20. Using Willie's Acid-Base Box for Blood Gas Analysis

    Science.gov (United States)

    Dietz, John R.

    2011-01-01

    In this article, the author describes a method developed by Dr. William T. Lipscomb for teaching blood gas analysis of acid-base status and provides three examples using Willie's acid-base box. Willie's acid-base box is constructed using three of the parameters of standard arterial blood gas analysis: (1) pH; (2) bicarbonate; and (3) CO[subscript…

  1. Assessing College Students' Understanding of Acid Base Chemistry Concepts

    Science.gov (United States)

    Wan, Yanjun Jean

    2014-01-01

    Typically most college curricula include three acid base models: Arrhenius', Bronsted-Lowry's, and Lewis'. Although Lewis' acid base model is generally thought to be the most sophisticated among these three models, and can be further applied in reaction mechanisms, most general chemistry curricula either do not include Lewis' acid base model, or…

  2. Teaching Acid/Base Physiology in the Laboratory

    Science.gov (United States)

    Friis, Ulla G.; Plovsing, Ronni; Hansen, Klaus; Laursen, Bent G.; Wallstedt, Birgitta

    2010-01-01

    Acid/base homeostasis is one of the most difficult subdisciplines of physiology for medical students to master. A different approach, where theory and practice are linked, might help students develop a deeper understanding of acid/base homeostasis. We therefore set out to develop a laboratory exercise in acid/base physiology that would provide…

  3. Interactions of Safranin T with Nucleic Acids

    Institute of Scientific and Technical Information of China (English)

    WANG, Zhen-Xin; LIU, Dian-Jun; DONG, Slmo-Jun

    2001-01-01

    The interactions of Safranin T (ST) with several mucleic acidshave been investigated by electrochemical, UV- visibIe and CDspectroscopic technipues. The form of the nucleic acid-STcomplexes is starve to the ratio of the two species. Twoelectrocbemically inactive complexes such as, nucleic acid- srand nucleic acid-2ST, were formed while ST interacts withnucleic acids. Two proceases were obtaened from spectral experiments: (1) at the high value of R (R is defined as the ratio of the total concentration of ST to that of nucleic acid), sris groove-binding with stacking, (2) at the low value of R,ST is groove-binding without stacking.Intrinsic binding constants were obtained by spectral methods.The experints also show that electrostatic binding prays an important role inthe interactinn of ST with nucleic acids.

  4. Methods for Identifying Ligands that Target Nucleic Acid Molecules and Nucleic Acid Structural Motifs

    Science.gov (United States)

    Disney, Matthew D. (Inventor); Childs-Disney, Jessica L. (Inventor)

    2017-01-01

    Disclosed are methods for identifying a nucleic acid (e.g., RNA, DNA, etc.) motif which interacts with a ligand. The method includes providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support; contacting the plurality of immobilized ligands with a nucleic acid motif library under conditions effective for one or more members of the nucleic acid motif library to bind with the immobilized ligands; and identifying members of the nucleic acid motif library that are bound to a particular immobilized ligand. Also disclosed are methods for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, as well as methods for identifying a nucleic acid which interacts with a ligand.

  5. Bedside Analysis of Acid-Base Balance

    Directory of Open Access Journals (Sweden)

    Yu. S. Podlesskikh

    2006-01-01

    Full Text Available Laboratory service is one of the most hang-the-expense items in the cost of treatment of patients in an intensive care unit. Isolated acid-base balance (ABB impairments are rare in clinical practice. These impairments are generally combined and they frequently cause a drastic change in the pH value of blood. Early detection of their origin and its elimination are of profound importance in these situations. Miniaturization of analyzers has made it possible to conduct some investigations and particularly to determine ABB just in the intensive care unit or operating suite. The attached software permits creation of a database and transmission of information to the laboratory network. One year’s experience has indicated that the quality of reagents and reference substances allows real-time determination of the values of ABB with a high degree of accuracy and reproducibility at a patient’s bed. 

  6. Cell number and transfection volume dependent peptide nucleic acid antisense activity by cationic delivery methods

    DEFF Research Database (Denmark)

    Llovera Nadal, Laia; Berthold, Peter; Nielsen, Peter E

    2012-01-01

    Efficient intracellular delivery is essential for high activity of nucleic acids based therapeutics, including antisense agents. Several strategies have been developed and practically all rely on auxiliary transfection reagents such as cationic lipids, cationic polymers and cell penetrating...... peptides as complexing agents and carriers of the nucleic acids. However, uptake mechanisms remain rather poorly understood, and protocols always require optimization of transfection parameters. Considering that cationic transfection complexes bind to and thus may up-concentrate on the cell surface, we...... have now quantitatively compared the cellular activity (in the pLuc705 HeLa cell splice correction system) of PNA antisense oligomers using lipoplex delivery of cholesterol- and bisphosphonate-PNA conjugates, polyplex delivery via a PNA-polyethyleneimine conjugate and CPP delivery via a PNA...

  7. Chip-based sequencing nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  8. Chip-based sequencing nucleic acids

    Science.gov (United States)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  9. Standardization of Nucleic Acid Tests for Clinical Measurements of Bacteria and Viruses.

    Science.gov (United States)

    Pavšič, Jernej; Devonshire, Alison S; Parkes, Helen; Schimmel, Heinz; Foy, Carole A; Karczmarczyk, Maria; Gutiérrez-Aguirre, Ion; Honeyborne, Isobella; Huggett, Jim F; McHugh, Timothy D; Milavec, Mojca; Zeichhardt, Heinz; Žel, Jana

    2015-07-01

    Nucleic acid-based tests for infectious diseases currently used in the clinical laboratory and in point-of-care devices are diverse. Measurement challenges associated with standardization of quantitative viral load testing are discussed in relation to human cytomegalovirus, BK virus, and Epstein-Barr virus, while the importance of defining the performance of qualitative methods is illustrated with Mycobacterium tuberculosis and influenza virus. The development of certified reference materials whose values are traceable to higher-order standards and reference measurement procedures, using, for instance, digital PCR, will further contribute to the understanding of analytical performance characteristics and promote clinical data comparability.

  10. Theory of ion transport with fast acid-base equilibrations in bioelectrochemical systems

    Science.gov (United States)

    Dykstra, J. E.; Biesheuvel, P. M.; Bruning, H.; Ter Heijne, A.

    2014-07-01

    Bioelectrochemical systems recover valuable components and energy in the form of hydrogen or electricity from aqueous organic streams. We derive a one-dimensional steady-state model for ion transport in a bioelectrochemical system, with the ions subject to diffusional and electrical forces. Since most of the ionic species can undergo acid-base reactions, ion transport is combined in our model with infinitely fast ion acid-base equilibrations. The model describes the current-induced ammonia evaporation and recovery at the cathode side of a bioelectrochemical system that runs on an organic stream containing ammonium ions. We identify that the rate of ammonia evaporation depends not only on the current but also on the flow rate of gas in the cathode chamber, the diffusion of ammonia from the cathode back into the anode chamber, through the ion exchange membrane placed in between, and the membrane charge density.

  11. Nucleic acids, proteins, and chirality

    Science.gov (United States)

    Usher, D. A.; Profy, A. T.; Walstrum, S. A.; Needels, M. C.; Bulack, S. C.; Lo, K. M.

    1984-01-01

    The present investigation is concerned with experimental results related, in one case, to the chirality of nucleotides, and, in another case, to the possibility of a link between the chirality of nucleic acids, and that of peptides. It has been found that aminoacylation of the 'internal' hydroxyl group of a dinucleoside monophosphate can occur stereoselectively. However, this reaction has not yet been made a part of a working peptide synthesis scheme. The formation and cleavage of oligonucleotides is considered. In the event of the formation of a helical complex between the oligonucleotide and the polymer, 1-prime,5-prime-bonds in the oligomer are found to become more resistant towards cleavage. The conditions required for peptide bond formation are examined, taking into account the known structures of RNA and possible mechanisms for prebiotic peptide bond formation. The possibility is considered that the 2-prime,5-prime-internucleotide linkage could have played an important part in the early days of biological peptide synthesis.

  12. Nucleic acid drugs: a novel approach

    African Journals Online (AJOL)

    Administrator

    In this way the nucleic acids act as drug for inhibiting gene expression or protein synthesis. This article examines ... The majority of currently employed pharmacological approaches for ..... of antiviral and anticancer in near future. REFERENCE.

  13. NMR studies of nucleic acid dynamics

    Science.gov (United States)

    Al-Hashimi, Hashim M.

    2013-12-01

    Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.

  14. Methods for analyzing nucleic acid sequences

    Science.gov (United States)

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2011-05-17

    The present invention is directed to a method of sequencing a target nucleic acid. The method provides a complex comprising a polymerase enzyme, a target nucleic acid molecule, and a primer, wherein the complex is immobilized on a support Fluorescent label is attached to a terminal phosphate group of the nucleotide or nucleotide analog. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The time duration of the signal from labeled nucleotides or nucleotide analogs that become incorporated is distinguished from freely diffusing labels by a longer retention in the observation volume for the nucleotides or nucleotide analogs that become incorporated than for the freely diffusing labels.

  15. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

    Directory of Open Access Journals (Sweden)

    Michael G. Mauk

    2015-10-01

    Full Text Available Microfluidic components and systems for rapid (<60 min, low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs are described. A microfluidic point-of-care (POC diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1 nucleic acids (NAs are extracted from relatively large (~mL volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane” to capture sample NAs in a flow-through, filtration mode; (2 NAs captured on the membrane are isothermally (~65 °C amplified; (3 amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4 paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

  16. Nucleic acid association to human prostasomes.

    Science.gov (United States)

    Olsson, I; Ronquist, G

    1990-01-01

    Human prostasomes isolated from seminal plasma were subjected to phenol extraction and then to absorbance (A) measurements at 260 nm (A260) and 280 nm (A280). The A260/A280 ratio was about 2 for prostasome extract and lower for seminal plasma extract, indicative of the presence of nucleic acid. The ratio of nucleic acid to protein in prostasomes was about 1:100, and the ratio in seminal plasma was 1:1,000. Hence nucleic acid is enriched in prostasomes (compared to seminal plasma of 10). Treatment of prostasome samples with 2% sodium dodecyl sulfate resulted in an efficient dissociation of nucleic acid from prostasomes as demonstrated by electrophoresis. The association of nucleic acids of various sizes (range; 200 to 20,000 base pairs) to prostasome membranes was most probably genuine and not the result of contamination from spermatozoa, erythrocytes, leukocytes, or bacteria. The results of experiments employing nucleic acid-degrading enzymes favored the concept that double-stranded DNA but not RNA is present at the prostasome membrane surface.

  17. [Characteristic vibration analysis of M-RNA nucleic acid bases complexes (M = Ca+ and Mg+) by DFT].

    Science.gov (United States)

    Zhang, Xing-Chu; Hu, Yi-Hua; Wang, Xiao-Juan

    2009-01-01

    A density functional investigation of the interaction between calcium and magnesium univalent cations and RNA pyrimidine base (cytosine, thymine and uracil) was performed to determine geometric coordinates and free energies for all possible stable isomers at B3LYP/6-311 + G (2df, 2p) level. The most stable isomers C1M, T1M and U1M (M = Ca+ and Mg+) with the lowest free energy among the same pyrimidine base tautomers were calculated to determine the characters of infrared vibrations. According to the results, two characteristic infrared vibrations at wave numbers 1,684 and 1,765 cm(-1) were found for single pyrimidine base C1, at 1,747 and 1,792 cm(-1) for T1, 1,763 and at 1,796 cm(-1) for U1. In addition, spectrum shifts were found when the cations interact with the pyrimidine base tautomers. For deeper analysis, we found that when the stable complexes are formed, the cations are prone to act on the oxygen atoms, and cause the vibrational frequencies to change, the spectral lines belonging to the vibration of C--O--M turn out to redshift and the others turn out to blueshift. When the stable complex C1M is formed, the characteristic infrared vibration at 1,684 cm(-1) mainly caused by the ring's vibration turns out to blueshift about 10 cm(-1), and the another characteristic vibration of 1,765 cm(-1) caused by vibration of bond C--O with oxygen atom acting on cations directly turns out to redshift by 112 cm(-1) for complex C1Ca+ and by 110 cm(-1) for C1Mg+. When the stable complexes T1M are formed, the characteristic vibration of bond C--O--M turns out to redshift about 130 cm(-1) and the vibration of bond C--O turns out to blueshift about 55 cm(-1). When the stable complexes U1M are formed, the vibration of bond C--O--M turns out to redshift about 90 cm(-1) and about 50 cm(-1) for another C--O. The characteristic infrared vibration frequencies are changed obviously when tautomers act on the cations, which is mainly because cations take part in molecule's vibrations and change the force constants and reduced masses.

  18. From proteins to nucleic acid-based drugs: the role of biotech in anti-VEGF therapy.

    Science.gov (United States)

    Gatto, Barbara; Cavalli, Marco

    2006-07-01

    Cancer cells, by releasing pro-angiogenic factors, stimulate the growth of the thick capillary net necessary for the nourishment of the tumor mass. The battle to defeat cancer uses today different approaches based on the inhibition of pathological angiogenesis: several compounds, either synthetic or biotech, aimed at this complex process, are under development. Vascular endothelial growth factor (VEGF) is considered the main target for an anti-cancer therapy based on angiogenesis inhibition; the goal is to block the interaction between this cytokine and its receptors in order to stop the intracellular signaling pathways leading to endothelium remodeling. FDA recently approved two drugs specifically aimed at VEGF, bevacizumab, a humanized monoclonal antibody, and pegaptinib, a pegylated aptamer with application in ophthalmic pathologies. These two approvals validate anti-VEGF therapy for clinical use, and show how biotech companies are investing on angiogenesis using different approaches, i.e. exploiting protein drugs and oligonucleotide-based therapeutics. Monoclonal antibodies, as well as other high molecular weight products like cytokine-traps, aptamers and short interfering RNA (siRNA), are designed to target VEGF and its receptors. Their design, production and clinical advancement in cancer and other pathological conditions linked to angiogenesis will be specifically addressed in this review.

  19. Application of Nucleic Acid-Based Tools for Monitoring Monitored Natural Attenuation (MNA), Biostimulation and Bioaugmentation at Chlorinated Solvent Sites

    Science.gov (United States)

    2011-02-01

    Dallas .......................................................................................... 25 4.1.3 MLP/ VAB , NASA Cape Canaveral...32 4.2.3 MLP/ VAB , NASA Cape Canaveral ....................................................................... 32 4.2.4...35 4.3.3 MLP/ VAB , NASA Cape Canaveral ....................................................................... 35 4.3.4 Vandenberg AFB

  20. Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra

    Energy Technology Data Exchange (ETDEWEB)

    Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav; Landau, Arie; Ahmed, Musahid; Krylov, Anna I.

    2010-08-02

    We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.

  1. Electron attachment to the guanine-cytosine nucleic acid base pair and the effects of monohydration and proton transfer.

    Science.gov (United States)

    Gupta, Ashutosh; Jaeger, Heather M; Compaan, Katherine R; Schaefer, Henry F

    2012-05-17

    The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.

  2. Creation of new molecules containing threading intercalator, which can bind strongly to unusual nucleic acid structures; Nuikomigata intakareta wo mochiita tokushu RNA kozo eno tokuiteki ketsugo bunshi no shoshutsu

    Energy Technology Data Exchange (ETDEWEB)

    Takenaka, Shigeori [Kyushu University, Fukuoka (Japan). Dept. of Chemical Systems and Engineering

    1999-12-16

    We have been studying the naphthalene diimide derivatives which can recognize the unusual nucleic acid structures due to the peculiar character of threading intercalator. Firstly, we synthesized the naphthalene diimide derivative carrying thymine moieties at the imide termini. This molecule was expected to have the preference for the non-alternating adenine sequence of single stranded nucleic acid. Circular dichroism and fluorescence energy transfer studies involving acridine orange, naphthalene diimide ligand, and d (GCGAAACGC) oligonucleotide showed that the ligand can prefer bulge form of the nucleic acid to hairpin structure. Secondly, we designed and synthesized the cyclic ligand linked between naphthalene diimide and ferrocene moieties. Cyclic ligand can strongly bind to nucleic acid base projecting out from double stranded nucleic acid such as mismatch base and this can be detected using electrochemical signal of the ligand. These ligands are not only suspected of anti-virus activity but also they are promising new probe of genetic polymorphism. (author)

  3. ACID-BASE INTERACTIONS BETWEEN POLYMERS AND FILLERS

    Institute of Scientific and Technical Information of China (English)

    WANG Qingguo; CHEN Fute; HUANG Yuanfu; ZHOU Qingli

    1987-01-01

    Inverse gas chromatography(IGC) and Fourier-transform infrared (FT-IR) techniques were applied to determining the relative acid-base strength of polymers and coupling agents. The acid-base characteristics of fillers such as CaCO3 could be altered by treatment with different coupling agents. It was shown that some mechanical properties of filled polymers were obviously associated with acid-base interactions between polymers and fillers.

  4. Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development.

    Science.gov (United States)

    Briones, Carlos; Moreno, Miguel

    2012-04-01

    Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.

  5. A Closer Look at Acid-Base Olfactory Titrations

    Science.gov (United States)

    Neppel, Kerry; Oliver-Hoyo, Maria T.; Queen, Connie; Reed, Nicole

    2005-01-01

    Olfactory titrations using raw onions and eugenol as acid-base indicators are reported. An in-depth investigation on olfactory titrations is presented to include requirements for potential olfactory indicators and protocols for using garlic, onions, and vanillin as acid-base olfactory indicators are tested.

  6. What is the Ultimate Goal in Acid-Base Regulation?

    Science.gov (United States)

    Balakrishnan, Selvakumar; Gopalakrishnan, Maya; Alagesan, Murali; Prakash, E. Sankaranarayanan

    2007-01-01

    It is common to see chapters on acid-base physiology state that the goal of acid-base regulatory mechanisms is to maintain the pH of arterial plasma and not arterial PCO [subscript 2] (Pa[subscript CO[subscript 2

  7. Disorders of Acid-Base Balance: New Perspectives.

    Science.gov (United States)

    Seifter, Julian L; Chang, Hsin-Yun

    2017-01-01

    Disorders of acid-base involve the complex interplay of many organ systems including brain, lungs, kidney, and liver. Compensations for acid-base disturbances within the brain are more complete, while limitations of compensations are more apparent for most systemic disorders. However, some of the limitations on compensations are necessary to survival, in that preservation of oxygenation, energy balance, cognition, electrolyte, and fluid balance are connected mechanistically. This review aims to give new and comprehensive perspective on understanding acid-base balance and identifying associated disorders. All metabolic acid-base disorders can be approached in the context of the relative losses or gains of electrolytes or a change in the anion gap in body fluids. Acid-base and electrolyte balance are connected not only at the cellular level but also in daily clinical practice. Urine chemistry is essential to understanding electrolyte excretion and renal compensations. Many constructs are helpful to understand acid-base, but these models are not mutually exclusive. Electroneutrality and the close interconnection between electrolyte and acid-base balance are important concepts to apply in acid-base diagnoses. All models have complexity and shortcuts that can help in practice. There is no reason to dismiss any of the present constructs, and there is benefit in a combined approach.

  8. A new representation of acid-base disturbances

    NARCIS (Netherlands)

    M. Hekking (Marcel); E.S. Gelsema; J. Lindemans (Jan)

    1994-01-01

    textabstractThe acid-base status of intensive care patients is monitored on the basis of three quantities. The graphical representation which may be of help for the monitoring task is therefore cumbersome. The classical Siggaard-Andersen acid-base chart is such a representation, but it is only suite

  9. Novel Biochip Platform for Nucleic Acid Analysis

    Directory of Open Access Journals (Sweden)

    Juan J. Diaz-Mochon

    2012-06-01

    Full Text Available This manuscript describes the use of a novel biochip platform for the rapid analysis/identification of nucleic acids, including DNA and microRNAs, with very high specificity. This approach combines a unique dynamic chemistry approach for nucleic acid testing and analysis developed by DestiNA Genomics with the STMicroelectronics In-Check platform, which comprises two microfluidic optimized and independent PCR reaction chambers, and a sequential microarray area for nucleic acid capture and identification by fluorescence. With its compact bench-top “footprint” requiring only a single technician to operate, the biochip system promises to transform and expand routine clinical diagnostic testing and screening for genetic diseases, cancers, drug toxicology and heart disease, as well as employment in the emerging companion diagnostics market.

  10. Conformational classification of functional nucleic acids.

    Science.gov (United States)

    Fujii, S

    1999-01-01

    The kink parameters would provide the tolerant aspect for irregular helical structure of nucleic acid. Using these kink parameters, the classification of conformation space was carried for the functional nucleic acid molecules. The kink parameters could afford us the simple structural aspects about the constructive parts of functional molecules. Local elastic kink phenomena can be classified by rod like models with the combination of kink parameters. The constructive parts, such as the stable tetra nucleotides loop, U-turn conformation and adenosine platform, were selected and the statistical analyses were carried on the parameters calculated by program BIOCON.

  11. Macromolecular mimicry of nucleic acid and protein

    DEFF Research Database (Denmark)

    Nautrup Pedersen, Gitte; Nyborg, Jens; Clark, Brian F

    1999-01-01

    of the concept of macromolecular mimicry. Macromolecular mimicry has further been proposed among initiation and release factors, thereby adding a new element to the description of protein synthesis in bacteria. Such mimicry has also been observed in other biological processes such as autoimmunity, DNA repair......Although proteins and nucleic acids consist of different chemical components, proteins can mimic structures and possibly also functions of nucleic acids. Recently, structural mimicry was observed between two elongation factors in bacterial protein biosynthesis leading to the introduction...

  12. Teaching acid/base physiology in the laboratory

    DEFF Research Database (Denmark)

    Friis, Ulla G; Plovsing, Ronni; Hansen, Klaus;

    2010-01-01

    Acid/base homeostasis is one of the most difficult subdisciplines of physiology for medical students to master. A different approach, where theory and practice are linked, might help students develop a deeper understanding of acid/base homeostasis. We therefore set out to develop a laboratory...... exercise in acid/base physiology that would provide students with unambiguous and reproducible data that clearly would illustrate the theory in practice. The laboratory exercise was developed to include both metabolic acidosis and respiratory alkalosis. Data were collected from 56 groups of medical...

  13. Respiratory Acid-Base Disorders in the Critical Care Unit.

    Science.gov (United States)

    Hopper, Kate

    2017-03-01

    The incidence of respiratory acid-base abnormalities in the critical care unit (CCU) is unknown, although respiratory alkalosis is suspected to be common in this population. Abnormal carbon dioxide tension can have many physiologic effects, and changes in Pco2 may have a significant impact on outcome. Monitoring Pco2 in CCU patients is an important aspect of critical patient assessment, and identification of respiratory acid-base abnormalities can be valuable as a diagnostic tool. Treatment of respiratory acid-base disorders is largely focused on resolution of the primary disease, although mechanical ventilation may be indicated in cases with severe respiratory acidosis. Published by Elsevier Inc.

  14. Multifunctional Nucleic Acids for Tumor Cell Treatment

    DEFF Research Database (Denmark)

    Pofahl, Monika; Wengel, Jesper; Mayer, Günter

    2014-01-01

    -proliferative and antimiR function in one 37-nucleotide nucleic acid molecule. It inhibits cancer cell growth and induces gene expression that is pathologically damped by an oncomir. These findings will have a strong impact on future developments regarding aptamer- and antimiR-related applications for tumor targeting...

  15. Miniaturized isothermal nucleic acid amplification, a review.

    Science.gov (United States)

    Asiello, Peter J; Baeumner, Antje J

    2011-04-21

    Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.

  16. Recognition of Nucleic Acid Junctions Using Triptycene-Based Molecules

    OpenAIRE

    Barros, Stephanie A.; Chenoweth, David M.

    2014-01-01

    Nucleic acid modulation by small molecules is an essential process across the kingdoms of life. Targeting nucleic acids with small molecules represents a significant challenge at the forefront of chemical biology. Nucleic acid junctions are ubiquitous structural motifs in nature and in designed materials. Herein, we describe a new class of structure specific nucleic acid junction stabilizers based on a triptycene scaffold. Triptycenes provide significant stabilization of DNA and RNA three-way...

  17. An Olfactory Indicator for Acid-Base Titrations.

    Science.gov (United States)

    Flair, Mark N.; Setzer, William N.

    1990-01-01

    The use of an olfactory acid-base indicator in titrations for visually impaired students is discussed. Potential olfactory indicators include eugenol, thymol, vanillin, and thiophenol. Titrations performed with each indicator with eugenol proved to be successful. (KR)

  18. Acid-base and potassium disorders in liver disease.

    Science.gov (United States)

    Ahya, Shubhada N; José Soler, Maria; Levitsky, Josh; Batlle, Daniel

    2006-11-01

    Acid-base and potassium disorders occur frequently in the setting of liver disease. As the liver's metabolic function worsens, particularly in the setting of renal dysfunction, hemodynamic compromise, and hepatic encephalopathy, acid-base disorders ensue. The most common acid-base disorder is respiratory alkalosis. Metabolic acidosis alone or in combination with respiratory alkalosis also is common. Acid-base disorders in patients with liver disease are complex. The urine anion gap may help to distinguish between chronic respiratory alkalosis and hyperchloremic metabolic acidosis when a blood gas is not available. A negative urine anion gap helps to rule out chronic respiratory alkalosis. In this disorder a positive urine anion gap is expected owing to suppressed urinary acidification. Distal renal tubular acidosis occurs in autoimmune liver disease such as primary biliary cirrhosis, but often is a functional defect from impaired distal sodium delivery. Potassium disorders are often the result of the therapies used to treat advanced liver disease.

  19. Synthesis and catalytic application of amino acid based dendritic macromolecules

    NARCIS (Netherlands)

    Koten, G. van; Gossage, R.A.; Jastrzebski, J.T.B.H.; Ameijde, J. van; Mulders, S.J.E.; Brouwer, Arwin J.; Liskamp, R.M.J.

    1999-01-01

    The use of amino acid based dendrimers as molecular scaffolds for the attachment of catalytically active organometallic Ni ''pincer'' complexes, via a urea functionality, is described; the dendrimer catalysts have comparable activity to their mononuclear (NCN)NiX analogues.

  20. Acid-base homeostasis in the human system

    Science.gov (United States)

    White, R. J.

    1974-01-01

    Acid-base regulation is a cooperative phenomena in vivo with body fluids, extracellular and intracellular buffers, lungs, and kidneys all playing important roles. The present account is much too brief to be considered a review of present knowledge of these regulatory systems, and should be viewed, instead, as a guide to the elements necessary to construct a simple model of the mutual interactions of the acid-base regulatory systems of the body.

  1. Non-enzymatic Polymerization of Nucleic Acids from Monomers

    DEFF Research Database (Denmark)

    Dörr, Mark; Löffler, Philipp M. G.; Monnard, Pierre-Alain

    2012-01-01

    synthesis of long nucleic acid polymers or to sequence-specifically amplify nucleic acid polymers, respectively. Starting from molecular requirements, details of the polymerization mechanisms and strategies are first presented and then compared. Finally, we discuss the relevance of these strategies...... to the investigation of possible early molecular information systems on the prebiotic earth and the development of novel synthetic methodologies for nucleic acids....

  2. An ion-exchange nanomembrane sensor for detection of nucleic acids using a surface charge inversion phenomenon.

    Science.gov (United States)

    Senapati, Satyajyoti; Slouka, Zdenek; Shah, Sunny S; Behura, Susanta K; Shi, Zonggao; Stack, M Sharon; Severson, David W; Chang, Hsueh-Chia

    2014-10-15

    We present a novel low-cost biosensor for rapid, sensitive and selective detection of nucleic acids based on an ionic diode feature of an anion exchange nanoporous membrane under DC bias. The ionic diode feature is associated with external surface charge inversion on the positively charged anion exchange nanomembrane upon hybridization of negatively charged nucleic acid molecules to single-stranded oligoprobes functionalized on the membrane surface resulting in the formation of a cation selective monolayer. The resulting bipolar membrane causes a transition from electroconvection-controlled to water-splitting controlled ion conductance, with a large ion current signature that can be used to accurately quantify the hybridized nucleic acids. The platform is capable of distinguishing two base-pair mismatches in a 22-base pairing segment of microRNAs associated with oral cancer, as well as serotype-specific detection of dengue virus. We also show the sensor' capability to selectively capture target nucleic acids from a heterogeneous mixture. The limit of detection is 1 pM for short 27 base target molecules in a 15-min assay. Similar hybridization results are shown for short DNA molecules as well as RNAs from Brucella and Escherichia coli. The versatility and simplicity of this low-cost biosensor should enable point-of-care diagnostics in food, medical and environmental safety markets.

  3. Development of a Generic Microfluidic Device for Simultaneous Detection of Antibodies and Nucleic Acids in Oral Fluids

    Directory of Open Access Journals (Sweden)

    Zongyuan Chen

    2013-01-01

    Full Text Available A prototype dual-path microfluidic device (Rheonix CARD capable of performing simultaneously screening (antigen or antibody and confirmatory (nucleic acid detection of pathogens is described. The device fully integrates sample processing, antigen or antibody detection, and nucleic acid amplification and detection, demonstrating rapid and inexpensive “sample-to-result” diagnosis with performance comparable to benchtop analysis. For the chip design, a modular approach was followed allowing the optimization of individual steps in the sample processing process. This modular design provides great versatility accommodating different disease targets independently of the production method. In the detection module, a lateral flow (LF protocol utilizing upconverting phosphor (UCP reporters was employed. The nucleic acid (NA module incorporates a generic microtube containing dry reagents. Lateral flow strips and PCR primers determine the target or disease that is diagnosed. Diagnosis of HIV infection was used as a model to investigate the simultaneous detection of both human antibodies against the virus and viral RNA. The serological result is available in less than 30 min, and the confirmation by RNA amplification takes another 60 min. This approach combines a core serological portable diagnostic with a nucleic acid-based confirmatory test.

  4. Direct Detection of Nucleic Acid with Minimizing Background and Improving Sensitivity Based on a Conformation-Discriminating Indicator.

    Science.gov (United States)

    Zhu, Lixuan; Qing, Zhihe; Hou, Lina; Yang, Sheng; Zou, Zhen; Cao, Zhong; Yang, Ronghua

    2017-08-25

    As is well-known, the nucleic acid indicator-based strategy is one of the major approaches to monitor the nucleic acid hybridization-mediated recognition events in biochemical analysis, displaying obvious advantages including simplicity, low cost, convenience, and generality. However, conventional indicators either hold strong self-fluorescence or can be lighted by both ssDNA and dsDNA, lacking absolute selectivity for a certain conformation, always with high background interference and low sensitivity in sensing; and additional processing (e.g., nanomaterial-mediated background suppression, and enzyme-catalyzed signal amplification) is generally required to improve the detection performance. In this work, a carbazole derivative, EBCB, has been synthesized and screened as a dsDNA-specific fluorescent indicator. Compared with conventional indicators under the same conditions, EBCB displayed a much higher selective coefficient for dsDNA, with little self-fluorescence and negligible effect from ssDNA. Based on its superior capability in DNA conformation-discrimination, high sensitivity with minimizing background interference was demonstrated for direct detection of nucleic acid, and monitoring nucleic acid-based circuitry with good reversibity, resulting in low detection limit and high capability for discriminating base-mismatching. Thus, we expect that this highly specific DNA conformation-discriminating indicator will hold good potential for application in biochemical sensing and molecular logic switching.

  5. Rapid One-Step Selection Method for Generating Nucleic Acid Aptamers: Development of a DNA Aptamer against alpha-Bungarotoxin

    DEFF Research Database (Denmark)

    Lauridsen, Lasse Holm; Shamaileh, Hadi A.; Edwards, Stacey L.

    2012-01-01

    Background: Nucleic acids based therapeutic approaches have gained significant interest in recent years towards the development of therapeutics against many diseases. Recently, research on aptamers led to the marketing of Macugen (R), an inhibitor of vascular endothelial growth factor (VEGF...... by PCR enrichment of the selected aptamers. One round of selection successfully identified a DNA aptamer sequence with a binding affinity of 7.58 mu M. Conclusion: We have demonstrated a one-step method for rapid production of nucleic acid aptamers. Although the reported binding affinity is in the low...... micromolar range, we believe that this could be further improved by using larger targets, increasing the stringency of selection and also by combining a capillary electrophoresis separation prior to the one-step selection. Furthermore, the method presented here is a user-friendly, cheap and an easy way...

  6. Diagnostic applications of nucleic acid circuits.

    Science.gov (United States)

    Jung, Cheulhee; Ellington, Andrew D

    2014-06-17

    CONSPECTUS: While the field of DNA computing and molecular programming was engendered in large measure as a curiosity-driven exercise, it has taken on increasing importance for analytical applications. This is in large measure because of the modularity of DNA circuitry, which can serve as a programmable intermediate between inputs and outputs. These qualities may make nucleic acid circuits useful for making decisions relevant to diagnostic applications. This is especially true given that nucleic acid circuits can potentially directly interact with and be triggered by diagnostic nucleic acids and other analytes. Chemists are, by and large, unaware of many of these advances, and this Account provides a means of touching on what might seem to be an arcane field. We begin by explaining nucleic acid amplification reactions that can lead to signal amplification, such as catalytic hairpin assembly (CHA) and the hybridization chain reaction (HCR). In these circuits, a single-stranded input acts on kinetically trapped substrates via exposed toeholds and strand exchange reactions, refolding the substrates and allowing them to interact with one another. As multiple duplexes (CHA) or concatemers of increasing length (HCR) are generated, there are opportunities to couple these outputs to different analytical modalities, including transduction to fluorescent, electrochemical, and colorimetric signals. Because both amplification and transduction are at their root dependent on the programmability of Waston-Crick base pairing, nucleic acid circuits can be much more readily tuned and adapted to new applications than can many other biomolecular amplifiers. As an example, robust methods for real-time monitoring of isothermal amplification reactions have been developed recently. Beyond amplification, nucleic acid circuits can include logic gates and thresholding components that allow them to be used for analysis and decision making. Scalable and complex DNA circuits (seesaw gates

  7. Digital Microfluidics for Nucleic Acid Amplification

    Directory of Open Access Journals (Sweden)

    Beatriz Coelho

    2017-06-01

    Full Text Available Digital Microfluidics (DMF has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.

  8. Nucleic acid compositions and the encoding proteins

    Science.gov (United States)

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  9. Nucleic acid protocols: Extraction and optimization

    Directory of Open Access Journals (Sweden)

    Saeed El-Ashram

    2016-12-01

    Full Text Available Yield and quality are fundamental features for any researchers during nucleic acid extraction. Here, we describe a simplified, semi-unified, effective, and toxic material free protocol for extracting DNA and RNA from different prokaryotic and eukaryotic sources exploiting the physical and chemical properties of nucleic acids. Furthermore, this protocol showed that DNA and RNA are under triple protection (i.e. EDTA, SDS and NaCl during lysis step, and this environment is improper for RNase to have DNA liberated of RNA and even for DNase to degrade the DNA. Therefore, the complete removal of RNA under RNase influence is achieved when RNase is added after DNA extraction, which gives optimal quality with any protocols. Similarly, DNA contamination in an isolated RNA is degraded by DNase to obtain high-quality RNA. Our protocol is the protocol of choice in terms of simplicity, recovery time, environmental safety, amount, purity, PCR and RT-PCR applicability.

  10. Rapid hybridization of nucleic acids using isotachophoresis

    Science.gov (United States)

    Bercovici, Moran; Han, Crystal M.; Liao, Joseph C.; Santiago, Juan G.

    2012-01-01

    We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants. PMID:22733732

  11. Thermodynamic Analysis of Interacting Nucleic Acid Strands

    OpenAIRE

    Dirks, Robert M.; Bois, Justin S.; Schaeffer, Joseph M.; Winfree, Erik; Pierce, Niles A.

    2007-01-01

    Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed...

  12. Assessment of acid-base balance. Stewart's approach.

    Science.gov (United States)

    Fores-Novales, B; Diez-Fores, P; Aguilera-Celorrio, L J

    2016-04-01

    The study of acid-base equilibrium, its regulation and its interpretation have been a source of debate since the beginning of 20th century. Most accepted and commonly used analyses are based on pH, a notion first introduced by Sorensen in 1909, and on the Henderson-Hasselbalch equation (1916). Since then new concepts have been development in order to complete and make easier the understanding of acid-base disorders. In the early 1980's Peter Stewart brought the traditional interpretation of acid-base disturbances into question and proposed a new method. This innovative approach seems more suitable for studying acid-base abnormalities in critically ill patients. The aim of this paper is to update acid-base concepts, methods, limitations and applications. Copyright © 2015 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.

  13. Renal acidification responses to respiratory acid-base disorders.

    Science.gov (United States)

    Madias, Nicolaos E

    2010-01-01

    Respiratory acid-base disorders are those abnormalities in acid-base equilibrium that are expressed as primary changes in the arterial carbon dioxide tension (PaCO2). An increase in PaCO2 (hypercapnia) acidifies body fluids and initiates the acid-base disturbance known as respiratory acidosis. By contrast, a decrease in PaCO2 (hypocapnia) alkalinizes body fluids and initiates the acid-base disturbance known as respiratory alkalosis. The impact on systemic acidity of these primary changes in PaCO2 is ameliorated by secondary, directional changes in plasma [HCO3¯] that occur in 2 stages. Acutely, hypercapnia or hypocapnia yields relatively small changes in plasma [HCO3¯] that originate virtually exclusively from titration of the body's nonbicarbonate buffers. During sustained hypercapnia or hypocapnia, much larger changes in plasma [HCO3¯] occur that reflect adjustments in renal acidification mechanisms. Consequently, the deviation of systemic acidity from normal is smaller in the chronic forms of these disorders. Here we provide an overview of the renal acidification responses to respiratory acid-base disorders. We also identify gaps in knowledge that require further research.

  14. Optimizing the specificity of nucleic acid hybridization.

    Science.gov (United States)

    Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

    2012-01-22

    The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed 'toehold exchange' probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg(2+) to 47 mM Mg(2+), and with nucleic acid concentrations from 1 nM to 5 µM. Experiments with RNA also showed effective single-base change discrimination.

  15. Speed limits for acid-base chemistry in aqueous solutions.

    Science.gov (United States)

    Donten, Mateusz L; Vandevondele, Joost; Hamm, Peter

    2012-01-01

    Proton transfer reactions, including acid-base recombination, are commonly considered to occur 'nearly instantaneously'. However, their actual time scales may stretch far into the microsecond range, as acid-base reactions are diffusion controlled and the concentrations are low near neutral pH. The interplay of competing bases in the pH relaxation is illustrated using a model acid-base system consisting of o-nitrobenzaldehyde (oNBA) as a proton cage and acetate ions and hydroxyl ions as bases. The kinetically controlled behavior leads to highly counterintuitive states, i.e. acetate ions are transiently protonated for hundreds of nanoseconds despite the presence of a much stronger base OH-.

  16. Acid-base patterns in acute severe asthma.

    Science.gov (United States)

    Raimondi, Guillermo A; Gonzalez, Silvia; Zaltsman, Jorge; Menga, Guillermo; Adrogué, Horacio J

    2013-12-01

    Acid-base status in acute severe asthma (ASA) remains undefined; some studies report complete absence of metabolic acidosis, whereas others describe it as present in one fourth of patients or more. Conclusion discrepancies would therefore appear to derive from differences in assessment methodology. Only a systematic approach centering on patient clinical findings can correctly establish true acid-base disorder prevalence levels. This study examines acid-base patterns in ASA (314 patients), taking into account both natural history of disease and treatment, in patients free of other diseases altering acid-base status. Data were collected from patients admitted for ASA without prior history of chronic bronchitis, emphysema, kidney or liver disease, heart failure, uncontrolled diabetes mellitus or gastrointestinal illness. Informed consent was obtained for all patients, after study protocol approval by the Institutional Review Board. Arterial blood gases, plasma electrolytes, lactate levels, and FEV(1) were measured on arrival. Severe airway obstruction was found with FEV(1) values of 25.6 ± 10.0%, substantial hypoxemia (PaO(2) 66.1 ± 11.9 mmHg) and increased A-a O(2) gradient (39.3 ± 12.3 mmHg) breathing room air. While respiratory alkalosis occurred in patients with better preservation of FEV1, respiratory acidosis was observed with more severe airway obstruction, as was increased lactate in the majority of patients, independent of PaO(2) and PaCO(2) levels. Predominant acid-base patterns observed in ASA in this patient population included primary hypocapnia, or less frequently, primary hypercapnia. Lactic acidosis occurred in 11% of patients and presented consistently as a mixed acid-base disorder. These findings suggest lactic acidosis results from the combined effects of both ASA and medication-related sympathetic effects.

  17. Acid-base bifunctional catalytic surfaces for nucleophilic addition reactions.

    Science.gov (United States)

    Motokura, Ken; Tada, Mizuki; Iwasawa, Yasuhiro

    2008-09-01

    This article illustrates the modification of oxide surfaces with organic amine functional groups to create acid-base bifunctional catalysts, summarizing our previous reports and also presenting new data. Immobilization of organic amines as bases on inorganic solid-acid surfaces afforded highly active acid-base bifunctional catalysts, which enabled various organic transformations including C--C coupling reactions, though these reactions did not proceed with either the homogeneous amine precursors or the acidic supports alone. Spectroscopic characterization, such as by solid-state MAS NMR and FTIR, revealed not only the interactions between acidic and basic sites but also bifunctional catalytic reaction mechanisms.

  18. Acid-base disturbance in patients with cirrhosis

    DEFF Research Database (Denmark)

    Henriksen, Jens H; Bendtsen, Flemming; Møller, Søren

    2015-01-01

    PURPOSE: Acid-base disturbances were investigated in patients with cirrhosis in relation to hemodynamic derangement to analyze the hyperventilatory effects and the metabolic compensation. METHODS: A total of 66 patients with cirrhosis and 44 controls were investigated during a hemodynamic study......, and effects of unidentified ions (all Pacid-base disturbances could not be identified. CONCLUSION: Hypocapnic alkalosis is related to disease severity and hyperdynamic systemic circulation in patients with cirrhosis. The metabolic compensation includes...... alterations in serum albumin and water retention that may result in a delicate acid-base balance in these patients....

  19. Acids and bases solvent effects on acid-base strenght

    CERN Document Server

    Cox, Brian G

    2013-01-01

    Acids and bases are ubiquitous in chemistry. Our understanding of them, however, is dominated by their behaviour in water. Transfer to non-aqueous solvents leads to profound changes in acid-base strengths and to the rates and equilibria of many processes: for example, synthetic reactions involving acids, bases and nucleophiles; isolation of pharmaceutical actives through salt formation; formation of zwitter- ions in amino acids; and chromatographic separation of substrates. This book seeks to enhance our understanding of acids and bases by reviewing and analysing their behaviour in non-aqueous solvents. The behaviour is related where possible to that in water, but correlations and contrasts between solvents are also presented.

  20. Whole-body acid-base modeling revisited

    DEFF Research Database (Denmark)

    Ring, Troels; Nielsen, Søren

    2017-01-01

    The textbook account of whole-body acid-base balance in terms of endogenous acid production, renal net acid excretion and gastrointestinal alkali absorption which is the only comprehensive model around, has never been applied in clinical practice or been formally validated. In order to improve...... understanding of acid-base modeling, we managed to write up this conventional model as an expression solely on urine chemistry. Renal net acid excretion and endogenous acid production was already formulated in terms of urine chemistry, and we could from the literature also see gastrointestinal alkali absorption...

  1. Enhanced Acid/Base Catalysis in High Temperature Liquid Water

    Institute of Scientific and Technical Information of China (English)

    Xiu Yang LU; Qi JING; Zhun LI; Lei YUAN; Fei GAO; Xin LIU

    2006-01-01

    Two novel and environmentally benign solvent systems, organic acids-enriched high temperature liquid water (HTLW) and NH3-enriched HTLW, were developed, which can enhance the reaction rate of acid/base-catalyzed organic reactions in HTLW. We investigated the decomposition of fructose in organic acids-enriched HTLW, hydrolysis of cinnamaldehyde and aldol condensation of phenylaldehyde with acetaldehyde in NH3-enriched HTLW. The experimental results demonstrated that organic acids-enriched or NH3-enriched HTLW can greatly accelerate acid/base-catalyzed organic reactions in HTLW.

  2. Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2011-01-01

    Full Text Available Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

  3. Nanoparticle strategies for cancer therapeutics: Nucleic acids, polyamines, bovine serum amine oxidase and iron oxide nanoparticles (Review).

    Science.gov (United States)

    Agostinelli, Enzo; Vianello, Fabio; Magliulo, Giuseppe; Thomas, Thresia; Thomas, T J

    2015-01-01

    Nanotechnology for cancer gene therapy is an emerging field. Nucleic acids, polyamine analogues and cytotoxic products of polyamine oxidation, generated in situ by an enzyme-catalyzed reaction, can be developed for nanotechnology-based cancer therapeutics with reduced systemic toxicity and improved therapeutic efficacy. Nucleic acid-based gene therapy approaches depend on the compaction of DNA/RNA to nanoparticles and polyamine analogues are excellent agents for the condensation of nucleic acids to nanoparticles. Polyamines and amine oxidases are found in higher levels in tumours compared to that of normal tissues. Therefore, the metabolism of polyamines spermidine and spermine, and their diamine precursor, putrescine, can be targets for antineoplastic therapy since these naturally occurring alkylamines are essential for normal mammalian cell growth. Intracellular polyamine concentrations are maintained at a cell type-specific set point through the coordinated and highly regulated interplay between biosynthesis, transport, and catabolism. In particular, polyamine catabolism involves copper-containing amine oxidases. Several studies showed an important role of these enzymes in developmental and disease-related processes in animals through the control of polyamine homeostasis in response to normal cellular signals, drug treatment, and environmental and/or cellular stress. The production of toxic aldehydes and reactive oxygen species (ROS), H2O2 in particular, by these oxidases suggests a mechanism by which amine oxidases can be exploited as antineoplastic drug targets. The combination of bovine serum amine oxidase (BSAO) and polyamines prevents tumour growth, particularly well if the enzyme has been conjugated with a biocompatible hydrogel polymer. The findings described herein suggest that enzymatically formed cytotoxic agents activate stress signal transduction pathways, leading to apoptotic cell death. Consequently, superparamagnetic nanoparticles or other

  4. Students' Understanding of Acids/Bases in Organic Chemistry Contexts

    Science.gov (United States)

    Cartrette, David P.; Mayo, Provi M.

    2011-01-01

    Understanding key foundational principles is vital to learning chemistry across different contexts. One such foundational principle is the acid/base behavior of molecules. In the general chemistry sequence, the Bronsted-Lowry theory is stressed, because it lends itself well to studying equilibrium and kinetics. However, the Lewis theory of…

  5. Soil Studies: Applying Acid-Base Chemistry to Environmental Analysis.

    Science.gov (United States)

    West, Donna M.; Sterling, Donna R.

    2001-01-01

    Laboratory activities for chemistry students focus attention on the use of acid-base chemistry to examine environmental conditions. After using standard laboratory procedures to analyze soil and rainwater samples, students use web-based resources to interpret their findings. Uses CBL probes and graphing calculators to gather and analyze data and…

  6. Liquid Crystalline Furandicarboxylic Acid-based Aaromatic Polyesters

    NARCIS (Netherlands)

    WILSENS, CAROLUS HENRICUS R. MARIA; RASTOGI, SANJAY; VELD, MARTIJN ARNOLDUS JOHANNES; KLOP, ENNO ANTON; NOORDOVER, BART ADRIANUS JOHANNES

    2013-01-01

    The invention pertains to a fully aromatic liquid crystalline furandicarboxylic acid- based aromatic polyester obtainable from a mixture of monomers comprising 2,5- furandicarboxylic acid, p-hydroxybenzoic acid, an aromatic diol, and 5-40 mol% of an aromatic monocarboxylic acid selected from vanilli

  7. Acid-Base Disorders--A Computer Simulation.

    Science.gov (United States)

    Maude, David L.

    1985-01-01

    Describes and lists a program for Apple Pascal Version 1.1 which investigates the behavior of the bicarbonate-carbon dioxide buffer system in acid-base disorders. Designed specifically for the preclinical medical student, the program has proven easy to use and enables students to use blood gas parameters to arrive at diagnoses. (DH)

  8. Soil Studies: Applying Acid-Base Chemistry to Environmental Analysis.

    Science.gov (United States)

    West, Donna M.; Sterling, Donna R.

    2001-01-01

    Laboratory activities for chemistry students focus attention on the use of acid-base chemistry to examine environmental conditions. After using standard laboratory procedures to analyze soil and rainwater samples, students use web-based resources to interpret their findings. Uses CBL probes and graphing calculators to gather and analyze data and…

  9. Students' Understanding of Acids/Bases in Organic Chemistry Contexts

    Science.gov (United States)

    Cartrette, David P.; Mayo, Provi M.

    2011-01-01

    Understanding key foundational principles is vital to learning chemistry across different contexts. One such foundational principle is the acid/base behavior of molecules. In the general chemistry sequence, the Bronsted-Lowry theory is stressed, because it lends itself well to studying equilibrium and kinetics. However, the Lewis theory of…

  10. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    Science.gov (United States)

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  11. Soybean phytase and nucleic acid encoding the same

    OpenAIRE

    1999-01-01

    Isolated soybean phytase polypeptides and isolated nucleic acids encoding soybean phytases are provided. The invention is also directed to nucleic acid expression constructs, vectors, and host cells comprising the isolated soybean phytase nucleic acids, as well as methods for producing recombinant and non-recombinant purified soybean phytase. The invention also relates to transgenic plants expressing the soybean phytase, particularly expression under seed-specific expression control elements.

  12. The Importance of the Ionic Product for Water to Understand the Physiology of the Acid-Base Balance in Humans

    OpenAIRE

    Adeva-Andany, María M.; Natalia Carneiro-Freire; Cristóbal Donapetry-García; Eva Rañal-Muíño; Yosua López-Pereiro

    2014-01-01

    Human plasma is an aqueous solution that has to abide by chemical rules such as the principle of electrical neutrality and the constancy of the ionic product for water. These rules define the acid-base balance in the human body. According to the electroneutrality principle, plasma has to be electrically neutral and the sum of its cations equals the sum of its anions. In addition, the ionic product for water has to be constant. Therefore, the plasma concentration of hydrogen ions depends on th...

  13. Discovery of two–dimensional condensation of nucleic acids components at the mercury electrodes – 45 years’ history

    Directory of Open Access Journals (Sweden)

    Stanislav Hason*

    2010-12-01

    Full Text Available Purine and pyrimidine derivatives currently occurring in nucleicacids posses an extraordinary high ability of self–association at theelectrode surface and can form there by a two–dimensional (2Dcondensation a compact self-assembled monolayer. By this highcondensation ability nucleic acid bases differ from most of the otherpurine and pyrimidine derivatives which currently do not occur innucleic acids. A regular arrangement of nucleic acid bases,nucleosides and nucleotides leading to 2D condensation takes placenot only at the liquid mercury surface, but also on the mercury filmmodified carbon/graphite, solid amalgam, or atomically flat singlecrystalmetal electrodes. With polymeric DNA and/orpolynucleotides this kind of 2D condensation has not been observed.Recently, we have shown that synthetic homo- and heteropyrimidinicoligodeoxynucleotides (ODNs can 2D condensate atthe negatively charged mercury and solid amalgam surfaces.Formation of the ODN condensed film took place even in theabsence of any ODN in the bulk solution (ex situ 2D condensation.No such 2D condensed monolayer was observed with homo- andhetero-purinic ODNs giving only tensammetric(desorption/reorientation peaks in weakly alkaline pHs within thesame potential region.

  14. Flexibility of nucleic acids: from DNA to RNA

    CERN Document Server

    Bao, Lei; Jin, Lei; Tan, Zhi-Jie

    2015-01-01

    The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid flexibility, extensive studies have been performed using various experimental methods and theoretical models. In this review, we will introduce the progress that has been made in understanding the flexibility of nucleic acids including DNAs and RNAs, and will emphasize the experimental findings and the effects of salt, temperature, and sequence. Finally, we will discuss the major unanswered questions in understanding the flexibility of nucleic acids.

  15. Nucleic acid interactions with pyrite surfaces

    Science.gov (United States)

    Mateo-Martí, E.; Briones, C.; Rogero, C.; Gomez-Navarro, C.; Methivier, Ch.; Pradier, C. M.; Martín-Gago, J. A.

    2008-09-01

    The study of the interaction of nucleic acid molecules with mineral surfaces is a field of growing interest in organic chemistry, origin of life, material science and biotechnology. We have characterized the adsorption of single-stranded peptide nucleic acid (ssPNA) on a natural pyrite surface, as well as the further adsorption of ssDNA on a PNA-modified pyrite surface. The characterization has been performed by means of reflection absorption infrared spectroscopy (RAIRS), atomic force microscopy (AFM) and X-ray photoemission spectroscopy (XPS) techniques. The N(1s) and S(2p) XPS core level peaks of PNA and PNA + DNA have been decomposed in curve-components that we have assigned to different chemical species. RAIRS spectra recorded for different concentrations show the presence of positive and negative adsorption bands, related to the semiconducting nature of the surface. The combination of the information gathered by these techniques confirms that PNA adsorbs on pyrite surface, interacting through nitrogen-containing groups of the nucleobases and the iron atoms of the surface, instead of the thiol group of the molecule. The strong PNA/pyrite interaction inhibits further hybridization of PNA with complementary ssDNA, contrary to the behavior reported on gold surfaces.

  16. Comparison of the acid-base properties of ribose and 2'-deoxyribose nucleotides.

    Science.gov (United States)

    Mucha, Ariel; Knobloch, Bernd; Jezowska-Bojczuk, Małgorzata; Kozłowski, Henryk; Sigel, Roland K O

    2008-01-01

    The extent to which the replacement of a ribose unit by a 2'-deoxyribose unit influences the acid-base properties of nucleotides has not hitherto been determined in detail. In this study, by potentiometric pH titrations in aqueous solution, we have measured the acidity constants of the 5'-di- and 5'-triphosphates of 2'-deoxyguanosine [i.e., of H(2)(dGDP)(-) and H(2)(dGTP)(2-)] as well as of the 5'-mono-, 5'-di-, and 5'-triphosphates of 2'-deoxyadenosine [i.e., of H(2)(dAMP)(+/-), H(2)(dADP)(-), and H(2)(dATP)(2-)]. These 12 acidity constants (of the 56 that are listed) are compared with those of the corresponding ribose derivatives (published data) measured under the same experimental conditions. The results show that all protonation sites in the 2'-deoxynucleotides are more basic than those in their ribose counterparts. The influence of the 2'-OH group is dependent on the number of 5'-phosphate groups as well as on the nature of the purine nucleobase. The basicity of N7 in guanine nucleotides is most significantly enhanced (by about 0.2 pK units), while the effect on the phosphate groups and the N1H or N1H(+) sites is less pronounced but clearly present. In addition, (1)H NMR chemical shift change studies in dependence on pD in D(2)O have been carried out for the dAMP, dADP, and dATP systems, which confirmed the results from the potentiometric pH titrations and showed the nucleotides to be in their anti conformations. Overall, our results are not only of relevance for metal ion binding to nucleotides or nucleic acids, but also constitute an exact basis for the calculation, determination, and understanding of perturbed pK(a) values in DNAzymes and ribozymes, as needed for the delineation of acid-base mechanisms in catalysis.

  17. [Blood acid-base balance of sportsmen during physical activity].

    Science.gov (United States)

    Petrushova, O P; Mikulyak, N I

    2014-01-01

    The aim of this study was to investigate the acid-base balance parameters in blood of sportsmen by physical activity. Before exercise lactate concentration in blood was normal. Carbon dioxide pressure (рСО2), bicarbonate concentration (НСО3 -), base excess (BE), were increased immediately after physical activity lactate concentration increased, while pH, BE, НСО3 -, рСО2 decreased in capillary blood of sportsmen. These changes show the development of lactate-acidosis which is partly compensated with bicarbonate buffering system and respiratory alkalosis. During postexercise recovery lactate concentration decreased, while рСО2, НСО3 -, BE increased. The results of this study can be used for diagnostics of acid-base disorders and their medical treatment for preservation of sportsmen physical capacity.

  18. Acid-base properties of bentonite rocks with different origins.

    Science.gov (United States)

    Nagy, Noémi M; Kónya, József

    2006-03-01

    Five bentonite samples (35-47% montmorillonite) from a Sarmatian sediment series with bentonite sites around Sajóbábony (Hungary) is studied. Some of these samples were tuffogenic bentonite (sedimentary), the others were bentonitized tuff with volcano sedimentary origin. The acid-base properties of the edge sites were studied by potentiometric titrations and surface complexation modeling. It was found that the number and the ratio of silanol and aluminol sites as well as the intrinsic stability constants are different for the sedimentary bentonite and bentonitized tuff. The characteristic properties of the edges sites depend on the origins. The acid-base properties are compared to other commercial and standard bentonites.

  19. Effects of acid-base imbalance on vascular reactivity

    Directory of Open Access Journals (Sweden)

    A.C. Celotto

    2008-06-01

    Full Text Available Acid-base homeostasis maintains systemic arterial pH within a narrow range. Whereas the normal range of pH for clinical laboratories is 7.35-7.45, in vivo pH is maintained within a much narrower range. In clinical and experimental settings, blood pH can vary in response to respiratory or renal impairment. This altered pH promotes changes in vascular smooth muscle tone with impact on circulation and blood pressure control. Changes in pH can be divided into those occurring in the extracellular space (pHo and those occurring within the intracellular space (pHi, although, extracellular and intracellular compartments influence each other. Consistent with the multiple events involved in the changes in tone produced by altered pHo, including type of vascular bed, several factors and mechanisms, in addition to hydrogen ion concentration, have been suggested to be involved. The scientific literature has many reports concerning acid-base balance and endothelium function, but these concepts are not clear about acid-base disorders and their relations with the three known mechanisms of endothelium-dependent vascular reactivity: nitric oxide (NO/cGMP-dependent, prostacyclin (PGI2/cAMP-dependent and hyperpolarization. During the last decades, many studies have been published and have given rise to confronting data on acid-base disorder and endothelial function. Therefore, the main proposal of this review is to provide a critical analysis of the state of art and incentivate researchers to develop more studies about these issues.

  20. Molecular mechanisms of acid-base sensing by the kidney.

    Science.gov (United States)

    Brown, Dennis; Wagner, Carsten A

    2012-05-01

    A major function of the kidney is to collaborate with the respiratory system to maintain systemic acid-base status within limits compatible with normal cell and organ function. It achieves this by regulating the excretion and recovery of bicarbonate (mainly in the proximal tubule) and the secretion of buffered protons (mainly in the distal tubule and collecting duct). How proximal tubular cells and distal professional proton transporting (intercalated) cells sense and respond to changes in pH, bicarbonate, and CO(2) status is a question that has intrigued many generations of renal physiologists. Over the past few years, however, some candidate molecular pH sensors have been identified, including acid/alkali-sensing receptors (GPR4, InsR-RR), kinases (Pyk2, ErbB1/2), pH-sensitive ion channels (ASICs, TASK, ROMK), and the bicarbonate-stimulated adenylyl cyclase (sAC). Some acid-sensing mechanisms in other tissues, such as CAII-PDK2L1 in taste buds, might also have similar roles to play in the kidney. Finally, the function of a variety of additional membrane channels and transporters is altered by pH variations both within and outside the cell, and the expression of several metabolic enzymes are altered by acid-base status in parts of the nephron. Thus, it is possible that a master pH sensor will never be identified. Rather, the kidney seems equipped with a battery of molecules that scan the epithelial cell environment to mount a coordinated physiologic response that maintains acid-base homeostasis. This review collates current knowledge on renal acid-base sensing in the context of a whole organ sensing and response process.

  1. Regulated acid-base transport in the collecting duct.

    Science.gov (United States)

    Wagner, Carsten A; Devuyst, Olivier; Bourgeois, Soline; Mohebbi, Nilufar

    2009-05-01

    The renal collecting system serves the fine-tuning of renal acid-base secretion. Acid-secretory type-A intercalated cells secrete protons via a luminally expressed V-type H(+)-ATPase and generate new bicarbonate released by basolateral chloride/bicarbonate exchangers including the AE1 anion exchanger. Efficient proton secretion depends both on the presence of titratable acids (mainly phosphate) and the concomitant secretion of ammonia being titrated to ammonium. Collecting duct ammonium excretion requires the Rhesus protein RhCG as indicated by recent KO studies. Urinary acid secretion by type-A intercalated cells is strongly regulated by various factors among them acid-base status, angiotensin II and aldosterone, and the Calcium-sensing receptor. Moreover, urinary acidification by H(+)-ATPases is modulated indirectly by the activity of the epithelial sodium channel ENaC. Bicarbonate secretion is achieved by non-type-A intercalated cells characterized by the luminal expression of the chloride/bicarbonate exchanger pendrin. Pendrin activity is driven by H(+)-ATPases and may serve both bicarbonate excretion and chloride reabsorption. The activity and expression of pendrin is regulated by different factors including acid-base status, chloride delivery, and angiotensin II and may play a role in NaCl retention and blood pressure regulation. Finally, the relative abundance of type-A and non-type-A intercalated cells may be tightly regulated. Dysregulation of intercalated cell function or abundance causes various syndromes of distal renal tubular acidosis underlining the importance of these processes for acid-base homeostasis.

  2. A fully automatic system for acid-base coulometric titrations

    OpenAIRE

    1990-01-01

    An automatic system for acid-base titrations by electrogeneration of H+ and OH- ions, with potentiometric end-point detection, was developed. The system includes a PC-compatible computer for instrumental control, data acquisition and processing, which allows up to 13 samples to be analysed sequentially with no human intervention. The system performance was tested on the titration of standard solutions, which it carried out with low errors and RSD. It was subsequently applied to the analysis o...

  3. [Acid-base status in patients treated with peritoneal dialysis].

    Science.gov (United States)

    Katalinić, Lea; Blaslov, Kristina; Pasini, Eva; Kes, Petar; Bašić-Jukić, Nikolina

    2014-04-01

    When compared to hemodialysis, peritoneal dialysis is very simple yet low cost method of renal replacement therapy. Series of studies have shown its superiority in preserving residual renal function, postponing uremic complications, maintaining the acid-base balance and achieving better post-transplant outcome in patients treated with this method. Despite obvious advantages, its role in the treatment of chronic kidney disease is still not as important as it should be. Metabolic acidosis is an inevitable complication associated with progressive loss of kidney function. Its impact on mineral and muscle metabolism, residual renal function, allograft function and anemia is very complex but can be successfully managed. The aim of our study was to evaluate the efficiency in preserving the acid-base balance in patients undergoing peritoneal dialysis at Zagreb University Hospital Center. Twenty-eight patients were enrolled in the study. The mean time spent on the treatment was 32.39 ± 43.43 months. Only lactate-buffered peritoneal dialysis fluids were used in the treatment. Acid-base balance was completely maintained in 73.07% of patients; 11.54% of patients were found in the state of mild metabolic acidosis, and the same percentage of patients were in the state of mild metabolic alkalosis. In one patient, mixed alkalosis with respiratory and metabolic component was present. The results of this study showed that acid-base balance could be maintained successfully in patients undergoing peritoneal dialysis, even only with lactate-buffered solutions included in the treatment, although they were continuously proclaimed as inferior in comparison with bicarbonate-buffered ones. In well educated and informed patients who carefully use this method, accompanied by the attentive and thorough care of their physicians, this method can provide quality continuous replacement of lost renal function as well as better quality of life.

  4. Carbonic anhydrase 5 regulates acid-base homeostasis in zebrafish.

    Directory of Open Access Journals (Sweden)

    Ruben Postel

    Full Text Available The regulation of the acid-base balance in cells is essential for proper cellular homeostasis. Disturbed acid-base balance directly affects cellular physiology, which often results in various pathological conditions. In every living organism, the protein family of carbonic anhydrases regulate a broad variety of homeostatic processes. Here we describe the identification, mapping and cloning of a zebrafish carbonic anhydrase 5 (ca5 mutation, collapse of fins (cof, which causes initially a collapse of the medial fins followed by necrosis and rapid degeneration of the embryo. These phenotypical characteristics can be mimicked in wild-type embryos by acetazolamide treatment, suggesting that CA5 activity in zebrafish is essential for a proper development. In addition we show that CA5 regulates acid-base balance during embryonic development, since lowering the pH can compensate for the loss of CA5 activity. Identification of selective modulators of CA5 activity could have a major impact on the development of new therapeutics involved in the treatment of a variety of disorders.

  5. Neurologic complications of electrolyte disturbances and acid-base balance.

    Science.gov (United States)

    Espay, Alberto J

    2014-01-01

    Electrolyte and acid-base disturbances are common occurrences in daily clinical practice. Although these abnormalities can be readily ascertained from routine laboratory findings, only specific clinical correlates may attest as to their significance. Among a wide phenotypic spectrum, acute electrolyte and acid-base disturbances may affect the peripheral nervous system as arreflexic weakness (hypermagnesemia, hyperkalemia, and hypophosphatemia), the central nervous system as epileptic encephalopathies (hypomagnesemia, dysnatremias, and hypocalcemia), or both as a mixture of encephalopathy and weakness or paresthesias (hypocalcemia, alkalosis). Disabling complications may develop not only when these derangements are overlooked and left untreated (e.g., visual loss from intracranial hypertension in respiratory or metabolic acidosis; quadriplegia with respiratory insufficiency in hypermagnesemia) but also when they are inappropriately managed (e.g., central pontine myelinolisis when rapidly correcting hyponatremia; cardiac arrhythmias when aggressively correcting hypo- or hyperkalemia). Therefore prompt identification of the specific neurometabolic syndromes is critical to correct the causative electrolyte or acid-base disturbances and prevent permanent central or peripheral nervous system injury. This chapter reviews the pathophysiology, clinical investigations, clinical phenotypes, and current management strategies in disorders resulting from alterations in the plasma concentration of sodium, potassium, calcium, magnesium, and phosphorus as well as from acidemia and alkalemia.

  6. Gene Targeting and Expression Modulation by Peptide Nucleic Acids (PNA)

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2010-01-01

    Peptide nucleic acids (PNA) are artificial structural mimics of nucleic acids capable of sequence specific hybridization to both RNA and DNA. Thus they have obvious potential as gene targeting agents for drug discovery approaches. An overview with emphasis on recent progress on RNA "interference"...

  7. Biological activity and biotechnological aspects of locked nucleic acids

    DEFF Research Database (Denmark)

    Lundin, Karin E; Højland, Torben; Hansen, Bo;

    2013-01-01

    Locked nucleic acid (LNA) is one of the most promising new nucleic acid analogues that has been produced under the past two decades. In this chapter, we have tried to cover many of the different areas, where this molecule has been used to improve the function of synthetic oligonucleotides (ONs). ...

  8. MEANS AND METHODS FOR CLONING NUCLEIC ACID SEQUENCES

    NARCIS (Netherlands)

    Geertsma, Eric Robin; Poolman, Berend

    2008-01-01

    The invention provides means and methods for efficiently cloning nucleic acid sequences of interest in micro-organisms that are less amenable to conventional nucleic acid manipulations, as compared to, for instance, E.coli. The present invention enables high-throughput cloning (and, preferably,

  9. Peptide Nucleic Acids Having Amino Acid Side Chains

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than the corresponding DNA or RNA strands, and exhibit increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from a group consisting...

  10. Nucleic Acid Therapy: from humble beginnings a dynamic technology

    CSIR Research Space (South Africa)

    Millroy, L

    2011-02-01

    Full Text Available The term “nucleic acid therapy” encompasses a wide range of technologies for the treatment of a range of plant and animal ailments. As the name implies, it makes use of nucleic acid (either DNA or RNA) as a therapeutic agent. There are six branches...

  11. EGVII endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-11-11

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  12. EGVII endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2009-05-05

    The present invention provides an endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  13. Peptide Nucleic Acids Having Enhanced Binding Affinity and Sequence Specificity

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. Methods of increasing binding affinity and sequence specificity of peptide nucleic aci...

  14. Peptide Nucleic Acids Having 2,6-Diaminopurine Nucleobases

    DEFF Research Database (Denmark)

    2003-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. The peptide nucleic acids of the invention comprise ligands selected from a group cons...

  15. EGVI endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2010-10-05

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  16. EGVI endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2010-10-12

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  17. EGVII endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2012-02-14

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  18. An Exact Method to Determine the Conductivity of Aqueous Solutions in Acid-Base Titrations

    Directory of Open Access Journals (Sweden)

    Norma Rodríguez-Laguna

    2015-01-01

    Full Text Available Several works in the literature show that it is possible to establish the analytic equations to estimate the volume V of a strong base or a strong acid (Vb and Va, resp. being added to a solution of a substance or a mix of substances during an acid-base titration, as well as the equations to estimate the first derivative of the titration plot dpH/dV, and algebraic expressions to determine the buffer β capacity with dilution βdil. This treatment allows establishing the conditions of thermodynamic equilibria for all species within a system containing a mix of species from one or from various polyacid systems. The present work shows that it is possible to determine exactly the electric conductivity of aqueous solutions for these Brønsted acid-base titrations, because the functional relation between this property and the composition of the system in equilibrium is well known; this is achieved using the equivalent conductivity λi values of each of the ions present in a given system. The model employed for the present work confirms the experimental outcomes with the H2SO4, B(OH3, CH3COOH, and H3PO4 aqueous solutions’ titration.

  19. Cellular nucleic acid binding protein binds G-rich single-stranded nucleic acids and may function as a nucleic acid chaperone.

    Science.gov (United States)

    Armas, Pablo; Nasif, Sofía; Calcaterra, Nora B

    2008-02-15

    Cellular nucleic acid binding protein (CNBP) is a small single-stranded nucleic acid binding protein made of seven Zn knuckles and an Arg-Gly rich box. CNBP is strikingly conserved among vertebrates and was reported to play broad-spectrum functions in eukaryotic cells biology. Neither its biological function nor its mechanisms of action were elucidated yet. The main goal of this work was to gain further insights into the CNBP biochemical and molecular features. We studied Bufo arenarum CNBP (bCNBP) binding to single-stranded nucleic acid probes representing the main reported CNBP putative targets. We report that, although bCNBP is able to bind RNA and single-stranded DNA (ssDNA) probes in vitro, it binds RNA as a preformed dimer whereas both monomer and dimer are able to bind to ssDNA. A systematic analysis of variant probes shows that the preferred bCNBP targets contain unpaired guanosine-rich stretches. These data expand the knowledge about CNBP binding stoichiometry and begins to dissect the main features of CNBP nucleic acid targets. Besides, we show that bCNBP presents a highly disordered predicted structure and promotes the annealing and melting of nucleic acids in vitro. These features are typical of proteins that function as nucleic acid chaperones. Based on these data, we propose that CNBP may function as a nucleic acid chaperone through binding, remodeling, and stabilizing nucleic acids secondary structures. This novel CNBP biochemical activity broadens the field of study about its biological function and may be the basis to understand the diverse ways in which CNBP controls gene expression.

  20. Scaffolding along Nucleic Acid Duplexes Using 2'-Amino-Locked Nucleic Acids

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Wengel, Jesper

    2014-01-01

    Conspectus Incorporation of chemically modified nucleotide scaffolds into nucleic acids to form assemblies rich in function is an innovative area with great promise for nanotechnology and biomedical and material science applications. The intrinsic biorecognition potential of nucleic acids combined......-LNA nucleotides. By application of different chemical reactions, modification of 2'-amino-LNA scaffolds can be efficiently performed in high yields and with various tags, postsynthetically or during the automated oligonucleotide synthesis. The choice of a synthetic method for scaffolding along 2'-amino-LNA mainly...... depends on the chemical nature of the modification, its price, its availability, and applications of the product. One of the most useful applications of the product LNA/DNA scaffolds containing 2'-amino-LNA is to detect complementary DNA and RNA targets. Examples of these applications include sensing...

  1. Intumescent features of nucleic acids and proteins

    Energy Technology Data Exchange (ETDEWEB)

    Alongi, Jenny, E-mail: jenny.alongi@polito.it; Cuttica, Fabio; Blasio, Alessandro Di; Carosio, Federico; Malucelli, Giulio

    2014-09-10

    Highlights: • The combustion resistance of DNA and caseins to different heat fluxes was studied. • Upon heating, DNA and caseins exhibited an intumescent behaviour. • The char derived from DNA was more stable and coherent than that from caseins. - Abstract: Are nucleic acids and proteins intumescent molecules? In order to get an answer, in the present manuscript, powders of deoxyribose nucleic acids (DNA) and caseins have been exposed to different heat fluxes under a cone calorimeter source and to the direct application of a propane flame. Under these conditions, DNA and caseins exhibited a typical intumescent behaviour, generating a coherent expanded cellular carbonaceous residue (char), extremely resistant to heat exposure. The resulting volumetric expansion as well as the resistance of the formed char turned out to be dependent on (i) the chemical structure of the chosen biomacromolecule, (ii) the evolution of ammonia and (iii) the adopted heat flux in cone calorimetry tests (namely, 25, 35, 50 and 75 kW/m{sup 2}). The presence of ribose units within the DNA backbone determined the formation of highly expanded and coherent residues as compared to those obtained from caseins. Indeed, under a heat flux of 35 kW/m{sup 2}, when a carbon source (i.e. common cane sugar) was added to caseins, the resulting char was similar to that formed by DNA. Furthermore, the char expansion was ascribed to the evolution of ammonia released by these biomacromolecules upon heating, as detected by thermogravimetry coupled to infrared spectroscopy, and confirmed by scanning electron microscopy experiments performed on the bubbles present in the residues of flammability tests.

  2. Quantitative thermodynamic predication of interactions between nucleic acid and non-nucleic acid species using Microsoft excel.

    Science.gov (United States)

    Zou, Jiaqi; Li, Na

    2013-09-01

    Proper design of nucleic acid sequences is crucial for many applications. We have previously established a thermodynamics-based quantitative model to help design aptamer-based nucleic acid probes by predicting equilibrium concentrations of all interacting species. To facilitate customization of this thermodynamic model for different applications, here we present a generic and easy-to-use platform to implement the algorithm of the model with Microsoft(®) Excel formulas and VBA (Visual Basic for Applications) macros. Two Excel spreadsheets have been developed: one for the applications involving only nucleic acid species, the other for the applications involving both nucleic acid and non-nucleic acid species. The spreadsheets take the nucleic acid sequences and the initial concentrations of all species as input, guide the user to retrieve the necessary thermodynamic constants, and finally calculate equilibrium concentrations for all species in various bound and unbound conformations. The validity of both spreadsheets has been verified by comparing the modeling results with the experimental results on nucleic acid sequences reported in the literature. This Excel-based platform described here will allow biomedical researchers to rationalize the sequence design of nucleic acid probes using the thermodynamics-based modeling even without relevant theoretical and computational skills. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  3. Salicylic Acid-Based Organic Dyes Acting as the Photosensitizer for Solar Cells.

    Science.gov (United States)

    Hong, Sungjun; Park, Jae-Hyeong; Han, Ah-Reum; Ko, Kwan-Woo; Eom, Jin Hee; Namgoong, Sung Keon; Lo, Alvie S V; Gordon, Keith C; Yoon, Sungho; Han, Chi-Hwan

    2016-05-01

    A D-π-A metal-free organic dye, featuring salicylic acid as a novel acceptor/anchoring unit, has been designed, synthesized and applied to dye-sensitized solar cell. The detailed photophysical, electrochemical, photovoltaic and sensitizing properties of the organic dye were investigated, in addition to the computational studies of the dye and dye-(TiO2)6 system. A solar cell device using this new organic dye as a sensitizer produced a solar to electric power conversion efficiency (PCE) of 3.49% (J(sc) = 6.69 mAcm-2, V(oc) = 0.74 V and ff = 0.70) under 100 mWcm(-2) simulated AM 1.5 G solar irradiation, demonstrating that the salicylic acid-based organic dye is a suitable alternative to currently used organometallic dyes.

  4. Electrochemical microfluidic biosensor for the detection of nucleic acid sequences.

    Science.gov (United States)

    Goral, Vasiliy N; Zaytseva, Natalya V; Baeumner, Antje J

    2006-03-01

    A microfluidic biosensor with electrochemical detection for the quantification of nucleic acid sequences was developed. In contrast to most microbiosensors that are based on fluorescence for signal generation, it takes advantage of the simplicity and high sensitivity provided by an amperometric and coulorimetric detection system. An interdigitated ultramicroelectrode array (IDUA) was fabricated in a glass chip and integrated directly with microchannels made of poly(dimethylsiloxane) (PDMS). The assembly was packaged into a Plexiglas housing providing fluid and electrical connections. IDUAs were characterized amperometrically and using cyclic voltammetry with respect to static and dynamic responses for the presence of a reversible redox couple-potassium hexacyanoferrate (ii)/hexacyanoferrate (iii) (ferri/ferrocyanide). A combined concentration of 0.5 microM of ferro/ferricyanide was determined as lower limit of detection with a dynamic range of 5 orders of magnitude. Background signals were negligible and the IDUA responded in a highly reversible manner to the injection of various volumes and various concentrations of the electrochemical marker. For the detection of nucleic acid sequences, liposomes entrapping the electrochemical marker were tagged with a DNA probe, and superparamagnetic beads were coated with a second DNA probe. A single stranded DNA target sequence hybridized with both probes. The sandwich was captured in the microfluidic channel just upstream of the IDUA via a magnet located in the outside housing. Liposomes were lysed using a detergent and the amount of released ferro/ferricyanide was quantified while passing by the IDUA. Optimal location of the magnet with respect to the IDUA was investigated, the effect of dextran sulfate on the hybridization reaction was studied and the amount of magnetic beads used in the assay was optimized. A dose response curve using varying concentrations of target DNA molecules was carried out demonstrating a limit of

  5. Rapid one-step selection method for generating nucleic acid aptamers: development of a DNA aptamer against α-bungarotoxin.

    Directory of Open Access Journals (Sweden)

    Lasse H Lauridsen

    Full Text Available BACKGROUND: Nucleic acids based therapeutic approaches have gained significant interest in recent years towards the development of therapeutics against many diseases. Recently, research on aptamers led to the marketing of Macugen®, an inhibitor of vascular endothelial growth factor (VEGF for the treatment of age related macular degeneration (AMD. Aptamer technology may prove useful as a therapeutic alternative against an array of human maladies. Considering the increased interest in aptamer technology globally that rival antibody mediated therapeutic approaches, a simplified selection, possibly in one-step, technique is required for developing aptamers in limited time period. PRINCIPAL FINDINGS: Herein, we present a simple one-step selection of DNA aptamers against α-bungarotoxin. A toxin immobilized glass coverslip was subjected to nucleic acid pool binding and extensive washing followed by PCR enrichment of the selected aptamers. One round of selection successfully identified a DNA aptamer sequence with a binding affinity of 7.58 µM. CONCLUSION: We have demonstrated a one-step method for rapid production of nucleic acid aptamers. Although the reported binding affinity is in the low micromolar range, we believe that this could be further improved by using larger targets, increasing the stringency of selection and also by combining a capillary electrophoresis separation prior to the one-step selection. Furthermore, the method presented here is a user-friendly, cheap and an easy way of deriving an aptamer unlike the time consuming conventional SELEX-based approach. The most important application of this method is that chemically-modified nucleic acid libraries can also be used for aptamer selection as it requires only one enzymatic step. This method could equally be suitable for developing RNA aptamers.

  6. Rapid one-step selection method for generating nucleic acid aptamers: development of a DNA aptamer against α-bungarotoxin.

    Science.gov (United States)

    Lauridsen, Lasse H; Shamaileh, Hadi A; Edwards, Stacey L; Taran, Elena; Veedu, Rakesh N

    2012-01-01

    Nucleic acids based therapeutic approaches have gained significant interest in recent years towards the development of therapeutics against many diseases. Recently, research on aptamers led to the marketing of Macugen®, an inhibitor of vascular endothelial growth factor (VEGF) for the treatment of age related macular degeneration (AMD). Aptamer technology may prove useful as a therapeutic alternative against an array of human maladies. Considering the increased interest in aptamer technology globally that rival antibody mediated therapeutic approaches, a simplified selection, possibly in one-step, technique is required for developing aptamers in limited time period. Herein, we present a simple one-step selection of DNA aptamers against α-bungarotoxin. A toxin immobilized glass coverslip was subjected to nucleic acid pool binding and extensive washing followed by PCR enrichment of the selected aptamers. One round of selection successfully identified a DNA aptamer sequence with a binding affinity of 7.58 µM. We have demonstrated a one-step method for rapid production of nucleic acid aptamers. Although the reported binding affinity is in the low micromolar range, we believe that this could be further improved by using larger targets, increasing the stringency of selection and also by combining a capillary electrophoresis separation prior to the one-step selection. Furthermore, the method presented here is a user-friendly, cheap and an easy way of deriving an aptamer unlike the time consuming conventional SELEX-based approach. The most important application of this method is that chemically-modified nucleic acid libraries can also be used for aptamer selection as it requires only one enzymatic step. This method could equally be suitable for developing RNA aptamers.

  7. Gamma Peptide Nucleic Acids: As Orthogonal Nucleic Acid Recognition Codes for Organizing Molecular Self-Assembly.

    Science.gov (United States)

    Sacui, Iulia; Hsieh, Wei-Che; Manna, Arunava; Sahu, Bichismita; Ly, Danith H

    2015-07-08

    Nucleic acids are an attractive platform for organizing molecular self-assembly because of their specific nucleobase interactions and defined length scale. Routinely employed in the organization and assembly of materials in vitro, however, they have rarely been exploited in vivo, due to the concerns for enzymatic degradation and cross-hybridization with the host's genetic materials. Herein we report the development of a tight-binding, orthogonal, synthetically versatile, and informationally interfaced nucleic acid platform for programming molecular interactions, with implications for in vivo molecular assembly and computing. The system consists of three molecular entities: the right-handed and left-handed conformers and a nonhelical domain. The first two are orthogonal to each other in recognition, while the third is capable of binding to both, providing a means for interfacing the two conformers as well as the natural nucleic acid biopolymers (i.e., DNA and RNA). The three molecular entities are prepared from the same monomeric chemical scaffold, with the exception of the stereochemistry or lack thereof at the γ-backbone that determines if the corresponding oligo adopts a right-handed or left-handed helix, or a nonhelical motif. These conformers hybridize to each other with exquisite affinity, sequence selectivity, and level of orthogonality. Recognition modules as short as five nucleotides in length are capable of organizing molecular assembly.

  8. Recognition of pathogen-associated nucleic acids by endosomal nucleic acid-sensing toll-like receptors

    Institute of Scientific and Technical Information of China (English)

    Xiaobing He; Huaijie Jia; Zhizhong Jing; Dingxiang Liu

    2013-01-01

    Foreign nucleic acids,the essential signature molecules of invading pathogens that act as danger signals for host cells,are detected by endosomal nucleic acid-sensing tolllike receptors (TLRs) 3,7,8,9,and 13.These TLRs have evolved to recognize ‘non-self' nucleic acids within endosomal compartments and rapidly initiate innate immune responses to ensure host protection through induction of type Ⅰ interferons,inflammatory cytokines,chemokines,and co-stimulatory molecules and maturation of immune cells.In this review,we highlight our understanding of the recognition of pathogen-associated nucleic acids and activation of corresponding signaling pathways through endosomal nucleic acid-sensing TLRs 3,7,8,9,and 13 for an enormous diversity of pathogens,with particular emphasis on their compartmentalization,intracellular trafficking,proteolytic cleavage,autophagy,and regulatory programs.

  9. Studies related to primitive chemistry. A proton and nitrogen-14 nuclear magnetic resonance amino acid and nucleic acid constituents and a and their possible relation to prebiotic

    Science.gov (United States)

    Manatt, S. L.; Cohen, E. A.; Shiller, A. M.; Chan, S. I.

    1973-01-01

    Preliminary proton nuclear magnetic resonance (NMR) studies were made to determine the applicability of this technique for the study of interactions between monomeric and polymeric amino acids with monomeric nucleic acid bases and nucleotides. Proton NMR results for aqueous solutions (D2O) demonstrated interactions between the bases cytosine and adenine and acidic and aromatic amino acids. Solutions of 5'-AMP admixed with amino acids exhibited more complex behavior but stacking between aromatic rings and destacking at high amino acids concentration was evident. The multisite nature of 5'-AMP was pointed out. Chemical shift changes for adenine and 5'-AMP with three water soluble polypeptides demonstrated that significant interactions exist. It was found that the linewidth-pH profile of each amino acid is unique. It is concluded that NMR techniques can give significant and quantitative data on the association of amino acid and nucleic acid constituents.

  10. History of medical understanding and misunderstanding of Acid base balance.

    Science.gov (United States)

    Aiken, Christopher Geoffrey Alexander

    2013-09-01

    To establish how controversies in understanding acid base balance arose, the literature on acid base balance was reviewed from 1909, when Henderson described how the neutral reaction of blood is determined by carbonic and organic acids being in equilibrium with an excess of mineral bases over mineral acids. From 1914 to 1930, Van Slyke and others established our acid base principles. They recognised that carbonic acid converts into bicarbonate all non-volatile mineral bases not bound by mineral acids and determined therefore that bicarbonate represents the alkaline reserve of the body and should be a physiological constant. They showed that standard bicarbonate is a good measure of acidosis caused by increased production or decreased elimination of organic acids. However, they recognised that bicarbonate improved low plasma bicarbonate but not high urine acid excretion in diabetic ketoacidosis, and that increasing pCO2 caused chloride to shift into cells raising plasma titratable alkali. Both indicate that minerals influence pH. In 1945 Darrow showed that hyperchloraemic metabolic acidosis in preterm infants fed milk with 5.7 mmol of chloride and 2.0 mmol of sodium per 100 kcal was caused by retention of chloride in excess of sodium. Similar findings were made but not recognised in later studies of metabolic acidosis in preterm infants. Shohl in 1921 and Kildeberg in 1978 presented the theory that carbonic and organic acids are neutralised by mineral base, where mineral base is the excess of mineral cations over anions and organic acid is the difference between mineral base, bicarbonate and protein anion. The degree of metabolic acidosis measured as base excess is determined by deviation in both mineral base and organic acid from normal.

  11. Acid-Base Balance in Uremic Rats with Vascular Calcification

    Directory of Open Access Journals (Sweden)

    Alan Peralta-Ramírez

    2014-07-01

    Full Text Available Background/Aims: Vascular calcification (VC, a major complication in humans and animals with chronic kidney disease (CKD, is influenced by changes in acid-base balance. The purpose of this study was to describe the acid-base balance in uremic rats with VC and to correlate the parameters that define acid-base equilibrium with VC. Methods: Twenty-two rats with CKD induced by 5/6 nephrectomy (5/6 Nx and 10 nonuremic control rats were studied. Results: The 5/6 Nx rats showed extensive VC as evidenced by a high aortic calcium (9.2 ± 1.7 mg/g of tissue and phosphorus (20.6 ± 4.9 mg/g of tissue content. Uremic rats had an increased pH level (7.57 ± 0.03 as a consequence of both respiratory (PaCO2 = 28.4 ± 2.1 mm Hg and, to a lesser degree, metabolic (base excess = 4.1 ± 1 mmol/l derangements. A high positive correlation between both anion gap (AG and strong ion difference (SID with aortic calcium (AG: r = 0.604, p = 0.02; SID: r = 0.647, p = 0.01 and with aortic phosphorus (AG: r = 0.684, p = 0.007; SID: r = 0.785, p = 0.01 was detected. Conclusions: In an experimental model of uremic rats, VC showed high positive correlation with AG and SID.

  12. Acid-base properties of Baltic Sea dissolved organic matter

    Science.gov (United States)

    Hammer, Karoline; Schneider, Bernd; Kuliński, Karol; Schulz-Bull, Detlef E.

    2017-09-01

    Calculations related to the marine CO2 system that are based on alkalinity data may be strongly biased if the contributions of organic compounds are ignored. In coastal seas, concentrations of dissolved organic matter (DOM) are frequently high and alkalinity from inorganic compounds is low. In this study, based on measurements of total alkalinity, total CO2, and pH, we determined the organic alkalinity, Aorg, in water from the central Baltic Sea. The maximum Aorg measured in the surface mixed layer during the spring bloom was > 50 μmol/kg-SW but the Aorg decreased with depth and approached zero below the permanent halocline. This behavior could be attributed to the decreased pH of deeper water layers. The data were used to calculate the bulk dissociation constant, KDOM, for marine DOM and the fraction f of dissolved organic carbon (DOC) that acts as a carrier for acid-base functional groups. The p KDOM (7.27) agreed well with the value (7.34) previously estimated in a preliminary study of organic alkalinity in the Baltic Sea. The fraction of carbon atoms carrying acid-base groups was 17% and was somewhat higher than previously reported (12%). Spike experiments performed using artificial seawater and three different humic/fulvic substances tested whether the acid-base properties of these substances explain the results of our field study. Specifically, Aorg was determined at different concentrations (DOC) of the added humic/fulvic substances. The relationship between Aorg and the DOC concentrations indicated that humic/fulvic substances are more acidic (p KDOM < 6.5) than the bulk DOC natural occurring in the Baltic Sea.

  13. A simple model for electrical charge in globular macromolecules and linear polyelectrolytes in solution

    Science.gov (United States)

    Krishnan, M.

    2017-05-01

    We present a model for calculating the net and effective electrical charge of globular macromolecules and linear polyelectrolytes such as proteins and DNA, given the concentration of monovalent salt and pH in solution. The calculation is based on a numerical solution of the non-linear Poisson-Boltzmann equation using a finite element discretized continuum approach. The model simultaneously addresses the phenomena of charge regulation and renormalization, both of which underpin the electrostatics of biomolecules in solution. We show that while charge regulation addresses the true electrical charge of a molecule arising from the acid-base equilibria of its ionizable groups, charge renormalization finds relevance in the context of a molecule's interaction with another charged entity. Writing this electrostatic interaction free energy in terms of a local electrical potential, we obtain an "interaction charge" for the molecule which we demonstrate agrees closely with the "effective charge" discussed in charge renormalization and counterion-condensation theories. The predictions of this model agree well with direct high-precision measurements of effective electrical charge of polyelectrolytes such as nucleic acids and disordered proteins in solution, without tunable parameters. Including the effective interior dielectric constant for compactly folded molecules as a tunable parameter, the model captures measurements of effective charge as well as published trends of pKa shifts in globular proteins. Our results suggest a straightforward general framework to model electrostatics in biomolecules in solution. In offering a platform that directly links theory and experiment, these calculations could foster a systematic understanding of the interrelationship between molecular 3D structure and conformation, electrical charge and electrostatic interactions in solution. The model could find particular relevance in situations where molecular crystal structures are not available or

  14. Enzymes for fatty acid-based hydrocarbon biosynthesis.

    Science.gov (United States)

    Herman, Nicolaus A; Zhang, Wenjun

    2016-12-01

    Surging energy consumption and environmental concerns have stimulated interest in the production of chemicals and fuels through sustainable and renewable approaches. Fatty acid-based hydrocarbons, such as alkanes and alkenes, are of particular interest to directly replace fossil fuels. Towards this effort, understanding of hydrocarbon-producing enzymes is the first indispensable step to bio-production of hydrocarbons. Here, we review recent advances in the discovery and mechanistic study of enzymes capable of converting fatty acid precursors into hydrocarbons, and provide perspectives on the future of this rapidly growing field. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. The comprehensive acid-base characterization of glutathione

    Science.gov (United States)

    Mirzahosseini, Arash; Somlyay, Máté; Noszál, Béla

    2015-02-01

    Glutathione in its thiol (GSH) and disulfide (GSSG) forms, and 4 related compounds were studied by 1H NMR-pH titrations and a case-tailored evaluation method. The resulting acid-base properties are quantified in terms of 128 microscopic protonation constants; the first complete set of such parameters for this vitally important pair of compounds. The concomitant 12 interactivity parameters were also determined. Since biological redox systems are regularly compared to the GSH-GSSG pair, the eight microscopic thiolate basicities determined this way are exclusive means for assessing subtle redox parameters in a wide pH range.

  16. Simple Protocol for Secondary School Hands-On Activity: Electrophoresis of Pre-Stained Nucleic Acids on Agar-Agar Borate Gels

    Science.gov (United States)

    Britos, Leticia; Goyenola, Guillermo; Orono, Silvia Umpierrez

    2004-01-01

    An extremely simple, inexpensive, and safe method is presented, which emulates nucleic acids isolation and electrophoretic analysis as performed in a research environment, in the context of a secondary school hands-on activity. The protocol is amenable to an interdisciplinary approach, taking into consideration the electrical and chemical…

  17. Nucleic acid detection system and method for detecting influenza

    Science.gov (United States)

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  18. Nucleic acid detection system and method for detecting influenza

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  19. Ion-Mediated Nucleic Acid Helix-Helix Interactions

    OpenAIRE

    Tan, Zhi-Jie; Chen, Shi-Jie

    2006-01-01

    Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free-energy landscape for two parallel nucleic acid helices in the solution of added salt. The theory is based on realistic atomic structures of the helices. In monovalent salt, the helices are predicted to repel each other. For divalent salt, while the mean-field Po...

  20. Opuntia ficus indica (L.) Fruit Extract as Natural Indicator in Acid-Base Titration

    OpenAIRE

    Manoj A. Suva

    2014-01-01

    In routine experiments synthetic indicators are the choice of acid base titrations. But there are some limitations like environmental pollution, availability and higher cost which leads to search for natural compounds as an acid base indicator was started. The present work highlights theexploit of the methanolic and aqueous extract of the fruit of Opuntia ficus indica plants as a natural acid base indicator in acid base titrations. Opuntia ficus indica plant was identified and fruits were was...

  1. Acid base catalyzed transesterification kinetics of waste cooking oil

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Siddharth; Sharma, M.P.; Rajvanshi, Shalini [Alternate Hydro Energy Centre, Indian Institute of Technology, Roorkee (India)

    2011-01-15

    The present study reports the results of kinetics study of acid base catalyzed two step transesterification process of waste cooking oil, carried out at pre-determined optimum temperature of 65 C and 50 C for esterification and transesterification process respectively under the optimum condition of methanol to oil ratio of 3:7 (v/v), catalyst concentration 1%(w/w) for H{sub 2}SO{sub 4} and NaOH and 400 rpm of stirring. The optimum temperature was determined based on the yield of ME at different temperature. Simply, the optimum concentration of H{sub 2}SO{sub 4} and NaOH was determined with respect to ME Yield. The results indicated that both esterification and transesterification reaction are of first order rate reaction with reaction rate constant of 0.0031 min{sup -1} and 0.0078 min{sup -1} respectively showing that the former is a slower process than the later. The maximum yield of 21.50% of ME during esterification and 90.6% from transesterification of pretreated WCO has been obtained. This is the first study of its kind which deals with simplified kinetics of two step acid-base catalyzed transesterification process carried under the above optimum conditions and took about 6 h for complete conversion of TG to ME with least amount of activation energy. Also various parameters related to experiments are optimized with respect to ME yield. (author)

  2. Acid-base interactions in microbial adhesion to hexadecane and chloroform

    NARCIS (Netherlands)

    Bos, R; Busscher, HJ; Geertsema-Doornbusch, GI; Van Der Mei, HC; Mittal, KL

    2000-01-01

    Acid-base interactions play an important role in adhesion, including microbial adhesion to surfaces. Qualitatively acid-base interactions in microbial adhesion can be demonstrated by comparing adhesion to hexadecane (a negatively charged interface in aqueous solutions, unable to exert acid-base inte

  3. How Do Undergraduate Students Conceptualize Acid-Base Chemistry? Measurement of a Concept Progression

    Science.gov (United States)

    Romine, William L.; Todd, Amber N.; Clark, Travis B.

    2016-01-01

    We developed and validated a new instrument, called "Measuring Concept progressions in Acid-Base chemistry" (MCAB) and used it to better understand the progression of undergraduate students' understandings about acid-base chemistry. Items were developed based on an existing learning progression for acid-base chemistry. We used the Rasch…

  4. Equilibrium of acidifying and alkalinizing metabolic acid-base disorders in cirrhosis.

    Science.gov (United States)

    Funk, Georg-Christian; Doberer, Daniel; Osterreicher, Christoph; Peck-Radosavljevic, Markus; Schmid, Monika; Schneeweiss, Bruno

    2005-06-01

    Conflicting results exist with regard to metabolic acid-base status in liver cirrhosis, when the classic concept of acid-base analysis is applied. The influence of the common disturbances of water, electrolytes and albumin on acid-base status in cirrhosis has not been studied. The aim of this study was to clarify acid-base status in cirrhotic patients by analyzing all parameters with possible impact on acid-base equilibrium. Fifty stable cirrhotic patients admitted to a university hospital. Arterial acid-base status was analyzed using the principles of physical chemistry and compared with 10 healthy controls. Apart from mild hypoalbuminemic alkalosis, acid-base state was normal in Child-Pugh A cirrhosis. Respiratory alkalosis was the net acid-base disorder in Child-Pugh B and C cirrhosis with a normal overall metabolic acid-base state (Base excess-1.0 (-3.6 to 1.6) vs 1.1 (-0.2 to 1.1) mmol/l, P = 0.136, compared with healthy controls, median (interquartile range)). Absence of an apparent metabolic acid-base disorder was based on an equilibrium of hypoalbuminemic alkalosis and of dilutional acidosis and hyperchloremic acidosis. A balance of offsetting acidifying and alkalinizing metabolic acid-base disorders leaves the net metabolic acid-base status unchanged in cirrhosis.

  5. Computational Approaches to Nucleic Acid Origami.

    Science.gov (United States)

    Jabbari, Hosna; Aminpour, Maral; Montemagno, Carlo

    2015-10-12

    Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.

  6. Fluorescent hybridization probes for nucleic acid detection.

    Science.gov (United States)

    Guo, Jia; Ju, Jingyue; Turro, Nicholas J

    2012-04-01

    Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.

  7. In vitro selection of functional nucleic acids

    Science.gov (United States)

    Wilson, D. S.; Szostak, J. W.

    1999-01-01

    In vitro selection allows rare functional RNA or DNA molecules to be isolated from pools of over 10(15) different sequences. This approach has been used to identify RNA and DNA ligands for numerous small molecules, and recent three-dimensional structure solutions have revealed the basis for ligand recognition in several cases. By selecting high-affinity and -specificity nucleic acid ligands for proteins, promising new therapeutic and diagnostic reagents have been identified. Selection experiments have also been carried out to identify ribozymes that catalyze a variety of chemical transformations, including RNA cleavage, ligation, and synthesis, as well as alkylation and acyl-transfer reactions and N-glycosidic and peptide bond formation. The existence of such RNA enzymes supports the notion that ribozymes could have directed a primitive metabolism before the evolution of protein synthesis. New in vitro protein selection techniques should allow for a direct comparison of the frequency of ligand binding and catalytic structures in pools of random sequence polynucleotides versus polypeptides.

  8. Isolated menthone reductase and nucleic acid molecules encoding same

    Science.gov (United States)

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L

    2013-04-23

    The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

  9. Nanopore biosensors for detection of proteins and nucleic acids

    NARCIS (Netherlands)

    Maglia, Giovanni; Soskine, Mikhael

    2014-01-01

    Described herein are nanopore biosensors based on a modified cytolysin protein. The nanopore biosensors accommodate macromoiecules including proteins and nucleic acids, and may additionally comprise ligands with selective binding properties.

  10. Nanopore biosensors for detection of proteins and nucleic acids

    NARCIS (Netherlands)

    Maglia, Giovanni; Soskine, Mikhael

    2014-01-01

    Described herein are nanopore biosensors based on a modified cytolysin protein. The nanopore biosensors accommodate macromoiecules including proteins and nucleic acids, and may additionally comprise ligands with selective binding properties.

  11. SAXS studies of ion-nucleic acid interactions.

    Science.gov (United States)

    Pollack, Lois

    2011-01-01

    Positively charged ions, atoms, or molecules compensate the high negative charge of the nucleic acid backbone. Their presence is critical to the biological function of DNA and RNA. This review focuses on experimental studies probing (a) interactions between small ions and nucleic acids and (b) ion-mediated interactions between nucleic acid duplexes. Experimental results on these simple model systems can be compared with specific theoretical models to validate their predictions. Small angle X-ray scattering (SAXS) provides unique insight into these interactions. Anomalous SAXS reports the spatial correlations of condensed (e.g., locally concentrated) counterions to individual DNA or RNA duplexes. SAXS very effectively reports interactions between nucleic acid helices, which range from strongly repulsive to strongly attractive depending on the ionic species present. The sign and strength of interparticle interactions are easily deduced from dramatic changes in the scattering profiles of interacting duplexes.

  12. Histological and nucleic acids alterations in Spodoptera littoralis ...

    African Journals Online (AJOL)

    plzfg

    A number of insecticidal proteins expressed and secreted during the vegetative growth .... To ascertain the effect on nucleic acids under the same conditions, the electrophoretic pattern of ... less densely packed layer of neurons and glial cells.

  13. Dioxaphosphorinane-constrained nucleic Acid dinucleotides as tools for structural tuning of nucleic acids.

    Science.gov (United States)

    Catana, Dan-Andrei; Renard, Brice-Loïc; Maturano, Marie; Payrastre, Corinne; Tarrat, Nathalie; Escudier, Jean-Marc

    2012-01-01

    We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion angles α to ζ defining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers of α,β-D-CNA exhibiting wether B-type canonical values or not.

  14. Scavenging nucleic acid debris to combat autoimmunity and infectious disease

    Science.gov (United States)

    Holl, Eda K.; Shumansky, Kara L.; Borst, Luke B.; Burnette, Angela D.; Sample, Christopher J.; Ramsburg, Elizabeth A.; Sullenger, Bruce A.

    2016-08-01

    Nucleic acid-containing debris released from dead and dying cells can be recognized as damage-associated molecular patterns (DAMPs) or pattern-associated molecular patterns (PAMPs) by the innate immune system. Inappropriate activation of the innate immune response can engender pathological inflammation and autoimmune disease. To combat such diseases, major efforts have been made to therapeutically target the pattern recognition receptors (PRRs) such as the Toll-like receptors (TLRs) that recognize such DAMPs and PAMPs, or the downstream effector molecules they engender, to limit inflammation. Unfortunately, such strategies can limit the ability of the immune system to combat infection. Previously, we demonstrated that nucleic acid-binding polymers can act as molecular scavengers and limit the ability of artificial nucleic acid ligands to activate PRRs. Herein, we demonstrate that nucleic acid scavengers (NASs) can limit pathological inflammation and nucleic acid-associated autoimmunity in lupus-prone mice. Moreover, we observe that such NASs do not limit an animal’s ability to combat viral infection, but rather their administration improves survival when animals are challenged with lethal doses of influenza. These results indicate that molecules that scavenge extracellular nucleic acid debris represent potentially safer agents to control pathological inflammation associated with a wide range of autoimmune and infectious diseases.

  15. Bioanalytical applications of isothermal nucleic acid amplification techniques.

    Science.gov (United States)

    Deng, Huimin; Gao, Zhiqiang

    2015-01-01

    The most popular in vitro nucleic acid amplification techniques like polymerase chain reaction (PCR) including real-time PCR are costly and require thermocycling, rendering them unsuitable for uses at point-of-care. Highly efficient in vitro nucleic acid amplification techniques using simple, portable and low-cost instruments are crucial in disease diagnosis, mutation detection and biodefense. Toward this goal, isothermal amplification techniques that represent a group of attractive in vitro nucleic acid amplification techniques for bioanalysis have been developed. Unlike PCR where polymerases are easily deactivated by thermally labile constituents in a sample, some of the isothermal nucleic acid amplification techniques, such as helicase-dependent amplification and nucleic acid sequence-based amplification, enable the detection of bioanalytes with much simplified protocols and with minimal sample preparations since the entire amplification processes are performed isothermally. This review focuses on the isothermal nucleic acid amplification techniques and their applications in bioanalytical chemistry. Starting off from their amplification mechanisms and significant properties, the adoption of isothermal amplification techniques in bioanalytical chemistry and their future perspectives are discussed. Representative examples illustrating the performance and advantages of each isothermal amplification technique are discussed along with some discussion on the advantages and disadvantages of each technique.

  16. Nucleic acid in-situ hybridization detection of infectious agents

    Science.gov (United States)

    Thompson, Curtis T.

    2000-04-01

    Limitations of traditional culture methods and newer polymerase chain reaction (PCR)-based methods for detection and speciation of infectious agents demonstrate the need for more rapid and better diagnostics. Nucleic acid hybridization is a detection technology that has gained wide acceptance in cancer and prenatal cytogenetics. Using a modification of the nucleic acid hybridization technique known as fluorescence in-situ hybridization, infectious agents can be detected in a variety of specimens with high sensitivity and specificity. The specimens derive from all types of human and animal sources including body fluids, tissue aspirates and biopsy material. Nucleic acid hybridization can be performed in less than one hour. The result can be interpreted either using traditional fluorescence microscopy or automated platforms such as micro arrays. This paper demonstrates proof of concept for nucleic acid hybridization detection of different infectious agents. Interpretation within a cytologic and histologic context is possible with fluorescence microscopic analysis, thereby providing confirmatory evidence of hybridization. With careful probe selection, nucleic acid hybridization promises to be a highly sensitive and specific practical diagnostic alternative to culture, traditional staining methods, immunohistochemistry and complicated nucleic acid amplification tests.

  17. Sensors of Infection: Viral Nucleic Acid PRRs in Fish

    Directory of Open Access Journals (Sweden)

    Sarah Poynter

    2015-07-01

    Full Text Available Viruses produce nucleic acids during their replication, either during genomic replication or transcription. These nucleic acids are present in the cytoplasm or endosome of an infected cell, or in the extracellular space to be sensed by neighboring cells during lytic infections. Cells have mechanisms of sensing virus-generated nucleic acids; these nucleic acids act as flags to the cell, indicating an infection requiring defense mechanisms. The viral nucleic acids are called pathogen-associated molecular patterns (PAMPs and the sensors that bind them are called pattern recognition receptors (PRRs. This review article focuses on the most recent findings regarding nucleic acids PRRs in fish, including: Toll-like receptors (TLRs, RIG-I-like receptors (RLRs, cytoplasmic DNA sensors (CDSs and class A scavenger receptors (SR-As. It also discusses what is currently known of the downstream signaling molecules for each PRR family and the resulting antiviral response, either type I interferons (IFNs or pro-inflammatory cytokine production. The review highlights what is known but also defines what still requires elucidation in this economically important animal. Understanding innate immune systems to virus infections will aid in the development of better antiviral therapies and vaccines for the future.

  18. [Diagnosis and treatment of disordered acid-base balance].

    Science.gov (United States)

    Kosch, M; Schaefer, R M

    2005-01-20

    Differential diagnosis in disordered acid-base homeostasis is usually possible by measuring the pH, pCO2, pO2 and bicarbonate concentration, and enables differentiation between respiratory alkalosis and acidosis, and metabolic alkalosis and acidosis. Compensatory counter-regulation (respiratory or renal) can make correct assessment of the primary disorder problematic. Treatment of the underlying disease, in particular the provision of adequate oxygenation in respiratory disorders is of the essence. In chronic forms of metabolic acidosis, for example in chronic renal insufficiency and elderly patients, bicarbonate substitution should be initiated in order to prevent the negative effects on various organ systems. Sodium bicarbonate formulations that can be assimilated from the small bowel are especially tolerable and suitable.

  19. Acid-base transport in pancreas-new challenges

    DEFF Research Database (Denmark)

    Novak, Ivana; Haanes, Kristian Agmund; Wang, Jing

    2013-01-01

    Along the gastrointestinal tract a number of epithelia contribute with acid or basic secretions in order to aid digestive processes. The stomach and pancreas are the most extreme examples of acid (H+) and base (HCO-3) transporters, respectively. Nevertheless, they share the same challenges...... to consider in pancreas are the proton pumps (H-K-ATPases), as well as the calcium-activated K and Cl channels, such as K3.1 and TMEM16A/ANO1. Local regulators, such as purinergic signaling, fine-tune, and coordinate pancreatic secretion. Lastly, we speculate whether dys-regulation of acid-base transport...... contributes to pancreatic diseases including cystic fibrosis, pancreatitis, and cancer. © 2013 Novak, Haanes and Wang....

  20. Incidence of Postoperative Acid-Base Disturbances in Abdominal Surgery

    Directory of Open Access Journals (Sweden)

    Taghavi Gilani M

    2014-04-01

    Full Text Available Introduction: Respiratory and blood pressure changes as well as fluid administration alter the acid-base balance during the perioperative period which may cause consciousness disturbance and additional hemodynamic disorders. The aim of this study was to identify frequent postoperative acid-base disturbances in order to control postoperative complications. Materials and Methods:This prospective, observational study design was used on patients who underwent abdominal surgery during a six-month period. Gasometry was performed immediately after the patients’ admittion to ICU and six and 12 hours postoperatively. SPSS v13 software was used, and PResults: 213 patients (123 male and 90 female aged 14-85 years (51.7± 22.4 were evaluated. During admission, PH and PaCO2 were (7.29±0.13 and (38.3±11.9, respectively; however, although PH increased gradually (P=0.001, PaCO2 was reduced (P=0.03. Bicarbonate and base excess had opposite effects; bicarbonate initially decreased but increased after 12 hours (P=0.001, whereas base excess initially increased (-6.3±11.6 and then decreased gradually (P=0.003. The arterial oxygen pressure was reduced for 22.5% of the patients throughout the admission period, and this did not significantly change (P=0.57. Conclusion: According to the results, in admission, 65.7% had metabolic acidosis, but metabolic alkalosis was the least. Gradually, metabolic acidosis was modified, but metabolic alkalosis increased. Intraoperative hypotension and fluid infusion may be the main factors of early metabolic acidosis and control of hypotension, or correction of acidosis may increase metabolic alkalosis.

  1. Pre-storage of gelified reagents in a lab-on-a-foil system for rapid nucleic acid analysis

    DEFF Research Database (Denmark)

    Yi, Sun; Høgberg, Jonas; Christine, Thanner

    2013-01-01

    required for PCR as a ready-to-use product. The approach was successfully implemented in a lab-on-a-foil system, and the gelification process was automated for mass production. Integration of reagents on-chip by gelification greatly facilitated the development of easy-to-use lab-on-a-chip (LOC) devices......Reagent pre-storage in a microfluidic chip can enhance operator convenience, simplify the system design, reduce the cost of storage and shipment, and avoid the risk of cross-contamination. Although dry reagents have long been used in lateral flow immunoassays, they have rarely been used for nucleic...... acid-based point-of-care (POC) assays due to the lack of reliable techniques to dehydrate and store fragile molecules involved in the reaction. In this study, we describe a simple and efficient method for prolonged on-chip storage of PCR reagents. The method is based on gelification of all reagents...

  2. Assessing the movement of Cucurbit yellow stunting disorder virus in susceptible and tolerant cucumber germplasms using serological and nucleic acid based methods

    Science.gov (United States)

    Cucurbit yellow stunting disorder virus (CYSDV) is an emerging virus causing significant yield losses in cucurbits. Simple but reliable detection and quantification methods constitute an important support to disease management. In a susceptible germplasm CYSDV was detected 5 days post-inoculation (D...

  3. Nucleic acid-based detection of influenza A virus subtypes H7 and N9 with a special emphasis on the avian H7N9 virus.

    Science.gov (United States)

    Kalthoff, D; Bogs, J; Harder, T; Grund, C; Pohlmann, A; Beer, M; Hoffmann, B

    2014-03-13

    In 2013, a novel influenza A virus of subtype H7N9 was transmitted from avian sources to humans in China, causing severe illness and substantial mortality. Rapid and sensitive diagnostic approaches are the basis of epidemiological studies and of utmost importance for the detection of infected humans and animals. We developed various quantitative reverse transcriptase PCR (RT-qPCR) assays for (i) the generic detection of the haemagglutinin (HA) gene of H7 viruses or the neuraminidase (NA) gene of N9 viruses, and (ii) the specific detection of HA and NA of the novel avian H7N9/2013 virus. The sensitivity of the newly developed assays was compared with previously published PCRs, and the specificity of all RT-qPCRs was examined using a panel of 42 different H7 and 16 different N9 isolates. Furthermore, we analysed the performance of the RT-qPCR assays with dilution series and diagnostic samples obtained from animal experiments. Our study provides a comprehensive set of RT-qPCR assays for the reliable detection of the novel avian H7N9 virus, with high sensitivity and improved and tailored specificity values compared with published assays. Finally, we also present data about the robustness of a duplex assay for the simultaneous detection of HA and NA of the avian influenza H7N9/2013 virus.

  4. Guidance Protocol: Application of Nucleic Acid-Based Tools for Monitoring Monitored Natural Attenuation (MNA), Biostimulation, and Bioaugmentation at Chlorinated Solvent Sites

    Science.gov (United States)

    2011-02-01

    representative solid and groundwater samples from an aquifer . The sampling and handling procedures described herein have been validated for Dhc assessment...pH 5.5. Under methanogenic conditions, ethene is sometimes reduced to ethane. VC, ethene and ethane can be mineralized to carbon dioxide under...dechlorinating bacteria are not rare in subsurface environments and aquifers and cis-DCE plumes likely reflect the activity of such microorganisms

  5. A label-free colorimetric isothermal cascade amplification for the detection of disease-related nucleic acids based on double-hairpin molecular beacon.

    Science.gov (United States)

    Wu, Dong; Xu, Huo; Shi, Haimei; Li, Weihong; Sun, Mengze; Wu, Zai-Sheng

    2017-03-08

    K-Ras mutations at codon 12 play an important role in an early step of carcinogenesis. Here, a label-free colorimetric isothermal cascade amplification for ultrasensitive and specific detection of K-Ras point mutation is developed based on a double-hairpin molecular beacon (DHMB). The biosensor consists of DHMB probe and a primer-incorporated polymerization template (PPT) designed partly complementary to DHMB. In the presence of polymerase, target DNA is designed to trigger strand displacement amplification (SDA) via promote the hybridization of PPT with DHMB and subsequently initiates cascade amplification process with the help of the nicking endonuclease. During the hybridization and enzymatic reaction, G-quadruplex/hemin DNAzymes are generated, catalyzing the oxidation of ABTS(2-) by H2O2 in the presence of hemin. Utilizing the proposed facile colorimetric scheme, the target DNA can be quantified down to 4 pM with the dynamic response range of 5 orders of magnitude, indicating the substantially improved detection capability. Even more strikingly, point mutation in K-ras gene can be readily observed by the naked eye without the need for the labeling or expensive equipment. Given the high-performance for K-Ras analysis, the enhanced signal transduction capability associated with double-hairpin structure of DHMB provides a novel rout to screen biomarkers, and the descripted colorimetric biosensor seems to hold great promise for diagnostic applications of genetic diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Locked Nucleic Acid-Based In Situ Hybridization Reveals miR-7a as a Hypothalamus-Enriched MicroRNA with a Distinct Expression Pattern

    DEFF Research Database (Denmark)

    Herzer, S; Silahtaroglu, A; Meister, B

    2012-01-01

    MicroRNAs (miRNAs) are short (22 nucleotides) non-coding ribonucleic acid (RNA) molecules that post-transcriptionally repress expression of protein-coding genes by binding to 3'-untranslated regions of the target mRNAs. In order to identify miRNAs selectively expressed within the hypothalamus...... present in the hypothalamus, miR-7a, was the only miRNA found to be enriched in the hypothalamus, with low or no expression in other parts of the central nervous system (CNS). Within the hypothalamus, strong miR-7a expression was distinct and restricted to some hypothalamic nuclei and adjacent areas. mi......R-7a expression was particularly prominent in the subfornical organ, suprachiasmatic, paraventricular, periventricular, supraoptic, dorsomedial and arcuate nuclei. Identical expression patterns for miR-7a was seen in mouse and rat hypothalamus. By combining LNA-FISH with immunohistochemistry...

  7. Locked Nucleic Acid-Based In Situ Hybridization Reveals miR-7a as a Hypothalamus-Enriched MicroRNA with a Distinct Expression Pattern

    DEFF Research Database (Denmark)

    Herzer, S; Silahtaroglu, A; Meister, B

    2012-01-01

    present in the hypothalamus, miR-7a, was the only miRNA found to be enriched in the hypothalamus, with low or no expression in other parts of the central nervous system (CNS). Within the hypothalamus, strong miR-7a expression was distinct and restricted to some hypothalamic nuclei and adjacent areas. mi...

  8. Microbial Nucleic Acid Sensing in Oral and Systemic Diseases.

    Science.gov (United States)

    Crump, K E; Sahingur, S E

    2016-01-01

    One challenge in studying chronic infectious and inflammatory disorders is understanding how host pattern recognition receptors (PRRs), specifically toll-like receptors (TLRs), sense and respond to pathogen- or damage-associated molecular patterns, their communication with each other and different components of the immune system, and their role in propagating inflammatory stages of disease. The discovery of innate immune activation through nucleic acid recognition by intracellular PRRs such as endosomal TLRs (TLR3, TLR7, TLR8, and TLR9) and cytoplasmic proteins (absent in melanoma 2 and DNA-dependent activator of interferon regulatory factor) opened a new paradigm: Nucleic acid sensing is now implicated in multiple immune and inflammatory conditions (e.g., atherosclerosis, cancer), viral (e.g., human papillomavirus, herpes virus) and bacterial (e.g., Helicobacter pylori, pneumonia) diseases, and autoimmune disorders (e.g., systemic lupus erythematosus, rheumatoid arthritis). Clinical investigations reveal the overexpression of specific nucleic acid sensors in diseased tissues. In vivo animal models show enhanced disease progression associated with receptor activation. The involvement of nucleic acid sensors in various systemic conditions is further supported by studies reporting receptor knockout mice being either protected from or prone to disease. TLR9-mediated inflammation is also implicated in periodontal diseases. Considering that persistent inflammation in the oral cavity is associated with systemic diseases and that oral microbial DNA is isolated at distal sites, nucleic acid sensing may potentially be a link between oral and systemic diseases. In this review, we discuss recent advances in how intracellular PRRs respond to microbial nucleic acids and emerging views on the role of nucleic acid sensors in various systemic diseases. We also highlight new information on the role of intracellular PRRs in the pathogenesis of oral diseases including periodontitis

  9. Model for acid-base chemistry in nanoparticle growth (MABNAG

    Directory of Open Access Journals (Sweden)

    T. Yli-Juuti

    2013-03-01

    Full Text Available Climatic effects of newly-formed atmospheric secondary aerosol particles are to a large extent determined by their condensational growth rates. However, all the vapors condensing on atmospheric nanoparticles and growing them to climatically relevant sizes are not identified yet and the effects of particle phase processes on particle growth rates are poorly known. Besides sulfuric acid, organic compounds are known to contribute significantly to atmospheric nanoparticle growth. In this study a particle growth model MABNAG (Model for Acid-Base chemistry in NAnoparticle Growth was developed to study the effect of salt formation on nanoparticle growth, which has been proposed as a potential mechanism lowering the equilibrium vapor pressures of organic compounds through dissociation in the particle phase and thus preventing their evaporation. MABNAG is a model for monodisperse aqueous particles and it couples dynamics of condensation to particle phase chemistry. Non-zero equilibrium vapor pressures, with both size and composition dependence, are considered for condensation. The model was applied for atmospherically relevant systems with sulfuric acid, one organic acid, ammonia, one amine and water in the gas phase allowed to condense on 3–20 nm particles. The effect of dissociation of the organic acid was found to be small under ambient conditions typical for a boreal forest site, but considerable for base-rich environments (gas phase concentrations of about 1010 cm−3 for the sum of the bases. The contribution of the bases to particle mass decreased as particle size increased, except at very high gas phase concentrations of the bases. The relative importance of amine versus ammonia did not change significantly as a function of particle size. While our results give a reasonable first estimate on the maximum contribution of salt formation to nanoparticle growth, further studies on, e.g. the thermodynamic properties of the atmospheric organics

  10. Model for acid-base chemistry in nanoparticle growth (MABNAG)

    Science.gov (United States)

    Yli-Juuti, T.; Barsanti, K.; Hildebrandt Ruiz, L.; Kieloaho, A.-J.; Makkonen, U.; Petäjä, T.; Ruuskanen, T.; Kulmala, M.; Riipinen, I.

    2013-12-01

    Climatic effects of newly-formed atmospheric secondary aerosol particles are to a large extent determined by their condensational growth rates. However, all the vapours condensing on atmospheric nanoparticles and growing them to climatically relevant sizes are not identified yet and the effects of particle phase processes on particle growth rates are poorly known. Besides sulfuric acid, organic compounds are known to contribute significantly to atmospheric nanoparticle growth. In this study a particle growth model MABNAG (Model for Acid-Base chemistry in NAnoparticle Growth) was developed to study the effect of salt formation on nanoparticle growth, which has been proposed as a potential mechanism lowering the equilibrium vapour pressures of organic compounds through dissociation in the particle phase and thus preventing their evaporation. MABNAG is a model for monodisperse aqueous particles and it couples dynamics of condensation to particle phase chemistry. Non-zero equilibrium vapour pressures, with both size and composition dependence, are considered for condensation. The model was applied for atmospherically relevant systems with sulfuric acid, one organic acid, ammonia, one amine and water in the gas phase allowed to condense on 3-20 nm particles. The effect of dissociation of the organic acid was found to be small under ambient conditions typical for a boreal forest site, but considerable for base-rich environments (gas phase concentrations of about 1010 cm-3 for the sum of the bases). The contribution of the bases to particle mass decreased as particle size increased, except at very high gas phase concentrations of the bases. The relative importance of amine versus ammonia did not change significantly as a function of particle size. While our results give a reasonable first estimate on the maximum contribution of salt formation to nanoparticle growth, further studies on, e.g. the thermodynamic properties of the atmospheric organics, concentrations of low

  11. Nucleic acids in circulation: Are they harmful to the host?

    Indian Academy of Sciences (India)

    Indraneel Mittra; Naveen Kumar Nair; Pradyumna Kumar Mishra

    2012-06-01

    It has been estimated that 1011–1012 cells, primarily of haematogenous origin, die in the adult human body daily, and a similar number is regenerated to maintain homeostasis. Despite the presence of an efficient scavenging system for dead cells, considerable amounts of fragmented genetic material enter the circulation in healthy individuals. Elevated blood levels of extracellular nucleic acids have been reported in various disease conditions; such as ageing and age-related degenerative disorders, cancer; acute and chronic inflammatory conditions, severe trauma and autoimmune disorders. In addition to genomic DNA and nucleosomes, mitochondrial DNA is also found in circulation, as are RNA and microRNA. There is extensive literature that suggests that extraneously added nucleic acids have biological actions. They can enter into cells in vitro and in vivo and induce genetic transformation and cellular and chromosomal damage; and experimentally added nucleic acids are capable of activating both innate and adaptive immune systems and inducing a sterile inflammatory response. The possibility as to whether circulating nucleic acids may, likewise, have biological activities has not been explored. In this review we raise the question as to whether circulating nucleic acids may have damaging effects on the host and be implicated in ageing and diverse acute and chronic human pathologies.

  12. Challenges and Perspectives in Nucleic Acid Enzyme Engineering.

    Science.gov (United States)

    Balke, Darko; Hieronymus, Robert; Müller, Sabine

    2017-08-04

    Engineering of nucleic acids has been a goal in research for many years. Since the discovery of catalytic nucleic acids (ribozymes and DNAzymes), this field has attracted even more attention. One reason for the increased interest is that a large number of ribozymes have been engineered that catalyze a broad range of reactions of relevance to the origin of life. Another reason is that the structures of ribozymes or DNAzymes have been modulated such that activity is dependent on allosteric regulation by an external cofactor. Such constructs have great potential for application as biosensors in medicinal or environmental diagnostics, and as molecular tools for control of cellular processes. In addition to the development of nucleic acid enzymes by in vitro selection, rational design is a powerful strategy for the engineering of ribozymes or DNAzymes with tailored features. The structures and mechanisms of a large number of nucleic acid catalysts are now well understood. Therefore, specific design of their functional properties by structural modulation is a good option for the development of custom-made molecular tools. For rational design, several parameters have to be considered, and a number of tools are available to help/guide sequence design. Here, we discuss sequence, structural and functional design using the example of hairpin ribozyme variants to highlight the challenges and opportunities of rational nucleic enzyme engineering. Graphical Abstract.

  13. Plasmonics-based SERS nanobiosensor for homogeneous nucleic acid detection.

    Science.gov (United States)

    Wang, Hsin-Neng; Fales, Andrew M; Vo-Dinh, Tuan

    2015-05-01

    Developing a simple and efficient nucleic acid detection technology is essential for clinical diagnostics. Here, we describe a new conceptually simple and selective "turn on" plasmonics-based nanobiosensor, which integrates non-enzymatic DNA strand-displacement hybridization for specific nucleic acid target identification with surface-enhanced Raman scattering (SERS) detection. This SERS nanobiosensor is a target label-free, and rapid nanoparticle-based biosensing system using a homogeneous assay format that offers a simple and efficient tool for nucleic acid diagnostics. Our results showed that the nanobiosensor provided a limit of detection of ~0.1nM (200amol) in the current bioassay system, and exhibited high specificity for single nucleotide mismatch discrimination. Surface-enhanced Raman scattering (SERS) is a sensitive technique that enhances Raman scattering by molecules adsorbed on rough metal surfaces. The enhancement means that the technique may even detect single molecules. In this article, the authors describe a simple and efficient nucleic acid detection technology using SERS, with "OFF-to-ON" signal switch upon nucleic acid target identification and capture, which provides high sensitivity and specificity for single nucleotide mismatch discrimination. This new technology will be most welcomed in clinical diagnostics. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation.

    Science.gov (United States)

    Kellersberger, Katherine A; Yu, Eizadora; Kruppa, Gary H; Young, Malin M; Fabris, Daniele

    2004-05-01

    . A new program called MS2Links was developed for the automated reduction and interpretation of fragmentation data obtained from modified nucleic acids. Based on an algorithm that searches for plausible isotopic patterns, the data reduction module is capable of discriminating legitimate signals from noise spikes of comparable intensity. The fragment identification module calculates the monoisotopic mass of ion products expected from a certain sequence and user-defined covalent modifications, which are finally matched with the signals selected by the data reduction program. Considering that MS2Links can generate similar fragment libraries for peptides and their covalent conjugates with other peptides or nucleic acids, this program provides an integrated platform for the structural investigation of protein-nucleic acid complexes based on cross-linking strategies and top-down ESI-FTMS.

  15. Acid-base metabolism: implications for kidney stones formation.

    Science.gov (United States)

    Hess, Bernhard

    2006-04-01

    The physiology and pathophysiology of renal H+ ion excretion and urinary buffer systems are reviewed. The main focus is on the two major conditions related to acid-base metabolism that cause kidney stone formation, i.e., distal renal tubular acidosis (dRTA) and abnormally low urine pH with subsequent uric acid stone formation. Both the entities can be seen on the background of disturbances of the major urinary buffer system, NH3+ NH4+. On the one hand, reduced distal tubular secretion of H+ ions results in an abnormally high urinary pH and either incomplete or complete dRTA. On the other hand, reduced production/availability of NH4+ is the cause of an abnormally low urinary pH, which predisposes to uric acid stone formation. Most recent research indicates that the latter abnormality may be a renal manifestation of the increasingly prevalent metabolic syndrome. Despite opposite deviations from normal urinary pH values, both the dRTA and uric acid stone formation due to low urinary pH require the same treatment, i.e., alkali. In the dRTA, alkali is needed for improving the body's buffer capacity, whereas the goal of alkali treatment in uric acid stone formers is to increase the urinary pH to 6.2-6.8 in order to minimize uric acid crystallization.

  16. Acid-base transport in pancreas – new challenges

    Directory of Open Access Journals (Sweden)

    Ivana eNovak

    2013-12-01

    Full Text Available Along the gastrointestinal tract a number of epithelia contribute with acid or basic secretions in order to aid digestive processes. The stomach and pancreas are the most extreme examples of acid (H+ and base (HCO3- transporters, respectively. Nevertheless, they share the same challenges of transporting acid and bases across epithelia and effectively regulating their intracellular pH. In this review, we will make use of comparative physiology to enlighten the cellular mechanisms of pancreatic HCO3- and fluid secretion, which is still challenging physiologists. Some of the novel transporters to consider in pancreas are the proton pumps (H+-K+-ATPases, as well as the calcium-activated K+ and Cl- channels, such as KCa3.1 and TMEM16A/ANO1. Local regulators, such as purinergic signalling, fine-tune and coordinate pancreatic secretion. Lastly, we speculate whether dys-regulation of acid-base transport contributes to pancreatic diseases including cystic fibrosis, pancreatitis and cancer.

  17. Ionic liquid supported acid/base-catalyzed production of biodiesel.

    Science.gov (United States)

    Lapis, Alexandre A M; de Oliveira, Luciane F; Neto, Brenno A D; Dupont, Jairton

    2008-01-01

    The transesterification (alcoholysis) reaction was successfully applied to synthesize biodiesel from vegetable oils using imidazolium-based ionic liquids under multiphase acidic and basic conditions. Under basic conditions, the combination of the ionic liquid 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BMINTf2), alcohols, and K2CO3 (40 mol %) results in the production of biodiesel from soybean oil in high yields (>98%) and purity. H2SO4 immobilized in BMINTf2 efficiently promotes the transesterification reaction of soybean oil and various primary and secondary alcohols. In this multiphase process the acid is almost completely retained in the ionic liquid phase, while the biodiesel forms a separate phase. The recovered ionic liquid containing the acid could be reused at least six times without any significant loss in the biodiesel yield or selectivity. In both catalytic processes (acid and base), the reactions proceed as typical multiphasic systems in which the formed biodiesel accumulates as the upper phase and the glycerol by-product is selectively captured by the alcohol-ionic liquid-acid/base phase. Classical ionic liquids such as 1-n-butyl-3-methylimidazolium tetrafluoroborate and hexafluorophosphate are not stable under these acidic or basic conditions and decompose.

  18. Kinetics of acid base catalyzed transesterification of Jatropha curcas oil.

    Science.gov (United States)

    Jain, Siddharth; Sharma, M P

    2010-10-01

    Out of various non-edible oil resources, Jatropha curcas oil (JCO) is considered as future feedstock for biodiesel production in India. Limited work is reported on the kinetics of transesterification of high free fatty acids containing oil. The present study reports the results of kinetic study of two-step acid base catalyzed transesterification process carried out at an optimum temperature of 65 °C and 50 °C for esterification and transesterification respectively under the optimum methanol to oil ratio of 3:7 (v/v), catalyst concentration 1% (w/w) for H₂SO₄ and NaOH. The yield of methyl ester (ME) has been used to study the effect of different parameters. The results indicate that both esterification and transesterification reaction are of first order with reaction rate constant of 0.0031 min⁻¹ and 0.008 min⁻¹ respectively. The maximum yield of 21.2% of ME during esterification and 90.1% from transesterification of pretreated JCO has been obtained.

  19. The Acid-Base balance history (Part I

    Directory of Open Access Journals (Sweden)

    Mario Tarantino

    2007-08-01

    Full Text Available In the History of Medicine, the Acid-Base balance is unusual in that it has undergone constant evolution, not merely and not so much as a result of the progress of knowledge in physiological and physiopathological and clinical fields - which is common to all fields of Medical Science, but rather in relation to its very biochemical foundations, as was demonstrated by P. Stewart’s recent critical review and the reviews of J. Corey and J.A. Kellum, which are still valid today - and this is rather unusual. Although it started centuries ago, the history of the acidbase balance has experienced a slow and difficult evolution, and modern concepts almost exploded a couple of decades into the 20th century. It is therefore with even greater wonder and admiration that we look back on the pioneering intuitions of scholars such as R. Boyle, J.B. van Helmont and A.L. Lavoisier, to mention but a few of the scientists who laid the foundations for current knowledge in this fascinating chapter of physiology and clinical practice that belongs transversally to all medical and clinical disciplines.

  20. Nucleic acid therapy for lifespan prolongation: Present and future

    Indian Academy of Sciences (India)

    Wing-Fu Lai

    2011-09-01

    Lifespan prolongation is a common desire of the human race. With advances in biotechnology, the mechanism of aging has been gradually unraveled, laying the theoretical basis of nucleic acid therapy for lifespan prolongation. Regretfully, clinically applicable interventions do not exist without the efforts of converting theory into action, and it is the latter that has been far from adequately addressed at the moment. This was demonstrated by a database search on PubMed and Web of Science, from which only seven studies published between 2000 and 2010 were found to directly touch on the development of nucleic acid therapy for anti-aging and/or longevity enhancing purposes. In light of this, the objective of this article is to overview the current understanding of the intimate association between genes and longevity, and to bring the prospect of nucleic acid therapy for lifespan prolongation to light.

  1. Application of peptide nucleic acid towards development of nanobiosensor arrays.

    Science.gov (United States)

    Singh, Ravindra P; Oh, Byung-Keun; Choi, Jeong-Woo

    2010-10-01

    Peptide nucleic acid (PNA) is the modified DNA or DNA analogue with a neutral peptide backbone instead of a negatively charged sugar phosphate. PNA exhibits chemical stability, resistant to enzymatic degradation inside living cell, recognizing specific sequences of nucleic acid, formation of stable hybrid complexes like PNA/DNA/PNA triplex, strand invasion, extraordinary thermal stability and ionic strength, and unique hybridization relative to nucleic acids. These unique physicobiochemical properties of PNA enable a new mode of detection, which is a faster and more reliable analytical process and finds applications in the molecular diagnostics and pharmaceutical fields. Besides, a variety of unique characteristic features, PNAs replace DNA as a probe for biomolecular tool in the molecular genetic diagnostics, cytogenetics, and various pharmaceutical potentials as well as for the development of sensors/arrays/chips and many more investigation purposes. This review paper discusses the various current aspects related with PNAs, making a new hot device in the commercial applications like nanobiosensor arrays.

  2. Soni-removal of nucleic acids from inclusion bodies.

    Science.gov (United States)

    Neerathilingam, Muniasamy; Mysore, Sumukh; Gandham, Sai Hari A

    2014-05-23

    Inclusion bodies (IBs) are commonly formed in Escherichia coli due to over expression of recombinant proteins in non-native state. Isolation, denaturation and refolding of these IBs is generally performed to obtain functional protein. However, during this process IBs tend to form non-specific interactions with sheared nucleic acids from the genome, thus getting carried over into downstream processes. This may hinder the refolding of IBs into their native state. To circumvent this, we demonstrate a methodology termed soni-removal which involves disruption of nucleic acid-inclusion body interaction using sonication; followed by solvent based separation. As opposed to conventional techniques that use enzymes and column-based separations, soni-removal is a cost effective alternative for complete elimination of buried and/or strongly bound short nucleic acid contaminants from IBs. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  3. A Polyaniline-based Sensor of Nucleic Acids.

    Science.gov (United States)

    Sengupta, Partha Pratim; Gloria, Jared N; Parker, Marcus K; Flynt, Alex S

    2016-11-01

    Detection of nucleic acids is at the center of diagnostic technologies used in research and the clinic. Standard approaches used in these technologies rely on enzymatic modification that can introduce bias and artifacts. A critical element of next generation detection platforms will be direct molecular sensing, thereby avoiding a need for amplification or labels. Advanced nanomaterials may provide the suitable chemical modalities to realize label-free sensors. Conjugated polymers are ideal for biological sensing, possessing properties compatible with biomolecules and exhibit high sensitivity to localized environmental changes. In this article, a method is presented for detecting nucleic acids using the electroconductive polymer polyaniline. Simple DNA "probe" oligonucleotides complementary to target nucleic acids are attached electrostatically to the polymer, creating a sensor system that can differentiate single nucleotide differences in target molecules. Outside the specific and unbiased nature of this technology, it is highly cost effective.

  4. Properties of nucleic acid staining dyes used in gel electrophoresis.

    Science.gov (United States)

    Haines, Alicia M; Tobe, Shanan S; Kobus, Hilton J; Linacre, Adrian

    2015-03-01

    Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically, the most common dye used for gel staining is ethidium bromide, however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now available and their sensitivity for detection of DNA and their ability to permeate the cell membrane. It was found that GelRed™ was the most sensitive and safest dye to use with UV light excitation, and both GelGreen™ and Diamond™ Nucleic Acid Dye were sensitive and the safer dyes using blue light excitation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids

    DEFF Research Database (Denmark)

    Pedersen, Erik Bjerregaard; Nielsen, Jakob Toudahl; Nielsen, Claus

    2011-01-01

    Two G-quadruplex forming sequences, 50-TGGGAG and the 17-mer sequence T30177, which exhibit anti-HIV-1 activity on cell lines, were modified using either locked nucleic acids (LNA) or via insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (intercalating nucleic acid, INA) or (R)-1-O-[4-(1-pyrenylet......Two G-quadruplex forming sequences, 50-TGGGAG and the 17-mer sequence T30177, which exhibit anti-HIV-1 activity on cell lines, were modified using either locked nucleic acids (LNA) or via insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (intercalating nucleic acid, INA) or (R)-1-O-[4......-(1-pyrenylethynyl)phenylmethyl]glycerol (twisted intercalating nucleic acid, TINA). Incorporation of LNA or INA/TINA monomers provide as much as 8-fold improvement of anti-HIV-1 activity. We demonstrate for the first time a detailed analysis of the effect the incorporation of INA/TINA monomers in quadruplex forming...

  6. Instrument-free nucleic acid amplification assays for global health settings

    Science.gov (United States)

    LaBarre, Paul; Boyle, David; Hawkins, Kenneth; Weigl, Bernhard

    2011-06-01

    Many infectious diseases that affect global health are most accurately diagnosed through nucleic acid amplification and detection. However, existing nucleic acid amplification tests are too expensive and complex for most low-resource settings. The small numbers of centralized laboratories that exist in developing countries tend to be in urban areas and primarily cater to the affluent. In contrast, rural area health care facilities commonly have only basic equipment and health workers have limited training and little ability to maintain equipment and handle reagents.1 Reliable electric power is a common infrastructure shortfall. In this paper, we discuss a practical approach to the design and development of non-instrumented molecular diagnostic tests that exploit the benefits of isothermal amplification strategies. We identify modular instrument-free technologies for sample collection, sample preparation, amplification, heating, and detection. By appropriately selecting and integrating these instrument-free modules, we envision development of an easy to use, infrastructure independent diagnostic test that will enable increased use of highly accurate molecular diagnostics at the point of care in low-resource settings.

  7. Fluidic MEMS based Biosensor for the Detection of Nucleic acids by using Schizophyllan

    Science.gov (United States)

    Isoda, Takaaki; Hasegawa, Satoshi; Noguchi, Kazuhiro; Takamatsu, Kana; Itho, Fuyumi; Kimura, Taro; Sakurai, Kazuo; Shinkai, Seiji

    Recently, a fluid micro electro mechanical system (fluid MEMS), which is composed of a micro pump, mixer, valve, reactor, sensor, an electric circuit, on a chip, is being applied to a biotechnology or a medical analysis. Authors developed a micro sensor mounted on a chip to measure a concentration of one drop of solution (1nL-10μL) which contained nuclear acids. The form of the micro sensor mounted on the chip was a pair of Cu electrode which was a diameter of 2mm and was a thickness of 10μm. The sensing function was evaluated by the changes in a concentration of poly(x) (x=adenine, guanine, uracil, and cytosine) solution which was dropped on a micro sensor. To increase a recognization against nucleic acid, various adsorbent was added in a droplet. Especially, high recognition against the nucleic acid was observed with the adsorbent which modified the surface of polystyrene micro beads(10μm) using schizophyllan: a kind of polysaccharide. This biosensor recognized a small quantity of total-RNA and m-RNA extracted from the yeast.

  8. Recent Advances in Chemical Modification of Peptide Nucleic Acids

    Directory of Open Access Journals (Sweden)

    Eriks Rozners

    2012-01-01

    Full Text Available Peptide nucleic acid (PNA has become an extremely powerful tool in chemistry and biology. Although PNA recognizes single-stranded nucleic acids with exceptionally high affinity and sequence selectivity, there is considerable ongoing effort to further improve properties of PNA for both fundamental science and practical applications. The present paper discusses selected recent studies that improve on cellular uptake and binding of PNA to double-stranded DNA and RNA. The focus is on chemical modifications of PNA's backbone and heterocyclic nucleobases. The paper selects representative recent studies and does not attempt to provide comprehensive coverage of the broad and vibrant field of PNA modification.

  9. Nucleic acid aptamers: an emerging frontier in cancer therapy.

    Science.gov (United States)

    Zhu, Guizhi; Ye, Mao; Donovan, Michael J; Song, Erqun; Zhao, Zilong; Tan, Weihong

    2012-11-04

    The last two decades have witnessed the development and application of nucleic acid aptamers in a variety of fields, including target analysis, disease therapy, and molecular and cellular engineering. The efficient and widely applicable aptamer selection, reproducible chemical synthesis and modification, generally impressive target binding selectivity and affinity, relatively rapid tissue penetration, low immunogenicity, and rapid systemic clearance make aptamers ideal recognition elements for use as therapeutics or for in vivo delivery of therapeutics. In this feature article, we discuss the development and biomedical application of nucleic acid aptamers, with emphasis on cancer cell aptamer isolation, targeted cancer therapy, oncology biomarker identification and drug discovery.

  10. Nanopore-based sequencing and detection of nucleic acids.

    Science.gov (United States)

    Ying, Yi-Lun; Zhang, Junji; Gao, Rui; Long, Yi-Tao

    2013-12-09

    Nanopore-based techniques, which mimic the functions of natural ion channels, have attracted increasing attention as unique methods for single-molecule detection. The technology allows the real-time, selective, high-throughput analysis of nucleic acids through both biological and solid-state nanopores. In this Minireview, the background and latest progress in nanopore-based sequencing and detection of nucleic acids are summarized, and light is shed on a novel platform for nanopore-based detection. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Multifunctional combinatorial-designed nanoparticles for nucleic acid therapy

    Science.gov (United States)

    Amiji, Mansoor M.

    2016-05-01

    Recent advances in biomedical sciences, especially in the field of human genetics, is increasingly considered to facilitate a new frontier in development of novel disease-modifying therapeutics. One of major challenges in the development of nucleic acid therapeutics is efficient and specific delivery of the molecules to the target tissue and cell upon systemic administration. In this report, I discuss our strategy to develop combinatorial-designed multifunctional nanoparticle assemblies based on natural biocompatible and biodegradable polymers for nucleic acid delivery in: (1) overcoming tumor drug resistance and (2) genetic modulation of macrophage functional phenotype from M1 to M2 in treatment of inflammatory diseases.

  12. Methods of introducing nucleic acids into cellular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Lajoie, Marc J.; Gregg, Christopher J.; Mosberg, Joshua A.; Church, George M.

    2017-06-27

    A method of introducing a nucleic acid sequence into a cell is provided where the cell has impaired or inhibited or disrupted DnaG primase activity or impaired or inhibited or disrupted DnaB helicase activity, or larger or increased gaps or distance between Okazaki fragments or lowered or reduced frequency of Okazaki fragment initiation, or the cell has increased single stranded DNA (ssDNA) on the lagging strand of the replication fork including transforming the cell through recombination with a nucleic acid oligomer.

  13. Biomimetic High Density Lipoprotein Nanoparticles For Nucleic Acid Delivery

    Science.gov (United States)

    McMahon, Kaylin M.; Mutharasan, R. Kannan; Tripathy, Sushant; Veliceasa, Dorina; Bobeica, Mariana; Shumaker, Dale K.; Luthi, Andrea J.; Helfand, Brian T.; Ardehali, Hossein; Mirkin, Chad A.; Volpert, Olga; Thaxton, C. Shad

    2014-01-01

    We report a gold nanoparticle-templated high density lipoprotein (HDL AuNP) platform for gene therapy which combines lipid-based nucleic acid transfection strategies with HDL biomimicry. For proof-of-concept, HDL AuNPs are shown to adsorb antisense cholesterylated DNA. The conjugates are internalized by human cells, can be tracked within cells using transmission electron microscopy (TEM), and regulate target gene expression. Overall, the ability to directly image the AuNP core within cells, the chemical tailorability of the HDL AuNP platform, and the potential for cell-specific targeting afforded by HDL biomimicry make this platform appealing for nucleic acid delivery. PMID:21319839

  14. Nucleic acid-binding glycoproteins which solubilize nucleic acids in dilute acid: re-examination of the Ustilago maydis glycoproteins

    Energy Technology Data Exchange (ETDEWEB)

    Unrau, P.; Champ, D.R.; Young, J.L.; Grant, C.E.

    1980-01-01

    Holloman reported the isolation from Ustilago maydis of a glycoprotein which prevented the precipitation of nucleic acids in cold 5% trichloroacetic acid. Two glycoprotein fractions from U. maydis with this nucleic acid-solubilizing activity were isolated in our laboratory using improved purification procedures. The activity was not due to nuclease contamination. The glycoproteins are distinguished by: their ability to bind to concanavalin A-Sepharose; their differential binding to double- and single-stranded deoxyribonucleic acid, and to ribonucleic acid; their molecular weights (46,000 and 69,000); and the relative amounts present in growing versus nongrowing cells. Both fractions required sulfhydryl-reducing conditions for optimal yields, specific activity, and stability. Nucleic acid binding was cooperative, the minimum number of glycoproteins required to make a native T7 DNA molecule soluble in dilute acid being estimated at 2 and 15, respectively.

  15. Fetal cardiotocography and acid-base status during cesarean section.

    Science.gov (United States)

    Matorras, R; Tacuri, C; Nieto, A; Pijoan, J I; Cortés, J

    1998-10-01

    To assess the fetal well-being during cesarean section, in relation to the previous fetal condition. Observational study. University Hospital. PATIENTS PARTICIPANTS: 204 women undergoing cesarean section (203 intrapartum cesarean sections): 177 with general anesthesia and 27 with spinal anesthesia. We compared the fetal heart records of the last 30 min before cesarean section (during the first stage of labor) with those during cesarean section. Scalp blood analysis 30 min before the beginning of anesthesia induction was compared with umbilical artery analysis at delivery. Cardiotocography. Acid-base analysis. Apgar scores. During cesarean section there was a reduction in uterine activity, an increase in silent tracings and a decrease in late decelerations. Umbilical artery pH was lower than scalp pH (7.23+/-0.06 vs 7.30+/-0.06). Oxygen saturation was also lower (14.43+/-8.58% vs 18.99+/-8.4%). The values of pCO2 and of base deficit were higher. During cesarean section low values of modified Fischer scores were associated with low pH values of umbilical artery and low Apgar scores. Silent tracings appearing during cesarean section usually do not indicate fetal distress. Poor intracesarean fetal heart tracings were associated with worse indicators of neonatal well-being. Although umbilical pH were lower than scalp values, when the correction described in the literature was applied, the difference was of little clinical relevance. It is concluded that anesthesic, pharmacological and surgical events have slight repercussion in fetal well being. However, in a few cases fetal heart monitoring during cesarean section could detect otherwise undiagnosed cases of transient acidemia or depression in the fetus.

  16. Acid-base thermochemistry of gaseous aliphatic α-aminoacids.

    Science.gov (United States)

    Bouchoux, Guy; Huang, Sihua; Inda, Bhawani Singh

    2011-01-14

    Acid-base thermochemistry of isolated aliphatic amino acids (denoted AAA): glycine, alanine, valine, leucine, isoleucine and proline has been examined theoretically by quantum chemical computations at the G3MP2B3 level. Conformational analysis on neutral, protonated and deprotonated species has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. Comparison of the G3MP2B3 theoretical proton affinities, PA, and ΔH(acid) with experimental results is shown to be correct if experimental thermochemistry is re-evaluated and adapted to the most recent acidity-basicity scales. From this point of view, a set of evaluated proton affinities of 887, 902, 915, 916, 919 and 941 kJ mol(-1), and a set of evaluated ΔH(acid) of 1433, 1430, 1423, 1423, 1422 and 1426 kJ mol(-1), is proposed for glycine, alanine, valine, leucine, isoleucine and proline, respectively. Correlations with structural parameters (Taft's σ(α) polarizability parameter and molecular size) suggest that polarizability of the side chain is the major origin of the increase in PA and decrease in ΔH(acid) along the homologous series glycine, alanine, valine and leucine/isoleucine. Heats of formation of gaseous species AAA, AAAH(+) and [AAA-H](-) were computed at the G3MP2B3 level. The present study provides previously unavailable Δ(f)H°(298) for the ionized species AAAH(+) and [AAA-H](-). Comparison with Benson's estimate, and correlation with molecular size, show that several experimental Δ(f)H°(298) values of neutral or gaseous AAA might be erroneous.

  17. Pathophysiological aspect of metabolic acid-base disorders

    Directory of Open Access Journals (Sweden)

    Nešović-Ostojić Jelena

    2016-01-01

    Full Text Available Maintaing the arterial pH values (in normal range of 7,35-7,45 is one of the main principles of homeostasis. Regulatory responses, including chemical buffering (extracellular, intracellular, sceletal, the regulation of pCO2 by the respiratory system, and the regulation of [HCO3-] by the kidneys, act in concert to maintain normal arterial pH value. The main extracellular chemical buffer is bicarbonate-carbonic acid buffer system. The kidneys contribute to the regulation of hydrogen (and bicarbonate in body fluids in two ways. Proximal tubules are important in bicarbonate reabsorption and distal tubules excrete hydrogen ion (as ammonium ion or titratable acid. There are four simple acid-base disorders: metabolic acidosis and metabolic alkalosis; respiratory acidosis and respiratory alkalosis. Metabolic acidosis can occur because of an increase in endogenous acid production (such as lactate and ketoacids, loss of bicarbonate (as in diarrhea, or accumulation of endogenous acids (as in renal failure. Metabolic acidosis can also be with high and normal (hyperchloremic metabolic acidosis anion gap. Renal tubular acidosis (RTA is a form of hyperchloremic metabolic acidosis which occurs when the renal damage primarily affects tubular function. The main problem in distal RTA is reduced H+ excretion in distal tubule. Type 2 RTA is also called proximal RTA because the main problem is greatly impaired reabsorption of bicarbonate in proximal tubule. Impaired cation exchange in distal tubule is the main problem in RTA type 4. Metabolic alkalosis occurs as a result of net gain of [HCO3-] or loss of nonvolatile acid from extracellular fluids. Metabolic alkalosis can be associated with reduced or increased extracellular volume.

  18. Electrospun poly(lactic acid) based conducting nanofibrous networks

    Energy Technology Data Exchange (ETDEWEB)

    Patra, S N; Bhattacharyya, D [Department of Mechanical Engineering, Centre for Advanced Composite Materials, University of Auckland, Private Bag 92019, Auckland (New Zealand); Ray, S; Easteal, A J, E-mail: d.bhattacharyya@auckland.ac.nz [Department of Chemistry, Centre for Advanced Composite Materials, University of Auckland, Private Bag 92019, Auckland (New Zealand)

    2009-08-15

    Multi-functionalised micro/nanostructures of conducting polymers in neat or blended forms have received much attention because of their unique properties and technological applications in electrical, magnetic and biomedical devices. Biopolymer-based conducting fibrous mats are of special interest for tissue engineering because they not only physically support tissue growth but also are electrically conductive, and thus are able to stimulate specific cell functions or trigger cell responses. They are effective for carrying current in biological environments and can thus be considered for delivering local electrical stimuli at the site of damaged tissue to promote wound healing. Electrospinning is an established way to process polymer solutions or melts into continuous fibres with diameter often in the nanometre range. This process primarily depends on a number of parameters, including the type of polymer, solution viscosity, polarity and surface tension of the solvent, electric field strength and the distance between the spinneret and the collector. The present research has included polyaniline (PANi) as the conducting polymer and poly(L-lactic acid) (PLLA) as the biopolymer. Dodecylbenzene sulphonic acid (DBSA) doped PANi and PLLA have been dissolved in a common solvent (mixtures of chloroform and dimethyl formamide (DMF)), and the solutions successfully electrospun. DMF enhanced the dielectric constant of the solvent, and tetra butyl ammonium bromide (TBAB) was used as an additive to increase the conductivity of the solution. DBSA-doped PANi/PLLA mat exhibits an almost bead-free network of nanofibres that have extraordinarily smooth surface and diameters in the range 75 to 100 nm.

  19. Electrospun poly(lactic acid) based conducting nanofibrous networks

    Science.gov (United States)

    Patra, S. N.; Bhattacharyya, D.; Ray, S.; Easteal, A. J.

    2009-08-01

    Multi-functionalised micro/nanostructures of conducting polymers in neat or blended forms have received much attention because of their unique properties and technological applications in electrical, magnetic and biomedical devices. Biopolymer-based conducting fibrous mats are of special interest for tissue engineering because they not only physically support tissue growth but also are electrically conductive, and thus are able to stimulate specific cell functions or trigger cell responses. They are effective for carrying current in biological environments and can thus be considered for delivering local electrical stimuli at the site of damaged tissue to promote wound healing. Electrospinning is an established way to process polymer solutions or melts into continuous fibres with diameter often in the nanometre range. This process primarily depends on a number of parameters, including the type of polymer, solution viscosity, polarity and surface tension of the solvent, electric field strength and the distance between the spinneret and the collector. The present research has included polyaniline (PANi) as the conducting polymer and poly(L-lactic acid) (PLLA) as the biopolymer. Dodecylbenzene sulphonic acid (DBSA) doped PANi and PLLA have been dissolved in a common solvent (mixtures of chloroform and dimethyl formamide (DMF)), and the solutions successfully electrospun. DMF enhanced the dielectric constant of the solvent, and tetra butyl ammonium bromide (TBAB) was used as an additive to increase the conductivity of the solution. DBSA-doped PANi/PLLA mat exhibits an almost bead-free network of nanofibres that have extraordinarily smooth surface and diameters in the range 75 to 100 nm.

  20. Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Vetcher, Alexandre A [Institute of Biomedical Sciences and Technology and Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 (United States); Srinivasan, Srimeenakshi [Institute of Biomedical Sciences and Technology and Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 (United States); Vetcher, Ivan A [Institute of Biomedical Sciences and Technology and Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 (United States); Abramov, Semen M [NanoTech Institute, University of Texas at Dallas, Richardson, TX 75083 (United States); Kozlov, Mikhail [NanoTech Institute, University of Texas at Dallas, Richardson, TX 75083 (United States); Baughman, Ray H [NanoTech Institute, University of Texas at Dallas, Richardson, TX 75083 (United States); Levene, Stephen D [Institute of Biomedical Sciences and Technology and Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 (United States)

    2006-08-28

    We show that aqueous dispersions of single-walled carbon nanotubes (SWNTs), prepared with the aid of nucleic acids (NAs) such as RNA or DNA, can be separated into fractions using agarose gel electrophoresis. In a DC electric field, SWNT/NA complexes migrate in the gel in the direction of positive potential to form well-defined bands. Raman spectroscopy as a function of band position shows that nanotubes having different spectroscopic properties possess different electrophoretic mobilities. The migration patterns for SWNT/RNA and SWNT/DNA complexes differ. Parallel elution of the SWNT/NA complexes from the gel during electrophoresis and subsequent characterization by AFM reveals differences in nanotube diameter, length and curvature. The results suggest that fractionation of nanotubes can be achieved by this procedure. We discuss factors affecting the mobility of the nanotube complexes and propose analytical applications of this technique.

  1. Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis.

    Science.gov (United States)

    Vetcher, Alexandre A; Srinivasan, Srimeenakshi; Vetcher, Ivan A; Abramov, Semen M; Kozlov, Mikhail; Baughman, Ray H; Levene, Stephen D

    2006-08-28

    We show that aqueous dispersions of single-walled carbon nanotubes (SWNTs), prepared with the aid of nucleic acids (NAs) such as RNA or DNA, can be separated into fractions using agarose gel electrophoresis. In a DC electric field, SWNT/NA complexes migrate in the gel in the direction of positive potential to form well-defined bands. Raman spectroscopy as a function of band position shows that nanotubes having different spectroscopic properties possess different electrophoretic mobilities. The migration patterns for SWNT/RNA and SWNT/DNA complexes differ. Parallel elution of the SWNT/NA complexes from the gel during electrophoresis and subsequent characterization by AFM reveals differences in nanotube diameter, length and curvature. The results suggest that fractionation of nanotubes can be achieved by this procedure. We discuss factors affecting the mobility of the nanotube complexes and propose analytical applications of this technique.

  2. Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis

    Science.gov (United States)

    Vetcher, Alexandre A.; Srinivasan, Srimeenakshi; Vetcher, Ivan A.; Abramov, Semen M.; Kozlov, Mikhail; Baughman, Ray H.; Levene, Stephen D.

    2006-08-01

    We show that aqueous dispersions of single-walled carbon nanotubes (SWNTs), prepared with the aid of nucleic acids (NAs) such as RNA or DNA, can be separated into fractions using agarose gel electrophoresis. In a DC electric field, SWNT/NA complexes migrate in the gel in the direction of positive potential to form well-defined bands. Raman spectroscopy as a function of band position shows that nanotubes having different spectroscopic properties possess different electrophoretic mobilities. The migration patterns for SWNT/RNA and SWNT/DNA complexes differ. Parallel elution of the SWNT/NA complexes from the gel during electrophoresis and subsequent characterization by AFM reveals differences in nanotube diameter, length and curvature. The results suggest that fractionation of nanotubes can be achieved by this procedure. We discuss factors affecting the mobility of the nanotube complexes and propose analytical applications of this technique.

  3. Mesoporous Silica Nanoparticles as Carriers for Intracellular Delivery of Nucleic Acids and Subsequent Therapeutic Applications.

    Science.gov (United States)

    Cha, Wenzhang; Fan, Rengen; Miao, Yufeng; Zhou, Yong; Qin, Chenglin; Shan, Xiangxiang; Wan, Xinqiang; Li, Jinbo

    2017-05-11

    Nucleic acids, including DNA, microRNA (miRNA), small interfering RNA (siRNA), and antisense oligonucleotide (ASO), are powerful gene regulators, which have been demonstrated as promising drug candidates for therapeutic treatments. Nevertheless, poor cellular membrane permeability and serum stability have greatly hindered the applications of nucleic acids in biomedicine. To address these issues, associate carriers that can encapsulate and protect nucleic acids are urgently required. Mesoporous silica nanoparticles (MSNs or MSNPs), which are nanomaterials with excellent biocompatibility, large surface area for functionalization, and tunable pore size for encapsulating different cargos, are emerging as novel and ideal biomaterials for different biomedical applications. In this review paper, we focus on the applications of MSNs in nucleic acid delivery and nucleic acid-guided therapeutic treatments. General strategies for the preparation of nucleic acid-MSN complexes will be firstly introduced, followed by a summary of recent applications of MSNs in nucleic acid delivery and nucleic acid-guided therapeutics.

  4. Watson-Crick hydrogen bonding of unlocked nucleic acids

    DEFF Research Database (Denmark)

    Langkjær, Niels; Wengel, Jesper; Pasternak, Anna

    2015-01-01

    We herein describe the synthesis of two new unlocked nucleic acid building blocks containing hypoxanthine and 2,6-diaminopurine as nucleobase moieties and their incorporation into oligonucleotides. The modified oligonucleotides were used to examine the thermodynamic properties of UNA against unmo...... unmodified oligonucleotides and the resulting thermodynamic data support that the hydrogen bonding face of UNA is Watson-Crick like....

  5. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2017-09-05

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  6. Predicting nucleic acid binding interfaces from structural models of proteins.

    Science.gov (United States)

    Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

    2012-02-01

    The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

  7. Biological activity and biotechnological aspects of peptide nucleic acid.

    Science.gov (United States)

    Lundin, Karin E; Good, Liam; Strömberg, Roger; Gräslund, Astrid; Smith, C I Edvard

    2006-01-01

    During the latest decades a number of different nucleic acid analogs containing natural nucleobases on a modified backbone have been synthesized. An example of this is peptide nucleic acid (PNA), a DNA mimic with a noncyclic peptide-like backbone, which was first synthesized in 1991. Owing to its flexible and neutral backbone PNA displays very good hybridization properties also at low-ion concentrations and has subsequently attracted large interest both in biotechnology and biomedicine. Numerous modifications have been made, which could be of value for particular settings. However, the original PNA does so far perform well in many diverse applications. The high biostability makes it interesting for in vivo use, although the very limited diffusion over lipid membranes requires further modifications in order to make it suitable for treatment in eukaryotic cells. The possibility to use this nucleic acid analog for gene regulation and gene editing is discussed. Peptide nucleic acid is now also used for specific genetic detection in a number of diagnostic techniques, as well as for site-specific labeling and hybridization of functional molecules to both DNA and RNA, areas that are also discussed in this chapter.

  8. Modulating gene function with peptide nucleic acids (PNA)

    DEFF Research Database (Denmark)

    Nielsen, Peter E.; Crooke, Stanley T.

    2008-01-01

    A review on peptide nucleic acid (PNA) oligomers as modulators of gene expression ranging from gene silencing at the mRNAor the dsDNA (antigene) level, and redirection of mRNA splicing to gene activation through transcription bubble mimicking. PNA chem., anti-infective agents, cellular delivery, ...

  9. Nucleic acid amplification: Alternative methods of polymerase chain reaction.

    Science.gov (United States)

    Fakruddin, Md; Mannan, Khanjada Shahnewaj Bin; Chowdhury, Abhijit; Mazumdar, Reaz Mohammad; Hossain, Md Nur; Islam, Sumaiya; Chowdhury, Md Alimuddin

    2013-10-01

    Nucleic acid amplification is a valuable molecular tool not only in basic research but also in application oriented fields, such as clinical medicine development, infectious diseases diagnosis, gene cloning and industrial quality control. A comperehensive review of the literature on the principles, applications, challenges and prospects of different alternative methods of polymerase chain reaction (PCR) was performed. PCR was the first nucleic acid amplification method. With the advancement of research, a no of alternative nucleic acid amplification methods has been developed such as loop mediated isothermal amplification, nucleic acid sequence based amplification, strand displacement amplification, multiple displacement amplification. Most of the alternative methods are isothermal obviating the need for thermal cyclers. Though principles of most of the alternate methods are relatively complex than that of PCR, they offer better applicability and sensitivity in cases where PCR has limitations. Most of the alternate methods still have to prove themselves through extensive validation studies and are not available in commercial form; they pose the potentiality to be used as replacements of PCR. Continuous research is going on in different parts of the world to make these methods viable technically and economically.

  10. Enhancing and targeting nucleic acid delivery by magnetic force.

    Science.gov (United States)

    Plank, Christian; Anton, Martina; Rudolph, Carsten; Rosenecker, Joseph; Krötz, Florian

    2003-08-01

    Insufficient contact of inherently highly active nucleic acid delivery systems with target cells is a primary reason for their often observed limited efficacy. Physical methods of targeting can overcome this limitation and reduce the risk of undesired side effects due to non-target site delivery. The authors and others have developed a novel means of physical targeting, exploiting magnetic force acting on nucleic acid vectors associated with magnetic particles in order to mediate the rapid contact of vectors with target cells. Here, the principles of magnetic drug and nucleic acid delivery are reviewed, and the facts and potentials of the technique for research and therapeutic applications are discussed. Magnetically enhanced nucleic acid delivery - magnetofection - is universally applicable to viral and non-viral vectors, is extraordinarily rapid, simple and yields saturation level transfection at low dose in vitro. The method is useful for site-specific vector targeting in vivo. Exploiting the full potential of the technique requires an interdisciplinary research effort in magnetic field physics, magnetic particle chemistry, pharmaceutical formulation and medical application.

  11. Peptide nucleic acid (PNA) antisense effects in Escherichia coli

    DEFF Research Database (Denmark)

    Good, L; Nielsen, P E

    1999-01-01

    Antisense peptide nucleic acid (PNA) can be used to control cell growth, gene expression and growth phenotypes in the bacteria Escherichia coli. PNAs targeted to the RNA components of the ribosome can inhibit translation and cell growth, and PNAs targeted to mRNA can limit gene expression with gene...

  12. PYRENE INTERCALATING NUCLEIC ACIDS WITH A CARBON LINKER

    DEFF Research Database (Denmark)

    Østergaard, Michael E.; Wamberg, Michael Chr.; Pedersen, Erik Bjerregaard

    2011-01-01

    geminally attached. Fluorescence studies of this intercalating nucleic acid with the pyrene moieties inserted as a bulge showed formation of an excimer band. When a mismatch was introduced at the site of the intercalator, an excimer band was formed for the destabilized duplexes whereas an exciplex band...

  13. Mosaic protein and nucleic acid vaccines against hepatitis C virus

    Science.gov (United States)

    Yusim, Karina; Korber, Bette T. M.; Kuiken, Carla L.; Fischer, William M.

    2013-06-11

    The invention relates to immunogenic compositions useful as HCV vaccines. Provided are HCV mosaic polypeptide and nucleic acid compositions which provide higher levels of T-cell epitope coverage while minimizing the occurrence of unnatural and rare epitopes compared to natural HCV polypeptides and consensus HCV sequences.

  14. A DNA origami nanorobot controlled by nucleic acid hybridization

    KAUST Repository

    Torelli, Emanuela

    2014-03-20

    A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Assays for urinary biomarkers of oxidatively damaged nucleic acids

    DEFF Research Database (Denmark)

    Weimann, Allan; Broedbaek, Kasper; Henriksen, Trine;

    2012-01-01

    and skills requirement. The available ELISA methods present considerable specificity problems and cannot be recommended at present. The oxidized nucleic acid metabolites in urine are assumed to originate from the DNA and RNA. However, direct evidence is not available. A possible contribution from...

  16. Peptide nucleic acids and their potential applications in biotechnology

    DEFF Research Database (Denmark)

    Buchardt, O.; Egholm, M.; Berg, R.H.

    1993-01-01

    Peptide nucleic acids (PNAs) are novel DNA mimics in which the sugar-phosphate backbone has been replaced with a backbone based on amino acids1-3. PNAs exhibit sequence-specific binding to DNA and RNA with higher affinities and specificities than unmodified DNA. They,are resistant to nuclease and...

  17. A DNA origami nanorobot controlled by nucleic acid hybridization.

    Science.gov (United States)

    Torelli, Emanuela; Marini, Monica; Palmano, Sabrina; Piantanida, Luca; Polano, Cesare; Scarpellini, Alice; Lazzarino, Marco; Firrao, Giuseppe

    2014-07-23

    A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators.

  18. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2016-08-09

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  19. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2014-09-30

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  20. Collaborative Strategies for Teaching Common Acid-Base Disorders to Medical Students

    Science.gov (United States)

    Petersen, Marie Warrer; Toksvang, Linea Natalie; Plovsing, Ronni R.; Berg, Ronan M. G.

    2014-01-01

    The ability to recognize and diagnose acid-base disorders is of the utmost importance in the clinical setting. However, it has been the experience of the authors that medical students often have difficulties learning the basic principles of acid-base physiology in the respiratory physiology curriculum, particularly when applying this knowledge to…

  1. High School Students' Understanding of Acid-Base Concepts: An Ongoing Challenge for Teachers

    Science.gov (United States)

    Damanhuri, Muhd Ibrahim Muhamad; Treagust, David F.; Won, Mihye; Chandrasegaran, A. L.

    2016-01-01

    Using a quantitative case study design, the "Acids-Bases Chemistry Achievement Test" ("ABCAT") was developed to evaluate the extent to which students in Malaysian secondary schools achieved the intended curriculum on acid-base concepts. Responses were obtained from 260 Form 5 (Grade 11) students from five schools to initially…

  2. The acid-base resistant zone in three dentin bonding systems.

    Science.gov (United States)

    Inoue, Go; Nikaido, Toru; Foxton, Richard M; Tagami, Junji

    2009-11-01

    An acid-base resistant zone has been found to exist after acid-base challenge adjacent to the hybrid layer using SEM. The aim of this study was to examine the acid-base resistant zone using three different bonding systems. Dentin disks were applied with three different bonding systems, and then a resin composite was light-cured to make dentin disk sandwiches. After acid-base challenge, the polished surfaces were observed using SEM. For both one- and two-step self-etching primer systems, an acid-base resistant zone was clearly observed adjacent to the hybrid layer - but with differing appearances. For the wet bonding system, the presence of an acid-base resistant zone was unclear. This was because the self-etching primer systems etched the dentin surface mildly, such that the remaining mineral phase of dentin and the bonding agent yielded clear acid-base resistant zones. In conclusion, the acid-base resistant zone was clearly observed when self-etching primer systems were used, but not so for the wet bonding system.

  3. Stewart analysis of apparently normal acid-base state in the critically ill

    NARCIS (Netherlands)

    Moviat, M.; Boogaard, M. van den; Intven, F.; Voort, P. van der; Hoeven, H. van der; Pickkers, P.

    2013-01-01

    PURPOSE: This study aimed to describe Stewart parameters in critically ill patients with an apparently normal acid-base state and to determine the incidence of mixed metabolic acid-base disorders in these patients. MATERIALS AND METHODS: We conducted a prospective, observational multicenter study of

  4. Acid-base crystalline complexes and the pK(a) rule

    NARCIS (Netherlands)

    Cruz-Cabeza, A.J.

    2012-01-01

    Differences in the predicted aqueous pKa values (ΔpKa) have been calculated for 6465 crystalline complexes containing ionised and non-ionised acid-base pairs in the Cambridge Structural Database. A linear relationship between ΔpKa and the probability of proton transfer between acid-base pairs has be

  5. Stewart analysis of apparently normal acid-base state in the critically ill

    NARCIS (Netherlands)

    Moviat, M.; Boogaard, M. van den; Intven, F.; Voort, P. van der; Hoeven, H. van der; Pickkers, P.

    2013-01-01

    PURPOSE: This study aimed to describe Stewart parameters in critically ill patients with an apparently normal acid-base state and to determine the incidence of mixed metabolic acid-base disorders in these patients. MATERIALS AND METHODS: We conducted a prospective, observational multicenter study of

  6. Thai Grade 11 Students' Alternative Conceptions for Acid-Base Chemistry

    Science.gov (United States)

    Artdej, Romklao; Ratanaroutai, Thasaneeya; Coll, Richard Kevin; Thongpanchang, Tienthong

    2010-01-01

    This study involved the development of a two-tier diagnostic instrument to assess Thai high school students' understanding of acid-base chemistry. The acid-base diagnostic test (ABDT) comprising 18 items was administered to 55 Grade 11 students in a science and mathematics programme during the second semester of the 2008 academic year. Analysis of…

  7. Canonical Pedagogical Content Knowledge by Cores for Teaching Acid-Base Chemistry at High School

    Science.gov (United States)

    Alvarado, Clara; Cañada, Florentina; Garritz, Andoni; Mellado, Vicente

    2015-01-01

    The topic of acid-base chemistry is one of the oldest in general chemistry courses and it has been almost continuously in academic discussion. The central purpose of documenting the knowledge and beliefs of a group of ten Mexican teachers with experience in teaching acid-base chemistry in high school was to know how they design, prepare and…

  8. A Comparative Study of French and Turkish Students' Ideas on Acid-Base Reactions

    Science.gov (United States)

    Cokelez, Aytekin

    2010-01-01

    The goal of this comparative study was to determine the knowledge that French and Turkish upper secondary-school students (grades 11 and 12) acquire on the concept of acid-base reactions. Following an examination of the relevant curricula and textbooks in the two countries, 528 students answered six written questions about the acid-base concept.…

  9. Using the Logarithmic Concentration Diagram, Log "C", to Teach Acid-Base Equilibrium

    Science.gov (United States)

    Kovac, Jeffrey

    2012-01-01

    Acid-base equilibrium is one of the most important and most challenging topics in a typical general chemistry course. This article introduces an alternative to the algebraic approach generally used in textbooks, the graphical log "C" method. Log "C" diagrams provide conceptual insight into the behavior of aqueous acid-base systems and allow…

  10. A knowledge based advisory system for acid/base titrations in non-aqueous solvents

    NARCIS (Netherlands)

    Bos, M.; Linden, van der W.E.

    1996-01-01

    A computer program was developed that could advice on the choice of solvent and titrant for acid/base titrations in nonaqueous media. It is shown that the feasibility of a titration in a given solvent can be calculated from solvent properties and intrinsic acid/base properties of the sample componen

  11. Mixed acid-base disorder secondary to topiramate use in traumatic brain injury

    Directory of Open Access Journals (Sweden)

    S Golla

    2016-01-01

    Full Text Available We report a case of a man with traumatic brain injury. He was started on to prophylactic topiramate which led to a mixed acid-base disorder. He had severe metabolic acidosis secondary to renal tubular acidification defect and respiratory alkalosis secondary to hyperventilation. Withdrawal of the offending drug led to the prompt resolution of the acid-base disturbance.

  12. Canonical Pedagogical Content Knowledge by Cores for Teaching Acid-Base Chemistry at High School

    Science.gov (United States)

    Alvarado, Clara; Cañada, Florentina; Garritz, Andoni; Mellado, Vicente

    2015-01-01

    The topic of acid-base chemistry is one of the oldest in general chemistry courses and it has been almost continuously in academic discussion. The central purpose of documenting the knowledge and beliefs of a group of ten Mexican teachers with experience in teaching acid-base chemistry in high school was to know how they design, prepare and…

  13. Thai Grade 11 Students' Alternative Conceptions for Acid-Base Chemistry

    Science.gov (United States)

    Artdej, Romklao; Ratanaroutai, Thasaneeya; Coll, Richard Kevin; Thongpanchang, Tienthong

    2010-01-01

    This study involved the development of a two-tier diagnostic instrument to assess Thai high school students' understanding of acid-base chemistry. The acid-base diagnostic test (ABDT) comprising 18 items was administered to 55 Grade 11 students in a science and mathematics programme during the second semester of the 2008 academic year. Analysis of…

  14. A Comparative Study of French and Turkish Students' Ideas on Acid-Base Reactions

    Science.gov (United States)

    Cokelez, Aytekin

    2010-01-01

    The goal of this comparative study was to determine the knowledge that French and Turkish upper secondary-school students (grades 11 and 12) acquire on the concept of acid-base reactions. Following an examination of the relevant curricula and textbooks in the two countries, 528 students answered six written questions about the acid-base concept.…

  15. Collaborative Strategies for Teaching Common Acid-Base Disorders to Medical Students

    Science.gov (United States)

    Petersen, Marie Warrer; Toksvang, Linea Natalie; Plovsing, Ronni R.; Berg, Ronan M. G.

    2014-01-01

    The ability to recognize and diagnose acid-base disorders is of the utmost importance in the clinical setting. However, it has been the experience of the authors that medical students often have difficulties learning the basic principles of acid-base physiology in the respiratory physiology curriculum, particularly when applying this knowledge to…

  16. Using the Logarithmic Concentration Diagram, Log "C", to Teach Acid-Base Equilibrium

    Science.gov (United States)

    Kovac, Jeffrey

    2012-01-01

    Acid-base equilibrium is one of the most important and most challenging topics in a typical general chemistry course. This article introduces an alternative to the algebraic approach generally used in textbooks, the graphical log "C" method. Log "C" diagrams provide conceptual insight into the behavior of aqueous acid-base systems and allow…

  17. "Clickable" LNA/DNA probes for fluorescence sensing of nucleic acids and autoimmune antibodies

    DEFF Research Database (Denmark)

    Jørgensen, Anna S; Gupta, Pankaj; Wengel, Jesper

    2013-01-01

    Herein we describe fluorescent oligonucleotides prepared by click chemistry between novel alkyne-modified locked nucleic acid (LNA) strands and a series of fluorescent azides for homogeneous (all-in-solution) detection of nucleic acids and autoimmune antibodies.......Herein we describe fluorescent oligonucleotides prepared by click chemistry between novel alkyne-modified locked nucleic acid (LNA) strands and a series of fluorescent azides for homogeneous (all-in-solution) detection of nucleic acids and autoimmune antibodies....

  18. An Alternative to Synthetic Acid Base Indicator-Tagetes Erecta Linn

    Directory of Open Access Journals (Sweden)

    *A. Elumalai

    2012-06-01

    Full Text Available The present work highlights the use of the methanolic extract of the flowers of Tagetes erecta as an acid-base indicator in acid-base titrations. This natural indicator is easy to extract as well as easily available. Indicators used in titration show well marked changes of colour in certain intervals of pH. Most of these indicators are organic dyes and are of synthetic origin. Today synthetic indicators are the choice of acid-base titrations. But due to environmental pollution, availability and cost, the search for natural compounds as an acid-base indicator was started. Herbal indicators are evaluated by using strong acid-strong base, strong acid-weak base, weak acid-strong base and weak acid weak base. In all these titrations the methanolic extract of the flowers of Tagetes erecta was found to be very useful, economical, simple and accurate for acid base titration.

  19. Polymerase-directed synthesis of C5-ethynyl locked nucleic acids

    DEFF Research Database (Denmark)

    Veedu, Rakesh N; Burri, Harsha Vardhan Reddy; Kumar, Pawan;

    2010-01-01

    Modified nucleic acids have considerable potential in nanobiotechnology for the development of nanomedicines and new materials. Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far and we herein for the first time report the enzymatic incorporation of LNA...

  20. DMPD: Nucleic acid-sensing TLRs as modifiers of autoimmunity. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17082566 Nucleic acid-sensing TLRs as modifiers of autoimmunity. Deane JA, Bolland ...S. J Immunol. 2006 Nov 15;177(10):6573-8. (.png) (.svg) (.html) (.csml) Show Nucleic acid-sensing TLRs as modifiers of autoimmunit...y. PubmedID 17082566 Title Nucleic acid-sensing TLRs as modifiers of autoimmunity. Aut

  1. Easily denaturing nucleic acids derived from intercalating nucleic acids: thermal stability studies, dual duplex invasion and inhibition of transcription start

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Vester, Birte; Hansen, Lykke Haastrup;

    2005-01-01

    The bulged insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (monomer P) in two complementary 8mer DNA strands (intercalating nucleic acids) opposite to each other resulted in the formation of an easily denaturing duplex, which had lower thermal stability (21.0 degrees C) than the wild-type double...

  2. Metabolic Effects of a Succinic Acid Substrate Antihypoxant

    Directory of Open Access Journals (Sweden)

    B. N. Shakh

    2014-01-01

    Full Text Available The paper discusses promises for clinical use of substrate antihypoxants.Objective: to investigate the efficacy of succinate containing  substrate  antihypoxants  on  systemic  oxygen  consumption,  blood  buffer  capacity,  and  changes  in  the  mixed venous blood level of lactate when they are used in gravely sick patients and victims with marked metabolic posthypoxic disorders.Subjects and methods. The trial enrolled 30 patients and victims who had sustained an episode of severe hypoxia of mixed genesis, the severity of which was evaluated by the APACHE II scale and amounted to 23 to 30 scores with a 46 to 70.3% risk of death. The standard infusion program in this group involved the succinate-containing drug 1.5% reamberin solution  in  a  total  dose  of  800  ml.  A  comparison  group  included  15  patients  who  had  undergone  emergency  extensive surgery for abdominal diseases. 400 ml of 10% glucose solution was used as an infusion medium. Oxygen consumption (VO2ml/min and carbon dioxide production (VCO2ml/min were measured before infusion and monitored for 2 hours. Arterial blood gases and acid-base balance (ABB parameters and mixed venous blood lactate levels were examined. Measurements were made before and 30 minutes after the infusion of reamberin or glucose solution.Results. Infusion of 1.5% reamberin solution was followed by a significant increase in minute oxygen consumption from 281.5±21.2 to 310.4±24.4 ml/min. CO2 production declined (on average, from 223.3±6.5 to 206.5±7.59 ml/min. During infusion of 10% glucose solution, all the patients of the comparison group showed a rise in oxygen consumption from 303.6±33.86 to 443.13±32.1 ml/min, i.e. about 1.5-fold. VCO2 changed similarly. The intravenous infusion of 800 ml of 1.5% reamberin solution raised arterial blood buffer capacity, which was reflected by changes in pH, BE, and HCO3. There was a clear trend for lactate values to drop in the

  3. [Procedural analysis of acid-base balance disorder: case serials in 4 patents].

    Science.gov (United States)

    Ma, Chunyuan; Wang, Guijie

    2017-05-01

    To establish the standardization process of acid-base balance analysis, analyze cases of acid-base balance disorder with the aid of acid-base balance coordinate graph. The acid-base balance theory were reviewed systematically on recent research progress, and the important concepts, definitions, formulas, parameters, regularity and inference in the analysis of acid-base balance were studied. The analysis of acid-base balance disordered processes and steps were figured. The application of acid-base balance coordinate graph in the cases was introduced. The method of "four parameters-four steps" analysis was put forward to analyze the acid-base balance disorders completely. "Four parameters" included pH, arterial partial pressure of carbon dioxide (PaCO2), HCO3(-) and anion gap (AG). "Four steps" were outlined by following aspects: (1) according to the pH, PaCO2 and HCO3(-), the primary or main types of acid-base balance disorder was determined; (2) primary or main types of acid-base disorder were used to choose the appropriate compensation formula and to determine the presence of double mixed acid-base balance disorder; (3) the primary acid-base balance disorders were divided into two parts: respiratory acidosis or respiratory alkalosis, at the same time, the potential HCO3(-) should be calculated, the measured HCO3(-) should be replaced with potential HCO3(-), to determine whether there were three mixed acid-base disorders; (4) based on the above analysis the data judged as the simple AG increased-metabolic acidosis was needed to be further analyzed. The ratio of ΔAG↑/ΔHCO3(-)↓ was also needed to be calculated, to determine whether there was normal AG metabolic acidosis or metabolic alkalosis. In the clinical practice, PaCO2 (as the abscissa) and HCO3(-) (as the ordinate) were used to establish a rectangular coordinate system, through origin (0, 0) and coordinate point (40, 24) could be a straight line, and all points on the straight line pH were equal to 7

  4. Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support

    Directory of Open Access Journals (Sweden)

    Leclerc Mario

    2005-04-01

    Full Text Available Abstract Background Nucleic acids detection using microarrays requires labelling of target nucleic acids with fluorophores or other reporter molecules prior to hybridization. Results Using surface-bound peptide nucleic acids (PNA probes and soluble fluorescent cationic polythiophenes, we show a simple and sensitive electrostatic approach to detect and identify unlabelled target nucleic acid on microarray. Conclusion This simple methodology opens exciting possibilities for applied genetic analysis for the diagnosis of infections, identification of genetic mutations, and forensic inquiries. This electrostatic strategy could also be used with other nucleic acid detection methods such as electrochemistry, silver staining, metallization, quantum dots, or electrochemical dyes.

  5. The Importance of the Ionic Product for Water to Understand the Physiology of the Acid-Base Balance in Humans

    Directory of Open Access Journals (Sweden)

    María M. Adeva-Andany

    2014-01-01

    Full Text Available Human plasma is an aqueous solution that has to abide by chemical rules such as the principle of electrical neutrality and the constancy of the ionic product for water. These rules define the acid-base balance in the human body. According to the electroneutrality principle, plasma has to be electrically neutral and the sum of its cations equals the sum of its anions. In addition, the ionic product for water has to be constant. Therefore, the plasma concentration of hydrogen ions depends on the plasma ionic composition. Variations in the concentration of plasma ions that alter the relative proportion of anions and cations predictably lead to a change in the plasma concentration of hydrogen ions by driving adaptive adjustments in water ionization that allow plasma electroneutrality while maintaining constant the ionic product for water. The accumulation of plasma anions out of proportion of cations induces an electrical imbalance compensated by a fall of hydroxide ions that brings about a rise in hydrogen ions (acidosis. By contrast, the deficiency of chloride relative to sodium generates plasma alkalosis by increasing hydroxide ions. The adjustment of plasma bicarbonate concentration to these changes is an important compensatory mechanism that protects plasma pH from severe deviations.

  6. The importance of the ionic product for water to understand the physiology of the acid-base balance in humans.

    Science.gov (United States)

    Adeva-Andany, María M; Carneiro-Freire, Natalia; Donapetry-García, Cristóbal; Rañal-Muíño, Eva; López-Pereiro, Yosua

    2014-01-01

    Human plasma is an aqueous solution that has to abide by chemical rules such as the principle of electrical neutrality and the constancy of the ionic product for water. These rules define the acid-base balance in the human body. According to the electroneutrality principle, plasma has to be electrically neutral and the sum of its cations equals the sum of its anions. In addition, the ionic product for water has to be constant. Therefore, the plasma concentration of hydrogen ions depends on the plasma ionic composition. Variations in the concentration of plasma ions that alter the relative proportion of anions and cations predictably lead to a change in the plasma concentration of hydrogen ions by driving adaptive adjustments in water ionization that allow plasma electroneutrality while maintaining constant the ionic product for water. The accumulation of plasma anions out of proportion of cations induces an electrical imbalance compensated by a fall of hydroxide ions that brings about a rise in hydrogen ions (acidosis). By contrast, the deficiency of chloride relative to sodium generates plasma alkalosis by increasing hydroxide ions. The adjustment of plasma bicarbonate concentration to these changes is an important compensatory mechanism that protects plasma pH from severe deviations.

  7. [Practical diagnostics of acid-base disorders: part I: differentiation between respiratory and metabolic disturbances].

    Science.gov (United States)

    Deetjen, P; Lichtwarck-Aschoff, M

    2012-11-01

    The first part of this overview on diagnostic tools for acid-base disorders focuses on basic knowledge for distinguishing between respiratory and metabolic causes of a particular disturbance. Rather than taking sides in the great transatlantic or traditional-modern debate on the best theoretical model for understanding acid-base physiology, this article tries to extract what is most relevant for everyday clinical practice from the three schools involved in these keen debates: the Copenhagen, the Boston and the Stewart schools. Each school is particularly strong in a specific diagnostic or therapeutic field. Appreciating these various strengths a unifying, simplified algorithm together with an acid-base calculator will be discussed.

  8. An Alternative to Synthetic Acid Base Indicator-Tagetes Erecta Linn

    OpenAIRE

    A. Elumalai; M. C. Eswariah; M. K. Chinna; B. A. Kumar

    2012-01-01

    The present work highlights the use of the methanolic extract of the flowers of Tagetes erecta as an acid-base indicator in acid-base titrations. This natural indicator is easy to extract as well as easily available. Indicators used in titration show well marked changes of colour in certain intervals of pH. Most of these indicators are organic dyes and are of synthetic origin. Today synthetic indicators are the choice of acid-base titrations. But due to environmental pollution, availability a...

  9. A REVIEW ON ACID BASE STATUS IN DAIRY COWS: IMPLICATIONS OF DIETARY CATION-ANION BALANCE

    Directory of Open Access Journals (Sweden)

    D. Afzaal, M. Nisa, M. A. Khan and M. Sarwar

    2004-10-01

    Full Text Available The acid base status of a dairy cow is maintained within a narrow range. The key mechanisms involving blood, cells and lungs, perform this function. Although other minerals have an impact on acid base metabolism, the minerals used in dietary cation-anion balance (DCAB namely sodium (Na, potassium (K and chloride (Cl have the greatest effect. Hence, acid base status implicates other biological functions of dairy cows. Low DCAB prepartum reduces the incidence of milk fever and increases the productivity by simmering down the severity of hypocalcaemia. High DCAB diets have proved to increase dry mater and water intake and production and to mitigate the effects of heat stress.

  10. Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges.

    Science.gov (United States)

    Qing, Taiping; He, Dinggeng; He, Xiaoxiao; Wang, Kemin; Xu, Fengzhou; Wen, Li; Shangguan, Jingfang; Mao, Zhengui; Lei, Yanli

    2016-04-01

    Owing to their highly efficient catalytic effects and substrate specificity, the nucleic acid tool enzymes are applied as 'nano-tools' for manipulating different nucleic acid substrates both in the test-tube and in living organisms. In addition to the function as molecular scissors and molecular glue in genetic engineering, the application of nucleic acid tool enzymes in biochemical analysis has also been extensively developed in the past few decades. Used as amplifying labels for biorecognition events, the nucleic acid tool enzymes are mainly applied in nucleic acids amplification sensing, as well as the amplification sensing of biorelated variations of nucleic acids. With the introduction of aptamers, which can bind different target molecules, the nucleic acid tool enzymes-aided signal amplification strategies can also be used to sense non-nucleic targets (e.g., ions, small molecules, proteins, and cells). This review describes and discusses the amplification strategies of nucleic acid tool enzymes-aided biosensors for biochemical analysis applications. Various analytes, including nucleic acids, ions, small molecules, proteins, and cells, are reviewed briefly. This work also addresses the future trends and outlooks for signal amplification in nucleic acid tool enzymes-aided biosensors.

  11. A pliable electroporation patch (ep-Patch) for efficient delivery of nucleic acid molecules into animal tissues with irregular surface shapes.

    Science.gov (United States)

    Wei, Zewen; Huang, Yuanyu; Zhao, Deyao; Hu, Zhiyuan; Li, Zhihong; Liang, Zicai

    2015-01-05

    Delivery of nucleic acids into animal tissues by electroporation is an appealing approach for various types of gene therapy, but efficiency of existing methodsis not satisfactory. Here we present the validation of novel electroporation patch (ep-Patch) for efficient delivery of DNA and siRNA into mouse tissues. Using micromachining technology, closely spaced gold electrodes were made on the pliable parylene substrate to form a patch-like electroporation metrics. It enabled large coverage of the target tissues and close surface contact between the tissues and electrodes, thus providing a uniform electric field to deliver nucleic acids into tissues, even beneath intact skin. Using this ep-Patch for efficiently delivery of both DNA and siRNA, non-invasive electroporation of healthy mouse muscle tissue was successfully achieved. Delivery of these nucleic acids was performed to intact tumors with satisfactory results. Silencing of tumor genes using the ep-Patch was also demonstrated on mice. This pliable electroporation patch method constitutes a novel way of in vivo delivery of siRNA and DNA to certain tissues or organs to circumvent the disadvantages of existing methodologies for in vivo delivery of nucleic acid molecules.

  12. Differential interactions of plasmid DNA, RNA and genomic DNA with amino acid-based affinity matrices.

    Science.gov (United States)

    Sousa, Angela; Sousa, Fani; Queiroz, João A

    2010-09-01

    The development of a strategy to plasmid DNA (pDNA) purification has become necessary for the development of gene therapy and DNA vaccine production processes in recent years, since this nucleic acid and most of contaminants, such as RNA, genomic DNA and endotoxins, are negatively charged. An ideal separation methodology may be achieved with the use of affinity interactions between immobilized amino acids and nucleic acids. In this study, the binding behaviour of nucleic acids under the influence of different environmental conditions, such as the composition and ionic strength of elution buffer, and the temperature, is compared with various amino acids immobilized on chromatography resins. Supercoiled (sc) plasmid isoform was isolated with all matrices used, but in some cases preferential interactions with other nucleic acids were found. Particularly, lysine chromatography showed to be an ideal technology mainly on RNA purification using low salt concentration. On the other hand, arginine ligands have shown a greater ability to retain the sc isoform comparatively to the other nucleic acids retention, becoming this support more adequate to sc pDNA purification. The temperature variation, competitive elution and oligonucleotides affinity studies also allowed to recognize the dominant interactions inherent to biorecognition of pDNA molecule and the affinity matrices.

  13. Nucleic acid aptamers: research tools in disease diagnostics and therapeutics.

    Science.gov (United States)

    Santosh, Baby; Yadava, Pramod K

    2014-01-01

    Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug "Macugen" is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions.

  14. Microwave-Assisted Rapid Enzymatic Synthesis of Nucleic Acids.

    Science.gov (United States)

    Hari Das, Rakha; Ahirwar, Rajesh; Kumar, Saroj; Nahar, Pradip

    2016-07-02

    Herein we report microwave-induced enhancement of the reactions catalyzed by Escherichia coli DNA polymerase I and avian myeloblastosis virus-reverse transcriptase. The reactions induced by microwaves result in a highly selective synthesis of nucleic acids in 10-50 seconds. In contrast, same reactions failed to give desired reaction products when carried out in the same time periods, but without microwave irradiation. Each of the reactions was carried out for different duration of microwave exposure time to find the optimum reaction time. The products produced by the respective enzyme upon microwave irradiation of the reaction mixtures were identical to that produced by the conventional procedures. As the microwave-assisted reactions are rapid, microwave could be a useful alternative to the conventional and time consuming procedures of enzymatic synthesis of nucleic acids.

  15. Nucleic acids encoding antifungal polypeptides and uses thereof

    Science.gov (United States)

    Altier, Daniel J.; Ellanskaya, I. A.; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-11-02

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  16. A quantitative measure of chirality inside nucleic acid databank.

    Science.gov (United States)

    Pietropaolo, Adriana; Parrinello, Michele

    2011-08-01

    We show the capability of a chirality index (Pietropaolo et al., Proteins 2008;70:667-677) to investigate nucleic acid structures because of its high sensitivity to helical conformations. By analyzing selected structures of DNA and RNA, we have found that sequences rich in cytosine and guanine have a tendency to left-handed chirality, in contrast to regions rich in adenine or thymine which show strong negative, right-handed, chirality values. We also analyze RNA structures, where specific loops and hairpin motifs are characterized by a well-defined chirality value. We find that in nucleosome the chirality is exalted, whereas in ribosome it is reduced. Our results illustrate the sensitivity of this descriptor for nucleic acid conformations.

  17. A nucleic acid dependent chemical photocatalysis in live human cells

    DEFF Research Database (Denmark)

    Arian, Dumitru; Cló, Emiliano; Gothelf, Kurt V

    2010-01-01

    Only two nucleic acid directed chemical reactions that are compatible with live cells have been reported to date. Neither of these processes generate toxic species from nontoxic starting materials. Reactions of the latter type could be applied as gene-specific drugs, for example, in the treatment...... of cancer. We report here the first example of a chemical reaction that generates a cytotoxic drug from a nontoxic prodrug in the presence of a specific endogeneous ribonucleic acid in live mammalian cells. In this case, the prodrug is triplet oxygen and the drug is singlet oxygen. The key component...... singlet oxygen per nucleic acid target. This reaction is highly sequence specific. To detect the generation of singlet oxygen in live cells, we prepared a membrane-permeable and water-soluble fluorescent scavenger, a derivative of 2,5-diphenylisobenzofurane. The scavenger decomposes upon reaction...

  18. Electroporation-enhanced delivery of nucleic acid vaccines.

    Science.gov (United States)

    Broderick, Kate E; Humeau, Laurent M

    2015-02-01

    The naked delivery of nucleic acid vaccines is notoriously inefficient, and an enabling delivery technology is required to direct efficiently these constructs intracellularly. A delivery technology capable of enhancing nucleic acid uptake in both cells in tissues and in culture is electroporation (EP). EP is a physical delivery mechanism that increases the permeability of mammalian cell membranes and allows the trafficking of large macromolecules into the cell. EP has now been used extensively in the clinic and been shown to be an effective method to increase both the uptake of the construct and the breadth and magnitude of the resulting immune responses. Excitingly, 2014 saw the announcement of the first EP-enhanced DNA vaccine Phase II trial demonstrating clinical efficacy. This review seeks to introduce the reader to EP as a technology to enhance the delivery of DNA and RNA vaccines and highlight several published clinical trials using this delivery modality.

  19. Hands-free sample preparation platform for nucleic acid analysis.

    Science.gov (United States)

    Baier, T; Hansen-Hagge, T E; Gransee, R; Crombé, A; Schmahl, S; Paulus, C; Drese, K S; Keegan, H; Martin, C; O'Leary, J J; Furuberg, L; Solli, L; Grønn, P; Falang, I M; Karlgård, A; Gulliksen, A; Karlsen, F

    2009-12-07

    A Lab-On-Chip system with an instrument is presented which is capable of performing total sample preparation and automated extraction of nucleic acid from human cell samples fixed in a methanol based solution. The target application is extraction of mRNA from cervical liquid based cytology specimens for detection of transformed HPV-infections. The device accepts 3 ml of sample and performs the extraction in a disposable polymer chip of credit card size. All necessary reagents for cell lysis, washing, and elution are stored on-chip and the extraction is performed in two filter stages; one for cell pre-concentration and the other for nucleic acid capture. Tests performed using cancer cell lines and cervical liquid based cytology specimens confirm the extraction of HPV-mRNA by the system.

  20. Physical chemistry of nucleic acids and their complexes.

    Science.gov (United States)

    Ghirlando, Rodolfo; Felsenfeld, Gary

    2013-12-01

    Studies of the physical properties of nucleic acids began almost immediately following the discovery of the DNA structure. Early investigations focused on the stability and specificity of multi-strand polynucleotide complexes, then gradually on their interaction with other molecules, particularly proteins. As molecular and structural biology expanded to provide detailed information about biochemical mechanisms, physical studies eventually acquired the additional constraint that they should be relevant to functioning biological systems. We describe work in our laboratory that began with investigations of relatively simple questions about the role of electrostatic interactions in the stabilization of multi-strand nucleic acid structures, and evolved to studies of chromatin structure in vitro and within the nucleus. Copyright © 2013 Wiley Periodicals, Inc.

  1. CANADA: designing nucleic acid sequences for nanobiotechnology applications.

    Science.gov (United States)

    Feldkamp, Udo

    2010-02-01

    The design of nucleic acid sequences for a highly specific and efficient hybridization is a crucial step in DNA computing and DNA-based nanotechnology applications. The CANADA package contains software tools for designing DNA sequences that meet these and other requirements, as well as for analyzing and handling sequences. CANADA is freely available, including a detailed manual and example input files, at http://ls11-www.cs.uni-dortmund.de/molcomp/downloads.

  2. NanoDrop microvolume quantitation of nucleic acids.

    Science.gov (United States)

    Desjardins, Philippe; Conklin, Deborah

    2010-11-22

    Biomolecular assays are continually being developed that use progressively smaller amounts of material, often precluding the use of conventional cuvette-based instruments for nucleic acid quantitation for those that can perform microvolume quantitation. The NanoDrop microvolume sample retention system (Thermo Scientific NanoDrop Products) functions by combining fiber optic technology and natural surface tension properties to capture and retain minute amounts of sample independent of traditional containment apparatus such as cuvettes or capillaries. Furthermore, the system employs shorter path lengths, which result in a broad range of nucleic acid concentration measurements, essentially eliminating the need to perform dilutions. Reducing the volume of sample required for spectroscopic analysis also facilitates the inclusion of additional quality control steps throughout many molecular workflows, increasing efficiency and ultimately leading to greater confidence in downstream results. The need for high-sensitivity fluorescent analysis of limited mass has also emerged with recent experimental advances. Using the same microvolume sample retention technology, fluorescent measurements may be performed with 2 μL of material, allowing fluorescent assays volume requirements to be significantly reduced. Such microreactions of 10 μL or less are now possible using a dedicated microvolume fluorospectrometer. Two microvolume nucleic acid quantitation protocols will be demonstrated that use integrated sample retention systems as practical alternatives to traditional cuvette-based protocols. First, a direct A260 absorbance method using a microvolume spectrophotometer is described. This is followed by a demonstration of a fluorescence-based method that enables reduced-volume fluorescence reactions with a microvolume fluorospectrometer. These novel techniques enable the assessment of nucleic acid concentrations ranging from 1 pg/ μL to 15,000 ng/ μL with minimal consumption of

  3. Targeted high-throughput sequencing of tagged nucleic acid samples

    OpenAIRE

    M.; Meyer; Stenzel, U.; Myles, S.; Prüfer, K; Hofreiter, M.

    2007-01-01

    High-throughput 454 DNA sequencing technology allows much faster and more cost-effective sequencing than traditional Sanger sequencing. However, the technology imposes inherent limitations on the number of samples that can be processed in parallel. Here we introduce parallel tagged sequencing (PTS), a simple, inexpensive and flexible barcoding technique that can be used for parallel sequencing any number and type of double-stranded nucleic acid samples. We demonstrate that PTS is particularly...

  4. Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification

    OpenAIRE

    Pregibon, Daniel C.; Doyle, Patrick S

    2009-01-01

    The accurate quantification of nucleic acids is of utmost importance for clinical diagnostics, drug discovery, and basic science research. These applications require the concurrent measurement of multiple targets while demanding high-throughput analysis, high sensitivity, specificity between closely related targets, and a wide dynamic range. In attempt to create a technology that can simultaneously meet these demands, we recently developed a method of multiplexed analysis using encoded hydrog...

  5. Caged molecular beacons: controlling nucleic acid hybridization with light.

    Science.gov (United States)

    Wang, Chunming; Zhu, Zhi; Song, Yanling; Lin, Hui; Yang, Chaoyong James; Tan, Weihong

    2011-05-28

    We have constructed a novel class of light-activatable caged molecular beacons (cMBs) that are caged by locking two stems with a photo-labile biomolecular interaction or covalent bond. With the cMBs, the nucleic acid hybridization process can be easily controlled with light, which offers the possibility for a high spatiotemporal resolution study of intracellular mRNAs. © The Royal Society of Chemistry 2011

  6. System for portable nucleic acid testing in low resource settings

    Science.gov (United States)

    Lu, Hsiang-Wei; Roskos, Kristina; Hickerson, Anna I.; Carey, Thomas; Niemz, Angelika

    2013-03-01

    Our overall goal is to enable timely diagnosis of infectious diseases through nucleic acid testing at the point-of-care and in low resource settings, via a compact system that integrates nucleic acid sample preparation, isothermal DNA amplification, and nucleic acid lateral flow (NALF) detection. We herein present an interim milestone, the design of the amplification and detection subsystem, and the characterization of thermal and fluidic control and assay execution within this system. Using an earlier prototype of the amplification and detection unit, comprised of a disposable cartridge containing flexible pouches, passive valves, and electrolysis-driven pumps, in conjunction with a small heater, we have demonstrated successful execution of an established and clinically validated isothermal loop-mediated amplification (LAMP) reaction targeting Mycobacterium tuberculosis (M.tb) DNA, coupled to NALF detection. The refined design presented herein incorporates miniaturized and integrated electrolytic pumps, novel passive valves, overall design changes to facilitate integration with an upstream sample preparation unit, and a refined instrument design that automates pumping, heating, and timing. Nucleic acid amplification occurs in a two-layer pouch that facilitates fluid handling and appropriate thermal control. The disposable cartridge is manufactured using low-cost and scalable techniques and forms a closed system to prevent workplace contamination by amplicons. In a parallel effort, we are developing a sample preparation unit based on similar design principles, which performs mechanical lysis of mycobacteria and DNA extraction from liquefied and disinfected sputum. Our next step is to combine sample preparation, amplification, and detection in a final integrated cartridge and device, to enable fully automated sample-in to answer-out diagnosis of active tuberculosis in primary care facilities of low-resource and high-burden countries.

  7. Synthesis and photoactivity of phenylazonaphthalene peptide nucleic acid monomers

    Institute of Scientific and Technical Information of China (English)

    Jin Du Li; Miao Chen; Sheng Liu; Hao Bo Zhang; Zhi Lu Liu

    2008-01-01

    Phenylazonaphthalene peptide nucleic acid (PNA) monomers were successfully synthesized,and their photoisomerization was examined.The new PNA monomers showed reversible trans-cis isomerization with UV and visible light irradiation,which might be the foundation of photo-regulating the hybridization between PNA containing phenylazonaphthalene unit and DNA.Simultaneously,the fluorescence of the new PNA monomers might make them especially useful as structural probes.

  8. Multicentre validation study of nucleic acids extraction from FFPE tissues.

    Science.gov (United States)

    Bonin, Serena; Hlubek, Falk; Benhattar, Jean; Denkert, Carsten; Dietel, Manfred; Fernandez, Pedro L; Höfler, Gerald; Kothmaier, Hannelore; Kruslin, Bozo; Mazzanti, Chiara Maria; Perren, Aurel; Popper, Helmuth; Scarpa, Aldo; Soares, Paula; Stanta, Giorgio; Groenen, Patricia J T A

    2010-09-01

    In most pathology laboratories worldwide, formalin-fixed paraffin embedded (FFPE) samples are the only tissue specimens available for routine diagnostics. Although commercial kits for diagnostic molecular pathology testing are becoming available, most of the current diagnostic tests are laboratory-based assays. Thus, there is a need for standardized procedures in molecular pathology, starting from the extraction of nucleic acids. To evaluate the current methods for extracting nucleic acids from FFPE tissues, 13 European laboratories, participating to the European FP6 program IMPACTS (www.impactsnetwork.eu), isolated nucleic acids from four diagnostic FFPE tissues using their routine methods, followed by quality assessment. The DNA-extraction protocols ranged from homemade protocols to commercial kits. Except for one homemade protocol, the majority gave comparable results in terms of the quality of the extracted DNA measured by the ability to amplify differently sized control gene fragments by PCR. For array-applications or tests that require an accurately determined DNA-input, we recommend using silica based adsorption columns for DNA recovery. For RNA extractions, the best results were obtained using chromatography column based commercial kits, which resulted in the highest quantity and best assayable RNA. Quality testing using RT-PCR gave successful amplification of 200 bp-250 bp PCR products from most tested tissues. Modifications of the proteinase-K digestion time led to better results, even when commercial kits were applied. The results of the study emphasize the need for quality control of the nucleic acid extracts with standardised methods to prevent false negative results and to allow data comparison among different diagnostic laboratories.

  9. Nucleic acids and survival of excised anthers in vitro.

    Science.gov (United States)

    VASIL, I K

    1959-05-29

    Excised anthers of Allium cepa and Rhoeo discolor have been successfully cultured in modified White's medium supplemented with various concentrations of ribonucleic acid and deoxyribonucleic acid. Ribonucleic acid proved to be much more useful than deoxyribonucleic acid and reduced the time required for the completion of meiosis from 48 hours to 24 hours. The role of nucleic acids in the control of nuclear divisions has been indicated.

  10. Bioluminescence regenerative cycle (BRC) system for nucleic acid quantification assays

    Science.gov (United States)

    Hassibi, Arjang; Lee, Thomas H.; Davis, Ronald W.; Pourmand, Nader

    2003-07-01

    A new label-free methodology for nucleic acid quantification has been developed where the number of pyrophosphate molecules (PPi) released during polymerization of the target nucleic acid is counted and correlated to DNA copy number. The technique uses the enzymatic complex of ATP-sulfurylase and firefly luciferase to generate photons from PPi. An enzymatic unity gain positive feedback is also implemented to regenerate the photon generation process and compensate any decay in light intensity by self regulation. Due to this positive feedback, the total number of photons generated by the bioluminescence regenerative cycle (BRC) can potentially be orders of magnitude higher than typical chemiluminescent processes. A system level kinetic model that incorporates the effects of contaminations and detector noise was used to show that the photon generation process is in fact steady and also proportional to the nucleic acid quantity. Here we show that BRC is capable of detecting quantities of DNA as low as 1 amol (10-18 mole) in 40μlit aqueous solutions, and this enzymatic assay has a controllable dynamic range of 5 orders of magnitude. The sensitivity of this technology, due to the excess number of photons generated by the regenerative cycle, is not constrained by detector performance, but rather by possible PPi or ATP (adenosine triphosphate) contamination, or background bioluminescence of the enzymatic complex.

  11. Nucleic acid-lipid membrane interactions studied by DSC.

    Science.gov (United States)

    Giatrellis, Sarantis; Nounesis, George

    2011-01-01

    The interactions of nucleic acids with lipid membranes are of great importance for biological mechanisms as well as for biotechnological applications in gene delivery and drug carriers. The optimization of liposomal vectors for clinical use is absolutely dependent upon the formation mechanisms, the morphology, and the molecular organization of the lipoplexes, that is, the complexes of lipid membranes with DNA. Differential scanning calorimetry (DSC) has emerged as an efficient and relatively easy-to-operate experimental technique that can straightforwardly provide data related to the thermodynamics and the kinetics of the DNA-lipid complexation and especially to the lipid organization and phase transitions within the membrane. In this review, we summarize DSC studies considering nucleic acid-membrane systems, accentuating DSC capabilities, and data analysis. Published work involving cationic, anionic, and zwitterionic lipids as well as lipid mixtures interacting with RNA and DNA of different sizes and conformations are included. It is shown that despite limitations, issues such as DNA- or RNA-induced phase separation and microdomain lipid segregation, liposomal aggregation and fusion, alterations of the lipid long-range molecular order, as well as membrane-induced structural changes of the nucleic acids can be efficiently treated by systematic high-sensitivity DSC studies.

  12. Self-assembly of proteins and their nucleic acids

    Directory of Open Access Journals (Sweden)

    Terrett Jon

    2003-01-01

    Full Text Available Abstract We have developed an artificial protein scaffold, herewith called a protein vector, which allows linking of an in-vitro synthesised protein to the nucleic acid which encodes it through the process of self-assembly. This protein vector enables the direct physical linkage between a functional protein and its genetic code. The principle is demonstrated using a streptavidin-based protein vector (SAPV as both a nucleic acid binding pocket and a protein display system. We have shown that functional proteins or protein domains can be produced in vitro and physically linked to their DNA in a single enzymatic reaction. Such self-assembled protein-DNA complexes can be used for protein cloning, the cloning of protein affinity reagents or for the production of proteins which self-assemble on a variety of solid supports. Self-assembly can be utilised for making libraries of protein-DNA complexes or for labelling the protein part of such a complex to a high specific activity by labelling the nucleic acid associated with the protein. In summary, self-assembly offers an opportunity to quickly generate cheap protein affinity reagents, which can also be efficiently labelled, for use in traditional affinity assays or for protein arrays instead of conventional antibodies.

  13. Nucleic acid-lipid membrane interactions studied by DSC

    Directory of Open Access Journals (Sweden)

    Sarantis Giatrellis

    2011-01-01

    Full Text Available The interactions of nucleic acids with lipid membranes are of great importance for biological mechanisms as well as for biotechnological applications in gene delivery and drug carriers. The optimization of liposomal vectors for clinical use is absolutely dependent upon the formation mechanisms, the morphology, and the molecular organization of the lipoplexes, that is, the complexes of lipid membranes with DNA. Differential scanning calorimetry (DSC has emerged as an efficient and relatively easy-to-operate experimental technique that can straightforwardly provide data related to the thermodynamics and the kinetics of the DNA-lipid complexation and especially to the lipid organization and phase transitions within the membrane. In this review, we summarize DSC studies considering nucleic acid-membrane systems, accentuating DSC capabilities, and data analysis. Published work involving cationic, anionic, and zwitterionic lipids as well as lipid mixtures interacting with RNA and DNA of different sizes and conformations are included. It is shown that despite limitations, issues such as DNA- or RNA-induced phase separation and microdomain lipid segregation, liposomal aggregation and fusion, alterations of the lipid long-range molecular order, as well as membrane-induced structural changes of the nucleic acids can be efficiently treated by systematic high-sensitivity DSC studies.

  14. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Science.gov (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit.

  15. Computational design of nucleic acid feedback control circuits.

    Science.gov (United States)

    Yordanov, Boyan; Kim, Jongmin; Petersen, Rasmus L; Shudy, Angelina; Kulkarni, Vishwesh V; Phillips, Andrew

    2014-08-15

    The design of synthetic circuits for controlling molecular-scale processes is an important goal of synthetic biology, with potential applications in future in vitro and in vivo biotechnology. In this paper, we present a computational approach for designing feedback control circuits constructed from nucleic acids. Our approach relies on an existing methodology for expressing signal processing and control circuits as biomolecular reactions. We first extend the methodology so that circuits can be expressed using just two classes of reactions: catalysis and annihilation. We then propose implementations of these reactions in three distinct classes of nucleic acid circuits, which rely on DNA strand displacement, DNA enzyme and RNA enzyme mechanisms, respectively. We use these implementations to design a Proportional Integral controller, capable of regulating the output of a system according to a given reference signal, and discuss the trade-offs between the different approaches. As a proof of principle, we implement our methodology as an extension to a DNA strand displacement software tool, thus allowing a broad range of nucleic acid circuits to be designed and analyzed within a common modeling framework.

  16. Approach to acid-base disorders – a clinical chemistry perspective

    African Journals Online (AJOL)

    Acid-base disorders are frequently encountered in clinical practice and have a significant impact on patient morbidity ... The first step in assessment of the arterial blood gas profile is .... amino acids in hyperalimentation are metabolised to HCl ...

  17. Superior SWNT dispersion by amino acid based amphiphiles: designing biocompatible cationic nanohybrids.

    Science.gov (United States)

    Brahmachari, Sayanti; Das, Dibyendu; Das, Prasanta Kumar

    2010-11-28

    Stable aqueous SWNT dispersion up to 92% was achieved using amino acid based amphiphiles through a structure-property investigation. The nanohybrids showed remarkable serum stability and biocompatibility to mammalian cells.

  18. When acid-base titrations are carried out in unusual conditions

    OpenAIRE

    Domenico De Marco; Rocco De Marco

    2012-01-01

    Uncommon aspects in acid-base titrations are presented, which occur in titrations between both mono- and/or poly-functional acid and bases but are rarely introduced in ordinary analytical chemistry courses.

  19. Acid-Base Chemistry of White Wine: Analytical Characterisation and Chemical Modelling

    OpenAIRE

    Enrico Prenesti; Silvia Berto; Simona Toso; Pier Giuseppe Daniele

    2012-01-01

    A chemical model of the acid-base properties is optimized for each white wine under study, together with the calculation of their ionic strength, taking into account the contributions of all significant ionic species (strong electrolytes and weak one sensitive to the chemical equilibria). Coupling the HPLC-IEC and HPLC-RP methods, we are able to quantify up to 12 carboxylic acids, the most relevant substances responsible of the acid-base equilibria of wine. The analytical concentration of car...

  20. Improving Pharmacy Students' Understanding and Long-term Retention of Acid-Base Chemistry

    OpenAIRE

    Roche, Victoria F.

    2007-01-01

    Despite repeated exposure to the principles underlying the behavior of organic acids and bases in aqueous solution, some pharmacy students remain confused about the topic of acid-base chemistry. Since a majority of organic drug molecules have acid-base character, the ability to predict their reactivity and the extent to which they will ionize in a given medium is paramount to students' understanding of essentially all aspects of drug action in vivo and in vitro. This manuscript presents a med...

  1. Towards bridging the gap between acid-base transporters and neuronal excitability modulation.

    Science.gov (United States)

    Liu, Ying; Chen, Li-Ming

    2014-01-01

    pH homeostasis is a fundamental regulator of the function of the central nervous system. Dysfunction of acid-base transporters often results in disturbance of neuronal excitability. In a latest issue of Journal of Neuroscience, Jones et al. report that increasing intracellular bicarbonate concentration substantially stimulates the excitability of pyramidal neurons from mouse hippocampus by inhibiting KCNQ potassium channel. The finding shed important new light in understanding the molecular mechanism underlying the regulation of neuronal excitability by acid-base transporters.

  2. Relationship between depression score and acid-base status in Japanese Black calves with diarrhea.

    Science.gov (United States)

    Nakagawa, Mitsuhide; Suzuki, Kazuyuki; Taguchi, Kiyoshi

    2007-05-01

    We evaluated the relationship between depression score and acid-base status in 84 purebred and crossbred Japanese Black calves. The bicarbonate (psystem is a useful tool for evaluation of the acid-base status of purebred and crossbred Japanese Black calves. In addition, a depression score of 6.5 suggests severe metabolic acidosis and that intravenous infusion of sodium bicarbonate solution is necessary.

  3. A Clinical Approach to the Diagnosis of Acid-Base Disorders

    OpenAIRE

    1986-01-01

    The ability to diagnose and manage acid-base disorders rapidly and effectively is essential to the care of critically ill patients. This article presents an approach to the diagnosis of pure and mixed acid-base disorders, metabolic or respiratory. The approach taken is based on using the law of mass-action equation as it applies to the bicarbonate buffer system (Henderson equation), using sub-classifications for diagnostic purposes of causes of metabolic acidosis and metabolic alkalosis, and ...

  4. Quantitative acid-base physiology using the Stewart model. Does it improve our understanding of what is really wrong?

    NARCIS (Netherlands)

    Derksen, R.; Scheffer, G.J.; Hoeven, J.G. van der

    2006-01-01

    Traditional theories of acid-base balance are based on the Henderson-Hasselbalch equation to calculate proton concentration. The recent revival of quantitative acid-base physiology using the Stewart model has increased our understanding of complicated acid-base disorders, but has also led to several

  5. Azide-alkyne cycloaddition for universal post-synthetic modifications of nucleic acids and effective synthesis of bioactive nucleic acid conjugates.

    Science.gov (United States)

    Su, Yu-Chih; Lo, Yu-Lun; Hwang, Chi-Ching; Wang, Li-Fang; Wu, Min Hui; Wang, Eng-Chi; Wang, Yun-Ming; Wang, Tzu-Pin

    2014-09-14

    The regioselective post-synthetic modifications of nucleic acids are essential to studies of these molecules for science and applications. Here we report a facile universal approach by harnessing versatile phosphoramidation reactions to regioselectively incorporate alkynyl/azido groups into post-synthetic nucleic acids primed with phosphate at the 5' termini. With and without the presence of copper, the modified nucleic acids were subjected to azide-alkyne cycloaddition to afford various nucleic acid conjugates including a peptide-oligonucleotide conjugate (POC) with high yield. The POC was inoculated with human A549 cells and demonstrated excellent cell-penetrating ability despite cell deformation caused by a small amount of residual copper chelated to the POC. The combination of phosphoramidation and azide-alkyne cycloaddition reactions thus provides a universal regioselective strategy to post-synthetically modify nucleic acids. This study also explicated the toxicity of residual copper in synthesized bioconjugates destined for biological systems.

  6. Metal speciation of historic and new copper mine tailings from Repparfjorden, Northern Norway, before and after acid, base and electrodialytic extraction

    DEFF Research Database (Denmark)

    Pedersen, Kristine B.; Jensen, Pernille Erland; Ottosen, Lisbeth M.

    2017-01-01

    tailings. Substantial desorption (>40%) for both historic and new mine tailings occurred at pH values below 3 and above 12. These results combined with metal speciation, showing that the binding of Cu in the sediment changes around pH values 3 and 10, indicate potential for extraction of more Cu from...... the new mine tailings. Electrodialysis, based on applying an electric field of low intensity to extract metals from polluted soils/sediments, was designed for acidic and alkaline extraction, and in both cases more Cu was extracted than in the pure acid/base extractions, while maintaining low mobilisation...

  7. Nucleic-acid characterization of the identity and activity of subsurface microorganisms

    Science.gov (United States)

    Madsen, E. L.

    Nucleic-acid approaches to characterizing naturally occurring microorganisms in their habitats have risen to prominence during the last decade. Extraction of deoxyribonucleic-acid (DNA) and ribonucleic-acid (RNA) biomarkers directly from environmental samples provides a new means of gathering information in microbial ecology. This review article defines: (1) the subsurface habitat; (2) what nucleic-acid procedures are; and (3) the types of information nucleic-acid procedures can and cannot reveal. Recent literature examining microbial nucleic acids in the terrestrial subsurface is tabulated and reviewed. The majority of effort to date has focused upon insights into the identity and phylogeny of subsurface microorganisms afforded by analysis of their 16S rRNA genes. Given the power of nucleic-acid-based procedures and their limited application to subsurface habitats to date, many future opportunities await exploration. Au cours des derniers dix ans, les approches basées sur les acides nucléiques sont apparues et devenues essentielles pour caractériser dans leurs habitats les microorganismes existant à l'état naturel. L'extraction directe de l'ADN et de l'ARN, qui sont des biomarqueurs, d'échantillons environnementaux a fourni un nouveau moyen d'obtenir des informations sur l'écologie microbienne. Cet article synthétique définit 1) l'habitat souterrain, 2) ce que sont les procédures basées sur les acides nucléiques, 3) quel type d'informations ces procéedures peuvent et ne peuvent pas révéler. Les travaux récemment publiés concernatn les acides nucléiques microbiens dans le milieu souterrain terrestre sont catalogués et passés en revue. La majorité des efforts pour obtenir es données s'est concentrée sur l'identité et la phylogénie des microorganismes souterrains fournies par l'analyse de leurs gènes 16S rRNA. Étant donné la puissance des procédures basées sur les acides nucléiques et leur application limitée aux habitats souterrains

  8. The association between low-grade inflammation, iron status and nucleic acid oxidation in the elderly

    DEFF Research Database (Denmark)

    Broedbaek, Kasper; Siersma, Volkert Dirk; Andersen, Jon T

    2011-01-01

    This study applied a case-control approach to investigate the association between low-grade inflammation, defined by high values within the normal range of C-reactive protein (CRP) and interleukin-6 (IL-6), and urinary markers of nucleic acid oxidation. No differences in excretion of urinary...... markers of nucleic acid oxidation between cases and controls were found and multivariable linear regression analysis showed no association between urinary markers of nucleic acid oxidation and inflammatory markers. Post-hoc multivariable linear regression analysis showed significant associations between...... nucleic acid oxidation and various iron status markers and especially a close relationship between nucleic acid oxidation and ferritin. This study shows no association between low-grade inflammation and urinary markers of nucleic acid oxidation in a population of elderly Italian people. The results...

  9. Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes.

    Science.gov (United States)

    Marras, Salvatore A E; Tyagi, Sanjay; Kramer, Fred Russell

    2006-01-01

    A number of formats for nucleic acid hybridization have been developed to identify DNA and RNA sequences that are involved in cellular processes and that aid in the diagnosis of genetic and infectious diseases. The introduction of hybridization probes with interactive fluorophore pairs has enabled the development of homogeneous hybridization assays for the direct identification of nucleic acids. A change in the fluorescence of these probes indicates the presence of a target nucleic acid, and there is no need to separate unbound probes from hybridized probes. The advantages of homogeneous hybridization assays are their speed and simplicity. In addition, homogeneous assays can be combined with nucleic acid amplification, enabling the detection of rare target nucleic acids. These assays can be followed in real time, providing quantitative determination of target nucleic acids over a broad range of concentrations.

  10. Introduction of structural affinity handles as a tool in selective nucleic acid separations

    Science.gov (United States)

    Willson, III, Richard Coale (Inventor); Cano, Luis Antonio (Inventor)

    2011-01-01

    The method is used for separating nucleic acids and other similar constructs. It involves selective introduction, enhancement, or stabilization of affinity handles such as single-strandedness in the undesired (or desired) nucleic acids as compared to the usual structure (e.g., double-strandedness) of the desired (or undesired) nucleic acids. The undesired (or desired) nucleic acids are separated from the desired (or undesired) nucleic acids due to capture by methods including but not limited to immobilized metal affinity chromatography, immobilized single-stranded DNA binding (SSB) protein, and immobilized oligonucleotides. The invention is useful to: remove contaminating genomic DNA from plasmid DNA; remove genomic DNA from plasmids, BACs, and similar constructs; selectively separate oligonucleotides and similar DNA fragments from their partner strands; purification of aptamers, (deoxy)-ribozymes and other highly structured nucleic acids; Separation of restriction fragments without using agarose gels; manufacture recombinant Taq polymerase or similar products that are sensitive to host genomic DNA contamination; and other applications.

  11. Polylactic Acid-Based Polymer Blends for Durable Applications

    Science.gov (United States)

    Finniss, Adam

    was fully protected by the more stable phase. Lastly, molded parts of differing thicknesses were hydrolytically degraded to examine the effects of diffusion resistance on the mechanical properties of untreated PC/PLA blends. It was determined that, similar to the droplet morphology study, the effect of PC content was the most dominating factor in the durability of the formulations. In fact, if molded parts reach a critical thickness, a transition from ductile to brittle failure modes can be observed. The rate of diffusion through the materials was also determined to be much faster than the rate of PLA hydrolysis. It is concluded that the most effective way to create a durable material containing a significant bio-based content is to completely encapsulate PLA polymer with the more stable polycarbonate phase. Materials containing up to about 30% PLA at maximum were shown to be sufficiently durable so that they may be employed in similar automotive and electrical applications as for pure polycarbonate. (Abstract shortened by UMI.)

  12. Non-viral gene delivery strategies for gene therapy: a 'menage a trois' among nucleic acids, materials, and the biological environment

    Energy Technology Data Exchange (ETDEWEB)

    Pezzoli, Daniele; Candiani, Gabriele, E-mail: gabriele.candiani@polimi.it [INSTM (National Interuniversity Consortium of Materials Science and Technology), Research Unit Milano Politecnico (Italy)

    2013-03-15

    Gene delivery is the science of transferring genetic material into cells by means of a vector to alter cellular function or structure at a molecular level. In this context, a number of nucleic acid-based drugs have been proposed and experimented so far and, as they act on distinct steps along the gene transcription-translation pathway, specific delivery strategies are required to elicit the desired outcome. Cationic lipids and polymers, collectively known as non-viral delivery systems, have thus made their breakthrough in basic and medical research. Albeit they are promising alternatives to viral vectors, their therapeutic application is still rather limited as high transfection efficiencies are normally associated to adverse cytotoxic side effects. In this scenario, drawing inspiration from processes naturally occurring in vivo, major strides forward have been made in the development of more effective materials for gene delivery applications. Specifically, smart vectors sensitive to a variety of physiological stimuli such as cell enzymes, redox status, and pH are substantially changing the landscape of gene delivery by helping to overcome some of the systemic and intracellular barriers that viral vectors naturally evade. Herein, after summarizing the state-of-the-art information regarding the use of nucleic acids as drugs, we review the main bottlenecks still limiting the overall effectiveness of non-viral gene delivery systems. Finally, we provide a critical outline of emerging stimuli-responsive strategies and discuss challenges still existing on the road toward conceiving more efficient and safer multifunctional vectors.

  13. Interaction of nucleic acids with carbon nanotubes and dendrimers.

    Science.gov (United States)

    Nandy, Bidisha; Santosh, Mogurampelly; Maiti, Prabal K

    2012-07-01

    Nucleic acid interaction with nanoscale objects like carbon nanotubes (CNTs) and dendrimers is of fundamental interest because of their potential application in CNT separation, gene therapy and antisense therapy. Combining nucleic acids with CNTs and dendrimers also opens the door towards controllable self-assembly to generate various supra-molecular and nano-structures with desired morphologies. The interaction between these nanoscale objects also serve as a model system for studying DNA compaction, which is a fundamental process in chromatin organization. By using fully atomistic simulations, here we report various aspects of the interactions and binding modes of DNA and small interfering RNA (siRNA) with CNTs, graphene and dendrimers. Our results give a microscopic picture and mechanism of the adsorption of single- and double-strand DNA (ssDNA and dsDNA) on CNT and graphene. The nucleic acid-CNT interaction is dominated by the dispersive van der Waals (vdW) interaction. In contrast, the complexation of DNA (both ssDNA and dsDNA) and siRNA with various generations of poly-amido-amine (PAMAM) dendrimers is governed by electrostatic interactions. Our results reveal that both the DNA and siRNA form stable complex with the PAMAM dendrimer at a physiological pH when the dendrimer is positively charged due to the protonation of the primary amines. The size and binding energy of the complex increase with increase in dendrimer generation. We also give a summary of the current status in these fields and discuss future prospects.

  14. Nucleic acid binding and other biomedical properties of artificial oligolysines

    Directory of Open Access Journals (Sweden)

    Roviello GN

    2016-11-01

    Full Text Available Giovanni N Roviello,1 Caterina Vicidomini,1 Vincenzo Costanzo,1 Valentina Roviello2 1CNR Istituto di Biostrutture e Bioimmagini, Via Mezzocannone site and Headquarters, 2Centro Regionale di Competenza (CRdC Tecnologie, Via Nuova Agnano, Napoli, Italy Abstract: In the present study, we report the interaction of an artificial oligolysine (referred to as AOL realized in our laboratory with targets of biomedical importance. These included polyinosinic acid (poly rI and its complex with polycytidylic acid (poly I:C, RNAs with well-known interferon-inducing ability, and double-stranded (ds DNA. The ability of the peptide to bind both single-stranded poly rI and ds poly I:C RNAs emerged from our circular dichroism (CD and ultraviolet (UV studies. In addition, we found that AOL forms complexes with dsDNA, as shown by spectroscopic binding assays and UV thermal denaturation experiments. These findings are encouraging for the possible use of AOL in biomedicine for nucleic acid targeting and oligonucleotide condensation, with the latter being a key step preceding their clinical application. Moreover, we tested the ability of AOL to bind to proteins, using serum albumin as a model protein. We demonstrated the oligolysine–protein binding by CD experiments which suggested that AOL, positively charged under physiological conditions, binds to the protein regions rich in anionic residues. Finally, the morphology characterization of the solid oligolysine, performed by scanning electron microscopy, showed different crystal forms including cubic-shaped crystals confirming the high purity of AOL. Keywords: nucleic acid binding, polyinosinic acid, double-stranded nucleic acids, oligolysine, circular dichroism

  15. Interaction of nucleic acids with carbon nanotubes and dendrimers

    Indian Academy of Sciences (India)

    Bidisha Nandy; Mogurampelly Santosh; Prabal K Maiti

    2012-07-01

    Nucleic acid interaction with nanoscale objects like carbon nanotubes (CNTs) and dendrimers is of fundamental interest because of their potential application in CNT separation, gene therapy and antisense therapy. Combining nucleic acids with CNTs and dendrimers also opens the door towards controllable self-assembly to generate various supra-molecular and nano-structures with desired morphologies. The interaction between these nanoscale objects also serve as a model system for studying DNA compaction, which is a fundamental process in chromatin organization. By using fully atomistic simulations, here we report various aspects of the interactions and binding modes of DNA and small interfering RNA (siRNA) with CNTs, graphene and dendrimers. Our results give a microscopic picture and mechanism of the adsorption of single- and double-strand DNA (ssDNA and dsDNA) on CNT and graphene. The nucleic acid–CNT interaction is dominated by the dispersive van der Waals (vdW) interaction. In contrast, the complexation of DNA (both ssDNA and dsDNA) and siRNA with various generations of poly-amido-amine (PAMAM) dendrimers is governed by electrostatic interactions. Our results reveal that both the DNA and siRNA form stable complex with the PAMAM dendrimer at a physiological pH when the dendrimer is positively charged due to the protonation of the primary amines. The size and binding energy of the complex increase with increase in dendrimer generation. We also give a summary of the current status in these fields and discuss future prospects.

  16. Ion-mediated nucleic acid helix-helix interactions.

    Science.gov (United States)

    Tan, Zhi-Jie; Chen, Shi-Jie

    2006-07-15

    Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free-energy landscape for two parallel nucleic acid helices in the solution of added salt. The theory is based on realistic atomic structures of the helices. In monovalent salt, the helices are predicted to repel each other. For divalent salt, while the mean-field Poisson-Boltzmann theory predicts only the repulsion, the TBI theory predicts an effective attraction between the helices. The helices are predicted to be stabilized at an interhelix distance approximately 26-36 A, and the strength of the attractive force can reach -0.37 k(B)T/bp for helix length in the range of 9-12 bp. Both the stable helix-helix distance and the strength of the attraction are strongly dependent on the salt concentration and ion size. With the increase of the salt concentration, the helix-helix attraction becomes stronger and the most stable helix-helix separation distance becomes smaller. For divalent ions, at very high ion concentration, further addition of ions leads to the weakening of the attraction. Smaller ion size causes stronger helix-helix attraction and stabilizes the helices at a shorter distance. In addition, the TBI model shows that a decrease in the solvent dielectric constant would enhance the ion-mediated attraction. The theoretical findings from the TBI theory agree with the experimental measurements on the osmotic pressure of DNA array as well as the results from the computer simulations.

  17. Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays

    OpenAIRE

    Yingfu Li; Wendy Mok

    2008-01-01

    As the key constituents of the genetic code, the importance of nucleic acids to life has long been appreciated. Despite being composed of only four structurally similar nucleotides, single-stranded nucleic acids, as in single-stranded DNAs and RNAs, can fold into distinct three-dimensional shapes due to specific intramolecular interactions and carry out functions beyond serving as templates for protein synthesis. These functional nucleic acids (FNAs) can catalyze chemical reactions, regulate ...

  18. Nucleic acid constructs containing orthogonal site selective recombinases (OSSRs)

    Energy Technology Data Exchange (ETDEWEB)

    Gilmore, Joshua M.; Anderson, J. Christopher; Dueber, John E.

    2017-08-29

    The present invention provides for a recombinant nucleic acid comprising a nucleotide sequence comprising a plurality of constructs, wherein each construct independently comprises a nucleotide sequence of interest flanked by a pair of recombinase recognition sequences. Each pair of recombinase recognition sequences is recognized by a distinct recombinase. Optionally, each construct can, independently, further comprise one or more genes encoding a recombinase capable of recognizing the pair of recombinase recognition sequences of the construct. The recombinase can be an orthogonal (non-cross reacting), site-selective recombinase (OSSR).

  19. Kinetic Monte Carlo method applied to nucleic acid hairpin folding.

    Science.gov (United States)

    Sauerwine, Ben; Widom, Michael

    2011-12-01

    Kinetic Monte Carlo on coarse-grained systems, such as nucleic acid secondary structure, is advantageous for being able to access behavior at long time scales, even minutes or hours. Transition rates between coarse-grained states depend upon intermediate barriers, which are not directly simulated. We propose an Arrhenius rate model and an intermediate energy model that incorporates the effects of the barrier between simulated states without enlarging the state space itself. Applying our Arrhenius rate model to DNA hairpin folding, we demonstrate improved agreement with experiment compared to the usual kinetic Monte Carlo model. Further improvement results from including rigidity of single-stranded stacking.

  20. Loop-mediated isothermal amplification for detection of nucleic acids.

    Science.gov (United States)

    Tanner, Nathan A; Evans, Thomas C

    2014-01-06

    Sequence-specific isothermal nucleic acid amplification techniques are ideally suited for use in molecular diagnostic applications because they do not require thermal cycling equipment and the reactions are typically fast. One of the most widely cited isothermal techniques is termed loop-mediated isothermal amplification (LAMP). This protocol allows amplification times as fast as 5 to 10 min. Furthermore, various methodologies to detect amplification have been applied to LAMP to increase its utility for the point-of-care market. Basic LAMP protocols are provided herein for detection of specific DNA and RNA targets, along with a method to perform multiplex LAMP reactions, permitting even greater flexibility from this powerful technique.

  1. Pyrene intercalating nucleic acids with a carbon linker.

    Science.gov (United States)

    Østergaard, Michael E; Wamberg, Michael C; Pedersen, Erik B

    2011-03-01

    We have synthesized a carbon linker analogue of INA (oligonucleotides containing insertions of 1-O-(1-pyrenylmethyl)glycerol). Thermal stability studies showed an increase in melting temperature in favor of the carbon linker analogue. We also synthesized a carbon linker analogue with two pyrenes geminally attached. Fluorescence studies of this intercalating nucleic acid with the pyrene moieties inserted as a bulge showed formation of an excimer band. When a mismatch was introduced at the site of the intercalator, an excimer band was formed for the destabilized duplexes whereas an exciplex band was observed when the stability of the duplex was retained.

  2. DNA-like double helix formed by peptide nucleic acid

    DEFF Research Database (Denmark)

    Wittung, P; Nielsen, Peter E.; Buchardt, O;

    1994-01-01

    Although the importance of the nucleobases in the DNA double helix is well understood, the evolutionary significance of the deoxyribose phosphate backbone and the contribution of this chemical entity to the overall helical structure and stability of the double helix is not so clear. Peptide nucleic...... acid (PNA) is a DNA analogue with a backbone consisting of N-(2-aminoethyl)glycine units (Fig. 1) which has been shown to mimic DNA in forming Watson-Crick complementary duplexes with normal DNA. Using circular dichroism spectroscopy we show here that two complementary PNA strands can hybridize to one...

  3. Electrostatic free energy landscapes for nucleic acid helix assembly

    OpenAIRE

    Tan, Zhi-Jie; Chen, Shi-Jie

    2006-01-01

    Metal ions are crucial for nucleic acid folding. From the free energy landscapes, we investigate the detailed mechanism for ion-induced collapse for a paradigm system: loop-tethered short DNA helices. We find that Na + and Mg2+ play distinctive roles in helix–helix assembly. High [Na+] (>0.3 M) causes a reduced helix–helix electrostatic repulsion and a subsequent disordered packing of helices. In contrast, Mg2+ of concentration >1 mM is predicted to induce helix–helix attraction and results i...

  4. Electrolyte and Acid-Base Disturbances in End-Stage Liver Disease: A Physiopathological Approach.

    Science.gov (United States)

    Jiménez, José Víctor; Carrillo-Pérez, Diego Luis; Rosado-Canto, Rodrigo; García-Juárez, Ignacio; Torre, Aldo; Kershenobich, David; Carrillo-Maravilla, Eduardo

    2017-08-01

    Electrolyte and acid-base disturbances are frequent in patients with end-stage liver disease; the underlying physiopathological mechanisms are often complex and represent a diagnostic and therapeutic challenge to the physician. Usually, these disorders do not develop in compensated cirrhotic patients, but with the onset of the classic complications of cirrhosis such as ascites, renal failure, spontaneous bacterial peritonitis and variceal bleeding, multiple electrolyte, and acid-base disturbances emerge. Hyponatremia parallels ascites formation and is a well-known trigger of hepatic encephalopathy; its management in this particular population poses a risky challenge due to the high susceptibility of cirrhotic patients to osmotic demyelination. Hypokalemia is common in the setting of cirrhosis: multiple potassium wasting mechanisms both inherent to the disease and resulting from its management make these patients particularly susceptible to potassium depletion even in the setting of normokalemia. Acid-base disturbances range from classical respiratory alkalosis to high anion gap metabolic acidosis, almost comprising the full acid-base spectrum. Because most electrolyte and acid-base disturbances are managed in terms of their underlying trigger factors, a systematic physiopathological approach to their diagnosis and treatment is required.

  5. Boron and nucleic acid chemistries: merging the best of both worlds.

    Science.gov (United States)

    Martin, Anthony R; Vasseur, Jean-Jacques; Smietana, Michael

    2013-07-07

    At the intersection of nucleic acid and boron chemistries lies a thriving world of possibilities. During the past decades, the merging of these research domains has led to fascinating discoveries in different fields ranging from material to medical sciences. In recent years the interplay of these two worlds has gained a lot of attention, as can be judged by the increasing number of articles in which boron and nucleic acids stand out for their potential medicinal, biotechnological or analytical applications. In this review, we present an outline of this crossroads by focusing on both the interaction of boronated compounds with nucleic acids and the modification of nucleic acids by boron containing moieties.

  6. Prefibrillar Tau oligomers alter the nucleic acid protective function of Tau in hippocampal neurons in vivo.

    Science.gov (United States)

    Violet, Marie; Chauderlier, Alban; Delattre, Lucie; Tardivel, Meryem; Chouala, Meliza Sendid; Sultan, Audrey; Marciniak, Elodie; Humez, Sandrine; Binder, Lester; Kayed, Rakez; Lefebvre, Bruno; Bonnefoy, Eliette; Buée, Luc; Galas, Marie-Christine

    2015-10-01

    The accumulation of DNA and RNA oxidative damage is observed in cortical and hippocampal neurons from Alzheimer's disease (AD) brains at early stages of pathology. We recently reported that Tau is a key nuclear player in the protection of neuronal nucleic acid integrity in vivo under physiological conditions and hyperthermia, a strong inducer of oxidative stress. In a mouse model of tauopathy (THY-Tau22), we demonstrate that hyperthermia selectively induces nucleic acid oxidative damage and nucleic acid strand breaks in the nucleus and cytoplasm of hippocampal neurons that display early Tau phosphorylation but no Tau fibrils. Nucleic acid-damaged neurons were exclusively immunoreactive for prefibrillar Tau oligomers. A similar association between prefibrillar Tau oligomers and nucleic acid oxidative damage was observed in AD brains. Pretreatment with Methylene Blue (MB), a Tau aggregation inhibitor and a redox cycler, reduced hyperthermia-induced Tau oligomerization as well as nucleic acid damage. This study clearly highlights the existence of an early and critical time frame for hyperthermia-induced Tau oligomerization, which most likely occurs through increased oxidative stress, and nucleic acid vulnerability during the progression of Tau pathology. These results suggest that at early stages of AD, Tau oligomerization triggers the loss of the nucleic acid protective function of monomeric Tau. This study highlights the existence of a short therapeutic window in which to prevent the formation of pathological forms of Tau and their harmful consequences on nucleic acid integrity during the progression of Tau pathology. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Oxalic acid based chemical systems for electrochemical mechanical planarization of copper

    Science.gov (United States)

    Lowalekar, Viral Pradeep

    In an ECMP process, a wafer is anodically baised during polishing. The electrical potential is the driving force to oxidize copper metal to ions. Copper ions then react with chemistry in the electrolyte to go in solution or form a passivation layer on the surface. The passivation layer is removed by a very low downforce (0.5--1 psi), causing copper to electrochemically dissolve in solution. Passive film formation during copper ECMP is key to the success of this process, since passivation reduces dissolution in the recessed areas, while elevations on the copper surface in direct contact with the ECMP pad are electrochemically planarized. If no passive film forms, then copper removal will be conformal from the elevated and recessed areas, and planarity will be lost. Chemical formulations for the electrochemical mechanical planarization (ECMP) of copper must contain constituents that are stable at anodic potentials. A key component of the formulation is a corrosion inhibitor, which is required to protect low lying areas while higher areas are selectively removed. Organic compounds, which adsorb on copper at low overpotentials and form a film by oxidation at higher overpotentials, may be particularly useful for ECMP. The main goal of the research reported in this dissertation is to understand and develop oxalic acid-based chemical systems suitable for ECMP of copper through electrochemical and surface investigations. Special attention was paid to the development of an inhibitor, which can function under applied potential conditions. Physical methods such as profilometry and four point probe were used to obtain copper removal rates. An organic compound, thiosalicylic acid (TSA), was identified and tested as a potential corrosion inhibitor for copper. TSA offers better protection than the conventionally used benzotriazole (BTA) by oxidizing at high anodic potentials to form a passive film on the copper surface. The passive film formed on the copper surface by addition of

  8. Rhizosphere bacterial carbon turnover is higher in nucleic acids than membrane lipids: implications for understanding soil carbon cycling

    Directory of Open Access Journals (Sweden)

    Ashish A. Malik

    2015-04-01

    Full Text Available Using a pulse-chase 13CO2 plant labeling experiment we compared the flow of plant carbon into macromolecular fractions of root-associated soil microorganisms. Time dependent 13C dilution patterns in microbial cellular fractions were used to calculate their turnover time. The turnover times of microbial biomolecules were found to vary: microbial RNA (19 h and DNA (30 h turned over fastest followed by chloroform fumigation extraction-derived soluble cell lysis products (14 d, while phospholipid fatty acids (PLFAs had the slowest turnover (42 d. PLFA/NLFA 13C analyses suggest that both mutualistic arbuscular mycorrhizal and saprophytic fungi are dominant in initial plant carbon uptake. In contrast, high initial 13C enrichment in RNA hints at bacterial importance in initial C uptake due to the dominance of bacterial derived RNA in total extracts of soil RNA. To explain this discrepancy, we observed low renewal rate of bacterial lipids, which may therefore bias lipid fatty acid based interpretations of the role of bacteria in soil microbial food webs. Based on our findings, we question current assumptions regarding plant-microbe carbon flux and suggest that the rhizosphere bacterial contribution to plant assimilate uptake could be higher. This highlights the need for more detailed quantitative investigations with nucleic acid biomarkers to further validate these findings.

  9. Electricity Customers

    Science.gov (United States)

    This page discusses key sectors and how they use electricity. Residential, commercial, and industrial customers each account for roughly one-third of the nation’s electricity use. The transportation sector also accounts for a small fraction of electricity.

  10. Learning in constructivist environments: a research based on the acid-base subject

    Directory of Open Access Journals (Sweden)

    Vera Gouveia

    2004-08-01

    Full Text Available This communication intends to show as a constructivist environment permits a better learning of some concepts related to the acid-base subject, where generally students have some misconceptions at the beginning, as many researches had proved. Based on a long epistemological, psychological and educational reflection, supported by a wide bibliographical research and our own experience, we make some considerations about learning constructivist environments in the classroom, emphasising the cooperative work of students. In the second part, the effects produced in the teaching of the acid-base by such kind of environment are described, according a quasi-experimental study involving 52 students in their 10th year of education, distributed by two equivalent groups, taught by the same teacher. The results indicate clearly that the constructivist environment promoted a better learning of the acid-base subject, as well as improved the educational relationship in the classroom. Furthermore, the students developed positive attitudes regarding themselves and the others.

  11. Absorption, fluorescence, and acid-base equilibria of rhodamines in micellar media of sodium dodecyl sulfate

    Science.gov (United States)

    Obukhova, Elena N.; Mchedlov-Petrossyan, Nikolay O.; Vodolazkaya, Natalya A.; Patsenker, Leonid D.; Doroshenko, Andrey O.; Marynin, Andriy I.; Krasovitskii, Boris M.

    2017-01-01

    Rhodamine dyes are widely used as molecular probes in different fields of science. The aim of this paper was to ascertain to what extent the structural peculiarities of the compounds influence their absorption, emission, and acid-base properties under unified conditions. The acid-base dissociation (HR+ ⇄ R + H+) of a series of rhodamine dyes was studied in sodium n-dodecylsulfate micellar solutions. In this media, the form R exists as a zwitterion R±. The indices of apparent ionization constants of fifteen rhodamine cations HR+ with different substituents in the xanthene moiety vary within the range of pKaapp = 5.04 to 5.53. The distinct dependence of emission of rhodamines bound to micelles on pH of bulk water opens the possibility of using them as fluorescent interfacial acid-base indicators.

  12. Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology

    Directory of Open Access Journals (Sweden)

    Cecilia R. Chambers

    2015-01-01

    Full Text Available With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information on in vitro activities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments. We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase from Pyrococcus furiosus and the RNA ligase from Methanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area.

  13. Design Considerations for RNA Spherical Nucleic Acids (SNAs).

    Science.gov (United States)

    Barnaby, Stacey N; Perelman, Grant A; Kohlstedt, Kevin L; Chinen, Alyssa B; Schatz, George C; Mirkin, Chad A

    2016-09-21

    Ribonucleic acids (RNAs) are key components in many cellular processes such as cell division, differentiation, growth, aging, and death. RNA spherical nucleic acids (RNA-SNAs), which consist of dense shells of double-stranded RNA on nanoparticle surfaces, are powerful and promising therapeutic modalities because they confer advantages over linear RNA such as high cellular uptake and enhanced stability. Due to their three-dimensional shell of oligonucleotides, SNAs, in comparison to linear nucleic acids, interact with the biological environment in unique ways. Herein, the modularity of the RNA-SNA is used to systematically study structure-function relationships in order to understand how the oligonucleotide shell affects interactions with a specific type of biological environment, namely, one that contains serum nucleases. We use a combination of experiment and theory to determine the key architectural properties (i.e., sequence, density, spacer moiety, and backfill molecule) that affect how RNA-SNAs interact with serum nucleases. These data establish a set of design parameters for SNA architectures that are optimized in terms of stability.

  14. Non-enzymatic depurination of nucleic acids: factors and mechanisms.

    Directory of Open Access Journals (Sweden)

    Ran An

    Full Text Available Depurination has attracted considerable attention since a long time for it is closely related to the damage and repair of nucleic acids. In the present study, depurination using a pool of 30-nt short DNA pieces with various sequences at diverse pH values was analyzed by High Performance Liquid Chromatography (HPLC. Kinetic analysis results showed that non-enzymatic depurination of oligodeoxynucleotides exhibited typical first-order kinetics, and its temperature dependence obeyed Arrhenius' law very well. Our results also clearly showed that the linear relationship between the logarithms of rate constants and pH values had a salient point around pH 2.5. Interestingly and unexpectedly, depurination depended greatly on the DNA sequences. The depurination of poly (dA was found to be extremely slow, and thymine rich sequences depurinated faster than other sequences. These results could be explained to some extent by the protonation of nucleotide bases. Moreover, two equations were obtained based on our data for predicting the rate of depurination under various conditions. These results provide basic data for gene mutagenesis and nucleic acids metabolism in acidic gastric juice and some acidic organelles, and may also help to rectify some misconceptions about depurination.

  15. Nucleic Acid-Peptide Complex Phase Controlled by DNA Hybridization

    Science.gov (United States)

    Vieregg, Jeffrey; Lueckheide, Michael; Leon, Lorraine; Marciel, Amanda; Tirrell, Matthew

    When polyanions and polycations are mixed, counterion release drives formation of polymer-rich complexes that can either be solid (precipitates) or liquid (coacervates) depending on the properties of the polyelectrolytes. These complexes are important in many fields, from encapsulation of industrial polymers to membrane-free segregation of biomolecules such as nucleic acids and proteins. Condensation of long double-stranded DNA has been studied for several decades, but comparatively little attention has been paid to the polyelectrolyte behavior of oligonucleotides. We report here studies of DNA oligonucleotides (10 - 88 nt) complexed with polylysine (10 - 100 aa). Unexpectedly, we find that the phase of the resulting complexes is controlled by the hybridization state of the nucleic acid, with double-stranded DNA forming precipitates and single-stranded DNA forming coacervates. Stability increases with polyelectrolyte length and decreases with solution salt concentration, with complexes of the longer double-stranded polymers undergoing precipitate/coacervate/soluble transitions as ionic strength is increased. Mixing coacervates formed by complementary single-stranded oligonucleotides results in precipitate formation, raising the possibility of stimulus-responsive material design.

  16. Fast hybridization solution for the detection of immobilized nucleic acids.

    Science.gov (United States)

    Yang, T T; Kain, S R

    1995-03-01

    We have developed a fast hybridization solution, termed ExpressHyb, for the rapid and sensitive detection of nucleic acids immobilized on membrane supports. This solution reduces typical hybridization times of 12-24 h to as little as 1 h while simultaneously increasing the sensitivity of detection in many applications. Using ExpressHyb, human beta-actin mRNA was detected on a human multiple tissue Northern (MTN) blot following a 30-min hybridization, with optimal detection occurring with a 1-h hybridization interval. The moderately abundant human glyceraldehyde-3-phosphate dehydrogenase (G3PDH) mRNA was detected using similar hybridization conditions and yielded improved signal-to-background characteristics relative to overnight hybridizations in conventional solutions. ExpressHyb can be used with either 32P- or digoxigenin-labeled probes and works effectively with both cDNA and oligonucleotide probes. For non-isotopic detection in particular, ExpressHyb reduces the nonspecific background commonly encountered with this technique. In cDNA library screening, ExpressHyb was found to both reduce the time required for effective hybridizations and to increase the number of positive colonies obtained relative to conventional overnight procedures. Taken together, these results illustrate the broad capability of ExpressHyb Hybridization Solution to improve nucleic acid detection in a variety of important techniques.

  17. 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.

  18. Nucleic Acid Drugs for Prevention of Cardiac Rejection

    Directory of Open Access Journals (Sweden)

    Jun-ichi Suzuki

    2009-01-01

    Full Text Available Heart transplantation has been broadly performed in humans. However, occurrence of acute and chronic rejection has not yet been resolved. Several inflammatory factors, such as cytokines and adhesion molecules, enhance the rejection. The graft arterial disease (GAD, which is a type of chronic rejection, is characterized by intimal thickening comprised of proliferative smooth muscle cells. Specific treatments that target the attenuation of acute rejection and GAD formation have not been well studied in cardiac transplantation. Recent progress in the nucleic acid drugs, such as antisense oligodeoxynucleotides (ODNs to regulate the transcription of disease-related genes, has important roles in therapeutic applications. Transfection of cis-element double-stranded DNA, named as “decoy,” has been also reported to be a useful nucleic acid drug. This decoy strategy has been not only a useful method for the experimental studies of gene regulation but also a novel clinical strategy. In this paper, we reviewed the experimental results of NF-κB, E2F, AP-1, and STAT-1 decoy and other ODNs using the experimental heart transplant models.

  19. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.

    Science.gov (United States)

    Derr, Julien; Manapat, Michael L; Rajamani, Sudha; Leu, Kevin; Xulvi-Brunet, Ramon; Joseph, Isaac; Nowak, Martin A; Chen, Irene A

    2012-05-01

    During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

  20. Foamy Virus Protein—Nucleic Acid Interactions during Particle Morphogenesis

    Science.gov (United States)

    Hamann, Martin V.; Lindemann, Dirk

    2016-01-01

    Compared with orthoretroviruses, our understanding of the molecular and cellular replication mechanism of foamy viruses (FVs), a subfamily of retroviruses, is less advanced. The FV replication cycle differs in several key aspects from orthoretroviruses, which leaves established retroviral models debatable for FVs. Here, we review the general aspect of the FV protein-nucleic acid interactions during virus morphogenesis. We provide a summary of the current knowledge of the FV genome structure and essential sequence motifs required for RNA encapsidation as well as Gag and Pol binding in combination with details about the Gag and Pol biosynthesis. This leads us to address open questions in FV RNA engagement, binding and packaging. Based on recent findings, we propose to shift the point of view from individual glycine-arginine-rich motifs having functions in RNA interactions towards envisioning the FV Gag C-terminus as a general RNA binding protein module. We encourage further investigating a potential new retroviral RNA packaging mechanism, which seems more complex in terms of the components that need to be gathered to form an infectious particle. Additional molecular insights into retroviral protein-nucleic acid interactions help us to develop safer, more specific and more efficient vectors in an era of booming genome engineering and gene therapy approaches. PMID:27589786

  1. Design, preparation and application of nucleic acid delivery carriers.

    Science.gov (United States)

    Yang, Jun; Liu, Hongmei; Zhang, Xin

    2014-01-01

    Gene delivery vectors must deliver their cargoes into the cytosol or the nucleus, where DNA or siRNA functions in vivo. Therefore it is crucial for the rational design of the nucleic acid delivery carriers. Compared with viral vectors, non-viral vectors have overcome some fatal defections in gene therapy. Whereas the most important issue for the non-viral vectors is the low transfection efficiency, which hinders the progress of non-viral carriers. Sparked by the structures of the virus and understanding of the process of virus infection, various biomimic structures of non-viral carriers were designed and prepared to improve the transfection issues in vitro and in vivo. However, less impressive results are achieved. In this review, we will investigate the evolution of the virus-mimicking carriers of nucleic acids for gene therapy, especially in cancer therapy; explore and discuss the relationship between the structures, materials and functions of the carriers, to provide guidance for establishing safe and highly efficient non-viral carriers for gene therapy. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Acid-base regulation in tadpoles of Rana catesbeiana exposed to environmental hypercapnia

    DEFF Research Database (Denmark)

    Busk, Morten; Larsen, Erik Hviid; Jensen, Frank B.

    1997-01-01

    Tadpoles of Rana catesbeiana were exposed to different levels of environmental hypercapnia. The acid-base regulatory response differed from that in adult amphibians in showing a high degree of pH compensation in the extracellular fluid (65-85%) and complete compensation in the intracellular fluid......). It is suggested that the large bicarbonate efflux from the animal is a consequence of the dissolution of CaCO3 stores and the delayed adjustment of bicarbonate-retaining mechanisms. Re-exposure of tadpoles to hypercapnia after 1-3 weeks of normocapnic recovery only affected transepithelial fluxes of acid-base...

  3. Studies on synthesis and property of novel acid-base proton exchange membranes

    Institute of Scientific and Technical Information of China (English)

    Yong Fang Liang; Hai Yan Pan; Xiu Ling Zhu; Yao Xia Zhang; Xi Gao Jian

    2007-01-01

    Sulfonated poly(phthalazinone)s (SPPENK, SPPESK and SPPBEK) were prepared by direct polymerization reaction from sulfonated monomers. The novel acid-base membranes were composed of sulfonated polymers as the acidic compounds, and polyetherimide (PEI) as the basic compounds, casting from their N-methylpyrrolidone (NMP) solution directly onto clean glass plates at 60 ℃ aiming at enhancing membrane toughness and other relative properties. The resulted acid-base composite membranes had excellent resistance to swelling, thermo-stability, hydrolysis resistance and oxidative resistance properties with highly ion-exchange capacity (IEC).

  4. Direct measurement of acid-base interaction energy at solid interfaces.

    Science.gov (United States)

    Kurian, Anish; Prasad, Shishir; Dhinojwala, Ali

    2010-12-07

    We have studied acid-base interactions at solid-liquid and solid-solid interfaces using interface-sensitive sum frequency generation (SFG) spectroscopy. The shift of the sapphire hydroxyl peak in contact with several polar and nonpolar liquids and polymers was used to determine the interaction energy. The trend in the interaction energies cannot be explained by measuring only water contact angles. Molecular rearrangements at the sapphire interface, to maximize the interaction of the acid-base groups, play a dominant role, and these effects are not accounted for in the current theoretical models. These results provide important insights into understanding adhesion, friction, and wetting on solid interfaces.

  5. A transition metal Lewis acid/base triad system for cooperative substrate binding.

    Science.gov (United States)

    Tutusaus, Oscar; Ni, Chengbao; Szymczak, Nathaniel K

    2013-03-06

    A frustrated Lewis pair accessory functionality is positioned in the secondary coordination sphere of a terpyridine ligand (Tpy(BN) = 6-morpholino-2,2':6',2″-terpyridine-6″-boronic acid pinacol ester) to promote directed Lewis acid/base interactions. Following metalation with VCl3, the utility of the metal Lewis acid/base triad (LABT) is highlighted with N2H4 as a cooperatively coordinated substrate, affording the first η(2)-[N2H3](-) vanadium complex.

  6. Neurologic presentations of acid-base imbalance, electrolyte abnormalities, and endocrine emergencies.

    Science.gov (United States)

    Yee, Alan H; Rabinstein, Alejandro A

    2010-02-01

    Accurate identification of nervous system dysfunction is vital in the assessment of any multisystem disorder. The neurologic manifestations of acid-base disturbances, abnormal electrolyte concentrations, and acute endocrinopathies are protean and typically determined by the acuity of the underlying derangement. Detailed history and physical examination may guide appropriate laboratory testing and lead to prompt and accurate diagnosis. Neurologic manifestations of primary and secondary systemic disorders are frequently encountered in all subspecialties of medicine. This article focuses on key neurologic presentations of respiratory and metabolic acid-base derangements and potentially life-threatening endocrinopathies.

  7. A knowledge based advisory system for acid/base titrations in non-aqueous solvents

    OpenAIRE

    1996-01-01

    A computer program was developed that could advice on the choice of solvent and titrant for acid/base titrations in nonaqueous media. It is shown that the feasibility of a titration in a given solvent can be calculated from solvent properties and intrinsic acid/base properties of the sample components. A consistent set of properties for various solvents and a large number of acidic and basic compounds was calculated from literature data with the use of a genetic algorithm. Test results show t...

  8. Essentials in the diagnosis of acid-base disorders and their high altitude application.

    Science.gov (United States)

    Paulev, P E; Zubieta-Calleja, G R

    2005-09-01

    This report describes the historical development in the clinical application of chemical variables for the interpretation of acid-base disturbances. The pH concept was already introduced in 1909. Following World War II, disagreements concerning the definition of acids and bases occurred, and since then two strategies have been competing. Danish scientists in 1923 defined an acid as a substance able to give off a proton at a given pH, and a base as a substance that could bind a proton, whereas the North American Singer-Hasting school in 1948 defined acids as strong non-buffer anions and bases as non-buffer cations. As a consequence of this last definition, electrolyte disturbances were mixed up with real acid-base disorders and the variable, strong ion difference (SID), was introduced as a measure of non-respiratory acid-base disturbances. However, the SID concept is only an empirical approximation. In contrast, the Astrup/Siggaard-Andersen school of scientists, using computer strategies and the Acid-base Chart, has made diagnosis of acid-base disorders possible at a glance on the Chart, when the data are considered in context with the clinical development. Siggaard-Andersen introduced Base Excess (BE) or Standard Base Excess (SBE) in the extracellular fluid volume (ECF), extended to include the red cell volume (eECF), as a measure of metabolic acid-base disturbances and recently replaced it by the term Concentration of Titratable Hydrogen Ion (ctH). These two concepts (SBE and ctH) represent the same concentration difference, but with opposite signs. Three charts modified from the Siggaard-Andersen Acid-Base Chart are presented for use at low, medium and high altitudes of 2500 m, 3500 m, and 4000 m, respectively. In this context, the authors suggest the use of Titratable Hydrogen Ion concentration Difference (THID) in the extended extracellular fluid volume, finding it efficient and better than any other determination of the metabolic component in acid-base

  9. [Disorders of the acid-base balance and the anion gap].

    Science.gov (United States)

    Kimmel, Martin; Alscher, Mark Dominik

    2016-10-01

    The regulation of the acid-base balance and pH is critical for the organism. The most important buffer system is CO2 / HCO3(-). The kidney controls systemic bicarbonate and therefore the metabolic regulation and the lung is relevant for respiratory regulation by an effective CO2 elimination. There are four acid-base disorders with two metabolic and two respiratory disorders (acidosis and alkalosis). The anion gap enables a further workup of metabolic acidosis. © Georg Thieme Verlag KG Stuttgart · New York.

  10. Mobile Clinical Decision Support System for Acid-base Balance Diagnosis and Treatment Recommendation.

    Science.gov (United States)

    Mandzuka, Mensur; Begic, Edin; Boskovic, Dusanka; Begic, Zijo; Masic, Izet

    2017-06-01

    This paper presents mobile application implementing a decision support system for acid-base disorder diagnosis and treatment recommendation. The application was developed using the official integrated development environment for the Android platform (to maximize availability and minimize investments in specialized hardware) called Android Studio. The application identifies disorder, based on the blood gas analysis, evaluates whether the disorder has been compensated, and based on additional input related to electrolyte imbalance, provides recommendations for treatment. The application is a tool in the hands of the user, which provides assistance during acid-base disorders treatment. The application will assist the physician in clinical practice and is focused on the treatment in intensive care.

  11. JAWS: Just Add Water System - A device for detection of nucleic acids in Martian ice caps

    DEFF Research Database (Denmark)

    Hansen, Anders J.; Willerslev, Eske; Mørk, Søren

    2002-01-01

    The design of a device for nucleic acid detection in the Martian ice caps is presented; the Just Add Water System (JAWS). It is based on fiber-optic PNA (peptide nucleic acid) light up probe random microsphere universal array technology. JAWS is designed to be part of a larger system with a regul...

  12. Apparatus for point-of-care detection of nucleic acid in a sample

    Science.gov (United States)

    Bearinger, Jane P.; Dugan, Lawrence C.

    2016-04-19

    Provided herein are methods and apparatus for detecting a target nucleic acid in a sample and related methods and apparatus for diagnosing a condition in an individual. The condition is associated with presence of nucleic acid produced by certain pathogens in the individual.

  13. Mesoporous Silica Nanoparticles as Carriers for Intracellular Delivery of Nucleic Acids and Subsequent Therapeutic Applications

    Directory of Open Access Journals (Sweden)

    Wenzhang Cha

    2017-05-01

    Full Text Available Nucleic acids, including DNA, microRNA (miRNA, small interfering RNA (siRNA, and antisense oligonucleotide (ASO, are powerful gene regulators, which have been demonstrated as promising drug candidates for therapeutic treatments. Nevertheless, poor cellular membrane permeability and serum stability have greatly hindered the applications of nucleic acids in biomedicine. To address these issues, associate carriers that can encapsulate and protect nucleic acids are urgently required. Mesoporous silica nanoparticles (MSNs or MSNPs, which are nanomaterials with excellent biocompatibility, large surface area for functionalization, and tunable pore size for encapsulating different cargos, are emerging as novel and ideal biomaterials for different biomedical applications. In this review paper, we focus on the applications of MSNs in nucleic acid delivery and nucleic acid-guided therapeutic treatments. General strategies for the preparation of nucleic acid-MSN complexes will be firstly introduced, followed by a summary of recent applications of MSNs in nucleic acid delivery and nucleic acid-guided therapeutics.

  14. 21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Quality control material for cystic fibrosis... Test Systems § 866.5910 Quality control material for cystic fibrosis nucleic acid assays. (a) Identification. Quality control material for cystic fibrosis nucleic acid assays. A quality control material...

  15. Nucleic acids encoding mosaic clade M human immunodeficiency virus type 1 (HIV-1) envelope immunogens

    Science.gov (United States)

    Korber, Bette T; Fischer, William; Liao, Hua-Xin; Haynes, Barton F; Letvin, Norman; Hahn, Beatrice H

    2015-04-21

    The present invention relates to nucleic acids encoding mosaic clade M HIV-1 Env polypeptides and to compositions and vectors comprising same. The nucleic acids of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

  16. Microfluidic Preparation of Polymer-Nucleic Acid Nanocomplexes Improves Nonviral Gene Transfer

    NARCIS (Netherlands)

    Grigsby, C.L.; Ho, Y.P.; Lin, C.; Engbersen, Johannes F.J.; Leong, K.W.

    2013-01-01

    As the designs of polymer systems used to deliver nucleic acids continue to evolve, it is becoming increasingly apparent that the basic bulk manufacturing techniques of the past will be insufficient to produce polymer-nucleic acid nanocomplexes that possess the uniformity, stability, and potency

  17. BGL7 beta-glucosidase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Ward, Michael (San Francisco, CA)

    2008-08-05

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

  18. Methods for point-of-care detection of nucleic acid in a sample

    Science.gov (United States)

    Bearinger, Jane P.; Dugan, Lawrence C.

    2015-12-29

    Provided herein are methods and apparatus for detecting a target nucleic acid in a sample and related methods and apparatus for diagnosing a condition in an individual. The condition is associated with presence of nucleic acid produced by certain pathogens in the individual.

  19. BGL4 beta-glucosidase and nucleic acids encoding the same

    Science.gov (United States)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2008-01-22

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  20. BGL6 beta-glucosidase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Ward, Michael (San Francisco, CA)

    2009-09-01

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

  1. Covering all the bases : Coarse-grained model design and application for nucleic acids

    NARCIS (Netherlands)

    Uusitalo, Jaakko Juhani

    2016-01-01

    Nucleic acids play a crucial role in the storage, transportation and expression of our genetic information. They have also become an interesting tool for many applications in nanotechnology. Studying biomolecular systems containing nucleic acids using experimental and imaging techniques has its

  2. Corrigendum: Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes

    DEFF Research Database (Denmark)

    Bentin, T.; Hansen, G.I.; Nielsen, P.E.

    2007-01-01

    This corrects the article "Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes" in volume 34 on page 5790.......This corrects the article "Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes" in volume 34 on page 5790....

  3. BGL3 beta-glucosidase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2011-06-14

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  4. BGL4 beta-glucosidase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2011-12-06

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  5. Microgel Tethering For Microarray-Based Nucleic Acid Diagnostics

    Science.gov (United States)

    Dai, Xiaoguang

    Molecular diagnostics (MDx) have radically changed the process of clinical microbial identification based on identifying genetic information, MDx approaches are both specific and fast. They can identify microbes to the species and strain level over a time scale that can be as short as one hour. With such information clinicians can administer the most effective and appropriate antimicrobial treatment at an early time point with substantial implications both for patient well-being and for easing the burden on the health-care system. Among the different MDx approaches, such as fluorescence in-situ hybridization, microarrays, next-generation sequencing, and mass spectrometry, point-of-care MDx platforms are drawing particular interest due to their low cost, robustness, and wide application. This dissertation develops a novel MDx technology platform capable of high target amplification and detection performance. For nucleic acid target detection, we fabricate an array of electron-beam-patterned microgels on a standard glass microscope slide. The microgels can be as small as a few hundred nanometers. The unique way of energy deposition during electron-beam lithography provides the microgels with a very diffuse water -gel interface that enables them to not only serve as substrates to immobilize DNA probes but do so while preserving them in a highly hydrated environment that optimizes their performance. Benefiting from the high spatial resolution provided by such techniques as position-sensitive microspotting and dip-pen nanolithography, multiple oligonucleotide probes known as molecular beacons (MBs) can be patterned on microgels. Furthermore, nucleic acid target amplification can be conducted in direct contact with the microgel-tethered detection array. Specifically, we use an isothermal RNA amplification reaction - nucleic acid sequence-based amplification (NASBA). ssRNA amplicons of from the NASBA reaction can directly hybridize with microgel-tethered MBs, and the

  6. Identification of acid-base catalytic residues of high-Mr thioredoxin reductase from Plasmodium falciparum.

    Science.gov (United States)

    McMillan, Paul J; Arscott, L David; Ballou, David P; Becker, Katja; Williams, Charles H; Müller, Sylke

    2006-11-03

    High-M(r) thioredoxin reductase from the malaria parasite Plasmodium falciparum (PfTrxR) contains three redox active centers (FAD, Cys-88/Cys-93, and Cys-535/Cys-540) that are in redox communication. The catalytic mechanism of PfTrxR, which involves dithiol-disulfide interchanges requiring acid-base catalysis, was studied by steady-state kinetics, spectral analyses of anaerobic static titrations, and rapid kinetics analysis of wild-type enzyme and variants involving the His-509-Glu-514 dyad as the presumed acid-base catalyst. The dyad is conserved in all members of the enzyme family. Substitution of His-509 with glutamine and Glu-514 with alanine led to TrxR with only 0.5 and 7% of wild type activity, respectively, thus demonstrating the crucial roles of these residues for enzymatic activity. The H509Q variant had rate constants in both the reductive and oxidative half-reactions that were dramatically less than those of wild-type enzyme, and no thiolateflavin charge-transfer complex was observed. Glu-514 was shown to be involved in dithiol-disulfide interchange between the Cys-88/Cys-93 and Cys-535/Cys-540 pairs. In addition, Glu-514 appears to greatly enhance the role of His-509 in acid-base catalysis. It can be concluded that the His-509-Glu-514 dyad, in analogy to those in related oxidoreductases, acts as the acid-base catalyst in PfTrxR.

  7. Effect of benzoic acid supplementation on acid-base status and mineralmetabolism in catheterized growing pigs

    DEFF Research Database (Denmark)

    Nørgaard, Jan Værum; Fernández, José Adalberto; Sørensen, Kristina Ulrich;

    2010-01-01

    Benzoic acid (BA) in diets for growing pigs results in urinary acidification and reduced ammonia emission. The objective was to study the impact of BA supplementation on the acid-base status and mineral metabolism in pigs. Eight female 50-kg pigs, fitted with a catheter in the abdominal aorta, were...

  8. Interactive Computer-Assisted Instruction in Acid-Base Physiology for Mobile Computer Platforms

    Science.gov (United States)

    Longmuir, Kenneth J.

    2014-01-01

    In this project, the traditional lecture hall presentation of acid-base physiology in the first-year medical school curriculum was replaced by interactive, computer-assisted instruction designed primarily for the iPad and other mobile computer platforms. Three learning modules were developed, each with ~20 screens of information, on the subjects…

  9. Acid-base titration curves in an integrated computer learning environment

    NARCIS (Netherlands)

    Heck, A.; Kędzierska, E.; Rodgers, L.; Chmurska, M.

    2008-01-01

    The topic of acid-base reactions is a regular component of many chemistry curricula that requires integrated understanding of various areas of introductory chemistry. Many students have considerable difficulties understanding the concepts and processes involved. It has been suggested and confirmed b

  10. Intracellular pH regulation by acid/base transporters in mammalian neurons

    Directory of Open Access Journals (Sweden)

    Vernon A. Ruffin

    2014-02-01

    Full Text Available Intracellular pH (pHi regulation in the brain is important in both physiological and physiopathological conditions because changes in pHi generally result in altered neuronal excitability. In this review, we will cover 4 major areas: [1] The effect of pHi on cellular processes in the brain, including channel activity and neuronal excitability. [2] pHi homeostasis and how it is determined by the balance between rates of acid loading (JL and extrusion (JE. The balance between JE and JL determine steady-state pHi, as well as the ability of the cell to defend pHi in the face of extracellular acid-base disturbances (e.g. metabolic acidosis. [3] The properties and importance of members of the SLC4 and SLC9 families of acid-base transporters expressed in the brain that contribute to JL (namely the Cl-HCO3 exchanger AE3 and JE (the Na-H exchangers NHE1, NHE3 and NHE5 as well as the Na+- coupled HCO3- transporters NBCe1, NBCn1, NDCBE, and NBCn2. [4] The effect of acid-base disturbances on neuronal function and the roles of acid-base transporters in defending neuronal pHi under physiopathologic conditions.

  11. Stereoselective assembly of amino acid-based metal-biomolecule nanofibers.

    Science.gov (United States)

    Wu, Hong; Tian, Chunyong; Zhang, Yufei; Yang, Chen; Zhang, Songping; Jiang, Zhongyi

    2015-04-14

    A series of amino acid-based metal-biomolecule nanofibers are fabricated through a coordination-directed assembly process. The chirality and carbon chain length of the amino acids exert a pronounced influence on the assembly process. This study may be extended to design diverse kinds of 1-D metal-biomolecule frameworks (MBioFs).

  12. Facile syntheses of dissymmetric ferrocene-functionalized Lewis acids and acid-base pairs.

    Science.gov (United States)

    Morgan, Ian R; Di Paolo, Angela; Vidovic, Dragoslav; Fallis, Ian A; Aldridge, Simon

    2009-12-21

    A facile synthetic approach is reported for the synthesis of dissymmetric 1,2-ferrocenediyl Lewis acids and mixed acid-base pairs including the first example of a 1-phosphino-2-borylferrocene; the use of non-racemic electrophiles allows for the isolation of single diastereomer products.

  13. The central role of chloride in the metabolic acid-base changes in canine parvoviral enteritis.

    Science.gov (United States)

    Burchell, Richard K; Schoeman, Johan P; Leisewitz, Andrew L

    2014-04-01

    The acid-base disturbances in canine parvoviral (CPV) enteritis are not well described. In addition, the mechanisms causing these perturbations have not been fully elucidated. The purpose of the present study was to assess acid-base changes in puppies suffering from CPV enteritis, using a modified strong ion model (SIM). The hypothesis of the study was that severe acid-base disturbances would be present and that the SIM would provide insights into pathological mechanisms, which have not been fully appreciated by the Henderson-Hasselbalch model. The study analysed retrospective data, obtained from 42 puppies with confirmed CPV enteritis and 10 healthy control dogs. The CPV-enteritis group had been allocated a clinical score, to allow classification of the data according to clinical severity. The effects of changes in free water, chloride, l-lactate, albumin and phosphate were calculated, using a modification of the base excess algorithm. When the data were summated for each patient, and correlated to each individual component, the most important contributor to the metabolic acid-base changes, according to the SIM, was chloride (Penteritis are multifactorial and complex, with the SIM providing information in terms of the origin of these changes.

  14. Analysis and Identification of Acid-Base Indicator Dyes by Thin-Layer Chromatography

    Science.gov (United States)

    Clark, Daniel D.

    2007-01-01

    Thin-layer chromatography (TLC) is a very simple and effective technique that is used by chemists by different purposes, including the monitoring of the progress of a reaction. TLC can also be easily used for the analysis and identification of various acid-base indicator dyes.

  15. A small-angle neutron scattering study of cholic acid-based organogel systems

    NARCIS (Netherlands)

    Willemen, H.M.; Marcelis, A.T.M.; Sudhölter, E.J.R.; Bouwman, W.G.; Deme, B.; Terech, P.

    2004-01-01

    Small-angle neutron scattering measurements were performed on some cholic acid-based gel systems in order to gain detailed information about the network structure. The presence of thin fibers with a radius of about 10-20 Å was found for various gelators. Two types of interaction between different so

  16. Thermodynamics of micellization of cholic acid based facial amphiphiles carrying three permanent ionic head groups

    NARCIS (Netherlands)

    Willemen, H.M.; Marcelis, A.T.M.; Sudhölter, E.J.R.

    2003-01-01

    This paper describes a series of cholic acid based facial amphiphiles carrying three ionic headgroups. Their micellization behavior in water was studied as a function of spacer length and alkyl tail length: both were found to have a small influence on the critical micellization concentration (cmc).

  17. Experienced Teachers' Pedagogical Content Knowledge of Teaching Acid-Base Chemistry

    Science.gov (United States)

    Drechsler, Michal; Van Driel, Jan

    2008-01-01

    We investigated the pedagogical content knowledge (PCK) of nine experienced chemistry teachers. The teachers took part in a teacher training course on students' difficulties and the use of models in teaching acid-base chemistry, electrochemistry, and redox reactions. Two years after the course, the teachers were interviewed about their PCK of (1)…

  18. The Acid-Base Titration of a Very Weak Acid: Boric Acid

    Science.gov (United States)

    Celeste, M.; Azevedo, C.; Cavaleiro, Ana M. V.

    2012-01-01

    A laboratory experiment based on the titration of boric acid with strong base in the presence of d-mannitol is described. Boric acid is a very weak acid and direct titration with NaOH is not possible. An auxiliary reagent that contributes to the release of protons in a known stoichiometry facilitates the acid-base titration. Students obtain the…

  19. Acid-Base Chemistry According to Robert Boyle: Chemical Reactions in Words as well as Symbols

    Science.gov (United States)

    Goodney, David E.

    2006-01-01

    Examples of acid-base reactions from Robert Boyle's "The Sceptical Chemist" are used to illustrate the rich information content of chemical equations. Boyle required lengthy passages of florid language to describe the same reaction that can be done quite simply with a chemical equation. Reading or hearing the words, however, enriches the student's…

  20. Examining the Mismatch between Pupil and Teacher Knowledge in Acid-Base Chemistry.

    Science.gov (United States)

    Erduran, Sibel

    2003-01-01

    Reports a mismatch between teacher and pupil knowledge of acid-base chemistry as a result of controversial episodes from three science lessons. Suggests that the teacher's knowledge is guided by textbook information while the pupil's knowledge is based on direct experimental experience. Proposes that classroom activities should support the…

  1. Analysis and Identification of Acid-Base Indicator Dyes by Thin-Layer Chromatography

    Science.gov (United States)

    Clark, Daniel D.

    2007-01-01

    Thin-layer chromatography (TLC) is a very simple and effective technique that is used by chemists by different purposes, including the monitoring of the progress of a reaction. TLC can also be easily used for the analysis and identification of various acid-base indicator dyes.

  2. Synthesis of 2D Hexagonal Mesoporous Silica Using Amino Acid-based Surfactant Templating

    Directory of Open Access Journals (Sweden)

    Xu Hailan

    2016-01-01

    Full Text Available Ordered 2D hexagonal and parallel arranged pore channel mesoporous silica materials with homogeneous size and spherical shape have been synthesized by using amino acid-based surfactant templating, their ordered mesostructures were characterized by infrared spectroscopy, X-ray diffraction patterns (XRD, scanning electron microscopy (SEM, transmission electron microscopy (TEM and nitrogen sorption analysis.

  3. The Effect of Voluntary Ventilation on Acid-base Responses to a Moo Duk Tkow Form.

    Science.gov (United States)

    Hetzler, Ronald K.; And Others

    1989-01-01

    Results are reported from a study that investigated the acid-base and lactate reponses to voluntary integration of breathing and exercise movements during beginning level form Ki Cho I, performed at competitive intensities. Findings suggest that respiratory compensation does not occur and that respiratory acidosis may contribute to metabolic…

  4. Re-Evaluation of Acid-Base Prediction Rules in Patients with Chronic Respiratory Acidosis

    Directory of Open Access Journals (Sweden)

    Tereza Martinu

    2003-01-01

    Full Text Available RATIONALE: The prediction rules for the evaluation of the acid-base status in patients with chronic respiratory acidosis, derived primarily from an experimental canine model, suggest that complete compensation should not occur. This appears to contradict frequent observations of normal or near-normal pH levels in patients with chronic hypercapnia.

  5. Effect of acute metabolic acid/base shifts on the human airway calibre.

    NARCIS (Netherlands)

    Brijker, F.; Elshout, F.J.J. van den; Heijdra, Y.F.; Bosch, F.H.; Folgering, H.T.M.

    2001-01-01

    Acute metabolic alkalosis (NaHCO(3)), acidosis (NH(4)Cl), and placebo (NaCl) were induced in 15 healthy volunteers (12 females, median age 34 (range 24-56) years) in a double blind, placebo controlled study to evaluate the presence of the effects on airway calibre. Acid-base shifts were determined b

  6. Acid-base regulation in tadpoles of Rana catesbeiana exposed to environmental hypercapnia

    DEFF Research Database (Denmark)

    Busk, Morten; Larsen, Erik Hviid; Jensen, Frank B.

    1997-01-01

    Tadpoles of Rana catesbeiana were exposed to different levels of environmental hypercapnia. The acid-base regulatory response differed from that in adult amphibians in showing a high degree of pH compensation in the extracellular fluid (65-85%) and complete compensation in the intracellular fluid...

  7. Experienced Teachers' Pedagogical Content Knowledge of Teaching Acid-Base Chemistry

    Science.gov (United States)

    Drechsler, Michal; Van Driel, Jan

    2008-01-01

    We investigated the pedagogical content knowledge (PCK) of nine experienced chemistry teachers. The teachers took part in a teacher training course on students' difficulties and the use of models in teaching acid-base chemistry, electrochemistry, and redox reactions. Two years after the course, the teachers were interviewed about their PCK of (1)…

  8. The Acid-Base Titration of a Very Weak Acid: Boric Acid

    Science.gov (United States)

    Celeste, M.; Azevedo, C.; Cavaleiro, Ana M. V.

    2012-01-01

    A laboratory experiment based on the titration of boric acid with strong base in the presence of d-mannitol is described. Boric acid is a very weak acid and direct titration with NaOH is not possible. An auxiliary reagent that contributes to the release of protons in a known stoichiometry facilitates the acid-base titration. Students obtain the…

  9. Interactive Computer-Assisted Instruction in Acid-Base Physiology for Mobile Computer Platforms

    Science.gov (United States)

    Longmuir, Kenneth J.

    2014-01-01

    In this project, the traditional lecture hall presentation of acid-base physiology in the first-year medical school curriculum was replaced by interactive, computer-assisted instruction designed primarily for the iPad and other mobile computer platforms. Three learning modules were developed, each with ~20 screens of information, on the subjects…

  10. Soluble adenylyl cyclase is an acid-base sensor in epithelial base-secreting cells.

    Science.gov (United States)

    Roa, Jinae N; Tresguerres, Martin

    2016-08-01

    Blood acid-base regulation by specialized epithelia, such as gills and kidney, requires the ability to sense blood acid-base status. Here, we developed primary cultures of ray (Urolophus halleri) gill cells to study mechanisms for acid-base sensing without the interference of whole animal hormonal regulation. Ray gills have abundant base-secreting cells, identified by their noticeable expression of vacuolar-type H(+)-ATPase (VHA), and also express the evolutionarily conserved acid-base sensor soluble adenylyl cyclase (sAC). Exposure of cultured cells to extracellular alkalosis (pH 8.0, 40 mM HCO3 (-)) triggered VHA translocation to the cell membrane, similar to previous reports in live animals experiencing blood alkalosis. VHA translocation was dependent on sAC, as it was blocked by the sAC-specific inhibitor KH7. Ray gill base-secreting cells also express transmembrane adenylyl cyclases (tmACs); however, tmAC inhibition by 2',5'-dideoxyadenosine did not prevent alkalosis-dependent VHA translocation, and tmAC activation by forskolin reduced the abundance of VHA at the cell membrane. This study demonstrates that sAC is a necessary and sufficient sensor of extracellular alkalosis in ray gill base-secreting cells. In addition, this study indicates that different sources of cAMP differentially modulate cell biology. Copyright © 2016 the American Physiological Society.

  11. Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.

    Science.gov (United States)

    Galperin, Michael Y; Cochrane, Guy R

    2009-01-01

    The current issue of Nucleic Acids Research includes descriptions of 179 databases, of which 95 are new. These databases (along with several molecular biology databases described in other journals) have been included in the Nucleic Acids Research online Molecular Biology Database Collection, bringing the total number of databases in the collection to 1170. In this introductory comment, we briefly describe some of these new databases and review the principles guiding the selection of databases for inclusion in the Nucleic Acids Research annual Database Issue and the Nucleic Acids Research online Molecular Biology Database Collection. The complete database list and summaries are available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

  12. RIG-I detects infection with live Listeria by sensing secreted bacterial nucleic acids

    Science.gov (United States)

    Abdullah, Zeinab; Schlee, Martin; Roth, Susanne; Mraheil, Mobarak Abu; Barchet, Winfried; Böttcher, Jan; Hain, Torsten; Geiger, Sergej; Hayakawa, Yoshihiro; Fritz, Jörg H; Civril, Filiz; Hopfner, Karl-Peter; Kurts, Christian; Ruland, Jürgen; Hartmann, Gunther; Chakraborty, Trinad; Knolle, Percy A

    2012-01-01

    Immunity against infection with Listeria monocytogenes is not achieved from innate immune stimulation by contact with killed but requires viable Listeria gaining access to the cytosol of infected cells. It has remained ill-defined how such immune sensing of live Listeria occurs. Here, we report that efficient cytosolic immune sensing requires access of nucleic acids derived from live Listeria to the cytoplasm of infected cells. We found that Listeria released nucleic acids and that such secreted bacterial RNA/DNA was recognized by the cytosolic sensors RIG-I, MDA5 and STING thereby triggering interferon β production. Secreted Listeria nucleic acids also caused RIG-I-dependent IL-1β-production and inflammasome activation. The signalling molecule CARD9 contributed to IL-1β production in response to secreted nucleic acids. In conclusion, cytosolic recognition of secreted bacterial nucleic acids by RIG-I provides a mechanistic explanation for efficient induction of immunity by live bacteria. PMID:23064150

  13. [Development and practice evaluation of blood acid-base imbalance analysis software].

    Science.gov (United States)

    Chen, Bo; Huang, Haiying; Zhou, Qiang; Peng, Shan; Jia, Hongyu; Ji, Tianxing

    2014-11-01

    To develop a blood gas, acid-base imbalance analysis computer software to diagnose systematically, rapidly, accurately and automatically determine acid-base imbalance type, and evaluate the clinical application. Using VBA programming language, a computer aided diagnostic software for the judgment of acid-base balance was developed. The clinical data of 220 patients admitted to the Second Affiliated Hospital of Guangzhou Medical University were retrospectively analyzed. The arterial blood gas [pH value, HCO(3)(-), arterial partial pressure of carbon dioxide (PaCO₂)] and electrolytes included data (Na⁺ and Cl⁻) were collected. Data were entered into the software for acid-base imbalances judgment. At the same time the data generation was calculated manually by H-H compensation formula for determining the type of acid-base imbalance. The consistency of judgment results from software and manual calculation was evaluated, and the judgment time of two methods was compared. The clinical diagnosis of the types of acid-base imbalance for the 220 patients: 65 cases were normal, 90 cases with simple type, mixed type in 41 cases, and triplex type in 24 cases. The accuracy of the judgment results of the normal and triplex types from computer software compared with which were calculated manually was 100%, the accuracy of the simple type judgment was 98.9% and 78.0% for the mixed type, and the total accuracy was 95.5%. The Kappa value of judgment result from software and manual judgment was 0.935, P=0.000. It was demonstrated that the consistency was very good. The time for software to determine acid-base imbalances was significantly shorter than the manual judgment (seconds:18.14 ± 3.80 vs. 43.79 ± 23.86, t=7.466, P=0.000), so the method of software was much faster than the manual method. Software judgment can replace manual judgment with the characteristics of rapid, accurate and convenient, can improve work efficiency and quality of clinical doctors and has great

  14. Digestion of Nucleic Acids Starts in the Stomach.

    Science.gov (United States)

    Liu, Yu; Zhang, Yanfang; Dong, Ping; An, Ran; Xue, Changhu; Ge, Yinlin; Wei, Liangzhou; Liang, Xingguo

    2015-07-14

    The ingestion of nucleic acids (NAs) as a nutritional supplement or in genetically modified food has attracted the attention of researchers in recent years. Discussions over the fate of NAs led us to study their digestion in the stomach. Interestingly, we found that NAs are digested efficiently by human gastric juice. By performing digests with commercial, recombinant and mutant pepsin, a protein-specific enzyme, we learned that the digestion of NAs could be attributed to pepsin rather than to the acidity of the stomach. Further study showed that pepsin cleaved NAs in a moderately site-specific manner to yield 3'-phosphorylated fragments and the active site to digest NAs is probably the same as that used to digest protein. Our results rectify the misunderstandings that the digestion of NAs in the gastric tract begins in the intestine and that pepsin can only digest protein, shedding new light on NA metabolism and pepsin enzymology.

  15. Optimization and comparative evaluation of nucleic acids extraction protocols

    Directory of Open Access Journals (Sweden)

    Lucian Negura

    2011-12-01

    Full Text Available Modern molecular applications have grown the need of biobanks, which contain DNA and RNA of high purety, quality, and quantity. Nucleic acid extraction methods have widely variate and evolve in time, from methods using toxic reagents to enzymatic protocols, and furthermore to DNA or RNA-binding polymers, separating membranes or highly eulogized commercially kits. In order to establish a constant, reproducible and ergonomic system in generating biobanks, we compared different available methods for the extraction of genomic DNA and total RNA, from peripheram blood or solid tumoral tissues. We evaluated the cost/effectiveness and time consumption of each method, tracking RNA/DNA quantity, quality and integrity. We imagined a “E-ratio” value to define these parameters, and a “NA- estimation” to integrate “E-ratio” with quality and integrity data.

  16. Development of PNA-Surfactant Systems for Nucleic Acid Separations

    Science.gov (United States)

    Vernille, James; Armitage, Bruce; Schneider, James

    2002-03-01

    We have been exploring the use of novel peptide nucleic acid (PNA) surfactants for use in sequence specific, scalable DNA separations. While the synthetic and physical characteristics of PNA make it a useful molecule for bioseparations, PNA shows limited water solubility. Here we describe a molecular design strategy to improve water solubility while maintaining sequence specificity. A candidate molecule has been identified which contains lysine residues and a short alkane tail. Melting temperature data show that lipid tail interactions with the DNA nucleobases have a small but significant effect on stability while the added lysines stabilize the complex in an ionic strength dependent way. We also discuss the incorporation of these surfactants into micellar systems for novel separations.

  17. Nucleic acids--genes, drugs, molecular lego and more.

    Science.gov (United States)

    Häner, Robert

    2010-01-01

    Chemically modified nucleic acids find widespread use as tools in research, as diagnostic reagents and even as pharmaceutical compounds. On the background of antisense research and development, the synthesis and evaluation of modified oligonucleotides was intensively pursued in the early to mid nineties in corporate research of former Ciba. Most of these efforts concentrated on the development of sugar and/or backbone-modified derivatives for pharmaceutical applications. Additionally, oligonucleotide metal conjugates were investigated with the goal to develop artificial ribonucleases. Since the turn of the millennium also the potential of non-nucleosidic and non-hydrogen bonding building blocks has increasingly been recognized. Such derivatives possess unique properties that may have an impact in the fields of materials and genetic research. In this brief account, we take a personal look back on some past as well as some recent results.

  18. Determination of Nucleic Acid Hydration Using Osmotic Stress

    Science.gov (United States)

    Rozners, Eriks

    2010-01-01

    Understanding the role water plays in biological processes requires detailed knowledge of the phenomena of biopolymer hydration. Crystal structures have identified exact sites occupied by the water molecules in immediate hydration layers. NMR and molecular modeling have provided information on dynamics of water molecules occupying these sites. However, these studies give little information on the thermodynamic contribution of water molecules to conformational equilibria and recognition affinity. This unit describes probing of nucleic acid hydration using osmotic stress, a method that provides thermodynamic information complementary to crystallography, NMR and molecular modeling. Osmotic stress monitors the depression of melting temperature upon decreasing the water activity and calculates the number of thermodynamically unique water molecules associated with the double helix and released from the single strands upon melting. PMID:21154532

  19. Thioarsenides: A case for long-range Lewis acid-base-directed van der Waals interactions

    Energy Technology Data Exchange (ETDEWEB)

    Gibbs, Gerald V.; Wallace, Adam F.; Downs, R. T.; Ross, Nancy L.; Cox, David F.; Rosso, Kevin M.

    2011-04-01

    Electron density distributions, bond paths, Laplacian and local energy density properties have been calculated for a number of As4Sn (n = 3,4,5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis base regions) with aligned regions of locally depleted electron density (Lewis acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for several other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long range Lewis acid-base directed van der Waals interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and β-AsS and the distorted hexagonal close-packed arrays adopted by α- and β-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.

  20. Metabolism, gas exchange, and acid-base balance of giant salamanders.

    Science.gov (United States)

    Ultsch, Gordon R

    2012-08-01

    The giant salamanders are aquatic and paedomorphic urodeles including the genera Andrias and Cryptobranchus (Cryptobranchidae), Amphiuma (Amphiumidae), Siren (Sirenidae), and Necturus (Proteidae, of which only N. maculosus is considered 'a giant'). Species in the genera Cryptobranchus and Necturus are considered aquatic salamanders well adapted for breathing water, poorly adapted for breathing air, and with limited abilities to compensate acid-base disturbances. As such, they are water-breathing animals with a somewhat fish-like respiratory and acid-base physiology, whose habitat selection is limited to waters that do not typically become hypoxic or hypercarbic (although this assertion has been questioned for N. maculosus). Siren and Amphiuma species, by contrast, are dependent upon air-breathing, have excellent lungs, inefficient (Siren) or no (Amphiuma) gills, and are obligate air-breathers with an acid-base status more similar to that of terrestrial tetrapods. As such, they can be considered to be air-breathing animals that live in water. Their response to the aquatic hypercarbia that they often encounter is to maintain intracellular pH (pH(i) ) and abandon extracellular pH regulation, a process that has been referred to as preferential pH(i) regulation. The acid-base status of some present-day tropical air-breathing fishes, and of Siren and Amphiuma, suggests that the acid-base transition from a low PCO(2) -low [] system typical of water-breathing fishes to the high PCO(2) -high [] systems of terrestrial tetrapods may have been completed before emergence onto land, and likely occurred in habitats that were typically both hypoxic and hypercarbic.