WorldWideScience

Sample records for chemical synthesis dna

  1. Synthesis of chemically modified DNA.

    Science.gov (United States)

    Shivalingam, Arun; Brown, Tom

    2016-06-15

    Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to 'write' long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion. PMID:27284032

  2. DNA and RNA induced enantioselectivity in chemical synthesis

    NARCIS (Netherlands)

    Roelfes, Gerard

    2007-01-01

    One of the hallmarks of DNA and RNA structures is their elegant chirality. Using these chiral structures to induce enantioselectivity in chemical synthesis is as enticing as it is challenging. In recent years, three general approaches have been developed to achieve this, including chirality transfer

  3. Ethics of Chemical Synthesis

    OpenAIRE

    Joachim Schummer

    2001-01-01

    Unlike other branches of science, the scientific products of synthetic chemistry are not only ideas but also new substances that change our material world, for the benefit or harm of living beings. This paper provides for the first time a systematical analysis of moral issues arising from chemical synthesis, based on concepts of responsibility and general morality. Topics include the questioning of moral neutrality of chemical synthesis as an end in itself, chemical weapons research, moral ob...

  4. Ethics of Chemical Synthesis

    Directory of Open Access Journals (Sweden)

    Joachim Schummer

    2001-10-01

    Full Text Available Unlike other branches of science, the scientific products of synthetic chemistry are not only ideas but also new substances that change our material world, for the benefit or harm of living beings. This paper provides for the first time a systematical analysis of moral issues arising from chemical synthesis, based on concepts of responsibility and general morality. Topics include the questioning of moral neutrality of chemical synthesis as an end in itself, chemical weapons research, moral objections against improving material conditions of life by chemical means, and freedom of research. The paper aims at providing both a sound basis for moral judgements of chemistry in a public discourse and a framework for chemists to reflect on the moral relevance of their activity.

  5. DNA adducts-chemical addons

    OpenAIRE

    T. R. Rajalakshmi; N AravindhaBabu; Shanmugam, K. T.; Masthan, K. M. K.

    2015-01-01

    DNA adduct is a piece of DNA covalently bond to a chemical (safrole, benzopyrenediol epoxide, acetaldehyde). This process could be the start of a cancerous cell. When a chemical binds to DNA, it gets damaged resulting in abnormal replication. This could be the start of a mutation and without proper DNA repair, this can lead to cancer. It is this chemical that binds with the DNA is our prime area of concern. Instead of performing the whole body analysis for diagnosing cancer, this test could b...

  6. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  7. DNA adducts-chemical addons

    Directory of Open Access Journals (Sweden)

    T R Rajalakshmi

    2015-01-01

    Full Text Available DNA adduct is a piece of DNA covalently bond to a chemical (safrole, benzopyrenediol epoxide, acetaldehyde. This process could be the start of a cancerous cell. When a chemical binds to DNA, it gets damaged resulting in abnormal replication. This could be the start of a mutation and without proper DNA repair, this can lead to cancer. It is this chemical that binds with the DNA is our prime area of concern. Instead of performing the whole body analysis for diagnosing cancer, this test could be carried out for early detection of cancer. When scanning tunneling microscope is used, the DNA results can be obtained earlier. DNA adducts in scientific experiments are used as biomarkers.

  8. DNA adducts-chemical addons

    Science.gov (United States)

    Rajalakshmi, T. R.; AravindhaBabu, N.; Shanmugam, K. T.; Masthan, K. M. K.

    2015-01-01

    DNA adduct is a piece of DNA covalently bond to a chemical (safrole, benzopyrenediol epoxide, acetaldehyde). This process could be the start of a cancerous cell. When a chemical binds to DNA, it gets damaged resulting in abnormal replication. This could be the start of a mutation and without proper DNA repair, this can lead to cancer. It is this chemical that binds with the DNA is our prime area of concern. Instead of performing the whole body analysis for diagnosing cancer, this test could be carried out for early detection of cancer. When scanning tunneling microscope is used, the DNA results can be obtained earlier. DNA adducts in scientific experiments are used as biomarkers. PMID:26015708

  9. Green chemistry for chemical synthesis

    Science.gov (United States)

    Li, Chao-Jun; Trost, Barry M.

    2008-01-01

    Green chemistry for chemical synthesis addresses our future challenges in working with chemical processes and products by inventing novel reactions that can maximize the desired products and minimize by-products, designing new synthetic schemes and apparati that can simplify operations in chemical productions, and seeking greener solvents that are inherently environmentally and ecologically benign. PMID:18768813

  10. Green chemistry for chemical synthesis

    OpenAIRE

    Li, Chao-Jun; Trost, Barry M.

    2008-01-01

    Green chemistry for chemical synthesis addresses our future challenges in working with chemical processes and products by inventing novel reactions that can maximize the desired products and minimize by-products, designing new synthetic schemes and apparati that can simplify operations in chemical productions, and seeking greener solvents that are inherently environmentally and ecologically benign.

  11. Chemical synthesis on SU-8

    DEFF Research Database (Denmark)

    Qvortrup, Katrine; Taveras, Kennedy; Thastrup, Ole;

    2011-01-01

    In this paper we describe a highly effective surface modification of SU-8 microparticles, the attachment of appropriate linkers for solid-supported synthesis, and the successful chemical modification of these particles via controlled multi-step organic synthesis leading to molecules attached...

  12. Expedient chemical synthesis of 75mer DNA binding domain of MafA: an insight on its binding to insulin enhancer.

    Science.gov (United States)

    Pellegrino, Sara; Annoni, Chiara; Contini, Alessandro; Clerici, Francesca; Gelmi, Maria Luisa

    2012-11-01

    An expedient chemical synthesis of a 75mer peptide corresponding to the DNA binding domain (DBD, 227-301) of the human MafA leucine zipper transcription factor is reported. The application of microwave-assisted solid phase peptide synthesis (MW-SPPS) with a protocol modified respect to the standard one allowed obtaining the desired 75mer peptide in a short time with high quantity and optimal purity. MW-SPPS methodology was thus demonstrated as a valuable alternative to recombinant methods to obtain protein domains. Considering that recent findings suggest an involvement of MafA in the pathogenesis of diabetes mellitus, we also performed circular dichroism studies both on DBD folding and its interaction with MafA recognition element (MARE) on insulin enhancer. From our results, it was evicted that a disorder to order transition occurs after DBD interaction with insulin MARE which is mediated by specific structural elements on the N-terminus of the DBD. PMID:22476346

  13. Recognition and repair of chemically heterogeneous structures at DNA ends.

    Science.gov (United States)

    Andres, Sara N; Schellenberg, Matthew J; Wallace, Bret D; Tumbale, Percy; Williams, R Scott

    2015-01-01

    Exposure to environmental toxicants and stressors, radiation, pharmaceutical drugs, inflammation, cellular respiration, and routine DNA metabolism all lead to the production of cytotoxic DNA strand breaks. Akin to splintered wood, DNA breaks are not "clean." Rather, DNA breaks typically lack DNA 5'-phosphate and 3'-hydroxyl moieties required for DNA synthesis and DNA ligation. Failure to resolve damage at DNA ends can lead to abnormal DNA replication and repair, and is associated with genomic instability, mutagenesis, neurological disease, ageing and carcinogenesis. An array of chemically heterogeneous DNA termini arises from spontaneously generated DNA single-strand and double-strand breaks (SSBs and DSBs), and also from normal and/or inappropriate DNA metabolism by DNA polymerases, DNA ligases and topoisomerases. As a front line of defense to these genotoxic insults, eukaryotic cells have accrued an arsenal of enzymatic first responders that bind and protect damaged DNA termini, and enzymatically tailor DNA ends for DNA repair synthesis and ligation. These nucleic acid transactions employ direct damage reversal enzymes including Aprataxin (APTX), Polynucleotide kinase phosphatase (PNK), the tyrosyl DNA phosphodiesterases (TDP1 and TDP2), the Ku70/80 complex and DNA polymerase β (POLβ). Nucleolytic processing enzymes such as the MRE11/RAD50/NBS1/CtIP complex, Flap endonuclease (FEN1) and the apurinic endonucleases (APE1 and APE2) also act in the chemical "cleansing" of DNA breaks to prevent genomic instability and disease, and promote progression of DNA- and RNA-DNA damage response (DDR and RDDR) pathways. Here, we provide an overview of cellular first responders dedicated to the detection and repair of abnormal DNA termini. PMID:25111769

  14. Small-molecule discovery from DNA-encoded chemical libraries.

    Science.gov (United States)

    Kleiner, Ralph E; Dumelin, Christoph E; Liu, David R

    2011-12-01

    Researchers seeking to improve the efficiency and cost effectiveness of the bioactive small-molecule discovery process have recently embraced selection-based approaches, which in principle offer much higher throughput and simpler infrastructure requirements compared with traditional small-molecule screening methods. Since selection methods benefit greatly from an information-encoding molecule that can be readily amplified and decoded, several academic and industrial groups have turned to DNA as the basis for library encoding and, in some cases, library synthesis. The resulting DNA-encoded synthetic small-molecule libraries, integrated with the high sensitivity of PCR and the recent development of ultra high-throughput DNA sequencing technology, can be evaluated very rapidly for binding or bond formation with a target of interest while consuming minimal quantities of material and requiring only modest investments of time and equipment. In this tutorial review we describe the development of two classes of approaches for encoding chemical structures and reactivity with DNA: DNA-recorded library synthesis, in which encoding and library synthesis take place separately, and DNA-directed library synthesis, in which DNA both encodes and templates library synthesis. We also describe in vitro selection methods used to evaluate DNA-encoded libraries and summarize successful applications of these approaches to the discovery of bioactive small molecules and novel chemical reactivity.

  15. Apparatus for chemical synthesis

    Science.gov (United States)

    Kong, Peter C.; Herring, J. Stephen; Grandy, Jon D.

    2011-05-10

    A method and apparatus for forming a chemical hydride is described and which includes a pseudo-plasma-electrolysis reactor which is operable to receive a solution capable of forming a chemical hydride and which further includes a cathode and a movable anode, and wherein the anode is moved into and out of fluidic, ohmic electrical contact with the solution capable of forming a chemical hydride and which further, when energized produces an oxygen plasma which facilitates the formation of a chemical hydride in the solution.

  16. DNA display III. Solid-phase organic synthesis on unprotected DNA.

    Directory of Open Access Journals (Sweden)

    David R Halpin

    2004-07-01

    Full Text Available DNA-directed synthesis represents a powerful new tool for molecular discovery. Its ultimate utility, however, hinges upon the diversity of chemical reactions that can be executed in the presence of unprotected DNA. We present a solid-phase reaction format that makes possible the use of standard organic reaction conditions and common reagents to facilitate chemical transformations on unprotected DNA supports. We demonstrate the feasibility of this strategy by comprehensively adapting solid-phase 9-fluorenylmethyoxycarbonyl-based peptide synthesis to be DNA-compatible, and we describe a set of tools for the adaptation of other chemistries. Efficient peptide coupling to DNA was observed for all 33 amino acids tested, and polypeptides as long as 12 amino acids were synthesized on DNA supports. Beyond the direct implications for synthesis of peptide-DNA conjugates, the methods described offer a general strategy for organic synthesis on unprotected DNA. Their employment can facilitate the generation of chemically diverse DNA-encoded molecular populations amenable to in vitro evolution and genetic manipulation.

  17. DNA polymerase δ and DNA repair: DNA repair synthesis in human fibroblasts requires DNA polymerase δ

    International Nuclear Information System (INIS)

    When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernate of similarly treated HeLa cells. Monoclonal antibody to KB cell DNA polymerase α, while binding to HeLa DNA polymerase α, did not bind to the HeLa DNA polymerase δ. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGT) and 2(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase α, but did not inhibit the DNA polymerase δ. Neither purified DNA polymerase α nor β could promote repair DNA synthesis in the permeabilized cells. Furthermore, if monoclonal antibodies to DNA polymerase α BuPdGTP, or BuAdATP was added to the reconstituted system, there was no significant inhibition

  18. DNA sequencing by synthesis with degenerate primers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The degenerate primer-based sequencing Was developed by a synthesis method(DP-SBS)for high-throughput DNA sequencing,in which a set of degenerate primers are hybridized on the arrayed DNA templates and extended by DNA polymerase on microarrays.In this method,adifferent set of degenerate primers containing a give nnumber(n)of degenerate nucleotides at the 3'-ends were annealed to the sequenced templates that were immobilized on the solid surface.The nucleotides(n+1)on the template sequences were determined by detecting the incorporation of fluorescent labeled nucleotides.The fluorescent labeled nucleotide was incorporated into the primer in a base-specific manner after the enzymatic primer extension reactions and nine-base length were read out accurately.The main advanmge of the DP-SBS is that the method only uses very conventional biochemical reagents and avoids the complicated special chemical reagents for removing the labeled nucleotides and reactivating the primer for further extension.From the present study,it is found that the DP-SBS method is reliable,simple,and cost-effective for laboratory-sequencing a large amount of short DNA fragments.

  19. DNA-synthesis inhibition and repair DNA-synthesis in CHO Ade- C cells: An alternative approach to genotoxicity testing

    International Nuclear Information System (INIS)

    We describe an alternative assay to determine genotoxicity. Its main feature is that it combines two measures in a single experiment; the inhibition of replicative DNA synthesis together with the stimulation of DNA repair. We show that, in tests of four different genotoxic agents, the assay gives results that are entirely consistent with what is known about the mode of action of these agents. In addition, we have demonstrated that chemical carcinogens requiring metabolic activation can be examined using a standard procedure of incubation with a microsomal activating fraction. We consider the combined assay for DNA synthesis inhibition and repair synthesis to be a useful way for the rapid pre-screening of chemicals suspected of genotoxic activity on the level of mammalian cells. (author)

  20. DNA synthesis on discontinuous templates by human DNA polymerases: implications for non-homologous DNA recombination.

    OpenAIRE

    Islas, L; Fairley, C F; Morgan, W. F.

    1998-01-01

    DNA polymerases catalyze the synthesis of DNA using a continuous uninterrupted template strand. However, it has been shown that a 3'-->5' exonuclease-deficient form of the Klenow fragment of Escherichia coli DNA polymerase I as well as DNA polymerase of Thermus aquaticus can synthesize DNA across two unlinked DNA templates. In this study, we used an oligonucleotide-based assay to show that discontinuous DNA synthesis was present in HeLa cell extracts. DNA synthesis inhibitor studies as well a...

  1. Analysis of Translesion DNA Synthesis by the Mitochondrial DNA Polymerase γ.

    Science.gov (United States)

    Copeland, William C; Kasiviswanathan, Rajesh; Longley, Matthew J

    2016-01-01

    Mitochondrial DNA is replicated by the nuclear-encoded DNA polymerase γ (pol γ) which is composed of a single 140 kDa catalytic subunit and a dimeric 55 kDa accessory subunit. Mitochondrial DNA is vulnerable to various forms of damage, including several types of oxidative lesions, UV-induced photoproducts, chemical adducts from environmental sources, as well as alkylation and inter-strand cross-links from chemotherapy agents. Although many of these lesions block DNA replication, pol γ can bypass some lesions by nucleotide incorporation opposite a template lesion and further extension of the DNA primer past the lesion. This process of translesion synthesis (TLS) by pol γ can occur in either an error-free or an error-prone manner. Assessment of TLS requires extensive analysis of oligonucleotide substrates and replication products by denaturing polyacrylamide sequencing gels. This chapter presents protocols for the analysis of translesion DNA synthesis.

  2. Analysis of Translesion DNA Synthesis by the Mitochondrial DNA Polymerase γ

    Science.gov (United States)

    Copeland, William C.; Kasiviswanathan, Rajesh; Longley, Matthew J.

    2016-01-01

    Summary Mitochondrial DNA is replicated by the nuclear encoded DNA polymerase γ (pol γ) which is composed of a single 140 kDa catalytic subunit and a dimeric 55 kDa accessory subunit. Mitochondrial DNA is vulnerable to various forms of damage, including several types of oxidative lesions, UV-induced photoproducts, chemical adducts from environmental sources, as well as alkylation and inter-strand crosslinks from chemotherapy agents. Although many of these lesions block DNA replication, Pol γ can bypass some lesions by nucleotide incorporation opposite a template lesion and further extension of the DNA primer past the lesion. This process of translesion synthesis (TLS) by Pol γ can occur in either an error-free or an error-prone manner. Assessment of TLS requires extensive analysis of oligonucleotide substrates and replication products by denaturing polyacrylamide sequencing gels. This chapter presents protocols for the analysis of translesion DNA synthesis. PMID:26530671

  3. Spontaneous unscheduled DNA synthesis in human lymphocytes

    International Nuclear Information System (INIS)

    The rate of spontaneous unscheduled DNA synthesis in human lymphocytes was estimated from measurements of tritiated thymidine incorporation into double-stranded DNA (ds-DNA) during incubation of cells in vitro. The contribution of scheduled DNA synthesis to the observed incorporation was reduced by inhibiting replication with hydroxyurea and by separating freshly replicated single-stranded DNA (ss-DNA) from repaired ds-DNA by column chromatography. The residual contribution of scheduled DNA synthesis was estimated by observing effects on thymidine incorporation of: (a) increasing the rate of production of apurinic sites, and alternatively, (b) increasing the number of cells in S-phase. Corrections based on estimates of endogenous pool size were also made. The rate of spontaneous unscheduled DNA synthesis is estimated to be 490 +- 120 thymidine molecules incorporated per cell per hour. These results compare favorably with estimates made from rates of depurination and depyrimidination of DNA, measured in molecular systems if we assume thymidine is incorporated by a short patch mechanism which incorporates an average of four bases per lesion

  4. Standardized chemical synthesis of Pseudomonas aeruginosa pyocyanin

    Directory of Open Access Journals (Sweden)

    Rajkumar Cheluvappa

    2014-01-01

    As we have extracted pyocyanin both from P. aeruginosa cultures, and via chemical synthesis; we know the procedural and product-quality differences. We endorse the relative ease, safety, and convenience of using the chemical synthesis described here. Crucially, our “naturally endotoxin-free” pyocyanin can be extracted easily without using infectious bacteria.

  5. 酶促DNA合成研究的进展%Advance in Enzymatic DNA Synthesis

    Institute of Scientific and Technical Information of China (English)

    向义和

    2011-01-01

    The advance in enzymatic DNA synthesis is introduced. Kornberg and his colleagues went through deoxyribonucleotide.de-oxynucleoside try phosphates and DNA synthesis. The immediate precursor of DNA synthesis was known. DNA polymerase was separated and purified. The chemical mechanism of DNA synthesis was revealed and infectious phage φX174DNA was synthesized.%笔者介绍了酶促DNA合成研究的进展.科恩伯格和他的同事经历了从合成核苷酸、核苷三磷酸到合成DNA的历程.他们分离并提纯了DNA聚合酶,弄清了合成DNA的最直接的前体,揭示了DNA合成的化学机理,合成了具有感染性的噬菌体φX174DNA.

  6. Tools for chemical synthesis in microsystems

    OpenAIRE

    Jensen, Klavs F.; Newman, Stephen G.; Reizman, Brandon Jacob

    2014-01-01

    Chemical synthesis in microsystems has evolved from simple proof-of-principle examples to become a general technique in academia and industry. Numerous such “flow chemistry” applications are now found in pharmaceutical and fine chemical synthesis. Much of the development has been based on systems employing macroscopic flow components and tubes, rather than the integrated chip technology envisioned by the lab-on-a-chip community. We review the major developments in systems for flow chemistry a...

  7. Opportunities for Merging Chemical and Biological Synthesis

    OpenAIRE

    Wallace, Stephen; Balskus, Emily P.

    2014-01-01

    Organic chemists and metabolic engineers use largely orthogonal technologies to access small molecules like pharmaceuticals and commodity chemicals. As the use of biological catalysts and engineered organisms for chemical production grows, it is becoming increasingly evident that future efforts for chemical manufacture will benefit from the integration and unified expansion of these two fields. This review will discuss approaches that combine chemical and biological synthesis for small molecu...

  8. DNA synthesis in ataxia telangiectasia

    OpenAIRE

    Jaspers, Nicolaas

    1985-01-01

    textabstractAfter the discovery that cultured cells from AT patients are hypersensitive to ionizing radiation the suggestion was made that AT-could be the 1 X-ray-analogue 1 of xeroderma pigmentosum. The latter syndrome (XP) is characterized by hypersensitivity to short-wave UV-radiation, caused by a reduced ability to properly remove UV-induced DNA damage. The evidence for a DNA repair defect in AT cells is not as strong as in the case of XP (see section 2.2.5 of this thesis). Different XP p...

  9. Stimulation of mouse DNA primase-catalyzed oligoribonucleotide synthesis by mouse DNA helicase B.

    OpenAIRE

    Saitoh, A; S. Tada; Katada, T; Enomoto, T.

    1995-01-01

    Many prokaryotic and viral DNA helicases involved in DNA replication stimulate their cognate DNA primase activity. To assess the stimulation of DNA primase activity by mammalian DNA helicases, we analyzed the synthesis of oligoribonucleotides by mouse DNA polymerase alpha-primase complex on single-stranded circular M13 DNA in the presence of mouse DNA helicase B. DNA helicase B was purified by sequential chromatography through eight columns. When the purified DNA helicase B was applied to a M...

  10. Methanol synthesis beyond chemical equilibrium

    NARCIS (Netherlands)

    van Bennekom, J. G.; Venderbosch, R. H.; Winkelman, J. G. M.; Wilbers, E.; Assink, D.; Lemmens, K. P. J.; Heeres, H. J.

    2013-01-01

    In commercial methanol production from syngas, the conversion is thermodynamically limited to 0.3-0.7 leading to large recycles of non-converted syngas. This problem can be overcome to a significant extent by in situ condensation of methanol during its synthesis which is possible nowadays due to the

  11. Thymidine Analogues for Tracking DNA Synthesis

    Directory of Open Access Journals (Sweden)

    Brenton L. Cavanagh

    2011-09-01

    Full Text Available Replicating cells undergo DNA synthesis in the highly regulated, S-phase of the cell cycle. Analogues of the pyrimidine deoxynucleoside thymidine may be inserted into replicating DNA, effectively tagging dividing cells allowing their characterisation. Tritiated thymidine, targeted using autoradiography was technically demanding and superseded by 5-bromo-2-deoxyuridine (BrdU and related halogenated analogues, detected using antibodies. Their detection required the denaturation of DNA, often constraining the outcome of investigations. Despite these limitations BrdU alone has been used to target newly synthesised DNA in over 20,000 reviewed biomedical studies. A recent breakthrough in “tagging DNA synthesis” is the thymidine analogue 5-ethynyl-2′-deoxyuridine (EdU. The alkyne group in EdU is readily detected using a fluorescent azide probe and copper catalysis using ‘Huisgen’s reaction’ (1,3-dipolar cycloaddition or ‘click chemistry’. This rapid, two-step biolabelling approach allows the tagging and imaging of DNA within cells whilst preserving the structural and molecular integrity of the cells. The bio-orthogonal detection of EdU allows its application in more experimental assays than previously possible with other “unnatural bases”. These include physiological, anatomical and molecular biological experimentation in multiple fields including, stem cell research, cancer biology, and parasitology. The full potential of EdU and related molecules in biomedical research remains to be explored.

  12. Programmable chemical controllers made from DNA.

    Science.gov (United States)

    Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

    2013-10-01

    Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents. PMID:24077029

  13. DNA Nanoparticles for Improved Protein Synthesis In Vitro.

    Science.gov (United States)

    Galinis, Robertas; Stonyte, Greta; Kiseliovas, Vaidotas; Zilionis, Rapolas; Studer, Sabine; Hilvert, Donald; Janulaitis, Arvydas; Mazutis, Linas

    2016-02-24

    The amplification and digital quantification of single DNA molecules are important in biomedicine and diagnostics. Beyond quantifying DNA molecules in a sample, the ability to express proteins from the amplified DNA would open even broader applications in synthetic biology, directed evolution, and proteomics. Herein, a microfluidic approach is reported for the production of condensed DNA nanoparticles that can serve as efficient templates for in vitro protein synthesis. Using phi29 DNA polymerase and a multiple displacement amplification reaction, single DNA molecules were converted into DNA nanoparticles containing up to about 10(4)  clonal gene copies of the starting template. DNA nanoparticle formation was triggered by accumulation of inorganic pyrophosphate (produced during DNA synthesis) and magnesium ions from the buffer. Transcription-translation reactions performed in vitro showed that individual DNA nanoparticles can serve as efficient templates for protein synthesis in vitro.

  14. Unscheduled DNA synthesis in frog lens at 50C

    International Nuclear Information System (INIS)

    Unscheduled DNA labeling occurs in the frog even at low temperatures. It is concluded tentatively that UV-induced labeling observed in cold incubated lenses represents repair synthesis of DNA. (author)

  15. New strategies in chemical synthesis and catalysis

    CERN Document Server

    Pignataro, Bruno

    2012-01-01

    Providing a comprehensive overview of the essential topics, this book covers the core areas of organic, inorganic, organometallic, biochemical synthesis and catalysis.The authors are among the rising stars in European chemistry, a selection of participants in the 2010 European Young Chemists Award competition, and their contributions deal with most of the frontier issues in chemical synthesis. They give an account of the latest research results in chemistry in Europe, as well as the state of the art in their field of research and the outlook for the future.

  16. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Peter J. Tijrn

    2000-09-30

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  17. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    2001-03-31

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  18. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Peter J. Tijrn

    2000-06-30

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  19. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-10-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  20. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    1999-07-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  1. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    2002-07-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  2. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    2000-10-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  3. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    1998-01-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  4. Alternative Fuels and Chemicals from Synthesis Gas

    Energy Technology Data Exchange (ETDEWEB)

    Peter Tijrn

    2003-01-02

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  5. Alternative Fuels and Chemicals from Synthesis Gas

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    1998-12-02

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  6. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    1999-01-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  7. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    1999-04-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  8. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Peter Tijrn

    2003-02-03

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  9. Alternative Fuels and Chemicals From Synthesis Gas

    Energy Technology Data Exchange (ETDEWEB)

    none

    1998-07-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  10. Alternative fuels and chemicals from synthesis gas

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    1998-08-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  11. The Chemical Synthesis of Discodermolide

    Science.gov (United States)

    Paterson, I.; Florence, G. J.

    The marine sponge-derived polyketide discodermolide is a potent antimitotic agent that represents a promising natural product lead structure in the treatment of cancer. Discodermolide shares the same microtubule-stabilising mechanism of action as Taxol®, inhibits the growth of solid tumours in animal models and shows synergy with Taxol. The pronounced cytotoxicity of discodermolide, which is maintained against cancer cell lines that display resistance to Taxol and other drugs, combined with its scarce availability from its natural source, has fuelled significant academic and industrial interest in devising a practical total synthesis as a means of ensuring a sustainable supply for drug development. This chapter surveys the various total syntheses of discodermolide that have been completed over the period 1993-2007, focusing on the strategies employed for introduction of the multiple stereocentres and achieving control over the alkene geometry, along with the various methods used for realising the pivotal fragment couplings to assemble progressively the full carbon skeleton. This dedicated synthetic effort has triumphed in removing the supply problem for discodermolide, providing sufficient material for extensive biological studies and enabling its early stage clinical development, as well as facilitating SAR studies for lead optimisation.

  12. Speciality chemicals from synthesis gas

    Energy Technology Data Exchange (ETDEWEB)

    Lin, J.J.; Knifton, J.F. (Shell Development Company, Houston, TX (USA))

    1992-04-01

    Texaco has undertaken research to investigate the use of carbon monoxide and hydrogen as building blocks for the manufacture of amidocarbonylation products. The amidocarbonylation reaction offers a convenient method to construct two functionalities - amido and carboxylate - simultaneously. Texaco has extended this chemistry to make a variety of speciality chemicals by tailoring cobalt catalysts. Products which have been made including: surface active agents such as the C{sub 14} - C{sub 16} alkyl amidoacids; surfactants; intermediates for sweeteners like aspartame; food additives like glutamic acid; and chelating agents such as polyamidoacids. 20 refs., 10 figs., 1 tab.

  13. Efficient Biocatalytic Synthesis of Chiral Chemicals.

    Science.gov (United States)

    Zhang, Zhi-Jun; Pan, Jiang; Ma, Bao-Di; Xu, Jian-He

    2016-01-01

    Chiral chemicals are a group of important chiral synthons for the synthesis of a series of pharmaceuticals, agrochemicals, and fine chemicals. In past decades, a number of biocatalytic approaches have been developed for the green and effective synthesis of various chiral chemicals. However, the practical application of these biocatalytic processes is still hindered by the lack of highly efficient and robust biocatalysts, which usually results in the low volumetric productivity and high cost of the bioprocesses. Further step forward of biocatalysis in industrial application strongly requires the development of versatile and highly efficient biocatalysts, aiming to increase the process efficiency and facilitate the downstream processing. Recently, the fast growth of genome sequences in the database in post-genomic era offers great opportunities for accessing numerous biocatalysts with practical application potential, and the so-called genome mining approach provides time-effective and highly specific strategy for the fast identification of target enzymes with desired properties and outperforms the traditional screening of soil samples for microbial enzyme producers of interest. A number of biocatalytic processes with industrial application potential were developed thereafter. Further development of protein engineering strategies, process optimization, and cooperative work between biologists, organic chemists, and engineers is expected to make biocatalysis technology the first choice approach for the eco-friendly, highly efficient, and cost-effective synthesis of chiral chemicals in the near future. PMID:25537446

  14. An autoradiographic demonstration of nuclear DNA replication by DNA polymerase alpha and of mitochondrial DNA synthesis by DNA polymerase gamma.

    OpenAIRE

    Geuskens, M.; Hardt, N; Pedrali-Noy, G; Spadari, S

    1981-01-01

    The incorporation of thymidine into the DNA of eukaryotic cells is markedly depressed, but not completely inhibited, by aphidicolin, a highly specific inhibitor of DNA polymerase alpha. An electron microscope autoradiographic analysis of the synthesis of nuclear and mitochondrial DNA in vivo in Concanavalin A stimulated rabbit spleen lymphocytes and in Hamster cell cultures, in the absence and in the presence of aphidicolin, revealed that aphidicolin inhibits the nuclear but not the mitochond...

  15. Differential sensitivity to aphidicolin of replicative DNA synthesis and ultraviolet-induced unscheduled DNA synthesis in vivo in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Seki,Shuji

    1984-06-01

    Full Text Available In vivo in mammalian cells, ultraviolet-induced unscheduled DNA synthesis was less sensitive to aphidicolin than was replicative DNA synthesis. Replicative DNA synthesis in HeLa, HEp-2, WI-38 VA-13 and CV-1 cells was inhibited more than 97% by aphidicolin at 10 micrograms/ml, whereas aphidicolin inhibition of DNA synthesis in ultraviolet-irradiated cells varied between 30% and 90% depending on cell types and assay conditions. Aphidicolin inhibition of unscheduled DNA synthesis (UDS in HeLa cells increased gradually with increasing aphidicolin concentration and reached approximately 90% at 100 micrograms/ml aphidicolin. A significant fraction of UDS in ultraviolet-irradiated HEp-2 cells was resistant to aphidicolin even at 300 micrograms/ml. Considered along with related information reported previously, the present results suggest that both aphidicolin-sensitive and insensitive DNA polymerases, DNA polymerase alpha and a non-alpha DNA polymerase (possibly DNA polymerase beta, are involved in in situ UDS in these ultraviolet-irradiated cells. Comparison of staphylococcal nuclease sensitivity between DNAs repaired in the presence and in the absence of aphidicolin in HEp-2 cells suggested that the involvement of DNA polymerase alpha in UDS favored DNA synthesis in the intranucleosomal region.

  16. Chemical Vapor Synthesis of Nanocrystalline Oxides

    Science.gov (United States)

    Djenadic, Ruzica; Winterer, Markus

    The generation of nanoparticles in the gas phase by Chemical Vapor Synthesis (CVS) may be described from the point of view of chemical engineering as a sequence of unit operations among which reactant delivery, reaction energy input, and product separation are key processes which determine the product characteristics and quality required by the applications of nanoparticles and powders. In case of CVS, the volatility of the reactants (precursors) may severely limit the possible type of products as well as the production rate. It is shown that these limits can be lifted by use of a laser flash evaporator which also enables the use of precursor mixtures for the production of complex oxides as shown for Co-doped ZnO and the pulsed operation to influence powder characteristics. The mode in which energy is supplied to the particle synthesis reactor has also substantial influence on particle and powder characteristics as is shown for TiO2 using different time-temperatureprofiles.

  17. Synthesis and optimization of integrated chemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Paul I.; Evans, Lawrence B.

    2002-04-26

    This is the final technical report for the project titled ''Synthesis and optimization of integrated chemical processes''. Progress is reported on novel algorithms for the computation of all heteroazeotropic compositions present in complex liquid mixtures; the design of novel flexible azeotropic separation processes using middle vessel batch distillation columns; and theory and algorithms for sensitivity analysis and numerical optimization of hybrid discrete/continuous dynamic systems.

  18. DNA ligase I selectively affects DNA synthesis by DNA polymerases delta and epsilon suggesting differential functions in DNA replication and repair.

    OpenAIRE

    Mossi, R; Ferrari, E.; Hübscher, U

    1998-01-01

    The joining of single-stranded breaks in double-stranded DNA is an essential step in many important processes such as DNA replication, DNA repair, and genetic recombination. Several data implicate a role for DNA ligase I in DNA replication, probably coordinated by the action of other enzymes and proteins. Since both DNA polymerases delta and epsilon show multiple functions in different DNA transactions, we investigated the effect of DNA ligase I on various DNA synthesis events catalyzed by th...

  19. Cell-free assay measuring repair DNA synthesis in human fibroblasts

    International Nuclear Information System (INIS)

    Osmotic disruption of confluent cultured human fibroblasts that have been irradiated or exposed to chemical carcinogens allows the specific measurement of repair DNA synthesis using dTTP as a precursor. Fibroblasts similarly prepared from various xeroderma pigmentosum cell lines show the deficiencies of uv-induced DNA synthesis predicted from in vivo studies, while giving normal responses to methylmethanesulfonate. A pyrimidine-dimer-specific enzyme, T4 endonuclease V, stimulated the rate of uv-induced repair synthesis with normal and xeroderma pigmentosum cell lines. This system should prove useful for identifying agents that induce DNA repair, and cells that respond abnormally to such induction. It should also be applicable to an in vitro complementation assay with repair-defective cells and proteins obtained from repair-proficient cells. Finally, by using actively growing fibroblasts and thymidine in the system, DNA replication can be measured and studied in vitro

  20. Impact and mechanism of TiO2 nanoparticles on DNA synthesis in vitro

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The impact of TiO2 nanoparticles on DNA synthesis in vitro in the dark and the molecular mechanism of such impact were studied. The impact of TiO2 nanoparticles on DNA synthesis was investigated by adding TiO2 nanoparticles in different sizes and at various concentrations into the polymerase chain reaction (PCR) system. TiO2 nanoparticles were premixed with the DNA polymerase, the primer or the template, respectively and then the supernatant and the precipitation of each mixture were added into the PCR system separately to observe the impact on DNA synthesis. Sequentially the interaction be- tween TiO2 nanoparticles and the DNA polymerase, the primer or the template was further analyzed by using UV-visible spectroscopy and polyacrylamide gel electrophoresis (PAGE). The results suggest that TiO2 nanoparticles inhibit DNA synthesis in the PCR system in the dark more severely than mi- croscale TiO2 particles at the equivalent concentration and the inhibition effect of TiO2 nanoparticles is concentration dependent. The molecular mechanism of such inhibition is that in the dark, TiO2 nanoparticles interact with the DNA polymerase through physical adsorption while TiO2 nanoparticles do with the primer or the template in a chemical adsorption manner. The disfunction levels of the bio-molecules under the impact of TiO2 nanoparticles are in the following order: the primer > the tem- plate > the DNA polymerase.

  1. Use of scintillometric quantitation of unscheduled DNA synthesis in isolated rat hepatocytes for the screening of genotoxic agents

    International Nuclear Information System (INIS)

    The induction of unscheduled DNA synthesis has been considered as a suitable endpoint for the screening of genotoxic agents. Experimentally, unscheduled DNA synthesis is most frequently measured by autoradiography. The purpose of this report was to examine the usefulness of the liquid scintillation counting technique in measuring unscheduled DNA synthesis response in isolated rat hepatocytes. The various liquid scintillation counting-based unscheduled DNA synthesis assay procedures were examined according to the following groupings: (1) procedures based on the acid precipitation of cellular macromolecules, (2) procedures based on isopycnic gradient centrifugation of solubilized cells, (3) procedures based on nuclei isolation in conjunction with other DNA purification methods, and (4) procedures based on the selective retention of hepatocellular DNA. Limited cases in which test chemicals gave positive unscheduled DNA synthesis response in liquid scintillation counting-based assays and negative unscheduled DNA synthesis response in autoradiography-based assays are presented. It is concluded that liquid scintillation counting-based unscheduled DNA synthesis assays represent an appropriate system for inclusion in carcinogenicity and mutagenicity testing programs

  2. Mapping student thinking in chemical synthesis

    Science.gov (United States)

    Weinrich, Melissa

    In order to support the development of learning progressions about central ideas and practices in different disciplines, we need detailed analyses of the implicit assumptions and reasoning strategies that guide students' thinking at different educational levels. In the particular case of chemistry, understanding how new chemical substances are produced (chemical synthesis) is of critical importance. Thus, we have used a qualitative research approach based on individual interviews with first semester general chemistry students (n = 16), second semester organic chemistry students (n = 15), advanced undergraduates (n = 9), first year graduate students (n = 15), and PhD candidates (n = 16) to better characterize diverse students' underlying cognitive elements (conceptual modes and modes of reasoning) when thinking about chemical synthesis. Our results reveal a great variability in the cognitive resources and strategies used by students with different levels of training in the discipline to make decisions, particularly at intermediate levels of expertise. The specific nature of the task had a strong influence on the conceptual sophistication and mode of reasoning that students exhibited. Nevertheless, our data analysis has allowed us to identify common modes of reasoning and assumptions that seem to guide students' thinking at different educational levels. Our results should facilitate the development of learning progressions that help improve chemistry instruction, curriculum, and assessment.

  3. Wet chemical synthesis of soluble gold nanogaps

    DEFF Research Database (Denmark)

    Jain, Titoo; Tang, Qingxin; Bjørnholm, Thomas;

    2014-01-01

    with little variation in the interface between molecule and electrode (AuNR). In this Account, we highlight recent progress in using chemically synthesized AuNRs as building blocks for molecular electronic applications. We outline the general synthesis and properties of AuNRs and describe the aqueous growth...... of dimeric AuNR structures from an insulating molecule linked to AuNR precursors (gold seeds). Conjugated, electronically active molecules are typically not soluble under the conditions required for the bottom-up growth of AuNRs. Therefore, we present a strategy that utilizes host-guest chemistry in order...

  4. Single-molecule chemical reactions on DNA origami

    DEFF Research Database (Denmark)

    Voigt, Niels Vinther; Tørring, Thomas; Rotaru, Alexandru;

    2010-01-01

    as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position...... on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally......DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve...

  5. Analytical Devices Based on Direct Synthesis of DNA on Paper.

    Science.gov (United States)

    Glavan, Ana C; Niu, Jia; Chen, Zhen; Güder, Firat; Cheng, Chao-Min; Liu, David; Whitesides, George M

    2016-01-01

    This paper addresses a growing need in clinical diagnostics for parallel, multiplex analysis of biomarkers from small biological samples. It describes a new procedure for assembling arrays of ssDNA and proteins on paper. This method starts with the synthesis of DNA oligonucleotides covalently linked to paper and proceeds to assemble microzones of DNA-conjugated paper into arrays capable of simultaneously capturing DNA, DNA-conjugated protein antigens, and DNA-conjugated antibodies. The synthesis of ssDNA oligonucleotides on paper is convenient and effective with 32% of the oligonucleotides cleaved and eluted from the paper substrate being full-length by HPLC for a 32-mer. These ssDNA arrays can be used to detect fluorophore-linked DNA oligonucleotides in solution, and as the basis for DNA-directed assembly of arrays of DNA-conjugated capture antibodies on paper, detect protein antigens by sandwich ELISAs. Paper-anchored ssDNA arrays with different sequences can be used to assemble paper-based devices capable of detecting DNA and antibodies in the same device and enable simple microfluidic paper-based devices.

  6. Synthesis and NMR of {sup 15}N-labeled DNA fragments

    Energy Technology Data Exchange (ETDEWEB)

    Jones, R.A. [Rutgers, The State Univ. of New Jersey, Piscataway, NJ (United States)

    1994-12-01

    DNA fragments labeled with {sup 15}N at the ring nitrogens and at the exocyclic amino groups can be used to obtain novel insight into interactions such as base pairing, hydration, drug binding, and protein binding. A number of synthetic routes to {sup 15}N-labeled pyrimidine nucleosides, purines, and purine nucleosides have been reported. Moreover, many of these labeled bases or monomers have been incorporated into nucleic acids, either by chemical synthesis or by biosynthetic procedures. The focus of this chapter will be on the preparation of {sup 15}N-labeled purine 2{prime}-deoxynucleosides, their incorporation into DNA fragments by chemical synthesis, and the results of NMR studies using these labeled DNA fragments.

  7. Replication stress activates DNA repair synthesis in mitosis

    DEFF Research Database (Denmark)

    Minocherhomji, Sheroy; Ying, Songmin; Bjerregaard, Victoria A;

    2015-01-01

    mitosis serves as the trigger for completion of DNA replication at CFS loci in human cells. Given that this POLD3-dependent mitotic DNA synthesis is enhanced in aneuploid cancer cells that exhibit intrinsically high levels of chromosomal instability (CIN(+)) and replicative stress, we suggest...

  8. Inhibition of DNA-dependent RNA synthesis by 8-methoxypsoralen.

    Science.gov (United States)

    Gniazdowski, M; Czyz, M; Wilmańska, D; Studzian, K; Frasunek, M; Płucienniczak, A; Szmigiero, L

    1988-09-01

    The effect of the photobinding of 8-methoxypsoralen to phage T7 DNA on different steps of RNA synthesis in vitro was assayed. Total RNA synthesis is reduced to a few percent and the transcript size is decreased, as shown by means of gel filtration on a Sepharose 4B column when DNA of the adduct content of six drug molecules per 10(3) nucleotides is used. The initiation of RNA chains seems to be less affected, as inferred from an abortive initiation assay. Synthesis of pppApU on DNA of the same adduct content is inhibited to 34% of the corresponding controls, while the overall RNA synthesis is inhibited to 6%. The amount of the enzyme needed for maximal retention of DNA, the kinetics of its binding and the decay of the polymerase-DNA complex at high ionic strength (or on decrease of the temperature) are similar with DNA either irradiated in the absence of the drug or DNA bearing six 8-methoxypsoralen molecules per 10(3) nucleotides. It is concluded from this study that 8-methoxypsoralen partially inhibits initiation and blocks movement of RNA polymerase along the template, inducing premature termination. It does not appear to influence the binding of the enzyme to DNA. PMID:3048406

  9. Total Chemical Synthesis,Assembly of Human Torque Teno Virus Genome

    Institute of Scientific and Technical Information of China (English)

    Zheng Hou; Gengfu Xiao

    2011-01-01

    Torque teno virus(TTV)is a nonenveloped virus containing a single-stranded,circular DNA genome of approximately 3.8kb.We completely synthesized the 3808 nucleotides of the TTV(SANBAN isolate)genome,which contains a hairpin structure and a GC-rich region.More than 100 overlapping oligonucleotides were chemically synthesized and assembled by polymerise chain assembly reaction(PCA),and the synthesis was completed with splicing by overlap extension(SOEing).This study establishes the methodological basis of the chemical synthesis of a viral genome for use as a live attenuated vaccine or gene therapy vector.

  10. Inhibition of DNA replication, DNA repair synthesis, and DNA polymerases α and δ by butylphenyl deoxyguanosine triphosphate

    International Nuclear Information System (INIS)

    Semiconservative DNA replication in growing mammalian cells and ultraviolet (UV)-induced DNA repair synthesis in nongrowing mammalian cells are mediated by one or both of the aphidicolin-sensitive DNA polymerases, α and/or δ. They have studied the inhibition of replication and repair synthesis in permeable human cells by N2 (p-n-butylphenyl)-2'-deoxyguanosine-5'-triphosphate (BuPh dGTP), an agent which inhibits polymerase α strongly and polymerase δ weakly. Both processes are inhibited by BuPh-dGTP in competition with dGTP. The K/sub i/'s are, for replication, 2-3 μM and, for repair synthesis, 3-4 μM, consistent with the involvement of the same DNA polymerase in both processes. Inhibition of isolated human polymerase α by BuPh-dGTP is also competitive with dGTP, but the K/sub i/ is approximately 10 nM, several hundred-fold lower than the K/sub i/'s of replication and repair synthesis. Isolated polymerase δ is inhibited by BuPh-dGTP at doses similar to those which inhibit replication and repair synthesis, however, attempts to determine the K/sub i/ of polymerase δ were hampered by the finding that the dependence of δ activity on deoxyribunucleotide concentration is parabolic at low doses. This behavior differs from the behavior of polymerase α and of cellular DNA replication and repair synthesis, all of which show a simple, hyperbolic relationship between activity and deoxyribonucleotide concentration. Thus, inhibition of DNA replication and UV induced DNA repair synthesis by BuPh dGTP is quantitatively similar to DNA polymerase δ, but some other characteristics of the cellular processes are more similar to those of polymerase α

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

    OpenAIRE

    LITOVCHICK, ALEXANDER; Clark, Matthew A.; Keefe, Anthony D

    2014-01-01

    The affinity-mediated selection of large libraries of DNA-encoded small molecules is increasingly being used to initiate drug discovery programs. We present universal methods for the encoding of such libraries using the chemical ligation of oligonucleotides. These methods may be used to record the chemical history of individual library members during combinatorial synthesis processes. We demonstrate three different chemical ligation methods as examples of information recording processes (writ...

  12. D-ribose inhibits DNA repair synthesis in human lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Zunica, G.; Marini, M.; Brunelli, M.A.; Chiricolo, M.; Franceschi, C.

    1986-07-31

    D-ribose is cytotoxic for quiescent human lymphocytes and severely inhibits their PHA-induced proliferation at concentrations (25-50 mM) at which other simple sugars are ineffective. In order to explain these effects, DNA repair synthesis was evaluated in PHA-stimulated human lymphocytes treated with hydroxyurea and irradiated. D-ribose, in contrast to other reducing sugars, did not induce repair synthesis and therefore did not apparently damage DNA in a direct way, although it markedly inhibited gamma ray-induced repair. Taking into account that lymphocytes must rejoin physiologically-formed DNA strand breaks in order to enter the cell cycle, we suggest that D-ribose exerts its cytotoxic activity by interfering with metabolic pathways critical for the repair of DNA breaks.

  13. Pyrimidine-specific chemical reactions useful for DNA sequencing.

    OpenAIRE

    Rubin, C M; Schmid, C. W.

    1980-01-01

    Potassium permanganate reacts selectively with thymidine residues in DNA (1) while hydroxylamine hydrochloride at pH 6 specifically attacks cytosine (2). We have adopted these reactions for use with the chemical sequencing method developed by Maxam and Gilbert (3).

  14. Stimulation of DNA synthesis in cultured primary human mesothelial cells by specific growth factors

    International Nuclear Information System (INIS)

    Monolayer cultures of human mesothelial cells made quiescent by serum deprivation are induced to undergo one round of DNA synthesis by platelet-derived growth factor (PDGF), epidermal growth factor (EGF), or transforming growth factor type beta 1 (TGF-beta 1). This one-time stimulation is independent of other serum components. The kinetics for induction of DNA synthesis observed for PDGF, EGF, and TGF-beta 1 are all similar to one another, with a peak of DNA synthesis occurring 24-36 h after the addition of the growth factors. Repetitive rounds of DNA synthesis and cell division do not ensue after addition of PDGF, EGF, or TGF-beta 1 alone or in combination; however, in media supplemented with chemically denatured serum, each of these factors is capable of sustaining continuous replication of mesothelial cells. Stimulation of growth by PDGF and TGF-beta 1 is unusual for an epithelial cell type, and indicates that mesothelial cells have growth regulatory properties similar to connective tissue cells

  15. Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays

    Directory of Open Access Journals (Sweden)

    Agbavwe Christy

    2011-12-01

    Full Text Available Abstract Background Light-directed in situ synthesis of DNA microarrays using computer-controlled projection from a digital micromirror device--maskless array synthesis (MAS--has proved to be successful at both commercial and laboratory scales. The chemical synthetic cycle in MAS is quite similar to that of conventional solid-phase synthesis of oligonucleotides, but the complexity of microarrays and unique synthesis kinetics on the glass substrate require a careful tuning of parameters and unique modifications to the synthesis cycle to obtain optimal deprotection and phosphoramidite coupling. In addition, unintended deprotection due to scattering and diffraction introduce insertion errors that contribute significantly to the overall error rate. Results Stepwise phosphoramidite coupling yields have been greatly improved and are now comparable to those obtained in solid phase synthesis of oligonucleotides. Extended chemical exposure in the synthesis of complex, long oligonucleotide arrays result in lower--but still high--final average yields which approach 99%. The new synthesis chemistry includes elimination of the standard oxidation until the final step, and improved coupling and light deprotection. Coupling Insertions due to stray light are the limiting factor in sequence quality for oligonucleotide synthesis for gene assembly. Diffraction and local flare are by far the largest contributors to loss of optical contrast. Conclusions Maskless array synthesis is an efficient and versatile method for synthesizing high density arrays of long oligonucleotides for hybridization- and other molecular binding-based experiments. For applications requiring high sequence purity, such as gene assembly, diffraction and flare remain significant obstacles, but can be significantly reduced with straightforward experimental strategies.

  16. Continuous induction of unscheduled DNA synthesis by gamma irradiation

    International Nuclear Information System (INIS)

    The induction of DNA-synthesis in non-S-phase cells is a very sensitive measure of a preceding damage of the DNA. Usually, in an in vivo -in vitro test (treatment of an animal, incorporation of H3-thymidine in a cell suspension) the damaging of DNA takes place hours to days before the evaluation. In this case, the time course of the UDS-induction after a single dose of 1 Gy gamma irradiation should be observed for a long time (21 months). C57 black mice served as test animals. In an age of about 80 days they were irradiated and the induction of unscheduled DNA synthesis was measured at ten points of time during the whole life-span of the animals. Although the repair in this gamma radiation damage in DNA is a very quick process - with centrifugation in alkaline sucrose you find a half time of some minutes - an induction of unscheduled DNA synthesis could be seen at the irradiated animals until the end of their life (640 days). The reason for this could be permanent disorders in cellular regulation caused by the gamma irradiation. 4 figs. (Author)

  17. Ethyl coumarin-3-carboxylate: synthesis and chemical properties

    Directory of Open Access Journals (Sweden)

    Bakr F. Abdel-Wahab

    2014-03-01

    Full Text Available Ethyl coumarin-3-carboxylate occupies an important position in the organic synthesis and is used in production of biologically active compounds. Thus, the data published over the last few years on the methods of synthesis and chemical properties of ethyl coumarin-3-carboxylate are reviewed here for the first time. The reactions were classified as coumarin ring reactions and ester group reactions, and some of these reactions have been applied successfully to the synthesis of biologically and industrially important compounds.

  18. Aliphatic nitro alcohols. Synthesis, chemical transformations and applications

    Energy Technology Data Exchange (ETDEWEB)

    Shvekhgeimer, Mai-Genrikh A [A.N. Kosygin Moscow State Textile Academy, Moscow (Russian Federation)

    1998-01-31

    The data on the synthesis, chemical transformations and practical use of aliphatic nitro alcohols published over the last 25 years are described systematically and analysed. The bibliography includes 316 references.

  19. DNA Chemical discontinuities and their biological consequences

    International Nuclear Information System (INIS)

    The stability of genetic material is a relative concept since under several conditions there are structural changes in cellular DNA which unchain enzimatic processes leading to their own repair. Under certain circunstances the replication mechanism may arrive to a lesion before it be eliminated. It is known that most cells can replicate the injured DNA, but it is not known how this occurs. This mechanism is of great importance because there is strong evidence that mutations can be introduced in this process. Data are reviewed and discussed relating to the present stage of knowledge of this mechanism in bacteria and in mammal cells kept in culture. (M.A.)

  20. The use of chemically stabilised proteolytic enzymes in peptide synthesis

    OpenAIRE

    Colleary, Sandra

    2003-01-01

    The aim of this project was to study various serine proteases, both native and chemically modified, with a view to their application in peptide synthesis. Various chemical modifications of these were carried out to improve their stability before peptide synthesis. Porcine trypsin was stabilised by reaction with ethylene glycol bis-(succinic acid Nhydroxy-succinimide ester) (EG). The enhanced stability is likely due to intramolecular crosslink(s) being formed in the enzyme. EG-tiypsin reta...

  1. DNA Charge Transport: from Chemical Principles to the Cell.

    Science.gov (United States)

    Arnold, Anna R; Grodick, Michael A; Barton, Jacqueline K

    2016-01-21

    The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology. PMID:26933744

  2. Efficient Synthesis of Peptide and Protein Functionalized Pyrrole-Imidazole Polyamides Using Native Chemical Ligation.

    Science.gov (United States)

    Janssen, Brian M G; van Ommeren, Sven P F I; Merkx, Maarten

    2015-06-04

    The advancement of DNA-based bionanotechnology requires efficient strategies to functionalize DNA nanostructures in a specific manner with other biomolecules, most importantly peptides and proteins. Common DNA-functionalization methods rely on laborious and covalent conjugation between DNA and proteins or peptides. Pyrrole-imidazole (Py-Im) polyamides, based on natural minor groove DNA-binding small molecules, can bind to DNA in a sequence specific fashion. In this study, we explore the use of Py-Im polyamides for addressing proteins and peptides to DNA in a sequence specific and non-covalent manner. A generic synthetic approach based on native chemical ligation was established that allows efficient conjugation of both peptides and recombinant proteins to Py-Im polyamides. The effect of Py-Im polyamide conjugation on DNA binding was investigated by Surface Plasmon Resonance (SPR). Although the synthesis of different protein-Py-Im-polyamide conjugates was successful, attenuation of DNA affinity was observed, in particular for the protein-Py-Im-polyamide conjugates. The practical use of protein-Py-Im-polyamide conjugates for addressing DNA structures in an orthogonal but non-covalent manner, therefore, remains to be established.

  3. Efficient Synthesis of Peptide and Protein Functionalized Pyrrole-Imidazole Polyamides Using Native Chemical Ligation

    Directory of Open Access Journals (Sweden)

    Brian M. G. Janssen

    2015-06-01

    Full Text Available The advancement of DNA-based bionanotechnology requires efficient strategies to functionalize DNA nanostructures in a specific manner with other biomolecules, most importantly peptides and proteins. Common DNA-functionalization methods rely on laborious and covalent conjugation between DNA and proteins or peptides. Pyrrole-imidazole (Py–Im polyamides, based on natural minor groove DNA-binding small molecules, can bind to DNA in a sequence specific fashion. In this study, we explore the use of Py–Im polyamides for addressing proteins and peptides to DNA in a sequence specific and non-covalent manner. A generic synthetic approach based on native chemical ligation was established that allows efficient conjugation of both peptides and recombinant proteins to Py–Im polyamides. The effect of Py–Im polyamide conjugation on DNA binding was investigated by Surface Plasmon Resonance (SPR. Although the synthesis of different protein-Py–Im-polyamide conjugates was successful, attenuation of DNA affinity was observed, in particular for the protein-Py–Im-polyamide conjugates. The practical use of protein-Py–Im-polyamide conjugates for addressing DNA structures in an orthogonal but non-covalent manner, therefore, remains to be established.

  4. DNA polymerase-α regulates type I interferon activation through cytosolic RNA:DNA synthesis

    Science.gov (United States)

    Starokadomskyy, Petro; Gemelli, Terry; Rios, Jonathan J.; Xing, Chao; Wang, Richard C.; Li, Haiying; Pokatayev, Vladislav; Dozmorov, Igor; Khan, Shaheen; Miyata, Naoteru; Fraile, Guadalupe; Raj, Prithvi; Xu, Zhe; Xu, Zigang; Ma, Lin; Lin, Zhimiao; Wang, Huijun; Yang, Yong; Ben-Amitai, Dan; Orenstein, Naama; Mussaffi, Huda; Baselga, Eulalia; Tadini, Gianluca; Grunebaum, Eyal; Sarajlija, Adrijan; Krzewski, Konrad; Wakeland, Edward K.; Yan, Nan; de la Morena, Maria Teresa; Zinn, Andrew R.; Burstein, Ezra

    2016-01-01

    Aberrant nucleic acids generated during viral replication are the main trigger for antiviral immunity, and mutations disrupting nucleic acid metabolism can lead to autoinflammatory disorders. Here we investigated the etiology of X-linked reticulate pigmentary disorder (XLPDR), a primary immunodeficiency with autoinflammatory features. We discovered that XLPDR is caused by an intronic mutation that disrupts expression of POLA1, the gene encoding the catalytic subunit of DNA polymerase-α. Unexpectedly, POLA1 deficiency results in increased type I interferon production. This enzyme is necessary for RNA:DNA primer synthesis during DNA replication and strikingly, POLA1 is also required for the synthesis of cytosolic RNA:DNA, which directly modulates interferon activation. Altogether, this work identified POLA1 as a critical regulator of the type I interferon response. PMID:27019227

  5. Synthesis and structural characterization of piperazino-modified DNA that favours hybridization towards DNA over RNA

    DEFF Research Database (Denmark)

    Skov, Joan; Bryld, Torsten; Lindegaard, Dorthe;

    2011-01-01

    We report the synthesis of two C4'-modified DNA analogues and characterize their structural impact on dsDNA duplexes. The 4'-C-piperazinomethyl modification stabilizes dsDNA by up to 5°C per incorporation. Extension of the modification with a butanoyl-linked pyrene increases the dsDNA stabilization...... multiple sites in intermediate exchange on the NMR timescale, resulting in broad lines in NMR spectra. We identified two intercalation sites with NOE data showing that the pyrene prefers to intercalate one base pair away from the modified nucleotide with its linker curled up in the minor groove. Both...... modifications are tolerated in DNA:RNA hybrids but leave their melting temperatures virtually unaffected. Fluorescence data indicate that the pyrene moiety is residing outside the helix. The available data suggest that the DNA discrimination is due to (i) the positive charge of the piperazino ring having a...

  6. Involvement of DNA polymerase δ in DNA repair synthesis in human fibroblasts at late times after ultraviolet irradiation

    International Nuclear Information System (INIS)

    DNA repair synthesis following UV irradiation of confluent human fibroblasts has a biphasic time course with an early phase of rapid nucleotide incorporation and a late phase of much slower nucleotide incorporation. The biphasic nature of this curve suggests that two distinct DNA repair systems may be operative. Previous studies have specifically implicated DNA polymerase δ as the enzyme involved in DNA repair synthesis occurring immediately after UV damage. In this paper, the authors describe studies of DNA polymerase involvement in DNA repair synthesis in confluent human fibroblasts at late times after UV irradiation. Late UV-induced DNA repair synthesis in both intact and permeable cells was found to be inhibited by aphidicolin, indicating the involvement of one of the aphidicolin-sensitive DNA polymerases, α or δ. In permeable cells, the process was further analyzed by using the nucleotide analogue (butylphenyl)-2'-deoxyguanosine 5'-triphosphate, which inhibits DNA polymerase α several hundred times more strongly than it inhibits DNA polymerase δ. The (butylphenyl)-2'-deoxyguanosine 5'-triphosphate inhibition curve for late UV-induced repair synthesis was very similar to that for polymerase δ. It appears that repair synthesis at late time after UV irradiation, like repair synthesis at early times, is mediated by DNA polymerase δ

  7. Flow Chemistry for Designing Sustainable Chemical Synthesis (journal article)

    Science.gov (United States)

    An efficiently designed continuous flow chemical process can lead to significant advantages in developing a sustainable chemical synthesis or process. These advantages are the direct result of being able to impart a higher degree of control on several key reactor and reaction par...

  8. Synthesis of Cross-Linked DNA Containing Oxidized Abasic Site Analogues

    Science.gov (United States)

    2015-01-01

    DNA interstrand cross-links are an important family of DNA damage that block replication and transcription. Recently, it was discovered that oxidized abasic sites react with the opposing strand of DNA to produce interstrand cross-links. Some of the cross-links between 2′-deoxyadenosine and the oxidized abasic sites, 5′-(2-phosphoryl-1,4-dioxobutane) (DOB) and the C4-hydroxylated abasic site (C4-AP), are formed reversibly. Chemical instability hinders biochemical, structural, and physicochemical characterization of these cross-linked duplexes. To overcome these limitations, we developed methods for preparing stabilized analogues of DOB and C4-AP cross-links via solid-phase oligonucleotide synthesis. Oligonucleotides of any sequence are attainable by synthesizing phosphoramidites in which the hydroxyl groups of the cross-linked product were orthogonally protected using photochemically labile and hydrazine labile groups. Selective unmasking of a single hydroxyl group precedes solid-phase synthesis of one arm of the cross-linked DNA. The method is compatible with commercially available phosphoramidites and other oligonucleotide synthesis reagents. Cross-linked duplexes containing as many as 54 nt were synthesized on solid-phase supports. Subsequent enzyme ligation of one cross-link product provided a 60 bp duplex, which is suitable for nucleotide excision repair studies. PMID:24949656

  9. Nanodispersed Oxides-Plasma-Chemical Synthesis and Properties

    Institute of Scientific and Technical Information of China (English)

    Gheorghi VISSOKOV; Katerina ZAHARIEVA

    2007-01-01

    We discuss the plasma-chemical synthesis and the properties of transition metals oxides, Al2O3, SiO2, rare-earth oxides, oxides for ceramics and metal-ceramics, and oxides used as catalysts. Bearing in mind the indisputable advantages of using plasma-chemically synthesized nanodispersed oxides for the needs of various industrial fields, we set out to review the articles published in the past few years devoted to the problems of plasma-chemical synthesis and characterization of nanodispersed oxides.

  10. Drug discovery with DNA-encoded chemical libraries.

    Science.gov (United States)

    Buller, Fabian; Mannocci, Luca; Scheuermann, Jörg; Neri, Dario

    2010-09-15

    DNA-encoded chemical libraries represent a novel avenue for the facile discovery of small molecule ligands against target proteins of biological or pharmaceutical importance. Library members consist of small molecules covalently attached to unique DNA fragments that serve as amplifiable identification barcodes. This encoding allows the in vitro selection of ligands at subpicomolar concentrations from large library populations by affinity capture on a target protein of interest, in analogy to established technologies for the selection of binding polypeptides (e.g., antibodies). Different library formats have been explored by various groups, allowing the construction of chemical libraries comprising up to millions of DNA-encoded compounds. Libraries before and after selection have been characterized by PCR amplification of the DNA codes and subsequent relative quantification of library members using high-throughput sequencing. The most enriched compounds have then been further analyzed in biological assays, in the presence or in the absence of linked DNA. This article reviews experimental strategies used for the construction of DNA-encoded chemical libraries, revealing how selection, decoding, and hit validation technologies have been used for drug discovery programs.

  11. Tunable Hydrophobicity in DNA Micelles : Design, Synthesis, and Characterization of a New Family of DNA Amphiphiles

    NARCIS (Netherlands)

    Anaya, Milena; Kwak, Minseok; Musser, Andrew J.; Muellen, Klaus; Herrmann, Andreas; Müllen, Klaus

    2010-01-01

    This work describes the synthesis and characterization of a new family of DNA amphiphiles containing modified nucleobases. The hydrophobicity was imparted by the introduction of a dodec-1-yne chain at the 5-position of the uracil base, which allowed precise and simple tuning of the hydrophobic prope

  12. Synthesis, DNA binding and cytotoxic evaluation of aminoquinoline scaffolds

    Indian Academy of Sciences (India)

    Gopal Senthil Kumar; Mohamed Ashraf Ali; Tan Soo Choon; Rajendra Prasad Karnam Jayarampillai

    2016-03-01

    An effortless synthetic route has been developed for the synthesis of a new class of aminoquinoline substituted isoindolin-1,3-diones from regio-isomerical hydrazinylquinolines with phthalic anhydride in presence of Eaton’s reagent. DNA binding studies of selected isomeric compounds showed interaction withDNA via intercalation mode with higher binding affinity of 4-substituted quinolines rather than 2-substituted counterparts. Further, all compounds were screened for cytotoxic activity against three human cancer cell lines,among them compound 2c outranged standard doxorubicin against CCRF-CEM cell line.

  13. The Yeast Mitochondrial RNA Polymerase and Transcription Factor Complex Catalyzes Efficient Priming of DNA Synthesis on Single-stranded DNA.

    Science.gov (United States)

    Ramachandran, Aparna; Nandakumar, Divya; Deshpande, Aishwarya P; Lucas, Thomas P; R-Bhojappa, Ramanagouda; Tang, Guo-Qing; Raney, Kevin; Yin, Y Whitney; Patel, Smita S

    2016-08-01

    Primases use single-stranded (ss) DNAs as templates to synthesize short oligoribonucleotide primers that initiate lagging strand DNA synthesis or reprime DNA synthesis after replication fork collapse, but the origin of this activity in the mitochondria remains unclear. Herein, we show that the Saccharomyces cerevisiae mitochondrial RNA polymerase (Rpo41) and its transcription factor (Mtf1) is an efficient primase that initiates DNA synthesis on ssDNA coated with the yeast mitochondrial ssDNA-binding protein, Rim1. Both Rpo41 and Rpo41-Mtf1 can synthesize short and long RNAs on ssDNA template and prime DNA synthesis by the yeast mitochondrial DNA polymerase Mip1. However, the ssDNA-binding protein Rim1 severely inhibits the RNA synthesis activity of Rpo41, but not the Rpo41-Mtf1 complex, which continues to prime DNA synthesis efficiently in the presence of Rim1. We show that RNAs as short as 10-12 nt serve as primers for DNA synthesis. Characterization of the RNA-DNA products shows that Rpo41 and Rpo41-Mtf1 have slightly different priming specificity. However, both prefer to initiate with ATP from short priming sequences such as 3'-TCC, TTC, and TTT, and the consensus sequence is 3'-Pu(Py)2-3 Based on our studies, we propose that Rpo41-Mtf1 is an attractive candidate for serving as the primase to initiate lagging strand DNA synthesis during normal replication and/or to restart stalled replication from downstream ssDNA. PMID:27311715

  14. Toxicity DNA damage and inhibition of DNA repair synthesis in human melanoma cells by concentrated sunlight

    International Nuclear Information System (INIS)

    A water lens was used to focus solar radiation, giving an 8-fold concentration of the total spectrum and a cytocidal flux similar to that of laboratory UV sources. Survival curves for human melanoma cells were similar for sunlight and 254 nm UV. An xeroderma pigmentosum lymphoblastoid line was equally sensitive to both agents and human cell lines sensitive to ionizing radiation (lymphoblastoid lines), crosslinking agents or monofunctional alkylating agents (melanoma lines) had the same 254 nm UV and solar survival responses as appropriate control lines. Two melanoma sublines derived separately by 16 cycles of treatment with sunlight or 254 nm UV were crossresistant to both agents. In one melanoma cell line, DNA strand breaks and DNA protein crosslinking were induced in melanoma cells by sunlight but pyrimidine dimers and DNA interstrand crosslinking could not be detected. The solar fluence response of DNA repair synthesis was much less than that from equitoxic 254 nm UV, reaching a maximum near the D0 value and then declining; but semiconservative DNA synthesis remained high. These effects were not due to changes in thymidine pool sizes. Solar exposure did not have a major effect on 254 nm UV-induced repair synthesis. (author)

  15. Different patterns of bacterial DNA synthesis during postantibiotic effect.

    OpenAIRE

    Gottfredsson, M; Erlendsdóttir, H; Gudmundsson, A.; Gudmundsson, S.

    1995-01-01

    Studies on bacterial metabolism during the postantibiotic effect (PAE) period are limited but might provide insight into the nature of the PAE. We evaluated the rate of DNA synthesis in bacteria during the PAE period after a 1-h exposure of organisms in the logarithmic growth phase to various antibiotics. Staphylococcus aureus ATCC 25923 was exposed to vancomycin, dicloxacillin, rifampin, and ciprofloxacin; Escherichia coli ATCC 25922 was exposed to gentamicin, tobramycin, rifampin, imipenem,...

  16. DNA microarray synthesis by using PDMS molecular stamps (Ⅲ)-- Optimization for the reaction conditions

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Optimization for the technological processes of fabricating oligonucleotide microarray by the molecular stamping method is studied in this note. Three factors that affect the pressing coupling reactions of the nucleosides are focused on: the stability of the chemical activities of the reaction solutions, the contamination of the remain of the reactive nucleotides among the different spots on the chip, and the influence of the capping reaction on the hybridization result. The experiments show that the acetonitrile solution of tetrazole and nucleoside monomer could maintain sufficient reactive activity for more than 10 h. An effective method has been used and proved to eliminate the residual reactive nucleosides on chip with small molecules containing hydroxyl group. Finally, the capping step-- a regular step in the conventional DNA chemical synthesis can be neglected in our on-chip DNA synthetic process, which would not affect its hybridization results.

  17. Psoralen plus near-ultraviolet light: a possible new method for measuring DNA repair synthesis

    International Nuclear Information System (INIS)

    A new method is proposed to inhibit semiconservative DNA synthesis in cultured cells while DNA repair synthesis is being measured. The cells are treated with the DNA-crosslinking agent Trioxalen (4,5,8-trimethylpsoralen) plus near-ultraviolet light, and consequently 99.5% inhibition of replicative DNA synthesis is achieved. Additional DNA-damaging agents induce thymidine incorporation into the double-stranded regions of the DNA. The new method gave results very similar to those obtained with the benzoylated naphthoylated DEAE (BND) cellulose method using three human fibroblast strains, of which one had deficient capacity for DNA repair synthesis following treatment with γ rays and methyl methanesulfonate. The advantages of the new method are simplicity and rapidity, as well as the high extent to which replicative DNA synthesis is inhibited

  18. Psoralen plus near-ultraviolet light: a possible new method for measuring DNA repair synthesis

    International Nuclear Information System (INIS)

    A new method is proposed to inhibit semiconservative DNA synthesis in cultured cells while DNA repair synthesis is being measured. The cells are treated with the DNA-crosslinking agent Trioxalen (4,5,8-trimethylpsoralen) plus near-ultraviolet light, and consequently 99.5% inhibition of replicative DNA synthesis is achieved. Additional DNA-damaging agents induce thymidine incorporation into the double-stranded regions of the DNA. The new method gave results very similar to those obtained with the benzoylated naphthoylated DEAE (BND) cellulose method using three human fibroblast strains, of which one had deficient capacity for DNA repair synthesis following treatment with gamma rays and methyl methanesulfonate. The advantages of the new method are simplicity and rapidity, as well as the high extent to which replicative DNA synthesis is inhibited

  19. Deoxyadenosine family: improved synthesis, DNA damage and repair, analogs as drugs.

    Science.gov (United States)

    Biswas, Himadri; Kar, Indrani; Chattopadhyaya, Rajagopal

    2013-08-01

    Improved synthesis of 2'-deoxyadenosine using Escherichia coli overexpressing some enzymes and gram-scale chemical synthesis of 2'-deoxynucleoside 5'-triphosphates reported recently are described in this review. Other topics include DNA damage induced by chromium(VI), Fenton chemistry, photoinduction with lumazine, or by ultrasound in neutral solution; 8,5'-cyclo-2'-deoxyadenosine isomers as potential biomarkers; and a recapitulation of purine 5',8-cyclonucleoside studies. The mutagenicities of some products generated by oxidizing 2'-deoxyadenosine 5'-triphosphate, nucleotide pool sanitization, and translesion synthesis are also reviewed. Characterizing cross-linking between nucleosides in opposite strands of DNA and endonuclease V-mediated deoxyinosine excision repair are discussed. The use of purine nucleoside analogs in the treatment of rarer chronic lymphoid leukemias is reviewed. Some analogs at the C8 position induced delayed polymerization arrest during HIV-1 reverse transcription. The susceptibility of clinically metronidazole-resistant Trichomonas vaginalis to two analogs, toyocamycin and 2-fluoro-2'-deoxyadenosine, were tested in vitro. GS-9148, a dAMP analog, was translocated to the priming site in a complex with reverse transcriptase and double-stranded DNA to gain insight into the mechanism of reverse transcriptase inhibition. PMID:25436589

  20. Replication stress activates DNA repair synthesis in mitosis.

    Science.gov (United States)

    Minocherhomji, Sheroy; Ying, Songmin; Bjerregaard, Victoria A; Bursomanno, Sara; Aleliunaite, Aiste; Wu, Wei; Mankouri, Hocine W; Shen, Huahao; Liu, Ying; Hickson, Ian D

    2015-12-10

    Oncogene-induced DNA replication stress has been implicated as a driver of tumorigenesis. Many chromosomal rearrangements characteristic of human cancers originate from specific regions of the genome called common fragile sites (CFSs). CFSs are difficult-to-replicate loci that manifest as gaps or breaks on metaphase chromosomes (termed CFS 'expression'), particularly when cells have been exposed to replicative stress. The MUS81-EME1 structure-specific endonuclease promotes the appearance of chromosome gaps or breaks at CFSs following replicative stress. Here we show that entry of cells into mitotic prophase triggers the recruitment of MUS81 to CFSs. The nuclease activity of MUS81 then promotes POLD3-dependent DNA synthesis at CFSs, which serves to minimize chromosome mis-segregation and non-disjunction. We propose that the attempted condensation of incompletely duplicated loci in early mitosis serves as the trigger for completion of DNA replication at CFS loci in human cells. Given that this POLD3-dependent mitotic DNA synthesis is enhanced in aneuploid cancer cells that exhibit intrinsically high levels of chromosomal instability (CIN(+)) and replicative stress, we suggest that targeting this pathway could represent a new therapeutic approach.

  1. Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

    Science.gov (United States)

    Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

    2010-05-04

    A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

  2. Synthesis, photochemical properties and DNA binding studies of dna cleaving agents based on chiral dipyridine dihydrodioxins salts

    Science.gov (United States)

    Shamaev, Alexei

    Control of chemical reactions becomes especially challenging when chemical processes have to work within the complexity of biological environments. This is one of the reasons why the ability to design "caged" molecules with structure, reactivity, and biological activity that can be activated externally by light continues to draw significant attention, from both the practical and fundamental points of view. Possible applications of such molecules include design of molecular machines and switches, logic gate mimics, optical sensors, drug delivery systems, etc. Since "caged" molecules are of particular use for processes that occur in biochemical systems and in the environment, interesting light-sensitive systems, anti-cancer drugs, have been developed recently to control DNA cleavage. Caged molecules may interact with or bind with DNA and can be classified by their mechanism of action. Each of these classes of molecules has a different structure and interacts with DNA in a different way, but some molecules can combine several functionalities. The preponderance of caged molecules, anti-cancer drugs, capable of DNA cleavage or their metabolites incorporate Electron Transfer (ET) functionalities, which play important roles in physiological responses. These main groups include quinones (or phenolic precursors), metal complexes, aromatic nitro compounds (or reduced derivatives), and conjugated imines (or iminium species). Redox cycling with oxygen can occur giving rise to Oxidation Stress (OS) through generation of Reactive Oxygen Species (ROS) which can contribute to drug efficacy or can lead to undesirable toxicity. In some cases, ET results in interference with normal electron transport chains. In this work a series of caged molecules-chiral Pyrene Dihydridioxins (PDHD)-DNA chiral DNA intecalators and PDHD-metal complexes bearing masked o-quinone functionality activated through intramolecular ET were synthesized. The o-quinone release and intramolecular ET can be easily

  3. Ultrafast chemical repair of DNA single and double strand break precursors in irradiated V79 cells

    International Nuclear Information System (INIS)

    The fast kinetics of reactions of free radical precursors of DNA single strand breaks (ssb) and double strand breaks (dsb) have been determined in Chinese hamster V79 cells by fast mixing and irradiation methods using the alkaline unwinding technique to assay breaks. Fast chemical repair of oxygen-dependent ssb and dsb precursors was observed and approached completion within 10 to 20 ms of irradiation. Treatment of cells with the glutathione synthesis blocking agent, buthionine sulphoximine, showed that approximately half of the chemical repair was attributable to intracellular non-protein thiols. The nature of the residual repair is obscure, but it is apparently not attributable to non-protein thiols. Similar repair rates and thiol dependences were also found for cell kill. With all three endpoints, oxygen competes with and blocks the chemical repair. 36 refs., 6 figs., 1 tab

  4. Studies on enzymes involved in DNA synthesis and thymine nucleotide formation in potato tuber slices

    International Nuclear Information System (INIS)

    Activity changes of several enzymes involved in DNA synthesis were investigated in potato tuber tissue in which DNA synthesis was induced by slicing. Nucleoside phosphotransferase activity increased only slightly during aging of the tissue discs. Thymidine monophosphate (TMP) kinase activity increased about 36% after aging for 24 hr. Protein synthesis in an early stage of aging was necessary for the activity increase. A 2.7-fold increase was observed in DNA polymerase activity after aging for 36 hr. The activity increase was due to continuous synthesis of enzyme protein. In vivo examination of TMP synthetase suggests that its activity does not necessarily increase before full development of DNA synthesis. It was concluded that among the enzymes examined, TMP kinase activity may increase shortly after slicing to support a massive supply of thymidine triphosphate and the increased activity of DNA polymerane may contribute to the active synthesis of DNA in aged discs. (auth.)

  5. Routes to deagglomerated nanopowder by chemical synthesis

    OpenAIRE

    Burgard, Detlef; Kropf, Christian; Nass, Rüdiger; Schmidt, Helmut K.

    1994-01-01

    The concept of tailored interfaces has been applied to the synthesis of nano-scaled Y2O3/ZrO2 powders. The microemulsion technique as well as the thermodynamically controlled growth reaction have been utilized for this purpose. Both methods yielded agglomerate free amorphous powders with particles sized of 8 nm and 15 nm, respectively. Cubic zirconia was obtained by calcination between 300 and 400°C and crystallite coarsening was not observed. The calcined powders could be redispersed by trea...

  6. Relative ultraviolet radiation sensitivity of certain functions of polyoma virus. Stimulation of cell DNA synthesis

    International Nuclear Information System (INIS)

    Peritoneal Mouse macrophages were used to study the stimulation of cell DNA synthesis by polyoma virus. Using ultraviolet-irradiated polyoma virus, it was possible to show a difference between the inactivation of infectivity and of induction of DNA synthesis. By statistical analysis of these two phenomena it was found that 39% of the viral genome is necessary for the induction of cell DNA synthesis

  7. Ion-exchange membranes in chemical synthesis – a review

    Directory of Open Access Journals (Sweden)

    Jaroszek Hanna

    2016-12-01

    Full Text Available The applicability of ion-exchange membranes (IEMs in chemical synthesis was discussed based on the existing literature. At first, a brief description of properties and structures of commercially available ion-exchange membranes was provided. Then, the IEM-based synthesis methods reported in the literature were summarized, and areas of their application were discussed. The methods in question, namely: membrane electrolysis, electro-electrodialysis, electrodialysis metathesis, ion-substitution electrodialysis and electrodialysis with bipolar membrane, were found to be applicable for a number of organic and inorganic syntheses and acid/base production or recovery processes, which can be conducted in aqueous and non-aqueous solvents. The number and the quality of the scientific reports found indicate a great potential for IEMs in chemical synthesis.

  8. Facile chemical synthesis and structure characterization of copper molybdate nanoparticles

    Science.gov (United States)

    Rahimi-Nasrabadi, Mehdi; Pourmortazavi, Seied Mahdi; Khalilian-Shalamzari, Morteza

    2015-03-01

    Experimental parameters of a synthesis route were optimized by Taguchi robust design for the facile and controllable synthesis of copper molybdate nanoparticles. CuMoO4 nanoparticles were synthesized by chemical precipitation followed by hydrothermal process. Effects of different parameters of synthesis procedure, i.e. concentrations of both reagents, copper feeding flow rate and temperature of reactor on the particle size of prepared copper molybdate nanoparticles were investigated. The results of statistical optimization revealed that the size of copper molybdate particles is dependent on the procedure variables involving copper concentrations, flow rate and temperature of the reactor; while, molybdate concentration has a no considerable role in determining the size of CuMoO4 particles. Based on the results obtained by statistical optimization process, the nanoparticles of copper molybdate were prepared and then their structure and chemical composition were characterized by various techniques, i.e. SEM, TEM, XRD, EDX, FT-IR, UV-Vis and photoluminescence spectroscopy.

  9. On the Plasma-Chemical Synthesis of Nanopowders

    Institute of Scientific and Technical Information of China (English)

    G. Vissokov; Iv. Grancharov; Tsv. Tsvetanov

    2003-01-01

    This paper presents an overview of nanopowders preparation using low-temperature plasma (LTP). LTP with its unique processing capabilities provides an attractive and chemically unspecific route for powder synthesis. Nanopowders such as oxides, nitrides, carbides, catalysts and other nanopowders have been successfully synthesized in LTP reactors based on high intensity arcs, plasma jets and radio-frequency (r. f.) inductively coupled discharges.

  10. Differential chromosomal and mitochondrial DNA synthesis in temperature-sensitive mutants of Ustilago maydis

    Energy Technology Data Exchange (ETDEWEB)

    Unrau, P.

    1977-01-01

    The amount and type of residual DNA synthesis was determined in eight temperature-sensitive mutants of the smut fungus Ustilago maydis after incubation at the restrictive temperature (32/sup 0/C) for eight hours. Mutants ts-220, ts-207, ts-432 and ts-346 were found to have an overall reduction in the synthesis of both nuclear and mitochondrial DNA in comparison to the wild-type. In mutants ts-20, tsd 1-1, ts-84 and pol 1-1 nuclear DNA synthesis was depressed relative to mitochondrial synthesis. The DNA-polymerase mutant pol 1-1 had persistent nuclear synthesis at about 50% of the rate of synthesis of mitochondrial DNA and similar behavior was observed in a diploid homozygous strain. Mutant ts-84 had an initial burst of DNA synthesis which was reduced for nuclear but not mitochondrial synthesis after three hours preincubation at 32/sup 0/C. tsd 1-1 and ts-20 had nuclear residual synthesis amounting to about 25% of the relative rate of mitochondrial synthesis which correlates to increasing UV sensitivity of these strains on incubation at 32/sup 0/C. A pol 1-1 ts-84 double mutant had an additive loss of nuclear DNA synthesis which indicates that the steps of replication involved may be sequential.

  11. Targeting deubiquitinases enabled by chemical synthesis of proteins.

    Science.gov (United States)

    Ohayon, Shimrit; Spasser, Liat; Aharoni, Amir; Brik, Ashraf

    2012-02-15

    Ubiquitination/ubiquitylation is involved in a wide range of cellular processes in eukaryotes, such as protein degradation and DNA repair. Ubiquitination is a reversible post-translational modification, with the removal of the ubiquitin (Ub) protein being catalyzed by a family of enzymes known as deubiquitinases (DUBs). Approximately 100 DUBs are encoded in the human genome and are involved in a variety of regulatory processes, such as cell-cycle progression, tissue development, and differentiation. DUBs were, moreover, found to be associated with several diseases and as such are emerging as potential therapeutic targets. Several directions have been pursued in the search for lead anti-DUB compounds. However, none of these strategies have delivered inhibitors reaching advanced clinical stages due to several challenges in the discovery process, such as the absence of a highly sensitive and practically available high-throughput screening assay. In this study, we report on the design and preparation of a FRET-based assay for DUBs based on the application of our recent chemical method for the synthesis of Ub bioconjugates. In the assay, the ubiquitinated peptide was specifically labeled with a pair of FRET labels and used to screen a library comprising 1000 compounds against UCH-L3. Such analysis identified a novel and potent inhibitor able to inhibit this DUB in time-dependent manner with k(inact) = 0.065 min(-1) and K(i) = 0.8 μM. Our assay, which was also found suitable for the UCH-L1 enzyme, should assist in the ongoing efforts targeting the various components of the ubiquitin system and studying the role of DUBs in health and disease.

  12. Radiation sensitizations at DNA-level by chemical and biological agents. Coordinated programme on improvement of radiotherapy of cancer using modifiers of radiosensitivity of cells

    International Nuclear Information System (INIS)

    Radiation sensitization by chemical agents at DNA level is discussed. Procaine, Halothan and Metronidazole showed no significant effect on unscheduled DNA synthesis (UDS) in mouse spleen cells, investigated by autoradiography and no effect on rejoining of DNA single strand breaks after gamma or UV irradiation. Oxyphenbutazon and prednisolone reduced the replicative DNA synthesis in vitro and in vivo but there was only little effect on DNA repair in the in vivo experiments. These two substances showed also a small reduction in poly(ADP-ribose) synthesis (PAR synthesis). 5-methoxypsoralen (5-MOP) and 8-methoxypsoralen (8-MOP) in combination with UV irradiation showed that 5-MOP was more toxic than mutagen, but induced much less DNA crosslinks than 8-MOP. Autoradiographic studies of radiation sensitization by biological agents showed significant inhibition of UDS in Yoshida tumor cells after acute mycoplasma infection in rats. Nucleoid sedimentation studies showed only in the case of Yoshida tumor cells after mycoplasma infection a dramatic effect in the sedimentation behaviour. Sensitization of cells by changing chromatin structure was also studied. Benzamide, 3-NH2-benzamide, 3-Methoxybenzamide, Spermine, Theophyllin and Caffeine were tested in different concentrations on replicative DNA synthesis, UDS after UV irradiation and PAR synthesis Chinese hamster ovary cells. 5-Methoxybenzamide was the strongest sensitizer and inhibitor of the PAR synthesis, and was used in further experiments. Results of KFA Juelich on sensitization of a mamma-adenocarcinoma EO 771 on C57 B1 mice are given. Replicative DNA synthesis, DNA repair and PAR synthesis were compared in spleen cells and adenocarcinoma cells after treatment with 5-Methoxybenzamide. An inhibitory effect on UDS could be shown only in adenocarcinoma cells but not in the mice spleen cells

  13. Radiation hypersensitivity and radioresistant DNA synthesis in ataxia-telangiectasia

    International Nuclear Information System (INIS)

    Patients with the autosomal recessive genetic disease, ataxia-telangiectasia (A-T), are cancer-prone and hypersensitive to the killing effects of ionizing radiation. In an attempt to isolate the gene(s) responsible for the hypersensitivity of A-T cells, they were transfected with normal human DNA in cosmid vectors containing a rescuable marker (G-418 resistance), and revertants to normal sensitivity were isolated and characterized. The failure of radioresistant revertants to demonstrate a reversion of the phenotype, radioresistant DNA synthesis, shows that this feature is dependent on a gene separate from the one conferring resistance to cell killing. Cells from every A-T patient thus far examined demonstrate both hypersensitivity, in terms of radiation-induced cell killing, and radioresistant DNA synthesis. The results reported here, however, show that the former is not a result of the latter, as previously proposed. Moreover, the fact that these two characteristics can be uncoupled obscures the role(s) that either of them plays in the etiology of the disease, or in the development in its other features, including cancer-proneness

  14. Studies on bleomycin-induced repair DNA synthesis in permeable mouse ascites sarcoma cells.

    Directory of Open Access Journals (Sweden)

    Mori,Shigeru

    1989-04-01

    Full Text Available To study the mechanism of DNA excision repair, a DNA repair system employing permeable mouse sarcoma (SR-C3H/He cells was established and characterized. SR-C3H/He cells were permeabilized with a 0.0175% Triton X-100 solution. The permeable cells were treated with 1 mM ATP and 0.11 mM bleomycin, and then washed thoroughly to remove ATP and bleomycin. Repair DNA synthesis occurred in the bleomycin-damaged, permeable SR-C3H/He cells when incubated with ATP and four deoxyribonucleoside triphosphates. The repair nature of the DNA synthesis was confirmed by the BrdUMP density shift technique, and by the reduced sensitivity of the newly synthesized DNA to Escherichia coli exonuclease III. The DNA synthesis was optimally enhanced by addition of 0.08 M NaCl. Studies using selective inhibitors of DNA synthesis showed that aphidicolin-sensitive DNA polymerase (DNA polymerase alpha and/or delta and DNA polymerase beta were involved in the repair process. The present DNA repair system is thought to be useful to study nuclear DNA damage by bleomycin, removal of the damaged ends by an exonuclease, repair DNA synthesis by DNA polymerases and repair patch ligation by DNA ligase(s.

  15. Microwave Technology--Applications in Chemical Synthesis

    Science.gov (United States)

    Microwave heating, being specific and instantaneous, is unique and has found a place for expeditious chemical syntheses. Specifically, the solvent-free reactions are convenient to perform and have advantages over the conventional heating protocols as summarized in the previous se...

  16. Approaches to chemical synthesis of pectic oligosaccharides

    DEFF Research Database (Denmark)

    Nepogodiev, Sergei A.; Field, Robert A.; Damager, Iben

    2011-01-01

    at the formation of specific glycosidic linkages as they are present in the target oligosaccharides. Challenges in synthesis of pectic oligosaccharides are associated with often poor stereoselectivity of glycosylation reactions between GA and GD, in particular for the construction of 1,2-cis-glycosidic linkages...... representing all three major types of pectic polysaccharide: homogalacturonan (HG), rhamnogalacturonan-I (RG-I) and rhamnogalacturonan-II (RG-II). Such molecules have been synthesized by sequential coupling of building blocks, the so-called glycosyl donors (GD) and glycosyl acceptors (GA), which aimed...... group strategies for GA and GD, glycosylation methodologies and general strategies for oligosaccharide assembly are described with the focus on pectin fragments. Synthetic routes to fragments of each type of pectic polysaccharides are discussed in detail in separate sections and structures of all...

  17. Metabolic design for cyanobacterial chemical synthesis.

    Science.gov (United States)

    Oliver, John W K; Atsumi, Shota

    2014-06-01

    Photosynthetic chemical production in cyanobacteria is a promising technology for renewable energy, CO2 mitigation, and fossil fuel replacement. Metabolic engineering has enabled a direct biosynthetic process from CO2 fixation to chemical feedstocks and biofuels, without requiring costly production, storage, and breakdown of cellulose or sugars. However, direct production technology is challenged by a need to achieve high-carbon partitioning to products in order to be competitive. This review discusses principles for the design of biosynthetic pathways in cyanobacteria and describes recent advances in relevant genetic tools. This field is at a critical juncture in assessing the strength and feasibility of carbon partitioning. To address this, we have included the stoichiometry of reducing equivalents and carbon conservation for heterologous pathways, and a method for calculating product yields against a theoretical maximum.

  18. Chemically stabilized subtilisins in peptide synthesis

    OpenAIRE

    Colleary, Sandra; Ó'Fágáin, Ciarán

    2008-01-01

    We have stabilized alcalaseTM and subtilisin Carlsberg (SC) against heat by chemical modification with ethylene glycol bis-succinimidyl succinate (EGNHS), a procedure not previously reported for subtilisins. The increases in thermal stability at 65oC were 1.8-fold and 4.7-fold respectively. Caseinolytic activity of alcalase in aqueous buffer was unchanged following modification but apparent Km of SC decreased 2.5-fold. Native and modified forms of both enzymes synthesized the tripeptide Z-...

  19. Synthesis of Ethyl Salicylate Using Household Chemicals

    Science.gov (United States)

    Solomon, Sally; Hur, Chinhyu; Lee, Alan; Smith, Kurt

    1996-02-01

    Ethyl salicylate is synthesized, isolated, and characterized in a three-step process using simple equipment and household chemicals. First, acetylsalicylic acid is extracted from aspirin tablets with isopropyl alcohol, then hydrolyzed to salicylic acid with muriatic acid, and finally, the salicylic acid is esterified using ethanol and a boric acid catalyst. The experiment can be directed towards high school or university level students who have sufficient background in organic chemistry to recognize the structures and reactions that are involved.

  20. RNA polymerase motors on DNA track: effects of traffic congestion on RNA synthesis

    CERN Document Server

    Tripathi, Tripti

    2007-01-01

    RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by a ssDNA. In some circumstances, which are described in this paper, a large number of RNAPs move simultaneously along the same track. We refer to such collective movements of the RNAPs as RNAP traffic because of the similarities between the collective dynamics of the RNAPs on ssDNA track and that of vehicles in highway traffic. In this paper we develop a theoretical model for RNAP traffic by incorporating the steric interactions between RNAPs as well as the mechano-chemical cycle of individual RNAPs during the elongation of the mRNA. By a combination of analytical and numerical techniques, we calculate the rates of mRNA synthesis and the average density profile of the RNAPs on the ssDNA track. We also suggest novel experiments for testing o...

  1. Peptide Synthesis on a Next-Generation DNA Sequencing Platform.

    Science.gov (United States)

    Svensen, Nina; Peersen, Olve B; Jaffrey, Samie R

    2016-09-01

    Methods for displaying large numbers of peptides on solid surfaces are essential for high-throughput characterization of peptide function and binding properties. Here we describe a method for converting the >10(7) flow cell-bound clusters of identical DNA strands generated by the Illumina DNA sequencing technology into clusters of complementary RNA, and subsequently peptide clusters. We modified the flow-cell-bound primers with ribonucleotides thus enabling them to be used by poliovirus polymerase 3D(pol) . The primers hybridize to the clustered DNA thus leading to RNA clusters. The RNAs fold into functional protein- or small molecule-binding aptamers. We used the mRNA-display approach to synthesize flow-cell-tethered peptides from these RNA clusters. The peptides showed selective binding to cognate antibodies. The methods described here provide an approach for using DNA clusters to template peptide synthesis on an Illumina flow cell, thus providing new opportunities for massively parallel peptide-based assays.

  2. Molecular cloning and chemical synthesis of a region of platelet glycoprotein IIb involved in adhesive function.

    OpenAIRE

    Loftus, J C; Plow, E F; Frelinger, A.L.; D'Souza, S E; Dixon, D; Lacy, J.; Sorge, J; Ginsberg, M H

    1987-01-01

    Membrane glycoprotein (GP) IIb-IIIa is a component of a platelet adhesive protein receptor. A region of the heavy chain of GPIIb, defined by the monoclonal antibody PMI-1, is involved in adhesion receptor function. We have localized and chemically synthesized this region of GPIIb. A cDNA clone that directs the synthesis of a fusion protein reactive with the PMI-1 antibody was isolated from a phage lambda gt11 expression library constructed with mRNA from an erythroleukemia (HEL) cell line. Th...

  3. Alternative fuels and chemicals from synthesis gas

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    1998-12-01

    A DOE/PETC funded study was conducted to examine the use of a liquid phase mixed alcohol synthesis (LPMAS) plant to produce gasoline blending ethers. The LPMAS plant was integrated into three utilization scenarios: a coal fed IGCC power plant, a petroleum refinery using coke as a gasification feedstock, and a standalone natural gas fed partial oxidation plant. The objective of the study was to establish targets for the development of catalysts for the LPMAS reaction. In the IGCC scenario, syngas conversions need only be moderate because unconverted syngas is utilized by the combined cycle system. A once through LPMAS plant achieving syngas conversions in the range of 38--49% was found to be suitable. At a gas hourly space velocity of 5,000 sL/Kg-hr and a methanol:isobutanol selectivity ratio of 1.03, the target catalyst productivity ranges from 370 to 460 g iBuOH/Kg-hr. In the petroleum refinery scenario, high conversions ({approximately}95%) are required to avoid overloading the refinery fuel system with low Btu content unconverted syngas. To achieve these high conversions with the low H{sub 2}/CO ratio syngas, a recycle system was required (because of the limit imposed by methanol equilibrium), steam was injected into the LPMAS reactor, and CO{sub 2} was removed from the recycle loop. At the most economical recycle ratio, the target catalyst productivity is 265 g iBuOH/Kg-hr. In the standalone LPMAS scenario, essentially complete conversions are required to achieve a fuel balanced plant. At the most economical recycle ratio, the target catalyst productivity is 285 g iBuOH/Kg-hr. The economics of this scenario are highly dependent on the cost of the natural gas feedstock and the location of the plant. For all three case scenarios, the economics of a LPMAS plant is marginal at current ether market prices. Large improvements over demonstrated catalyst productivity and alcohol selectivity are required.

  4. DNA precursor compartmentation in mammalian cells: metabolic and antimetabolic studies of nuclear and mitochondrial DNA synthesis

    International Nuclear Information System (INIS)

    HeLa cells were used for the quantitation of cellular and mitochondrial deoxyribonucleoside triphosphate (dNTP) and ribonucleoside triphosphate (rNTP) pools and of changes in pools in response to treatment with the antimetabolites methotrexate (mtx) and 5-fluorodeoxyuridine (FUdR). Use of an enzymatic assay of dNTPs and of improved nucleotide extraction methods allowed quantitation of mitochondrial dNTP pools. All four mitochondrial dNTP pools expand following treatment with mtx or FUdR whereas cellular dTTP and dGTP pools are depleted. Mitochrondrial rNTP pools were also found to expand in response to these antimetabolites. Mouse L-cells were used to determine the relative contributions of an exogenously supplied precursor to nuclear and mitochrondrial DNA replication. Cells were labeled to near steady state specific activities with 32P-orthophosphate and subsequently labeled with [3H]uridine, a general pyrimidine precursor, in the continuing presence of 32P. Deoxyribonucleoside monophosphates derived from these DNAs were separated by HPLC and the 3H/32P ratio in each pyrimidine determined. The dCMP residues in mitochondrial DNA (mtDNA) were found to be derived exclusively from the exogenous supplied uridine. The dTMP residues from nuclear and mtDNA and the dCMP residues from nuclear DNA were seen to be synthesized partly from exogenous sources and partly from other sources, presumably de novo pyrimidine synthesis

  5. Role of noble metal nanoparticles in DNA base damage and catalysis: a radiation chemical investigation

    International Nuclear Information System (INIS)

    In the emerging field of nanoscience and nanotechnology, tremendous focus has been made by researcher to explore the applications of nanomaterials for human welfare by converting the findings into technology. Some of the examples have been the use of nanoparticles in the field of opto-electronic, fuel cells, medicine and catalysis. These wide applications and significance lies in the fact that nanoparticles possess unique physical and chemical properties very different from their bulk precursors. Numerous methods for the synthesis of noble nanoparticles with tunable shape and size have been reported in literature. The goal of our group is to use different methods of synthesis of noble metal nanoparticles (Au, Ag, Pt and Pd) and test their protective/damaging role towards DNA base damage induced by ionizing radiation (Au and Ag) and to test the catalytic activity of nanoparticles (Pt and Pd) in certain known organic synthesis/electron transfer reactions. Using radiation chemical techniques such as pulse radiolysis and steady state radiolysis complemented by the product analysis using HPLC/LC-MS, a detailed mechanism for the formation of transient species, kinetics leading to the formation of stable end products is studied in the DNA base damage induced by ionizing radiation in presence and absence of Au and Ag nanoparticles. Unraveling the complex interaction between catalysts and reactants under operando conditions is a key step towards gaining fundamental insight in catalysis. The catalytic activity of Pt and Pd nanoparticles in electron transfer and Suzuki coupling reactions has been determined. Investigations are currently underway to gain insight into the interaction between catalysts and reactants using time resolved spectroscopic measurements. These studies will be detailed during the presentation. (author)

  6. The Evolving Role of Chemical Synthesis in Antibacterial Drug Discovery

    OpenAIRE

    Wright, Peter M.; Seiple, Ian B.; Myers, Andrew G.

    2014-01-01

    The discovery and implementation of antibiotics in the early twentieth century transformed human health and wellbeing. Chemical synthesis enabled the development of the first antibacterial substances, organoarsenicals and sulfa drugs, but these were soon outshone by a host of more powerful and vastly more complex antibiotics from nature: penicillin, streptomycin, tetracycline, and erythromycin, among others. These primary defences are now significantly less effective as an unavoidable consequ...

  7. DNA synthesis in the imaginal wing discs of the American bollworm Helicoverpa armigera (Hübner)

    Indian Academy of Sciences (India)

    A Josephrajkumar; B Subrahmanyam

    2002-03-01

    The effect of two insect growth regulators of plant origin viz. plumbagin and azadirachtin and the ecdysteroids 20-hydroxyecdysone, makisterone A and a phytoecdysteroid on DNA synthesis in imaginal wing discs of day 4 final instar Helicoverpa armigera larvae was studied. DNA synthesis increased with increase in time of incubation up to 8 h and decreased later without the addition of moulting hormone. Addition of 20-hydroxyecdysone supported long term acquisition of competence for DNA synthesis in the wing discs. Both DNA synthesis and protein content were drastically reduced in plumbagin and azadirachtin-treated insects. Under in vitro conditions, plumbagin had a more pronounced inhibitory effect than azadirachtin. All the ecdysteroids tested, viz. makisterone A, 20-hydroxyecdysone and the ecdysteroidal fraction from the silver fern Cheilanthes farinosa enhanced DNA synthesis.

  8. Multi-line split DNA synthesis: a novel combinatorial method to make high quality peptide libraries

    Directory of Open Access Journals (Sweden)

    Ueno Shingo

    2004-09-01

    Full Text Available Abstract Background We developed a method to make a various high quality random peptide libraries for evolutionary protein engineering based on a combinatorial DNA synthesis. Results A split synthesis in codon units was performed with mixtures of bases optimally designed by using a Genetic Algorithm program. It required only standard DNA synthetic reagents and standard DNA synthesizers in three lines. This multi-line split DNA synthesis (MLSDS is simply realized by adding a mix-and-split process to normal DNA synthesis protocol. Superiority of MLSDS method over other methods was shown. We demonstrated the synthesis of oligonucleotide libraries with 1016 diversity, and the construction of a library with random sequence coding 120 amino acids containing few stop codons. Conclusions Owing to the flexibility of the MLSDS method, it will be able to design various "rational" libraries by using bioinformatics databases.

  9. ER-mitochondria contacts couple mtDNA synthesis with mitochondrial division in human cells.

    Science.gov (United States)

    Lewis, Samantha C; Uchiyama, Lauren F; Nunnari, Jodi

    2016-07-15

    Mitochondrial DNA (mtDNA) encodes RNAs and proteins critical for cell function. In human cells, hundreds to thousands of mtDNA copies are replicated asynchronously, packaged into protein-DNA nucleoids, and distributed within a dynamic mitochondrial network. The mechanisms that govern how nucleoids are chosen for replication and distribution are not understood. Mitochondrial distribution depends on division, which occurs at endoplasmic reticulum (ER)-mitochondria contact sites. These sites were spatially linked to a subset of nucleoids selectively marked by mtDNA polymerase and engaged in mtDNA synthesis--events that occurred upstream of mitochondrial constriction and division machine assembly. Our data suggest that ER tubules proximal to nucleoids are necessary but not sufficient for mtDNA synthesis. Thus, ER-mitochondria contacts coordinate licensing of mtDNA synthesis with division to distribute newly replicated nucleoids to daughter mitochondria.

  10. Effects of uniconazole waterless-dressing seed on DNA synthesis in seed germination of wheat

    International Nuclear Information System (INIS)

    Effects of uniconazole waterless-dressing seed on the synthesis of DNA in seed germination of wheat, c.v. Mianyang 26, were studied with the method of 3H-TdR. The results showed that uniconazole treatments could promote DNA synthesis, when the concentration of uniconazole was 20 mg/kg, the speed of DNA synthesis was the quickest. At the same time, the incorporating 3H-TdR indicated that uniconazole treatment were beneficial to the DNA repairing in the early period of wheat seed germination. (authors)

  11. Bleomycin-induced DNA synthesis in a cell-free system using a permeable mouse sarcoma cell Extract.

    Directory of Open Access Journals (Sweden)

    Seki,Shuji

    1987-10-01

    Full Text Available To investigate factors involved in excision repair DNA synthesis, a soluble extract was prepared from permeable mouse sarcoma (SR-C3H/He cells by homogenization and ultracentrifugation. DNA synthesis measured by using native calf thymus DNA as the template-primer and the extract as the polymerase source showed low activity. The DNA synthesis was enhanced more than ten-fold by the addition of an appropriate concentration of bleomycin, a radiomimetic DNA-damaging drug. Using selective inhibitors of DNA polymerases, it was shown that the DNA polymerase involved in the bleomycin-induced DNA synthesis was DNA polymerase beta. In addition to DNA polymerase beta, an exonuclease which converts bleomycin-damaged DNA into suitable template-primers for repair DNA synthesis appeared to be present in the permeable cell extract.

  12. Synthesis and applications of 2-aminopyrimidine derivatives as key intermediates in chemical synthesis of biomolecules

    Science.gov (United States)

    Koroleva, Elena V.; Gusak, K. N.; Ignatovich, Zh V.

    2010-10-01

    Published data on the main approaches to the formation of the heterocyclic 2-aminopyrimidine system, which is one of important pharmacophores responsible for the biological properties of its derivatives, are described systematically. Main chemical transformations of functionalized 2-aminopyrimidines and their application in the synthesis of modern pharmaceuticals are considered.

  13. Synthesis and applications of 2-aminopyrimidine derivatives as key intermediates in chemical synthesis of biomolecules

    Energy Technology Data Exchange (ETDEWEB)

    Koroleva, Elena V; Gusak, K N; Ignatovich, Zh V [Institute of Chemistry of New Materials of the National Academy of Sciences of Belarus (Belarus)

    2010-10-19

    Published data on the main approaches to the formation of the heterocyclic 2-aminopyrimidine system, which is one of important pharmacophores responsible for the biological properties of its derivatives, are described systematically. Main chemical transformations of functionalized 2-aminopyrimidines and their application in the synthesis of modern pharmaceuticals are considered.

  14. Enzymatic synthesis of long double-stranded DNA labeled with haloderivatives of nucleobases in a precisely pre-determined sequence

    Directory of Open Access Journals (Sweden)

    Rak Janusz

    2011-08-01

    Full Text Available Abstract Background Restriction endonucleases are widely applied in recombinant DNA technology. Among them, enzymes of class IIS, which cleave DNA beyond recognition sites, are especially useful. We use BsaI enzyme for the pinpoint introduction of halogen nucleobases into DNA. This has been done for the purpose of anticancer radio- and phototherapy that is our long-term objective. Results An enzymatic method for synthesizing long double-stranded DNA labeled with the halogen derivatives of nucleobases (Hal-NBs with 1-bp accuracy has been put forward and successfully tested on three different DNA fragments containing the 5-bromouracil (5-BrU residue. The protocol assumes enzymatic cleavage of two Polymerase-Chain-Reaction (PCR fragments containing two recognition sequences for the same or different class IIS restriction endonucleases, where each PCR fragment has a partially complementary cleavage site. These sites are introduced using synthetic DNA primers or are naturally present in the sequence used. The cleavage sites are not compatible, and therefore not susceptible to ligation until they are partially filled with a Hal-NB or original nucleobase, resulting in complementary cohesive end formation. Ligation of these fragments ultimately leads to the required Hal-NB-labeled DNA duplex. With this approach, a synthetic, extremely long DNA fragment can be obtained by means of a multiple assembly reaction (n × maximum PCR product length: n × app. 50 kb. Conclusions The long, precisely labeled DNA duplexes obtained behave in very much the same manner as natural DNA and are beyond the range of chemical synthesis. Moreover, the conditions of synthesis closely resemble the natural ones, and all the artifacts accompanying the chemical synthesis of DNA are thus eliminated. The approach proposed seems to be completely general and could be used to label DNA at multiple pre-determined sites and with halogen derivatives of any nucleobase. Access to DNAs

  15. EFFECT OF GLYCYRRHETINIC ACID ON DNA DAMAGE AND UNSCHEDULED DNA SYNTHESIS INDUCED BY BENZO (α) PYRENE

    Institute of Scientific and Technical Information of China (English)

    陈晓光; 韩锐

    1995-01-01

    Glycyrrhetinic acid (GA) is an active component of Glycyrrhiza uraleusis fisch. In this study, GA was found to inhibit ear edema and ornithine decarboxykase (ODC)activity induced by croton oil in mice. GA could also protect rapid DNA damage and decrease the unscheduled DNA synthesis induced by benzo(α)pyrene, The results demonstrate that GA has a potential cancer chemopreventive activity.

  16. The initiation mechanism of translesion DNA synthesis in response to UV irradiation

    International Nuclear Information System (INIS)

    Ultraviolet (UV) light causes DNA damage and increases a person's risk for both melanoma and non-melanoma skin cancer. If the DNA damage is unrepaired, cells can often tolerate it by using specialized DNA polymerases during DNA replication to insert a base opposite a lesion and bypass the damage, in a process called translesion DNA synthesis (TLS). This review addresses recent advances in our understanding of TLS. (author)

  17. Temperature lowering in cryogenic chemical-synthesis techniques and system

    International Nuclear Information System (INIS)

    When evaluating a chemical synthesis process for a reaction that occurs on the cryogenically cooled walls, it is sometimes necessary to reduce the wall temperatures to enhance the chemical process. To evaluate the chemical process at lower than atmospheric boiling of liquid nitrogen, we built a system and used it to reduce the temperature of the liquid nitrogen. The technique of lowering the liquid nitrogen temperature by reducing the pressure of the boil-off is established knowledge. This paper presents the engineering aspects of the system, design features, equipment requirements, methods of control, and results of the chemical synthesis. The heat input to the system was ∼400 watts, placing a relatively large demand on the pumping system. Our system is a scale-up of the small laboratory experiment, and it provides the information needed to design an effective system. The major problem encountered was the large quantity of liquid escaping the system during the processing, placing a large gas load on the vacuum system

  18. DNA-content and synthesis rate in human melanoma cells in vitro after hyperthermia and radiation

    International Nuclear Information System (INIS)

    Human melanoma cells were cultured over 168 hours. DNA-content and 3H-thymidine incorporation were measured after 800 R and hyperthermia of 400C and 440C for 3 and 6 hours. An early and a late effect could be distinguished. 3 and 6 hours after irradiation alone no alteration of DNA-synthesis was observed. After heat treatment at 400C for 6 hours the DNA-synthesis was increased immediately. 420C and 440C deminished the rate of DNA-synthesis. The combined treatment (heat and irradiation) suppressed the overshooting rate of DNA-synthesis. Accordingly after heat treatment at 400C for 6 hours the DNA-content was higher than the controls and the 3 hours-400C treated cultures measured over a period of 48 hours. Thereafter the DNA-content showed little or no alterations compared with the controls. The heat treatment at 440C reduced the DNA-content heavily, followed by a relative increase at 120 hours. The DNA-synthesis rate showed the same effect. The combined treatment suppressed this late increase. However, 24 hours after combined treatment the incorporation of thymidine into the DNA was higher at 440C-6 than 440C-3 hours, 40C-3 hours, than 400C-6 hours, although the DNA-content was very low. The results show synergistic effects of hyperthermia and radiation on the DNA-synthesis and content if one considers the effects at the later periods (120-168 hours). However, a stimulating effect is found on the DNA-synthesis if the melanoma cells are incubated at 400C for 6 hours. (orig.)

  19. Nerve growth factor enhances DNA synthesis in cultured cerebellar neuroblasts.

    Science.gov (United States)

    Confort, C; Charrasse, S; Clos, J

    1991-10-01

    The cerebellar neuroblasts in primary cultures from five-day-old rats bore NGF receptor immunoreactivity, suggesting a potential responsive to NGF. At low plating density, NGF was found to enhance DNA synthesis in these cells in a dose-dependent manner. As these cells synthesize NGF, one possibility to account for the lack of response of neuroblasts plated at high density is that the amount of endogenous trophic agent produced in this culture condition is sufficient to ensure an optimal effect. The results demonstrate that premitotic neuroblasts in the CNS, as well postmitotic neurons, are responsive to NGF. At the early stage of its development, the cerebellum therefore appears to be a very good autocrine model of NGF action. PMID:1661619

  20. Nerve growth factor enhances DNA synthesis in cultured cerebellar neuroblasts.

    Science.gov (United States)

    Confort, C; Charrasse, S; Clos, J

    1991-10-01

    The cerebellar neuroblasts in primary cultures from five-day-old rats bore NGF receptor immunoreactivity, suggesting a potential responsive to NGF. At low plating density, NGF was found to enhance DNA synthesis in these cells in a dose-dependent manner. As these cells synthesize NGF, one possibility to account for the lack of response of neuroblasts plated at high density is that the amount of endogenous trophic agent produced in this culture condition is sufficient to ensure an optimal effect. The results demonstrate that premitotic neuroblasts in the CNS, as well postmitotic neurons, are responsive to NGF. At the early stage of its development, the cerebellum therefore appears to be a very good autocrine model of NGF action.

  1. Synthesis, DNA binding and topoisomerase inhibition of mononaphthalimide homospermidine derivatives

    Institute of Scientific and Technical Information of China (English)

    Zhi Yong Tian; Hong Xia Ma; Song Qiang Xie; Xue Wang; Jin Zhao; Chao Jie Wang; Wen Yuan Gao

    2008-01-01

    Two novel mononaphthalimide homospermidine derivatives (2a, 2b) with three or four methylene unit as linkages weresynthesized and evaluated for cytotoxicity against human leukemia K562, murine melanoma B 16 and Chinese hamster ovary CHOcell lines. The presence of homospermidine motif could greatly elevate the potency of 1,8-naphthalimide. Conjugate 2b with longerspacer exhibited higher in vitro cytotoxicity than 2a. The DNA binding experiments indicated that conjugates 2b could bind toherring sperm DNA. The topoisomerase Ⅱ poison trials revealed that 2b could inhibit the activity of top. Ⅱ.2008 Chao Jie Wang. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.

  2. Inhibition of adenovirus DNA synthesis in vitro by sera from patients with systemic lupus erythematosus

    Energy Technology Data Exchange (ETDEWEB)

    Horwitz, M.S.; Friefeld, B.R.; Keiser, H.D.

    1982-12-01

    Sera containing antinuclear antibodies from patients with systemic lupus erythematosus (SLE) and related disorders were tested for their effect on the synthesis of adenovirus (Ad) DNA in an in vitro replication system. After being heated at 60/sup 0/C for 1 h, some sera from patients with SLE inhibited Ad DNA synthesis by 60 to 100%. Antibodies to double-stranded DNA were present in 15 of the 16 inhibitory sera, and inhibitory activity copurified with anti-double-stranded DNA in the immunoglobulin G fraction. These SLE sera did not inhibit the DNA polymerases ..cap alpha.., BETA, ..gamma.. and had no antibody to the 72,000-dalton DNA-binding protein necessary for Ad DNA synthesis. The presence of antibodies to single-stranded DNA and a variety of saline-extractable antigens (Sm, Ha, nRNP, and rRNP) did not correlate with SLE serum inhibitory activity. Methods previously developed for studying the individual steps in Ad DNA replication were used to determine the site of inhibition by the SLE sera that contained antibody to double-stranded DNA. Concentrations of the SLE inhibitor that decreased the elongation of Ad DNA by greater than 85% had no effect on either the initiation of Ad DNA synthesis or the polymerization of the first 26 deoxyribonucleotides.

  3. DNA polymerase I-mediated ultraviolet repair synthesis in toluene-treated Escherichia coli

    International Nuclear Information System (INIS)

    DNA synthesis after ultraviolet irradiation is low in wild type toluene-treated cells. The level of repair incorporation is greater in strains deficient in DNA polymerase I. The low level of repair synthesis is attributable to the concerted action of DNA polymerase I and polynucleotide ligase. Repair synthesis is stimulated by blocking ligase activity with the addition of nicotinamide mononucleotide (NMN) or the use of a ligase temperature-sensitive mutant. NMN stimulation is specific for DNA polymerase I-mediated repair synthesis, as it is absent in isogenic strains deficient in the polymerase function or the 5' yields 3' exonuclease function associated with DNA polymerase I. DNA synthesis that is stimulated by NMN is proportional to the ultraviolet exposure at low doses, nonconservative in nature, and is dependent on the uvrA gene product but is independent of the recA gene product. These criteria place this synthesis in the excision repair pathway. The NMN-stimulated repair synthesis requires ATP and is N-ethylmaleimide-resistant. The use of NMN provides a direct means for evaluating the involvement of DNA polymerase I in excision repair

  4. Interacting RNA polymerase motors on DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis

    CERN Document Server

    Tripathi, Tripti

    2007-01-01

    RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by a DNA. In many circumstances, which are described in this paper, a large number of RNAPs move simultaneously along the same track; we refer to such collective movements of the RNAPs as RNAP traffic. Here we develop a theoretical model for RNAP traffic by incorporating the steric interactions between RNAPs as well as the mechano-chemical cycle of individual RNAPs during the elongation of the mRNA. By a combination of analytical and numerical techniques, we calculate the rates of mRNA synthesis and the average density profile of the RNAPs on the DNA track. We also introduce, and compute, two new measures of {\\it fluctuations} in the synthesis of RNA. Analyzing these fluctuations, we show how the level of intrinsic noise in mRNA synthesis dep...

  5. Synthesis, characterization, DNA binding, DNA cleavage, protein binding and cytotoxic activities of Ru(II) complexes.

    Science.gov (United States)

    Thota, Sreekanth; Vallala, Srujana; Yerra, Rajeshwar; Rodrigues, Daniel Alencar; Raghavendra, Nulgumnalli Manjunathaiah; Barreiro, Eliezer J

    2016-01-01

    We report on the synthesis of novel Ru(II) compounds (Ru-1 to Ru-8) bearing R-pdc, 4-Cl-pbinh ligands (where R=4-CF3, 4-F, 4-OH pdc=3-phenyl-5-(1H-pyrrol-2-yl)-4,5-dihydro-1H-pyrazole-1-carbothioamide, pbinh=phenoxybenzylidene isonicotinyl hydrazides) and their in vitro antitumor activity toward the cell lines murine leukemia L1210, human lymphocyte CEM, human epithelial cervical carcinoma HeLa, BEL-7402 and Molt4/C8. Some of the complexes exhibited more potent antiproliferative activity against cell lines than the standard drug cisplatin. Ruthenium complex Ru-2 displayed potent cytotoxicity with than that of cisplatin. DNA-binding, DNA cleavage and protein binding properties of ruthenium complexes with these ligands are reported. Interactions of these ruthenium complexes with DNA revealed an intercalative mode of binding between them. Synchronous fluorescence spectra proved that the interaction of ruthenium complexes with bovine serum albumin (BSA) resulted in a conformational change of the latter.

  6. Enabling Technologies for the Future of Chemical Synthesis.

    Science.gov (United States)

    Fitzpatrick, Daniel E; Battilocchio, Claudio; Ley, Steven V

    2016-03-23

    Technology is evolving at breakneck pace, changing the way we communicate, travel, find out information, and live our lives. Yet chemistry as a science has been slower to adapt to this rapidly shifting world. In this Outlook we use highlights from recent literature reports to describe how progresses in enabling technologies are altering this trend, permitting chemists to incorporate new advances into their work at all levels of the chemistry development cycle. We discuss the benefits and challenges that have arisen, impacts on academic-industry relationships, and future trends in the area of chemical synthesis. PMID:27163040

  7. Cdt2-mediated XPG degradation promotes gap-filling DNA synthesis in nucleotide excision repair

    OpenAIRE

    Han, Chunhua; Wani, Gulzar; Zhao, Ran; Qian, Jiang; Sharma, Nidhi; He, Jinshan; Zhu, Qianzheng; Wang, Qi-En; Wani, Altaf A.

    2014-01-01

    Xeroderma pigmentosum group G (XPG) protein is a structure-specific repair endonuclease, which cleaves DNA strands on the 3′ side of the DNA damage during nucleotide excision repair (NER). XPG also plays a crucial role in initiating DNA repair synthesis through recruitment of PCNA to the repair sites. However, the fate of XPG protein subsequent to the excision of DNA damage has remained unresolved. Here, we show that XPG, following its action on bulky lesions resulting from exposures to UV ir...

  8. Nucleotide excision repair DNA synthesis by excess DNA polymerase beta: a potential source of genetic instability in cancer cells.

    Science.gov (United States)

    Canitrot, Y; Hoffmann, J S; Calsou, P; Hayakawa, H; Salles, B; Cazaux, C

    2000-09-01

    The nucleotide excision repair pathway contributes to genetic stability by removing a wide range of DNA damage through an error-free reaction. When the lesion is located, the altered strand is incised on both sides of the lesion and a damaged oligonucleotide excised. A repair patch is then synthesized and the repaired strand is ligated. It is assumed that only DNA polymerases delta and/or epsilon participate to the repair DNA synthesis step. Using UV and cisplatin-modified DNA templates, we measured in vitro that extracts from cells overexpressing the error-prone DNA polymerase beta exhibited a five- to sixfold increase of the ultimate DNA synthesis activity compared with control extracts and demonstrated the specific involvement of Pol beta in this step. By using a 28 nt gapped, double-stranded DNA substrate mimicking the product of the incision step, we showed that Pol beta is able to catalyze strand displacement downstream of the gap. We discuss these data within the scope of a hypothesis previously presented proposing that excess error-prone Pol beta in cancer cells could perturb the well-defined specific functions of DNA polymerases during error-free DNA transactions. PMID:10973926

  9. DNA synthesis as an index of the cell reaction to irradiation and other damaging exposures

    International Nuclear Information System (INIS)

    Recent investigation results, showing the outlook of DNA synthesis suppresion determination method as a test for estimating and predicting cell sensitivity to irradiation and other damageing exposures are presented. Advantages of such a method are noted

  10. Peptide protected gold clusters: chemical synthesis and biomedical applications

    Science.gov (United States)

    Yuan, Qing; Wang, Yaling; Zhao, Lina; Liu, Ru; Gao, Fuping; Gao, Liang; Gao, Xueyun

    2016-06-01

    Bridging the gap between atoms and nanoparticles, noble metal clusters with atomic precision continue to attract considerable attention due to their important applications in catalysis, energy transformation, biosensing and biomedicine. Greatly different to common chemical synthesis, a one-step biomimetic synthesis of peptide-conjugated metal clusters has been developed to meet the demand of emerging bioapplications. Under mild conditions, multifunctional peptides containing metal capturing, reactive and targeting groups are rationally designed and elaborately synthesized to fabricate atomically precise peptide protected metal clusters. Among them, peptide-protected Au Cs (peptide-Au Cs) possess a great deal of exceptional advantages such as nanometer dimensions, high photostability, good biocompatibility, accurate chemical formula and specific protein targeting capacity. In this review article, we focus on the recent advances in potential theranostic fields by introducing the rising progress of peptide-Au Cs for biological imaging, biological analysis and therapeutic applications. The interactions between Au Cs and biological systems as well as potential mechanisms are also our concerned theme. We expect that the rapidly growing interest in Au Cs-based theranostic applications will attract broader concerns across various disciplines.

  11. UV-assisted photocatalytic synthesis of highly dispersed Ag nanoparticles supported on DNA decorated graphene for quantitative iodide analysis.

    Science.gov (United States)

    Kong, Fen-Ying; Li, Wei-Wei; Wang, Jing-Yi; Wang, Wei

    2015-07-15

    Herein, we report, for the first time, the synthesis of reduced graphene oxide-DNA-Ag (RGO-DNA-Ag) nanohybrids by ultraviolet (UV) irradiation of aqueous solutions of GO and Ag ions in the presence of DNA. The morphology and microstructure characterizations of the resultant nanohybrids reveal that the proposed method leads to the simultaneous reduction of GO and Ag ions together with efficient dispersion of Ag nanoparticles on the surface of RGO sheets. This simple and fast synthesis route is carried out at ambient conditions without using any additional chemical reducing agents, which has the potential to provide new avenues for the green fabrication of various RGO-based nanomaterials. Additionally, the RGO-DNA-Ag nanohybrids can be utilized as a novel sensing interfacial for direct determination of iodide by simple differential pulse voltammetry (DPV), without requiring any preceding preconcentration of the analyte. Based on the RGO-DNA-Ag nanohybrids modified electrode, a wide linear range of 1μM-1mM and a low detection limit of 0.2μM were obtained. This sensitive and direct method of analysis can be applied successfully to the determination of iodide in real samples.

  12. Effect of DNA polymerase inhibitors on DNA repair in intact and permeable human fibroblasts: Evidence that DNA polymerases. delta. and. beta. are involved in DNA repair synthesis induced by N-methyl-N prime -nitro-N-nitrosoguanidine

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, R.A.; Miller, M.R. (West Virginia Univ. Health Sciences Center, Morgantown (USA)); McClung, J.K. (Samuel Roberts Noble Foundation, Inc., East Ardmore, OK (USA))

    1990-01-09

    The involvement of DNA polymerases {alpha}, {beta}, and {delta} in DNA repair synthesis induced by N-methyl-N{prime}-nitro-N-nitrosoguanidine (MNNG) was investigated in human fibroblasts (HF). The effects of anti-(DNA polymerase {alpha}) monoclonal antibody, (p-n-butylphenyl)deoxyguanosine triphosphate (BuPdGTP), dideoxythymidine triphosphate (ddTTP), and aphidicolin on MNNG-induced DNA repair synthesis were investigated to dissect the roles of the different DNA polymerases. A subcellular system (permeable cells), in which DNA repair synthesis and DNA replication were differentiated by CsCl gradient centrifugation of BrdUMP density-labeled DNA, was used to examine the effects of the polymerase inhibitors. Another approach investigated the effects of several of these inhibitors of MNNG-induced DNA repair synthesis in intact cells by measuring the amount of ({sup 3}H)thymidine incorporated into repair DNA as determined by autoradiography and quantitation with an automated video image analysis system. In permeable cells, MNNG-induced DNA repair synthesis was inhibited 56% by 50 {mu}g of aphidicolin/mL, 6% by 10 {mu}M BuPdGTP, 13% by anti-(DNA polymerse {alpha}) monoclonal antibodies, and 29% by ddTTP. In intact cells, MNNG-induced DNA repair synthesis was inhibited 57% by 50 {mu}g of aphidicolin/mL and was not significantly inhibited by microinjecting anti-(DNA polymerase {alpha}) antibodies into HF nuclei. These results indicate that both DNA polymerase {delta} and {beta} are involved in repairing DNA damage caused by MNNG.

  13. In vitro synthesis of ribosomal proteins directed by Escherichia coli DNA.

    Science.gov (United States)

    Kaltschmidt, E; Kahan, L; Nomura, M

    1974-02-01

    In vitro synthesis of a number of E. coli 30S ribosomal proteins has been demonstrated in a cell-free system consisting of ribosomes, initiation factors, RNA polymerase, a fraction containing soluble enzymes and factors, and E. coli DNA. DNA-dependent synthesis of the following 30S proteins has been demonstrated: S4, S5, S7, S8, S9, S10, S13, S14, S16, S19, and S20.

  14. Stimulation of rat bladder epithelial DNA synthesis intravesical instillation of distilled water

    International Nuclear Information System (INIS)

    Two commonly used cystoscopic infusion fluids were examined to determine whether their infusion stimulates DNA synthesis of the bladder epithelium. Following a single intravesical dose of 0.5 ml of distilled water or 1.5% L-glycine solution, rats were killed periodically up to 1 week. A transient but significant increase in epithelial cell [3H]thymidine labeling was observed at 48 hr after distilled water instillation. Glycine solution did not stimulate DNA synthesis

  15. DNA polymerase-α regulates the activation of type I interferons through cytosolic RNA:DNA synthesis.

    Science.gov (United States)

    Starokadomskyy, Petro; Gemelli, Terry; Rios, Jonathan J; Xing, Chao; Wang, Richard C; Li, Haiying; Pokatayev, Vladislav; Dozmorov, Igor; Khan, Shaheen; Miyata, Naoteru; Fraile, Guadalupe; Raj, Prithvi; Xu, Zhe; Xu, Zigang; Ma, Lin; Lin, Zhimiao; Wang, Huijun; Yang, Yong; Ben-Amitai, Dan; Orenstein, Naama; Mussaffi, Huda; Baselga, Eulalia; Tadini, Gianluca; Grunebaum, Eyal; Sarajlija, Adrijan; Krzewski, Konrad; Wakeland, Edward K; Yan, Nan; de la Morena, Maria Teresa; Zinn, Andrew R; Burstein, Ezra

    2016-05-01

    Aberrant nucleic acids generated during viral replication are the main trigger for antiviral immunity, and mutations that disrupt nucleic acid metabolism can lead to autoinflammatory disorders. Here we investigated the etiology of X-linked reticulate pigmentary disorder (XLPDR), a primary immunodeficiency with autoinflammatory features. We discovered that XLPDR is caused by an intronic mutation that disrupts the expression of POLA1, which encodes the catalytic subunit of DNA polymerase-α. Unexpectedly, POLA1 deficiency resulted in increased production of type I interferons. This enzyme is necessary for the synthesis of RNA:DNA primers during DNA replication and, strikingly, we found that POLA1 is also required for the synthesis of cytosolic RNA:DNA, which directly modulates interferon activation. Together this work identifies POLA1 as a critical regulator of the type I interferon response.

  16. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips.

    Science.gov (United States)

    Kosuri, Sriram; Eroshenko, Nikolai; Leproust, Emily M; Super, Michael; Way, Jeffrey; Li, Jin Billy; Church, George M

    2010-12-01

    Development of cheap, high-throughput and reliable gene synthesis methods will broadly stimulate progress in biology and biotechnology. Currently, the reliance on column-synthesized oligonucleotides as a source of DNA limits further cost reductions in gene synthesis. Oligonucleotides from DNA microchips can reduce costs by at least an order of magnitude, yet efforts to scale their use have been largely unsuccessful owing to the high error rates and complexity of the oligonucleotide mixtures. Here we use high-fidelity DNA microchips, selective oligonucleotide pool amplification, optimized gene assembly protocols and enzymatic error correction to develop a method for highly parallel gene synthesis. We tested our approach by assembling 47 genes, including 42 challenging therapeutic antibody sequences, encoding a total of ∼35 kilobase pairs of DNA. These assemblies were performed from a complex background containing 13,000 oligonucleotides encoding ∼2.5 megabases of DNA, which is at least 50 times larger than in previously published attempts.

  17. Inhibitory effect of benzene metabolites on nuclear DNA synthesis in bone marrow cells

    International Nuclear Information System (INIS)

    Effects of endogenously produced and exogenously added benzene metabolites on the nuclear DNA synthetic activity were investigated using a culture system of mouse bone marrow cells. Effects of the metabolites were evaluated by a 30-min incorporation of [3H]thymidine into DNA following a 30-min interaction with the cells in McCoy's 5a medium with 10% fetal calf serum. Phenol and muconic acid did not inhibit nuclear DNA synthesis. However, catechol, 1,2,4-benzenetriol, hydroquinone, and p-benzoquinone were able to inhibit 52, 64, 79, and 98% of the nuclear DNA synthetic activity, respectively, at 24 μM. In a cell-free DNA synthetic system, catechol and hydroquinone did not inhibit the incorporation of [3H]thymidine triphosphate into DNA up to 24 μM but 1,2,4-benzenetriol and p-benzoquinone did. The effect of the latter two benzene metabolites was completely blocked in the presence of 1,4-dithiothreitol (1 mM) in the cell-free assay system. Furthermore, when DNA polymerase α, which requires a sulfhydryl (SH) group as an active site, was replaced by DNA polymerase 1, which does not require an SH group for its catalytic activity, p-benzoquinone and 1,2,4-benzenetriol were unable to inhibit DNA synthesis. Thus, the data imply the p-benzoquinone and 1,2,4-benzenetriol inhibited DNA polymerase α, consequently resulting in inhibition of DNA synthesis in both cellular and cell-free DNA synthetic systems. The present study identifies catechol, hydroquinone, p-benzoquinone, and 1,2,4-benzenetriol as toxic benzene metabolites in bone marrow cells and also suggests that their inhibitory action on DNA synthesis is mediated by mechanism(s) other than that involving DNA damage as a primary cause

  18. DNA mismatch repair efficiency and fidelity are elevated during DNA synthesis in human cells

    International Nuclear Information System (INIS)

    DNA mismatch repair (MMR) within human cells is hypothesized to occur primarily at the replication fork. However, experimental models measuring MMR activity at specific phases of the cell cycle and during genomic DNA synthesis are lacking. We have investigated MMR activity within the nuclear environment of HeLa cells after enriching for G1, S and G2/M phase of the cell cycle by centrifugal elutriation. This approach preserves physiologically normal MMR activity in cell populations subdivided into different phases of the cell cycle. Here we have shown that nuclear protein concentration of hMutSα and hMutLα increases as cells progress into S phase during routine cell culture. MMR activity, as measured by both in vitro and in vivo approaches, increases during S phase to the highest extent within normally growing cells. Both fidelity and activity of MMR are highest on actively replicating templates within intact cells during S phase. The MMR pathway however, is also active at lower levels at other phases of the cell cycle, and on nonreplicating templates

  19. A proposed role played by benzene itself in the induction of acute cytopenia: inhibition of DNA synthesis.

    Science.gov (United States)

    Lee, E W; Garner, C D; Johnson, J T

    1988-04-01

    A single intraperitoneal dose of benzene (880 mg/kg) in mice inhibited DNA synthesis of bone marrow cells within one hour postinjection. However, there was no inhibitory effect on the synthesis of heme and protein at that dosage. Dose-dependent inhibition of DNA synthesis by benzene was observed over the range of 440 to 1760 mg/kg, supporting the idea that cytopenia which was observed by others following multiple doses of benzene (e.g., 440 or 880 mg/kg) might be due to the inhibitory effect of benzene on DNA synthesis. In our studies, benzene concentrations above 81 micrograms/g wet bone marrow resulted in inhibition of DNA synthesis, regardless of whether it was given ip or by inhalation. The effect of benzene itself, rather than its toxic metabolites, on DNA synthesis was further seen in experiments using a bone marrow cell culture system and cell-free DNA synthetic system. Experimental results demonstrated that benzene alone was capable of inhibiting the DNA synthesis of bone marrow cells and that the reduced DNA synthesis resulted from the inhibitory effect of benzene on DNA polymerase alpha, the enzyme that catalyzes the last step of the DNA synthetic pathway. Thus, benzene itself could play a significant role in inducing myelotoxicity in the case of acute or subacute toxicity by exerting its inhibitory effect on DNA synthesis.

  20. Synergistic bombesin and insulin stimulation of DNA synthesis in human fetal kidney in serum-free culture.

    Science.gov (United States)

    Brière, N; Chailler, P

    1993-05-01

    The respective influences of growth factors during kidney development can be directly evaluated using the chemically-defined serum-free culture system perfected in our laboratory. Since, in this culture model, conditions are minimal for growth and differentiation, DNA synthesis sharply decreases during the first 48 h. The addition of epidermal growth factor (EGF, 100 ng/ml), insulin (5 micrograms/ml) and transferrin (5 micrograms/ml) significantly restores this important cellular function. The objective of the present study was to determine the influence of bombesin, a potent mitogen, supplemented alone or in combination with insulin, transferrin and/or EGF. Cortical explants of human fetal kidneys (17-20 weeks) were maintained during 5 days in culture. When compared with 5 day controls (L-15 medium only), bombesin generated a maximal though weak effect on DNA synthesis at a concentration of 0.3 nM, corresponding to a stimulation index (SI) of 22%. When combined with either transferrin or EGF, or with transferrin plus EGF, bombesin did not alter the SI of individual factors. Insulin, in turn, greatly increased DNA synthesis (SI = 169%), while bombesin strongly potentiated this effect (SI = 275%). Transferrin also enhanced insulin SI from 169 to 240%. When added as a third factor, bombesin further potentiated the effectiveness (SI = 338%) of the combination insulin plus transferrin. These results indicate that bombesin controls cell proliferation in synergism with other regulators and hence may act as a competence growth factor during nephrogenesis.

  1. Does trans-lesion synthesis explain the UV-radiation resistance of DNA synthesis in C. elegans embryos

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, Phil; Reddy, Jennifer; Svendsen, Betty-Ann (Texas Christian Univ., Fort Worth, TX (United States). Dept. of Biology)

    1991-09-01

    Over 10-fold larger fluences were required to inhibit both DNA synthesis and cell division in wild-type C.elegans embryos as compared with other model systems or C.elegans rad mutants. In addition, unlike in other organisms, the molecular weight of daughter DNA strands was reduced only after large, superlethal fluences. The molecular weight of nascent DNA fragments exceeded the interdimer distance by up to 19-fold, indicating that C.elegans embryos can replicate through non-instructional lesions. This putative trans-lesion synthetic capability may explain the refractory nature of UV-radiation on embryonic DNA synthesis and nuclear division in C.elegans. (author). 42 refs.; 7 figs.

  2. Recent Developments in Chemical Synthesis with Biocatalysts in Ionic Liquids

    Directory of Open Access Journals (Sweden)

    Mahesh K. Potdar

    2015-09-01

    Full Text Available Over the past decade, a variety of ionic liquids have emerged as greener solvents for use in the chemical manufacturing industries. Their unique properties have attracted the interest of chemists worldwide to employ them as replacement for conventional solvents in a diverse range of chemical transformations including biotransformations. Biocatalysts are often regarded as green catalysts compared to conventional chemical catalysts in organic synthesis owing to their properties of low toxicity, biodegradability, excellent selectivity and good catalytic performance under mild reaction conditions. Similarly, a selected number of specific ionic liquids can be considered as greener solvents superior to organic solvents owing to their negligible vapor pressure, low flammability, low toxicity and ability to dissolve a wide range of organic and biological substances, including proteins. A combination of biocatalysts and ionic liquids thus appears to be a logical and promising opportunity for industrial use as an alternative to conventional organic chemistry processes employing organic solvents. This article provides an overview of recent developments in this field with special emphasis on the application of more sustainable enzyme-catalyzed reactions and separation processes employing ionic liquids, driven by advances in fundamental knowledge, process optimization and industrial deployment.

  3. Recent Developments in Chemical Synthesis with Biocatalysts in Ionic Liquids.

    Science.gov (United States)

    Potdar, Mahesh K; Kelso, Geoffrey F; Schwarz, Lachlan; Zhang, Chunfang; Hearn, Milton T W

    2015-09-15

    Over the past decade, a variety of ionic liquids have emerged as greener solvents for use in the chemical manufacturing industries. Their unique properties have attracted the interest of chemists worldwide to employ them as replacement for conventional solvents in a diverse range of chemical transformations including biotransformations. Biocatalysts are often regarded as green catalysts compared to conventional chemical catalysts in organic synthesis owing to their properties of low toxicity, biodegradability, excellent selectivity and good catalytic performance under mild reaction conditions. Similarly, a selected number of specific ionic liquids can be considered as greener solvents superior to organic solvents owing to their negligible vapor pressure, low flammability, low toxicity and ability to dissolve a wide range of organic and biological substances, including proteins. A combination of biocatalysts and ionic liquids thus appears to be a logical and promising opportunity for industrial use as an alternative to conventional organic chemistry processes employing organic solvents. This article provides an overview of recent developments in this field with special emphasis on the application of more sustainable enzyme-catalyzed reactions and separation processes employing ionic liquids, driven by advances in fundamental knowledge, process optimization and industrial deployment.

  4. Synthesis of Codon-optimized Human Interleukin-18 Gene by Combination of Chemical and Enzymatic Method

    Institute of Scientific and Technical Information of China (English)

    GAO Chao-hui; SHI Xiao-yue; HOU Xin-tong; MENG Qing-fan; Zhang Ying-jiu; TENG Li-rong

    2008-01-01

    According to the amino acid sequence and codon preference of E,coli,the human interleukin-18(IL-18)gene was optimized to avoid the rare codons,The total length of the synthesized gene is 571 bp;18 oligonucleotides,DNA fragments were designed and synthesized by the phosphoramidite four-step chemical method,The whole DNAsequence was synthesized by a one-step total gene synthesis method,and then inserted in pUC18 vector,Five positive clones identified by blue-white colony screening were sent to Shanghai Sangon Biological Engineering Technology and Service Co.,Ltd,for sequencing,The sequencing result shows that one clone contained the complete correct gene in all the five positive clones.

  5. Plasma-Chemical Synthesis of Nanosized Powders-Nitrides, Carbides, Oxides, Carbon Nanotubes and Fullerenes

    Institute of Scientific and Technical Information of China (English)

    Katerina ZAHARIEVA; Gheorghi VISSOKOV; Janis GRABIS; Slavcho RAKOVSKY

    2012-01-01

    In this article the plasma-chemical synthesis of nanosized powders (nitrides, car- bides, oxides, carbon nanotubes and fullerenes) is reviewed. Nanosized powders - nitrides, carbides, oxides, carbon nanotubes and fullerenes have been successfully produced using different techniques, technological apparatuses and conditions for their plasma-chemical synthesis.

  6. An optimized chemical synthesis of human relaxin-2.

    Science.gov (United States)

    Barlos, Kostas K; Gatos, Dimitrios; Vasileiou, Zoe; Barlos, Kleomenis

    2010-04-01

    Human gene 2 relaxin (RLX) is a member of the insulin superfamily and is a multi-functional factor playing a vital role in pregnancy, aging, fibrosis, cardioprotection, vasodilation, inflammation, and angiogenesis. RLX is currently applied in clinical trials to cure among others acute heart failure, fibrosis, and preeclampsia. The synthesis of RLX by chemical methods is difficult because of the insolubility of its B-chain and the required laborious and low yielding site-directed combination of its A (RLXA) and B (RLXB) chains. We report here that oxidation of the Met(25) residue of RLXB improves its solubility, allowing its effective solid-phase synthesis and application in random interchain combination reactions with RLXA. Linear Met(O)(25)-RLX B-chain (RLXBO) reacts with a mixture of isomers of bicyclic A-chain (bcRLXA) giving exclusively the native interchain combination. Applying this method Met(O)(25)-RLX (RLXO) was obtained in 62% yield and was easily converted to RLX in 78% yield, by reduction with ammonium iodide. PMID:20191607

  7. New approach for direct chemical synthesis of hexagonal Co nanoparticles

    Science.gov (United States)

    Abel, Frank M.; Tzitzios, Vasilis; Hadjipanayis, George C.

    2016-02-01

    In this paper, we explore the possibility of producing hexagonal Cobalt nanoparticles, with high saturation magnetization by direct chemical synthesis. The nanoparticles were synthesized by reduction of anhydrous cobalt (II) chloride by NaBH4 in tetraglyme at temperatures in the range of 200-270 °C under a nitrogen-hydrogen atmosphere. The reactions were done at high temperatures to allow for the formation of as-made hexagonal cobalt. The size of the particles was controlled by the addition of different surfactants. The best magnetic properties so far were obtained on spherical hexagonal Co nanoparticles with an average size of 45 nm, a saturation magnetization of 143 emu/g and coercivity of 500 Oe. the saturation magnetization and coercivity were further improved by annealing the Co nanoparticles leading to saturation magnetization of 160 emu/g and coercivity of 540 Oe.

  8. Chemical Synthesis of Human Insulin-Like Peptide-6.

    Science.gov (United States)

    Wu, Fangzhou; Mayer, John P; Zaykov, Alexander N; Zhang, Fa; Liu, Fa; DiMarchi, Richard D

    2016-07-01

    Human insulin-like peptide-6 (INSL-6) belongs to the insulin superfamily and shares the distinctive disulfide bond configuration of human insulin. In this report we present the first chemical synthesis of INSL-6 utilizing fluorenylmethyloxycarbonyl-based (Fmoc) solid-phase peptide chemistry and regioselective disulfide bond construction protocols. Due to the presence of an oxidation-sensitive tryptophan residue, two new orthogonal synthetic methodologies were developed. The first method involved the identification of an additive to suppress the oxidation of tryptophan during iodine-mediated S-acetamidomethyl (Acm) deprotection and the second utilized iodine-free, sulfoxide-directed disulfide bond formation. The methodologies presented here offer an efficient synthetic route to INSL-6 and will further improve synthetic access to other multiple-disulfide-containing peptides with oxidation-sensitive residues. PMID:27259101

  9. Modern catalysis in the synthesis of some pharmaceuticals and fine chemicals

    OpenAIRE

    Petrović Slobodan D.; Mišić-Vuković Milica M.; Mijin Dušan Ž.

    2002-01-01

    Catalysis in the synthesis of Pharmaceuticals and line chemicals nowadays becomes more and more important. Synthesis that minimizes wastes is important from the economical aspect, as well as from the environmental aspect. "Green chemistry" or "green technology" is an effort to protect the environment by increasing the efficiency of the overall synthetic processes in the chemical industry by minimizing or eliminating wasteful by-products. Modern catalytic methods in the synthesis of some Pharm...

  10. Effect of Microwave Radiation on Enzymatic and Chemical Peptide Bond Synthesis on Solid Phase

    Directory of Open Access Journals (Sweden)

    Alessandra Basso

    2009-01-01

    Full Text Available Peptide bond synthesis was performed on PEGA beads under microwave radiations. Classical chemical coupling as well as thermolysin catalyzed synthesis was studied, and the effect of microwave radiations on reaction kinetics, beads' integrity, and enzyme activity was assessed. Results demonstrate that microwave radiations can be profitably exploited to improve reaction kinetics in solid phase peptide synthesis when both chemical and biocatalytic strategies are used.

  11. Chemical Incorporation of Chain-Terminating Nucleoside Analogs as 3'-Blocking DNA Damage and Their Removal by Human ERCC1-XPF Endonuclease.

    Science.gov (United States)

    Yamamoto, Junpei; Takahata, Chiaki; Kuraoka, Isao; Hirota, Kouji; Iwai, Shigenori

    2016-01-01

    Nucleoside/nucleotide analogs that lack the 3'-hydroxy group are widely utilized for HIV therapy. These chain-terminating nucleoside analogs (CTNAs) block DNA synthesis after their incorporation into growing DNA, leading to the antiviral effects. However, they are also considered to be DNA damaging agents, and tyrosyl-DNA phosphodiesterase 1, a DNA repair enzyme, is reportedly able to remove such CTNA-modifications of DNA. Here, we have synthesized phosphoramidite building blocks of representative CTNAs, such as acyclovir, abacavir, carbovir, and lamivudine, and oligonucleotides with the 3'-CTNAs were successfully synthesized on solid supports. Using the chemically synthesized oligonucleotides, we investigated the excision of the 3'-CTNAs in DNA by the human excision repair cross complementing protein 1-xeroderma pigmentosum group F (ERCC1-XPF) endonuclease, which is one of the main components of the nucleotide excision repair pathway. A biochemical analysis demonstrated that the ERCC1-XPF endonuclease cleaved 2-7 nt upstream from the 3'-blocking CTNAs, and that DNA synthesis by the Klenow fragment was resumed after the removal of the CTNAs, suggesting that ERCC1-XPF participates in the repair of the CTNA-induced DNA damage. PMID:27294910

  12. Synthesis and cell-free cloning of DNA libraries using programmable microfluidics

    OpenAIRE

    Yehezkel, Tuval Ben; Rival, Arnaud; Raz, Ofir; Cohen, Rafael; Marx, Zipora; Camara, Miguel; Dubern, Jean-Frédéric; Koch, Birgit; Heeb, Stephan; Krasnogor, Natalio; Delattre, Cyril; Shapiro, Ehud

    2015-01-01

    Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and a...

  13. Revisiting Plus-Strand DNA Synthesis in Retroviruses and Long Terminal Repeat Retrotransposons: Dynamics of Enzyme: Substrate Interactions

    Directory of Open Access Journals (Sweden)

    Stuart F. J. Le Grice

    2009-11-01

    Full Text Available Although polypurine tract (PPT-primed initiation of plus-strand DNA synthesis in retroviruses and LTR-containing retrotransposons can be accurately duplicated, the molecular details underlying this concerted series of events remain largely unknown. Importantly, the PPT 3’ terminus must be accommodated by ribonuclease H (RNase H and DNA polymerase catalytic centers situated at either terminus of the cognate reverse transcriptase (RT, and in the case of the HIV-1 enzyme, ~70Å apart. Communication between RT and the RNA/DNA hybrid therefore appears necessary to promote these events. The crystal structure of the HIV-1 RT/PPT complex, while informative, positions the RNase H active site several bases pairs from the PPT/U3 junction, and thus provides limited information on cleavage specificity. To fill the gap between biochemical and crystallographic approaches, we review a multidisciplinary approach combining chemical probing, mass spectrometry, NMR spectroscopy and single molecule spectroscopy. Our studies also indicate that nonnucleoside RT inhibitors affect enzyme orientation, suggesting initiation of plus-strand DNA synthesis as a potential therapeutic target.

  14. Three Novel cis-Acting Elements Required for Efficient Plus-Strand DNA Synthesis of the Hepatitis B Virus Genome

    OpenAIRE

    Lee, Jehan; Shin, Myeong-Kyun; Lee, Hye-Jin; Yoon, Gyesoon; Ryu, Wang-Shick

    2004-01-01

    Synthesis of the relaxed-circular (RC) DNA genomes of hepadnaviruses by reverse transcriptase involves two template switches during plus-strand DNA synthesis. These template switches require repeat sequences (so-called donor and acceptor sites) between which a complementary strand of nucleic acid is transferred. To determine cis-acting elements apart from the donor and acceptor sites that are required for plus-strand RC DNA synthesis by hepatitis B virus (HBV), a series of mutants bearing a s...

  15. Measurement of unscheduled DNA synthesis and S-phase synthesis in rodent hepatocytes following in vivo treatment: Testing of 24 compounds

    International Nuclear Information System (INIS)

    The in vivo-in vitro hepatocyte DNA repair assay has been shown to be useful for studying genotoxic hepatocarcinogens. In addition, measurement of S-phase synthesis (SPS) provides an indirect indicator of hepatocellular proliferation, which may be an important mechanism in rodent carcinogenesis. This assay was used to examine 24 chemicals for their ability to induce unscheduled DNA synthesis (UDS) or SPS in Fischer-344 rats or B6C3F1 mice following in vivo treatment. Hepatocytes were isolated by liver perfusion and incubated with 3H-thymidine following in vivo treatment by gavage. Chemicals chosen for testing were from the National Toxicology Program (NTP) genetic toxicology testing program and most were also evaluated in long-term animal studies conducted by the NTP. Dinitrotoluene and Michler's Ketone induced positive UDS response in rat, while N-nitrosodiethanolamine and selenium sulfide induced equivocal UDS results in mouse and rat, respectively. BCMEE, bromoform, chloroform, PBB, 1,1,2-trichloroethane, and trichloroethylene were all potent inducers of SPS in mouse liver, while C.I. Solvent Yellow 14, and 1,1,2,2-tetrachloroethane yielded equivocal SPS results in rat and mouse, respectively. These results indicate that most of the test compounds do not induced UDS in the liver; however, the significant S-phase response induced by many of these compounds, especially the halogenated solvents, may be an important mechanism in their hepatocarinogenicity

  16. Protein synthesis by native chemical ligation: Expanded scope by using straightforward methodology

    OpenAIRE

    Tilman M Hackeng; Griffin, John H.; Dawson, Philip E.

    1999-01-01

    The total chemical synthesis of proteins has great potential for increasing our understanding of the molecular basis of protein function. The introduction of native chemical ligation techniques to join unprotected peptides next to a cysteine residue has greatly facilitated the synthesis of proteins of moderate size. Here, we describe a straightforward methodology that has enabled us to rapidly analyze the compatibility of the native chemical ligation strategy for X–Cys ligation sites, where X...

  17. Discovery of small-molecule interleukin-2 inhibitors from a DNA-encoded chemical library.

    Science.gov (United States)

    Leimbacher, Markus; Zhang, Yixin; Mannocci, Luca; Stravs, Michael; Geppert, Tim; Scheuermann, Jörg; Schneider, Gisbert; Neri, Dario

    2012-06-18

    Libraries of chemical compounds individually coupled to encoding DNA tags (DNA-encoded chemical libraries) hold promise to facilitate exceptionally efficient ligand discovery. We constructed a high-quality DNA-encoded chemical library comprising 30,000 drug-like compounds; this was screened in 170 different affinity capture experiments. High-throughput sequencing allowed the evaluation of 120 million DNA codes for a systematic analysis of selection strategies and statistically robust identification of binding molecules. Selections performed against the tumor-associated antigen carbonic anhydrase IX (CA IX) and the pro-inflammatory cytokine interleukin-2 (IL-2) yielded potent inhibitors with exquisite target specificity. The binding mode of the revealed pharmacophore against IL-2 was confirmed by molecular docking. Our findings suggest that DNA-encoded chemical libraries allow the facile identification of drug-like ligands principally to any protein of choice, including molecules capable of disrupting high-affinity protein-protein interactions.

  18. Correlation between the levels of N6-(Δ2-isopentenyl)-adenosine and synthesis of DNA in germinating rice seeds

    International Nuclear Information System (INIS)

    Levels of N6(Δ2-isopentenyl) adenosine as determined by radioimmunoassay increased up to 18 hr, then decreased till 24 hr and again increased up to 48 hr, during the germination of rice seeds. The synthesis of isopentenyl-adenosine as followed by the incorporation of 14C-adenine and precipitation with the antibodies for the hormone showed no significant change up to 24 hr. This may imply that the hormone was generated from the stored precursors. Synthesis of DNA proceeded in cycles with the peaks of incorporation of 3H-thymidine at 18 and 36 hr suggesting a correlation between the levels of cytokinin and the synthesis of DNA up to 24 hr. Cordycopin inhibited the synthesis of isopentenyladenosine and DNA and the inhibition of the synthesis of DNA was reversed by the presence of the hormone. This indicated the involvement of cytokinin in the synthesis of DNA. (author)

  19. Enzymatic Synthesis of Rhamnose Containing Chemicals by Reverse Hydrolysis.

    Directory of Open Access Journals (Sweden)

    Lili Lu

    Full Text Available Rhamnose containing chemicals (RCCs are widely occurred in plants and bacteria and are known to possess important bioactivities. However, few of them were available using the enzymatic synthesis method because of the scarcity of the α-L-rhamnosidases with wide acceptor specificity. In this work, an α-L-rhamnosidase from Alternaria sp. L1 was expressed in Pichia pastroris strain GS115. The recombinant enzyme was purified and used to synthesize novel RCCs through reverse hydrolysis in the presence of rhamnose as donor and mannitol, fructose or esculin as acceptors. The effects of initial substrate concentrations, reaction time, and temperature on RCC yields were investigated in detail when using mannitol as the acceptor. The mannitol derivative achieved a maximal yield of 36.1% by incubation of the enzyme with 0.4 M L-rhamnose and 0.2 M mannitol in pH 6.5 buffers at 55°C for 48 h. In identical conditions except for the initial acceptor concentrations, the maximal yields of fructose and esculin derivatives reached 11.9% and 17.9% respectively. The structures of the three derivatives were identified to be α-L-rhamnopyranosyl-(1→6'-D-mannitol, α-L-rhamnopyranosyl-(1→1'-β-D-fructopyranose, and 6,7-dihydroxycoumarin α-L-rhamnopyranosyl-(1→6'-β-D-glucopyranoside by ESI-MS and NMR spectroscopy. The high glycosylation efficiency as well as the broad acceptor specificity of this enzyme makes it a powerful tool for the synthesis of novel rhamnosyl glycosides.

  20. DNA Synthesis, Assembly and Applications in Synthetic Biology

    OpenAIRE

    Ma, Siying; Tang, Nicholas; Tian, Jingdong

    2012-01-01

    The past couple of years saw exciting new developments in microchip-based gene synthesis technologies. Such technologies hold the potential for significantly increasing the throughput and decreasing the cost of gene synthesis. Together with more efficient enzymatic error correction and genome assembly methods, these new technologies are pushing the field of synthetic biology to a higher level.

  1. The effect of nitroimidazole and nitroxyl radiosensitizers on the post-irradiation synthesis of DNA

    International Nuclear Information System (INIS)

    The modification of DNA damage by three radiosensitizing drugs, present during γ-irradiation of hypoxic Chinese hamster cells, was investigated. Both 2-methyl-5-nitroimidazole-1-ethanol (metronidazole) and 1-(2-nitro-1-imidazole)-3-methoxy-2-propanol (Ro-07-0582) were found to cause large increases in the yield of DNA single-strand breaks (SSB); triacetoneamine-N-oxyl (TAN) was found to have only a small effect on SSB production. The three drugs tested did not inhibit the rejoining of SSB. A pulse label and chase procedure was used to examine post-irradiation DNA synthesis. TAN present during irradiation under hypoxia was found to cause interruptions in subsequent DNA synthesis. Metronidazole and Ro-07-0582 had no effect on post-irradiation DNA synthesis. In addition, the effects of pre- and post-irradiation exposure to TAN were investigated, since these treatments have shown increased cell-killing in survival studies. TAN pre- and post-treatments were found to have no significant effect on subsequent DNA synthesis. (author)

  2. Chemical cleavage reactions of DNA on solid support: application in mutation detection

    Directory of Open Access Journals (Sweden)

    Cotton Richard GH

    2003-05-01

    Full Text Available Abstract Background The conventional solution-phase Chemical Cleavage of Mismatch (CCM method is time-consuming, as the protocol requires purification of DNA after each reaction step. This paper describes a new version of CCM to overcome this problem by immobilizing DNA on silica solid supports. Results DNA test samples were loaded on to silica beads and the DNA bound to the solid supports underwent chemical modification reactions with KMnO4 (potassium permanganate and hydroxylamine in 3M TEAC (tetraethylammonium chloride solution. The resulting modified DNA was then simultaneously cleaved by piperidine and removed from the solid supports to afford DNA fragments without the requirement of DNA purification between reaction steps. Conclusions The new solid-phase version of CCM is a fast, cost-effective and sensitive method for detection of mismatches and mutations.

  3. Flexible double-headed cytosine-linked 2'-deoxycytidine nucleotides. Synthesis, polymerase incorporation to DNA and interaction with DNA methyltransferases.

    Science.gov (United States)

    Kielkowski, Pavel; Cahová, Hana; Pohl, Radek; Hocek, Michal

    2016-03-15

    New types of double-headed 2'-deoxycytidine 5'-O-triphosphates (dC(XC)TPs) bearing another cytosine or 5-fluorocytosine linked through a flexible propargyl, homopropargyl or pent-1-ynyl linker to position 5 were prepared by the aqueous Sonogashira cross-coupling reactions of 5-iodo-dCTP with the corresponding (fluoro)cytosine-alkynes. The modified dC(XC)TPs were good substrates for DNA polymerases and were used for enzymatic synthesis of cytosine-functionalized DNA by primer extension or PCR. The cytosine- or fluorocytosine-linked DNA probes did not significantly inhibit DNA methyltransferases and did not cross-link to these proteins. PMID:26899597

  4. Regulation of chloroplast number and DNA synthesis in higher plants. Final report, August 1995--August 1996

    Energy Technology Data Exchange (ETDEWEB)

    Mullet, J.E.

    1997-06-17

    The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focused on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The research focused on the isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.

  5. Synthesis and Characterization of Chemically Etched Nanostructured Silicon

    KAUST Repository

    Mughal, Asad Jahangir

    2012-05-01

    Silicon is an essential element in today’s modern world. Nanostructured Si is a more recently studied variant, which has currently garnered much attention. When its spatial dimensions are confined below a certain limit, its optical properties change dramatically. It transforms from an indirect bandgap material that does not absorb or emit light efficiently into one which can emit visible light at room temperatures. Although much work has been conducted in understanding the properties of nanostructured Si, in particular porous Si surfaces, a clear understanding of the origin of photoluminescence has not yet been produced. Typical synthesis approaches used to produce nanostructured Si, in particular porous Si and nanocrystalline Si have involved complex preparations used at high temperatures, pressures, or currents. The purpose of this thesis is to develop an easier synthesis approach to produce nanostructured Si as well as arrive at a clearer understanding of the origin of photoluminescence in these systems. We used a simple chemical etching technique followed by sonication to produce nanostructured Si suspensions. The etching process involved producing pores on the surface of a Si substrate in a solution containing hydrofluoric acid and an oxidant. Nanocrystalline Si as well as nanoscale amorphous porous Si suspensions were successfully synthesized using this process. We probed into the phase, composition, and origin of photoluminescence in these materials, through the use of several characterization techniques. TEM and SEM were used to determine morphology and phase. FT-IR and XPS were employed to study chemical compositions, and steady state and time resolved optical spectroscopy techniques were applied to resolve their photoluminescent properties. Our work has revealed that the type of oxidant utilized during etching had a significant impact on the final product. When using nitric acid as the oxidant, we formed nanocrystalline Si suspensions composed of

  6. Ribonucleotide reductase activity is coupled to DNA synthesis via proliferating cell nuclear antigen.

    Science.gov (United States)

    Salguero, Israel; Guarino, Estrella; Shepherd, Marianne E A; Deegan, Tom D; Havens, Courtney G; MacNeill, Stuart A; Walter, Johannes C; Kearsey, Stephen E

    2012-04-24

    Synthesis of deoxynucleoside triphosphates (dNTPs) is required for both DNA replication and DNA repair and is catalyzed by ribonucleotide reductases (RNR), which convert ribonucleotides to their deoxy forms [1, 2]. Maintaining the correct levels of dNTPs for DNA synthesis is important for minimizing the mutation rate [3-7], and this is achieved by tight regulation of RNR [2, 8, 9]. In fission yeast, RNR is regulated in part by a small protein inhibitor, Spd1, which is degraded in S phase and after DNA damage to allow upregulation of dNTP supply [10-12]. Spd1 degradation is mediated by the activity of the CRL4(Cdt2) ubiquitin ligase complex [5, 13, 14]. This has been reported to be dependent on modulation of Cdt2 levels, which are cell cycle regulated, peaking in S phase, and which also increase after DNA damage in a checkpoint-dependent manner [7, 13]. We show here that Cdt2 level fluctuations are not sufficient to regulate Spd1 proteolysis and that the key step in this event is the interaction of Spd1 with the polymerase processivity factor proliferating cell nuclear antigen (PCNA), complexed onto DNA. This mechanism thus provides a direct link between DNA synthesis and RNR regulation. PMID:22464192

  7. Typical xeroderma pigmentosum complementation group A fibroblasts have detectable ultraviolet light-induced unscheduled DNA synthesis

    International Nuclear Information System (INIS)

    Ultraviolet-induced nuclear uptake of tritiated thymidine [3H]dThd demonstrable by autoradiography in non-synthesis phases of the cell cycle is known as unscheduled DNA synthesis and reflects repair replication of ultraviolet-damaged DNA. We have reported that the rate of any such unscheduled DNA synthesis in typical group A xeroderma pigmentosum fibroblasts, if present, is less than 2% of the normal rate. We have now performed experiments to determine whether these fibroblasts have any unscheduled DNA synthesis. Fibroblast coverslip cultures of four xeroderma pigmentosum group A strains were prepared. Irradiated (254 nm ultraviolet light) and unirradiated cultures from each strain were incubated with [3H]dThd at 37degC, and autoradiograms were prepared using NTB-3 emulsion. A nuclear grain count was made of 100 consecutive nuclei of non-S-phase irradiated and unirradiated cells. A slide background grain count was simultaneously made from an acellular area adjacent to each cell analyzed. When a strain's irradiated and unirradiated autoradiograms having similar slide background grain count averages were compared, the nuclear grain count average of the irradiated cells was always higher than that of the unirradiated cells. This ultraviolet-induced increase in the mean nuclear grain count ranged from 0.4 to 1.3% of that given by normal non-xeroderma pigmentosum fibroblasts and was not reduced by 10-2M hydroxyurea. Planimetric studies showed that the ultraviolet-induced increase in nuclear grain count is not due to an increased nuclear area in irradiated cells. We conclude that these typical group A xeroderma pigmentosum strains perform very low, but detectable, ultraviolet-induced unscheduled DNA synthesis which probably reflects repair replication. We cannot, however, determine if there are significantly different rates of ultraviolet-induced unscheduled DNA synthesis among these ultraviolet strains

  8. A cell-free system for DNA repair synthesis using purified enzymes from the Novikoff hepatoma

    International Nuclear Information System (INIS)

    Novikoff DNA polymerase-β and Novikoff DNase V have been used in a cell-free DNA excision repair system for UV-irradiated substrates to determine their DNA repair capabilities. The repair system was shown to depend upon UV-irradiated DNA, incision by phage T4 UV-endonuclease, excision by DNase V and synthesis by DNA polymerase-β; ligation was not included. Highly purified calf thymus DNA was UV-irradiated at 500-750 J/m2 and incised by T4 UV-endonuclease. The repair system was used to follow the purification of DNase V and DNA polymerase-β. For increased specificity, the parameters of UV-irradiation, incision, excision and synthesis were confirmed on highly supercoiled, covalently closed, phage PM2 DNA. Optimal DNA and Mg2+ concentrations were determined for the repair assay, which was shown to be linear with respect to time. Excision of the 3'-apyrimidinic site and the 5'-pyrimidine dimer by bidirectional DNase V, presumed to occur from the above experiments, was studied more thoroughly using lightly UV-irradiated [3H]poly(dT)poly (dA), labeled in both the base and the sugar, and incised with T4 UV-endonuclease

  9. Effect of α-Particle and X-Ray Irradiation on DNA Synthesis in Tissue Cultures

    International Nuclear Information System (INIS)

    The effect of both a-particle and X-ray irradiation on the rate of DNA synthesis in mouse fibroblast and HeLa cells in tissue culture is described. Tritiated thymidine micro autoradiography was used to indicate the rate of synthesis in the single layer cultures used. The results of the experiments show that: (1) The fraction of cells in a culture synthesizing DNA is unaffected by α-particles and X-rays in the doses used in the experiment. (2) The effect of either type of radiation is to reduce the rate of synthesis of DNA of the irradiated cells in synthesis. (3) The effect of a given dose of either type of radiation is to reduce the rate of synthesis of all the cells to a constant fraction of what it was in the unirradiated cells. (4) The rate of DNA synthesis is reduced to 37% (1/e) by a dose of ca. 25 α/μ2 or an X-ray dose of 14000 rad for mouse fibroblast cultures. In Hela cell cultures a dose of ca. 90000 rad is needed to reduce the rate of DNA synthesis to 37% of the initial value. (5) The reduction in synthesis occurs not more than a half hour after irradiation and may be an immediate effect. From (4) above the target shape can be roughly calculated and if it is assumed to be cylindrical it appears to have dimensions ca. 16 Å in one direction and 16 000 Å in the other, i. e. a long thin thread with a MW of ca. 5 * 107 in the case of the mouse fibroblast experiments. In the case of the Hela cell experiments the target volume gives a MW of ca. 107. The results are consistent with the view that the target may possibly be the DNA template (or maybe DNAP because of the high MW in one case). If the effects described reflect damage to the DNA (or DNAP) template during the exponential phase of synthesis then observations (1), (2) and (3) above follow as obvious correlatives. (author)

  10. Synthesis and characterization of a lamellar hydroxyapatite/DNA nanohybrid

    International Nuclear Information System (INIS)

    Research highlights: → A lamellar hydroxyapatite (HAp)/DNA nanohybrid was prepared as a novel gene delivering vector. → Gel electrophoresis analysis confirmed that the lamellar HAp could protect DNA from degradation of DNase I. → The protected DNA in the HAp/DNA nanohybrid could be recovered readily under acid conditions. - Abstract: Two-dimensional layered materials exhibit desired functionalities when being used as gene delivery materials. In this study, a novel gene delivering vector, lamellar hydroxyapatite (HAp)/DNA nanohybrid was prepared. The structure of HAp/DNA nanohybrid was investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Fourier transform infrared (FT-IR) spectroscopy analysis revealed that ion-exchange occurred during the process. Gel electrophoresis analysis confirmed that the lamellar HAp could protect DNA from degradation of DNase I and the protected DNA could be recovered readily under acid conditions. Furthermore, the integrity of released DNA was confirmed by UV-vis spectra.

  11. 3D printing of versatile reactionware for chemical synthesis.

    Science.gov (United States)

    Kitson, Philip J; Glatzel, Stefan; Chen, Wei; Lin, Chang-Gen; Song, Yu-Fei; Cronin, Leroy

    2016-05-01

    In recent decades, 3D printing (also known as additive manufacturing) techniques have moved beyond their traditional applications in the fields of industrial manufacturing and prototyping to increasingly find roles in scientific research contexts, such as synthetic chemistry. We present a general approach for the production of bespoke chemical reactors, termed reactionware, using two different approaches to extrusion-based 3D printing. This protocol describes the printing of an inert polypropylene (PP) architecture with the concurrent printing of soft material catalyst composites, using two different 3D printer setups. The steps of the PROCEDURE describe the design and preparation of a 3D digital model of the desired reactionware device and the preparation of this model for use with fused deposition modeling (FDM) type 3D printers. The protocol then further describes the preparation of composite catalyst-silicone materials for incorporation into the 3D-printed device and the steps required to fabricate a reactionware device. This combined approach allows versatility in the design and use of reactionware based on the specific needs of the experimental user. To illustrate this, we present a detailed procedure for the production of one such reactionware device that will result in the production of a sealed reactor capable of effecting a multistep organic synthesis. Depending on the design time of the 3D model, and including time for curing and drying of materials, this procedure can be completed in ∼3 d. PMID:27077333

  12. Nanograined WC-Co Composite Powders by Chemical Vapor Synthesis

    Science.gov (United States)

    Ryu, Taegong; Sohn, H. Y.; Han, Gilsoo; Kim, Young-Ugk; Hwang, Kyu Sup; Mena, M.; Fang, Zhigang Z.

    2008-02-01

    Nanograined tungsten carbide (WC) Co composite powders were prepared by a chemical vapor synthesis (CVS) process that has previously been used for preparing the aluminides of titanium and nickel and other metallic and intermetallic powders at the University of Utah. To determine the optimum condition for producing nanograined WC-Co composite powders, the effects of carburization temperature, CH4 to WCl6 ratio, CH4 to H2 ratio, CoCl2 contents, and residence time of WC on the powder composition and particle size were investigated. The reduction and carburization of the vaporized chlorides by CH4-H2 mixtures produced nanograined WC and Co composite powder, which sometimes contained small levels of W2C, W, or the η (Co3W3C) phase. The presence of these incompletely carburized phases can be tolerated because they can be fully carburized during the subsequent sintering process. These phases can also be fully carburized by a separate post-treatment. The products were characterized by using X-ray diffraction (XRD) and a transmission electron microscope (TEM). As a result, nanograined WC-Co composite with the particle size less than 30 nm was obtained.

  13. 3D printing of versatile reactionware for chemical synthesis.

    Science.gov (United States)

    Kitson, Philip J; Glatzel, Stefan; Chen, Wei; Lin, Chang-Gen; Song, Yu-Fei; Cronin, Leroy

    2016-05-01

    In recent decades, 3D printing (also known as additive manufacturing) techniques have moved beyond their traditional applications in the fields of industrial manufacturing and prototyping to increasingly find roles in scientific research contexts, such as synthetic chemistry. We present a general approach for the production of bespoke chemical reactors, termed reactionware, using two different approaches to extrusion-based 3D printing. This protocol describes the printing of an inert polypropylene (PP) architecture with the concurrent printing of soft material catalyst composites, using two different 3D printer setups. The steps of the PROCEDURE describe the design and preparation of a 3D digital model of the desired reactionware device and the preparation of this model for use with fused deposition modeling (FDM) type 3D printers. The protocol then further describes the preparation of composite catalyst-silicone materials for incorporation into the 3D-printed device and the steps required to fabricate a reactionware device. This combined approach allows versatility in the design and use of reactionware based on the specific needs of the experimental user. To illustrate this, we present a detailed procedure for the production of one such reactionware device that will result in the production of a sealed reactor capable of effecting a multistep organic synthesis. Depending on the design time of the 3D model, and including time for curing and drying of materials, this procedure can be completed in ∼3 d.

  14. Chemical synthesis and immunosuppressive activity of dipalmitoyl phosphatidylinositol hexamannoside.

    Science.gov (United States)

    Ainge, Gary D; Compton, Benjamin J; Hayman, Colin M; Martin, William John; Toms, Steven M; Larsen, David S; Harper, Jacquie L; Painter, Gavin F

    2011-06-17

    Phosphatidylinositol mannosides (PIMs) isolated from mycobacteria have been identified as an important class of phosphoglycolipids with significant immune-modulating properties. We present here the synthesis of dipalmitoyl phosphatidylinositol hexamannoside (PIM(6)) 1 and the first reported functional biology of a synthetic PIM(6). Key steps in the synthetic protocol included the selective glycosylation of an inositol 2,6-diol with a suitably protected mannosyl donor and construction of the glycan core utilizing a [3 + 4] thio-glycosylation strategy. The target 1 was purified by reverse phase chromatography and characterized by standard spectroscopic methods, HPLC, and chemical modification by deacylation to dPIM(6). The (1)H NMR spectrum of synthetic dPIM(6) obtained from 1 matched that of dPIM(6) obtained from nature. PIM(6) (1) exhibited dendritic cell-dependent suppression of CD8(+) T cell expansion in a human mixed lymphocyte reaction consistent with the well established immunosuppressive activity of whole mycobacteria. PMID:21574597

  15. Size-controlled synthesis of transition metal nanoparticles through chemical and photo-chemical routes

    Science.gov (United States)

    Tangeysh, Behzad

    The central objective of this work is developing convenient general procedures for controlling the formation and stabilization of nanoscale transition metal particles. Contemporary interest in developing alternative synthetic approaches for producing nanoparticles arises in large part from expanding applications of the nanomaterials in areas such as catalysis, electronics and medicine. This research focuses on advancing the existing nanoparticle synthetic routes by using a new class of polymer colloid materials as a chemical approach, and the laser irradiation of metal salt solution as a photo-chemical method to attain size and shape selectivity. Controlled synthesis of small metal nanoparticles with sizes ranging from 1 to 5nm is still a continuing challenge in nanomaterial synthesis. This research utilizes a new class of polymer colloid materials as nano-reactors and protective agents for controlling the formation of small transition metal nanoparticles. The polymer colloid particles were formed from cross-linking of dinegatively charged metal precursors with partially protonated poly dimethylaminoethylmethacrylate (PDMAEMA). Incorporation of [PtCl6]2- species into the colloidal particles prior to the chemical reduction was effectively employed as a new strategy for synthesis of unusually small platinum nanoparticles with narrow size distributions (1.12 +/-0.25nm). To explore the generality of this approach, in a series of proof-of-concept studies, this method was successfully employed for the synthesis of small palladium (1.4 +/-0.2nm) and copper nanoparticles (1.5 +/-0.6nm). The polymer colloid materials developed in this research are pH responsive, and are designed to self-assemble and/or disassemble by varying the levels of protonation of the polymer chains. This unique feature was used to tune the size of palladium nanoparticles in a small range from 1nm to 5nm. The procedure presented in this work is a new convenient room temperature route for synthesis of

  16. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Directory of Open Access Journals (Sweden)

    Jiang-Ke Yang

    Full Text Available In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp and Aspergillus niger phytase gene phyA (1404 bp. Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  17. Recovery from DNA synthesis in V 79 chinese hamster cells irradiated with UV light

    International Nuclear Information System (INIS)

    Mammalian cells recover from DNA synthesis inhibition by UV light before most of the pyrimidine dimers have been removed from the genome. Most of the rodent cells show a deficient dimer excision repair compared with normal human fibroblasts. Despite this fact they recover efficiently from DNA synthesis inhibition after UV. In Chinese hamster V 79 cells was found that this recovery takes place in the absence of a significant excision repair, and it seems to be directly coupled to a recovery in the rate of movement of the replication fork. 120 refs, 31 figs. (author)

  18. Assessment of potential damage to DNA in urine of coke oven workers: an assay of unscheduled DNA synthesis.

    OpenAIRE

    Roos, F.; Renier, A.; Ettlinger, J; Iwatsubo, Y; Letourneux, M; Haguenoer, J M; Jaurand, M C; Pairon, J C

    1997-01-01

    OBJECTIVES: A study was conducted in coke oven workers to evaluate the biological consequences of the exposure of these workers, particularly production of potential genotoxic factors. METHODS: 60 coke oven workers and 40 controls were recruited in the same iron and steel works. Exposure to polycyclic aromatic hydrocarbons (PAHs) was assessed by job and measurement of 1-hydroxypyrene (1OHP) in urine samples. An unscheduled DNA synthesis assay was performed on rat pleural mesothelial cells use...

  19. DEVELOPMENT OF ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Peter J. Tijrn

    2003-05-31

    This Final Report for Cooperative Agreement No. DE-FC22-95PC93052, the ''Development of Alternative Fuels and Chemicals from Synthesis Gas,'' was prepared by Air Products and Chemicals, Inc. (Air Products), and covers activities from 29 December 1994 through 31 July 2002. The overall objectives of this program were to investigate potential technologies for the conversion of synthesis gas (syngas), a mixture primarily of hydrogen (H{sub 2}) and carbon monoxide (CO), to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at the LaPorte, Texas Alternative Fuels Development Unit (AFDU). Laboratory work was performed by Air Products and a variety of subcontractors, and focused on the study of the kinetics of production of methanol and dimethyl ether (DME) from syngas, the production of DME using the Liquid Phase Dimethyl Ether (LPDME{trademark}) Process, the conversion of DME to fuels and chemicals, and the production of other higher value products from syngas. Four operating campaigns were performed at the AFDU during the performance period. Tests of the Liquid Phase Methanol (LPMEOH{trademark}) Process and the LPDME{trademark} Process were made to confirm results from the laboratory program and to allow for the study of the hydrodynamics of the slurry bubble column reactor (SBCR) at a significant engineering scale. Two campaigns demonstrated the conversion of syngas to hydrocarbon products via the slurry-phase Fischer-Tropsch (F-T) process. Other topics that were studied within this program include the economics of production of methyl tert-butyl ether (MTBE), the identification of trace components in coal-derived syngas and the means to economically remove these species, and the study of systems for separation of wax from catalyst in the F-T process. The work performed under this Cooperative Agreement has continued to promote the development of technologies that use clean syngas produced

  20. DEVELOPMENT OF ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    Energy Technology Data Exchange (ETDEWEB)

    Peter J. Tijrn

    2003-05-31

    This Final Report for Cooperative Agreement No. DE-FC22-95PC93052, the ''Development of Alternative Fuels and Chemicals from Synthesis Gas,'' was prepared by Air Products and Chemicals, Inc. (Air Products), and covers activities from 29 December 1994 through 31 July 2002. The overall objectives of this program were to investigate potential technologies for the conversion of synthesis gas (syngas), a mixture primarily of hydrogen (H{sub 2}) and carbon monoxide (CO), to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at the LaPorte, Texas Alternative Fuels Development Unit (AFDU). Laboratory work was performed by Air Products and a variety of subcontractors, and focused on the study of the kinetics of production of methanol and dimethyl ether (DME) from syngas, the production of DME using the Liquid Phase Dimethyl Ether (LPDME{trademark}) Process, the conversion of DME to fuels and chemicals, and the production of other higher value products from syngas. Four operating campaigns were performed at the AFDU during the performance period. Tests of the Liquid Phase Methanol (LPMEOH{trademark}) Process and the LPDME{trademark} Process were made to confirm results from the laboratory program and to allow for the study of the hydrodynamics of the slurry bubble column reactor (SBCR) at a significant engineering scale. Two campaigns demonstrated the conversion of syngas to hydrocarbon products via the slurry-phase Fischer-Tropsch (F-T) process. Other topics that were studied within this program include the economics of production of methyl tert-butyl ether (MTBE), the identification of trace components in coal-derived syngas and the means to economically remove these species, and the study of systems for separation of wax from catalyst in the F-T process. The work performed under this Cooperative Agreement has continued to promote the development of technologies that use clean syngas produced

  1. Chemical carcinogenesis — the price for DNA-repair?

    Science.gov (United States)

    Wintersberger, Ulrike

    1982-03-01

    This essay examines the possibility of merging the mutation theory of cancer with the hypothesis that cancer is a change in the state of the differentiation of cells. It is suggested that during normal development DNA rearrangements occur, concerning genes which code for differentiation specific cell communication proteins. These proteins are responsible for the proper functioning of growth control in a multicellular organism. DNA-damaging agents — mutagens — induce DNA repair enzymes, some of which may catalyse illegitimate genome rearrangements, thus leading to a change of the balance between growth and differentiation. A cell with a selective advantage may arise and become the origin of a tumor.

  2. Chemical Synthesis of Proanthocyanidins in Vitro and Their Reactions in Aging Wines

    Directory of Open Access Journals (Sweden)

    Qiu-Hong Pan

    2008-12-01

    Full Text Available Proanthocyanidins are present in many fruits and plant products like grapes and wine, and contribute to their taste and health benefits. In the past decades of years, substantial progresses has been achieved in the identification of composition and structure of proanthocyanidins, but the debate concerning the existence of an enzymatic or nonenzymatic mechanism for proanthocyanidin condensation still goes on. Substantial attention has been paid to elucidating the potential mechanism of formation by means of biomimetic and chemical synthesis in vitro. The present paper aims at summarizing the research status on chemical synthesis of proanthocyanidins, including non-enzymatic synthesis of proanthocyanidin precursors, chemical synthesis of proanthocyanidins with direct condensation of flavanols and stereoselective synthesis of proanthocyanidins. Proanthocyanidin-involved reactions in aging wines are also reviewed such as direct and indirect reactions among proanthocyanidins, flavanols and anthocyanins. Topics for future research in this field are also put forward in this paper.

  3. Stimulation of DNA synthesis in cultured rat alveolar type II cells

    Energy Technology Data Exchange (ETDEWEB)

    Leslie, C.C.; McCormick-Shannon, K.; Robinson, P.C.; Mason, R.J.

    1985-01-01

    Restoration of the alveolar epithelium after injury is thought to be dependent on the proliferation of alveolar type II cells. To understand the factors that may be involved in promoting type II cell proliferation in vivo, we determined the effect of potential mitogens and culture substrata on DNA synthesis in rat alveolar type II cells in primary culture. Type II cells cultured in basal medium containing 10% fetal bovine serum (FBS) exhibited essentially no DNA synthesis. Factors that stimulated /sup 3/H-thymidine incorporation included cholera toxin, epidermal growth factor, and rat serum. The greatest degree of stimulation was achieved by plating type II cells on an extracellular matrix prepared from bovine corneal endothelial cells and then by culturing the pneumocytes in medium containing rat serum, cholera toxin, insulin, and epidermal growth factor. Under conditions of stimulation of /sup 3/H-thymidine incorporation there was an increased DNA content per culture dish but no increase in cell number. The ability of various culture conditions to promote DNA synthesis in type II cells was verified by autoradiography. Type II cells were identified by the presence of cytoplasmic inclusions, which were visualized by tannic acid staining before autoradiography. These results demonstrate the importance of soluble factors and culture substratum in stimulating DNA synthesis in rat alveolar type II cells in primary culture.

  4. Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis.

    Science.gov (United States)

    Gao, Yang; Yang, Wei

    2016-06-10

    It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.

  5. Synthesis and cell-free cloning of DNA libraries using programmable microfluidics.

    Science.gov (United States)

    Ben Yehezkel, Tuval; Rival, Arnaud; Raz, Ofir; Cohen, Rafael; Marx, Zipora; Camara, Miguel; Dubern, Jean-Frédéric; Koch, Birgit; Heeb, Stephan; Krasnogor, Natalio; Delattre, Cyril; Shapiro, Ehud

    2016-02-29

    Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development. PMID:26481354

  6. Synthesis and cell-free cloning of DNA libraries using programmable microfluidics

    Science.gov (United States)

    Yehezkel, Tuval Ben; Rival, Arnaud; Raz, Ofir; Cohen, Rafael; Marx, Zipora; Camara, Miguel; Dubern, Jean-Frédéric; Koch, Birgit; Heeb, Stephan; Krasnogor, Natalio; Delattre, Cyril; Shapiro, Ehud

    2016-01-01

    Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development. PMID:26481354

  7. Quantitative Transcript Analysis in Plants: Improved First-strand cDNA Synthesis

    Institute of Scientific and Technical Information of China (English)

    Nai-Zhong XIAO; Lei BA; Preben Bach HOLM; Xing-Zhi WANG; Steve BOWRA

    2005-01-01

    The quantity and quality of first-strand cDNA directly influence the accuracy of transcriptional analysis and quantification. Using a plant-derived α-tubulin as a model system, the effect of oligo sequence and DTT on the quality and quantity of first-strand cDNA synthesis was assessed via a combination of semi-quantitative PCR and real-time PCR. The results indicated that anchored oligo dT significantly improved the quantity and quality of α-tubulin cDNA compared to the conventional oligo dT. Similarly, omitting DTT from the first-strand cDNA synthesis also enhanced the levels of transcript. This is the first time that a comparative analysis has been undertaken for a plant system and it shows conclusively that small changes to current protocols can have very significant impact on transcript analysis.

  8. Bringing the science of proteins into the realm of organic chemistry: total chemical synthesis of SEP (synthetic erythropoiesis protein).

    Science.gov (United States)

    Kent, Stephen B H

    2013-11-11

    Erythropoietin, commonly known as EPO, is a glycoprotein hormone that stimulates the production of red blood cells. Recombinant EPO has been described as "arguably the most successful drug spawned by the revolution in recombinant DNA technology". Recently, the EPO glycoprotein molecule has re-emerged as a major target of synthetic organic chemistry. In this article I will give an account of an important body of earlier work on the chemical synthesis of a designed EPO analogue that had full biological activity and improved pharmacokinetic properties. The design and synthesis of this "synthetic erythropoiesis protein" was ahead of its time, but has gained new relevance in recent months. Here I will document the story of one of the major accomplishments of synthetic chemistry in a more complete way than is possible in the primary literature, and put the work in its contemporaneous context.

  9. Translesion synthesis by yeast DNA polymerase ζ from templates containing lesions of ultraviolet radiation and acetylaminofluorene

    OpenAIRE

    Guo, Dongyu; Wu, Xiaohua; Deepak K Rajpal; Taylor, John-Stephen; Wang, Zhigang

    2001-01-01

    In the yeast Saccharomyces cerevisiae, DNA polymerase ζ (Polζ) is required in a major lesion bypass pathway. To help understand the role of Polζ in lesion bypass, we have performed in vitro biochemical analyses of this polymerase in response to several DNA lesions. Purified yeast Polζ performed limited translesion synthesis opposite a template TT (6-4) photoproduct, incorporating A or T with similar efficiencies (and less frequently G) opposite the 3′ T, and pr...

  10. [Analysis of effectiveness of cDNA synthesis, induced using complementary primers and primers containing a noncomplementary base matrix].

    Science.gov (United States)

    D'iachenko, L B; Chenchik, A A; Khaspekov, G L; Tatarenko, A O; Bibilashvili, R Sh

    1994-01-01

    We have studied the efficiency of DNA synthesis catalyzed by M-MLV reverse transcriptase or Thermus aquaticus DNA polymerase for primers (4-17 nucleotides long) either completely matched or possessing a single mismatched base pair at all possible positions in the primer. It has been shown that DNA synthesis efficiency depends not only on the position of mismatched base pair but on the length and primary structure of the primer. The enzyme, template, and primer concentrations determine the relative level of mismatched DNA synthesis.

  11. Preparation of fluorescent DNA probe by solid-phase organic synthesis

    Directory of Open Access Journals (Sweden)

    2009-08-01

    Full Text Available Fluorescent DNA probe based on fluorescence resonance energy transfer (FRET was prepared by solid-phase organic synthesis when CdTe quantum dots (QDs were as energy donors and Au nanoparticles (AuNPs were as energy accepters. The poly(divinylbenzene core/poly(4-vinylpyridine shell microspheres, as solid-phase carriers, were prepared by seeds distillation-precipitation polymerization with 2,2′-azobisisobutyronitrile (AIBN as initiator in neat acetonitrile. The CdTe QDs and AuNPs were self-assembled on the surface of core/shell microspheres, and then the linkage of CdTe QDs with oligonucleotides (CdTe-DNA and AuNPs with complementary single-stranded DNA (Au-DNA was on the solid-phase carriers instead of in aqueous solution. The hybridization of complementary double stranded DNA (dsDNA bonded to the QDs and AuNPs (CdTe-dsDNA-Au determined the FRET distance of CdTe QDs and AuNPs. Compared with the fluorescence of CdTe-DNA, the fluorescence of CdTe-dsDNA-Au conjugates (DNA probes decreased extremely, which indicated that the FRET occurred between CdTe QDs and AuNPs. The probe system would have a certain degree recovery of fluorescence when the complementary single stranded DNA was introduced into this system, which showed that the distance between CdTe QDs and AuNPs was increased.

  12. Role of amidation in bile acid effect on DNA synthesis by regenerating mouse liver.

    Science.gov (United States)

    Barbero, E R; Herrera, M C; Monte, M J; Serrano, M A; Marin, J J

    1995-06-01

    Effect of bile acids on DNA synthesis by the regenerating liver was investigated in mice in vivo after partial hepatectomy (PH). Radioactivity incorporation into DNA after [14C]thymidine intraperitoneal administration peaked at 48 h after PH. At this time a significant taurocholate-induced dose-dependent reduction in DNA synthesis without changes in total liver radioactivity content was found (half-maximal effect at approximately 0.1 mumol/g body wt). Effect of taurocholate (0.5 mumol/g body wt) was mimicked by chocolate, ursodeoxycholate, deoxycholate, dehydrocholate, tauroursodeoxycholate, taurochenodeoxycholate, and taurodeoxycholate. In contrast, chenodeoxycholate, glycocholate, glycochenodeoxycholate, glycoursodeoxycholate, glycodeoxycholate, 5 beta-cholestane, bromosulfophthalein, and free taurine lacked this effect. No relationship between hydrophobic-hydrophilic balance and inhibitory effect was observed. Analysis by high-performance liquid chromatography indicated that inhibition of thymidine incorporation into DNA was not accompanied by an accumulation of phosphorylated DNA precursors in the liver but rather by a parallel increase in nucleotide catabolism. Bile acid-induced modifications in DNA synthesis were observed in vivo even in the absence of changes in toxicity tests, which suggests that the inhibitory effect shared by most unconjugated and tauroconjugated bile acids but not by glycoconjugated bile acids should be accounted for by mechanisms other than nonselective liver cell injury. PMID:7611405

  13. Cleavage enhancement of specific chemical bonds in DNA-Cisplatin complexes induced by X-rays

    International Nuclear Information System (INIS)

    The chemical bond transformation of cisplatin-DNA complexes can be probed efficiently by XPS which provides a concomitant X-ray irradiation source as well. The presence to Pt could considerably increase formation of the SE induced by X-ray and that the further interaction of these LEE with DNA leads to the enhancement of bond cleavages.

  14. Synthesis, DNA interaction and antimicrobial activities of three rimantadine analogues

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Bing-Mi; Zhang, Jun [Department of Pharmacy, Liaoning University, Shenyang 110036 (China); Wang, Xin, E-mail: wangxinlnu@163.com [Department of Pharmacy, Liaoning University, Shenyang 110036 (China); Zhang, Li-Ping; Liu, Yang [Department of Pharmacy, Liaoning University, Shenyang 110036 (China); Niu, Hua-Ying [Jinan Dachpharm Development Co., Ltd., Jinan 250100 (China); Liu, Bin, E-mail: liubinzehao@163.com [Department of Pharmacy, Liaoning University, Shenyang 110036 (China)

    2015-03-15

    The interactions of three rimantadine analogues (RAs) with calf thymus deoxyribonucleic acid (ct-DNA) in buffer solution (pH 7.4) were investigated using berberine (BR) as a probe by various methods. Fluorescence studies revealed that the RAs interacted with DNA in vitro and the quenchings were all static. Furthermore, the binding modes of these compounds to DNA were disclosed as groove binding supported by absorption spectroscopy, viscosity measurement and denatured DNA experiment. The antimicrobial activities of the RAs were also evaluated in Staphylococcus aureus and Escherichia coli, and they all exhibited good bacteriostasic effects. The results might provide an important reference for investigation of the molecular mechanism associated with the DNA binding of the RAs. - Highlights: • Three rimantadine analogues were synthesized. • The RAs effectively quenched the intrinsic fluorescence of DNA via a static combination. • These analogues can bind to DNA via groove binding mode. • The antimicrobial activities of three analogues were also evaluated by the disk diffusion method.

  15. Novel synthesis of O 6-alkylguanine containing oligodeoxyribonucleotides as substrates for the human DNA repair protein, O 6-methylguanine DNA methyltransferase (MGMT)

    OpenAIRE

    Shibata, Takayuki; Glynn, Nicola; McMurry, T. Brian H.; McElhinney, R. Stanley; Margison, Geoffrey P.; David M. Williams

    2006-01-01

    The human DNA repair protein O 6-methylguanine DNA methyltransferase (MGMT) dealkylates mutagenic O 6-alkylguanine lesions within DNA in an irreversible reaction which results in inactivation of the protein. MGMT also provides resistance of tumours to alkylating agents used in cancer chemotherapy and its inactivation is therefore of particular clinical importance. We describe a post-DNA synthesis strategy which exploits the novel, modified base 2-amino-6-methylsulfonylpurine and allows access...

  16. Chemical synthesis and modification of target phases of chalcogenide nanomaterials

    Science.gov (United States)

    Sines, Ian T.

    Inorganic nanoparticles have been at the forefront of materials research in recent years due to their utility in modern technological processes. Chalcogenide nanomaterials are of particular interest because of their wide range of desirable properties for semiconductors, magnetic devices, and energy industries. Primary factors that dictate the properties of the material are the elemental composition, crystal structure, stoichiometry, crystallite size, and particle morphology. One of the most common approaches to synthesize these materials is through solution mediated routes. This approach offers unique advantages in controlling the morphology and particle size that other methods lack. This dissertation describes our recent work on exploiting solution chemical routes to control the crystal structure and composition of chalcogenide nanomaterials. We will start by discussing solution chemistry routes to synthesize non-equilibrium phases of chaclogenide nanomaterials. By using low-temperature bottom-up techniques it is possible to trap kinetically stable phases that cannot be accessed using traditional high-temperature techniques. We used solution chemistry to synthesize and characterize, for the first time, wurtzite-type MnSe. Wurtzite-type MnSe is the end-member of the highly investigated ZnxMn1-xSe solid solution, a classic magnetic semiconductor system. We will then discuss PbO-type FeS, another non-equilibrium phase that is isostructural with the superconducting phase of FeSe. We synthesized phase-pure PbO-type FeS using a low-temperature solvothermal route. We will then discuss the post-synthetic modification of chalcogenides nanomaterials. By exploiting the solubility of Se and S in tri-n-octylphosphine we can selectively extract the chalcogen from preformed chalcogenide nanomaterials. This gives chemists a technique for purification and phase-targeting of particular chalcogenide phases. This method can be modified to facilitate anion exchange. When Te is

  17. Cdt2-mediated XPG degradation promotes gap-filling DNA synthesis in nucleotide excision repair.

    Science.gov (United States)

    Han, Chunhua; Wani, Gulzar; Zhao, Ran; Qian, Jiang; Sharma, Nidhi; He, Jinshan; Zhu, Qianzheng; Wang, Qi-En; Wani, Altaf A

    2015-01-01

    Xeroderma pigmentosum group G (XPG) protein is a structure-specific repair endonuclease, which cleaves DNA strands on the 3' side of the DNA damage during nucleotide excision repair (NER). XPG also plays a crucial role in initiating DNA repair synthesis through recruitment of PCNA to the repair sites. However, the fate of XPG protein subsequent to the excision of DNA damage has remained unresolved. Here, we show that XPG, following its action on bulky lesions resulting from exposures to UV irradiation and cisplatin, is subjected to proteasome-mediated proteolytic degradation. Productive NER processing is required for XPG degradation as both UV and cisplatin treatment-induced XPG degradation is compromised in NER-deficient XP-A, XP-B, XP-C, and XP-F cells. In addition, the NER-related XPG degradation requires Cdt2, a component of an E3 ubiquitin ligase, CRL4(Cdt2). Micropore local UV irradiation and in situ Proximity Ligation assays demonstrated that Cdt2 is recruited to the UV-damage sites and interacts with XPG in the presence of PCNA. Importantly, Cdt2-mediated XPG degradation is crucial to the subsequent recruitment of DNA polymerase δ and DNA repair synthesis. Collectively, our data support the idea of PCNA recruitment to damage sites which occurs in conjunction with XPG, recognition of the PCNA-bound XPG by CRL4(Cdt2) for specific ubiquitylation and finally the protein degradation. In essence, XPG elimination from DNA damage sites clears the chromatin space needed for the subsequent recruitment of DNA polymerase δ to the damage site and completion of gap-filling DNA synthesis during the final stage of NER. PMID:25483071

  18. Deoxyribonucleotide synthesis and the emergence of DNA in molecular evolution

    Science.gov (United States)

    Follmann, Hartmut

    1982-02-01

    DNA replication requires monomeric deoxyribonucleotides, which cannot be regarded as primary products of organic syntheses on a primitive earth. However, the present biosynthetic pathway — reductive elimination of the 2'-OH group from ribonucleotides, catalyzed by ribonucleotide reductases and thioredoxins — suggests an early, polyphyletic combination of protein-nucleotide interactions and metal catalysis. That key process had to precede the upcome of RNA-DNA dualism on the way from RNA-protein protocells to true organisms.

  19. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Binladen, Jonas; Miller, Webb;

    2007-01-01

    Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed to PCR polymerase amplification error...... strand of origin of observed damage events. With the advent of emulsion-based clonal amplification (emPCR) and the sequencing-by-synthesis technology this has changed. In this paper we demonstrate how data produced on the Roche GS20 genome sequencer can determine miscoding lesion strands of origin...

  20. Dissociation between insulin secretion and DNA synthesis in cultured pancreatic islets

    DEFF Research Database (Denmark)

    Nielsen, Jens Høiriis

    1985-01-01

    Glucose has been suggested to be the most important stimulus for beta cell replication in vivo and in vitro. In order to study the relationship between insulin secretion and DNA synthesis, newborn rat islets were cultured in the presence of different concentrations of glucose, theophylline and 3-...

  1. Labelling of Cells Engaged in DNA Synthesis: Autoradiography and BrdU Staining

    DEFF Research Database (Denmark)

    Madsen, Peder Søndergaard

    2010-01-01

    The cell cycle is divided in four phases: G1 phase, S phase (DNA-synthesis), G2 phase (together termed interphase) and M phase (mitosis). Cells that have ceased proliferation enter a state of quiescence called G0. M phase is itself composed of two tightly coupled processes: mitosis, in which...

  2. Human CD4+ T cells require exogenous cystine for glutathione and DNA synthesis

    DEFF Research Database (Denmark)

    Levring, Trine B; Kongsbak-Wismann, Martin; Rode, Anna Kathrine Obelitz;

    2015-01-01

    aim of this study was to elucidate why activated human T cells require exogenous Cys2 in order to proliferate. We activated purified naïve human CD4+ T cells and found that glutathione (GSH) levels and DNA synthesis were dependent on Cys2 and increased in parallel with increasing concentrations of Cys...

  3. Inhibitory effect of syphilitic rabbit serum on DNA synthesis in rabbit cells in vitro.

    OpenAIRE

    Wong, G H; Steiner, B; Strugnell, R; Faine, S.; Graves, S.

    1984-01-01

    A previously described toxic factor associated with Treponema pallidum (Nichols) and found in extracts of syphilitic rabbit testes has now also been detected in syphilitic rabbit serum. The toxic factor, which inhibits DNA synthesis in baby rabbit genital organ (BRGO) cells in vitro, is present in rabbit serum up to 30 days after infection with T pallidum.

  4. Unscheduled DNA synthesis in xeroderma pigmentosum cells after microinjection of yeast photoreactivating enzyme.

    NARCIS (Netherlands)

    J.C.M. Zwetsloot; J.H.J. Hoeijmakers (Jan); W. Vermeulen (Wim); A.P.M. Eker (André); D. Bootsma (Dirk)

    1986-01-01

    textabstractPhotoreactivating enzyme (PRE) from yeast causes a light-dependent reduction of UV-induced unscheduled DNA synthesis (UDS) when injected into the cytoplasm of repair-proficieint human fibroblasts (Zwetsloot et al., 1985). This result indicates that the exogenous PRE monomerizers UV-induc

  5. Ruthenium(II) arene complexes with oligocationic triarylphosphine ligands: synthesis, DNA interactions and in vitro properties

    NARCIS (Netherlands)

    Snelders, D.J.M.; Casini, A.; Edafe, F.; van Koten, G.; Klein Gebbink, R.J.M.; Dyson, P.J.

    2011-01-01

    The synthesis, DNA binding properties and cytotoxicity of a series of Ru(II)-arene complexes containing oligocationic ammonium-functionalized triarylphosphines, of the type Ru(p-cymene)Cl2(L) (L ¼ oligocationic phosphine), are reported. The complexes are highly charged (the overall charge states bei

  6. Free electron laser irradiation at 200 microns affects DNA synthesis in living cells

    International Nuclear Information System (INIS)

    We describe the effect of a 200-microns wavelength free electron laser beam on the ability of asynchronized and synchronized mammalian tissue culture cells to incorporate tritiated thymidine. Compared to controls (unexposed cells), a significant proportion of exposed cells exhibited a reduction in isotope incorporation. The results suggest that this wavelength may affect DNA synthesis

  7. Design, synthesis, and characterization of nucleosomes containing site-specific DNA damage.

    Science.gov (United States)

    Taylor, John-Stephen

    2015-12-01

    How DNA damaged is formed, recognized, and repaired in chromatin is an area of intense study. To better understand the structure activity relationships of damaged chromatin, mono and dinucleosomes containing site-specific damage have been prepared and studied. This review will focus on the design, synthesis, and characterization of model systems of damaged chromatin for structural, physical, and enzymatic studies.

  8. Calculations of physical and chemical reactions with DNA in aqueous solution from Auger cascades

    International Nuclear Information System (INIS)

    Monte Carlo calculations are performed of the physical and chemical interactions in liquid water by electrons produced during Auger cascades resulting from the decay of various radionuclides. Estimates are also made of the number of direct physical and indirect chemical interactions that would be produced on DNA located near the decay site. 13 refs., 8 figs

  9. DNA Polymerases Drive DNA Sequencing-by-Synthesis Technologies: Both Past and Present

    Directory of Open Access Journals (Sweden)

    Cheng-Yao eChen

    2014-06-01

    Full Text Available Next-generation sequencing (NGS technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. E. coli DNA polymerase I proteolytic (Klenow fragment was originally utilized in Sanger's dideoxy chain terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ⱷ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ⱷ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies.

  10. In vivo effects of T-2 mycotoxin on synthesis of proteins and DNA in rat tissues

    International Nuclear Information System (INIS)

    Rats were given an ip injection of T-2 mycotoxin (T-2), the T-2 metabolite, T-2 tetraol (tetraol), or cycloheximide. Serum, liver, heart, kidney, spleen, muscle, and intestine were collected at 3, 6, and 9 hr postinjection after a 2-hr pulse at each time with [14C]leucine and [3H]thymidine. Protein and DNA synthesis levels in rats were determined by dual-label counting of the acid-precipitable fraction of tissue homogenates. Rats given a lethal dose of T-2, tetraol, or cycloheximide died between 14 and 20 hr. Maximum inhibition of protein synthesis at the earliest time period was observed in additional rats given the same lethal dose of the three treatments and continued for the duration of the study (9 hr). With sublethal doses of T-2 or tetraol, the same early decrease in protein synthesis was observed but, in most of the tissues, recovery was seen with time. In the T-2-treated rats. DNA synthesis in the six tissues studied was also suppressed, although to a lesser degree. With sublethal doses, complete recovery of DNA synthesis took place in four of the six tissues by 9 hr after toxin exposure. The appearance of newly translated serum proteins did not occur in the animals treated with T-2 mycotoxin or cycloheximide, as evidenced by total and PCA-soluble serum levels of labeled leucine. An increase in tissue-pool levels of free leucine and thymidine in response to T-2 mycotoxin was also noted. T-2 mycotoxin, its metabolite, T-2 tetraol, and cycloheximide cause a rapid inhibition of protein and DNA synthesis in all tissue types studied. These results are compared with the responses seen in in vitro studies

  11. Native Chemical Ligation to Minimize Aspartimide Formation during Chemical Synthesis of Small LDLa Protein.

    Science.gov (United States)

    Tailhades, Julien; Sethi, Ashish; Petrie, Emma J; Gooley, Paul R; Bathgate, Ross A; Wade, John D; Hossain, Mohammed A

    2016-01-18

    The inhibition of the G protein-coupled receptor, relaxin family peptide receptor 1 (RXFP1), by a small LDLa protein may be a potential approach for prostate cancer treatment. However, it is a significant challenge to chemically produce the 41-residue and three-disulfide cross-bridged LDLa module which is highly prone to aspartimide formation due to the presence of several aspartic acid residues. Known palliative measures, including addition of HOBt to piperidine for N(α) -deprotection, failed to completely overcome this side reaction. For this reason, an elegant native chemical ligation approach was employed in which two segments were assembled for generating the linear LDLa protein. Acquisition of correct folding was achieved by using either a regioselective disulfide bond formation or global oxidation strategies. The final synthetic LDLa protein obtained was characterized by NMR spectroscopic structural analysis after chelation with a Ca(2+) ion and confirmed to be equivalent to the same protein obtained by recombinant DNA production. PMID:26612092

  12. Base J glucosyltransferase does not regulate the sequence specificity of J synthesis in trypanosomatid telomeric DNA.

    Science.gov (United States)

    Bullard, Whitney; Cliffe, Laura; Wang, Pengcheng; Wang, Yinsheng; Sabatini, Robert

    2015-12-01

    Telomeric DNA of trypanosomatids possesses a modified thymine base, called base J, that is synthesized in a two-step process; the base is hydroxylated by a thymidine hydroxylase forming hydroxymethyluracil (hmU) and a glucose moiety is then attached by the J-associated glucosyltransferase (JGT). To examine the importance of JGT in modifiying specific thymine in DNA, we used a Leishmania episome system to demonstrate that the telomeric repeat (GGGTTA) stimulates J synthesis in vivo while mutant telomeric sequences (GGGTTT, GGGATT, and GGGAAA) do not. Utilizing an in vitro GT assay we find that JGT can glycosylate hmU within any sequence with no significant change in Km or kcat, even mutant telomeric sequences that are unable to be J-modified in vivo. The data suggests that JGT possesses no DNA sequence specificity in vitro, lending support to the hypothesis that the specificity of base J synthesis is not at the level of the JGT reaction.

  13. Base J glucosyltransferase does not regulate the sequence specificity of J synthesis in trypanosomatid telomeric DNA.

    Science.gov (United States)

    Bullard, Whitney; Cliffe, Laura; Wang, Pengcheng; Wang, Yinsheng; Sabatini, Robert

    2015-12-01

    Telomeric DNA of trypanosomatids possesses a modified thymine base, called base J, that is synthesized in a two-step process; the base is hydroxylated by a thymidine hydroxylase forming hydroxymethyluracil (hmU) and a glucose moiety is then attached by the J-associated glucosyltransferase (JGT). To examine the importance of JGT in modifiying specific thymine in DNA, we used a Leishmania episome system to demonstrate that the telomeric repeat (GGGTTA) stimulates J synthesis in vivo while mutant telomeric sequences (GGGTTT, GGGATT, and GGGAAA) do not. Utilizing an in vitro GT assay we find that JGT can glycosylate hmU within any sequence with no significant change in Km or kcat, even mutant telomeric sequences that are unable to be J-modified in vivo. The data suggests that JGT possesses no DNA sequence specificity in vitro, lending support to the hypothesis that the specificity of base J synthesis is not at the level of the JGT reaction. PMID:26815240

  14. Synthesis of furan-based DNA binders and their interaction with DNA

    International Nuclear Information System (INIS)

    In recent years, many substances, based on naturally occurring DNA-binding molecules have been developed for the use in cancer therapy and as virostatica. Most of these substances are binding specifically to A-T rich sequences in the DNA minor groove. Neutral and positively charged DNA-binders are known. BNCT is most effective, which the boron is directly located in the cellular nucleus, so that the intercation with thermal neutrons can directly damage the DNA. To reach this aim, we have connected ammonioundecahydrododecaborate(1-) to DNA-binding structures such as 2,5-bis(4-formylphenyl)furan via a Schiff-Base reaction followed by a reduction of the imine to a secondary amine. In a following step the amine can be alkylated to insert positive charges to prevent repulsion between the compounds and the negatively charged sugar-phosphate-backbone of the DNA. (author)

  15. Systematic methods for synthesis and design of sustainable chemical and biochemical processes

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    for process intensification, sustainable process design, identification of optimal biorefinery models as well as integrated process-control design, and chemical product design. The lecture will present the main concepts, the decomposition based solution approach, the developed methods and tools together......Chemical and biochemical process design consists of designing the process that can sustainably manufacture an identified chemical product through a chemical or biochemical route. The chemical product tree is potentially very large; starting from a set of basic raw materials (such as petroleum...... with illustrative examples covering chemical and biochemical process synthesis and design....

  16. Design and Synthesis of Triangulated DNA Origami Trusses.

    Science.gov (United States)

    Matthies, Michael; Agarwal, Nayan P; Schmidt, Thorsten L

    2016-03-01

    DNA nanotechnology offers unique control over matter on the nanoscale. Here, we extend the DNA origami method to cover a range of wireframe truss structures composed of equilateral triangles, which use less material per volume than standard multiple-helix bundles. From a flat truss design, we folded tetrahedral, octahedral, or irregular dodecahedral trusses by exchanging few connector strands. Other than standard origami designs, the trusses can be folded in low-salt buffers that make them compatible with cell culture buffers. The structures also have defined cavities that may in the future be used to precisely position functional elements such as metallic nanoparticles or enzymes. Our graph routing program and a simple design pipeline will enable other laboratories to make use of this valuable and potent new construction principle for DNA-based nanoengineering.

  17. Synthesis and enhanced hydrogen desorption kinetics of magnesium hydride using hydriding chemical vapor synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin-Ho [Icheon Branch, Korea Institute of Ceramic Engineering and Technology (KICET), Icheon-si, Gyeonggi-do (Korea, Republic of); Kim, Byung-Goan [Korea Energy Materials Co.Ltd., 409, Daegu Technopark, 1-11, Hosan-Dong, Dalse-Gu 704-230 (Korea, Republic of); Kang, Yong-Mook, E-mail: dake@kaist.ac.kr [Department of Chemistry, Dongguk University-Seoul, 100715 Seoul (Korea, Republic of)

    2012-07-15

    Highlights: Black-Right-Pointing-Pointer We synthesized pure MgH{sub 2} by a hydriding chemical vapor synthesis process in a hydrogen atmosphere. Black-Right-Pointing-Pointer The particle size HCVS-MgH{sub 2} was drastically reduced to the sub-micron or micrometer-scale. Black-Right-Pointing-Pointer HCVS-MgH{sub 2} showed different shapes (needle-like nanofibers and angulated plate) depending on the deposited position. Black-Right-Pointing-Pointer HCVS-MgH{sub 2} desorbed hydrogen up to about 7.2 wt% and 7.1 wt%. - Abstract: This paper describes the hydriding chemical vapor synthesis (HCVS) of the hydrogen storage alloy MgH{sub 2} in a hydrogen atmosphere and the product's hydrogenation properties. Mg powder was used as a starting material to produce submicron MgH{sub 2} and uniformly heated to a temperature of 600 Degree-Sign C for Mg vaporization. The effects of deposited positions in HCVS reactor on the morphology and the composition of the obtained products were examined by using X-ray diffraction (XRD), scanning electron microscopy (SEM), and Brunauer-Emmett-Teller (BET) analyses. It is clearly seen that after the HCVS process, the particle size of synthesized MgH{sub 2} was drastically reduced to the sub-micron or micrometer-scale and these showed different shapes (needle-like nanofibers and angulated plate) depending on the deposited position. The hydrogen desorption temperatures of HCVS-MgH{sub 2} were measured using a differential scanning calorimeter (DSC). It was found that after the HCVS process, the desorption temperature of HCVS-MgH{sub 2} decreased from 430 to 385 Degree-Sign C and, simultaneously, the smallest particle size and the highest specific surface area were obtained. These observations indicate that the minimum hydrogen desorption temperature of HCVS-MgH{sub 2} powder with needle-like form can be obtained, and that this temperature is dependent on the particle size and the specific surface area of the products. The thermogravimetric

  18. DNA display I. Sequence-encoded routing of DNA populations.

    Directory of Open Access Journals (Sweden)

    David R Halpin

    2004-07-01

    Full Text Available Recently reported technologies for DNA-directed organic synthesis and for DNA computing rely on routing DNA populations through complex networks. The reduction of these ideas to practice has been limited by a lack of practical experimental tools. Here we describe a modular design for DNA routing genes, and routing machinery made from oligonucleotides and commercially available chromatography resins. The routing machinery partitions nanomole quantities of DNA into physically distinct subpools based on sequence. Partitioning steps can be iterated indefinitely, with worst-case yields of 85% per step. These techniques facilitate DNA-programmed chemical synthesis, and thus enable a materials biology that could revolutionize drug discovery.

  19. Design and synthesis of threading intercalators to target DNA.

    Science.gov (United States)

    Howell, Lesley A; Gulam, Rosul; Mueller, Anja; O'Connell, Maria A; Searcey, Mark

    2010-12-01

    Threading intercalators are high affinity DNA binding agents that bind by inserting a chromophore into the duplex and locating one group in each groove. The first threading intercalators that can be conjugated to acids, sulfonic acids and peptides to target them to duplex DNA are described, based upon the well studied acridine-3- or 4-carboxamides. Cellular uptake of the parent acridine is rapid and it can be visualized in the nucleus of cells. Both the parent compounds and their conjugates maintain antitumor activity.

  20. An autonomous molecular assembler for programmable chemical synthesis

    Science.gov (United States)

    Meng, Wenjing; Muscat, Richard A.; McKee, Mireya L.; Milnes, Phillip J.; El-Sagheer, Afaf H.; Bath, Jonathan; Davis, Benjamin G.; Brown, Tom; O'Reilly, Rachel K.; Turberfield, Andrew J.

    2016-06-01

    Molecular machines that assemble polymers in a programmed sequence are fundamental to life. They are also an achievable goal of nanotechnology. Here, we report synthetic molecular machinery made from DNA that controls and records the formation of covalent bonds. We show that an autonomous cascade of DNA hybridization reactions can create oligomers, from building blocks linked by olefin or peptide bonds, with a sequence defined by a reconfigurable molecular program. The system can also be programmed to achieve combinatorial assembly. The sequence of assembly reactions and thus the structure of each oligomer synthesized is recorded in a DNA molecule, which enables this information to be recovered by PCR amplification followed by DNA sequencing.

  1. DNA Oxidation Profiles of Copper Phenanthrene Chemical Nucleases

    Directory of Open Access Journals (Sweden)

    Zara eMolphy

    2015-04-01

    Full Text Available The deleterious effects of metal-catalyzed reactive oxygen species (ROS in biological systems can be seen in a wide variety of pathological conditions including cancer, cardiovascular disease, ageing, and neurodegenerative disorder. On the other hand however, targeted ROS production in the vicinity of nucleic acids – as demonstrated by metal-activated bleomycin – has paved the way for ROS-active chemotherapeutic drug development. Herein we report mechanistic investigations into the oxidative nuclease activity and redox properties of copper(II developmental therapeutics [Cu(DPQ(phen]2+ (Cu-DPQ-Phen, [Cu(DPPZ(phen]2+ (Cu-DPPZ-Phen, and [{Cu(phen2}2(μ-terph](terph (Cu-Terph, with results being compared directly to Sigman’s reagent [Cu(phen2]2+ throughout (phen = 1,10-phenanthroline; DPQ = dipyridoquinoxaline; DPPZ = dipyridophenazine. Oxidative DNA damage was identified at the minor groove through use of surface bound recognition elements of methyl green, netropsin, and [Co(NH36]Cl3 that functioned to control complex accessibility at selected regions. ROS-specific scavengers and stabilisers were employed to identify the cleavage process, the results of which infer hydrogen peroxide produced metal-hydroxo or free hydroxyl radicals (•OH as the predominant species. The extent of DNA damage owing to these radicals was then quantified through 8-oxo-2'-deoxyguanosine (8-oxo-dG lesion detection under ELISA protocol with the overall trend following Cu-DPQ-Phen > Cu-Terph > Cu-Phen > Cu-DPPZ. Finally, the effects of oxidative damage on DNA replication processes were investigated using the polymerase chain reaction (PCR where amplification of 120 base pair DNA sequences of varying base content were inhibited – particularly along A-T rich chains – through oxidative damage of the template strands.

  2. DNA Oxidation Profiles of Copper Phenanthrene Chemical Nucleases

    Science.gov (United States)

    Molphy, Zara; Slator, Creina; Chatgilialoglu, Chryssostomos; Kellett, Andrew

    2015-04-01

    The deleterious effects of metal-catalyzed reactive oxygen species (ROS) in biological systems can be seen in a wide variety of pathological conditions including cancer, cardiovascular disease, ageing, and neurodegenerative disorder. On the other hand however, targeted ROS production in the vicinity of nucleic acids - as demonstrated by metal-activated bleomycin - has paved the way for ROS-active chemotherapeutic drug development. Herein we report mechanistic investigations into the oxidative nuclease activity and redox properties of copper(II) developmental therapeutics [Cu(DPQ)(phen)]2+ (Cu-DPQ-Phen), [Cu(DPPZ)(phen)]2+ (Cu-DPPZ-Phen), and [{Cu(phen)2}2(μ-terph)](terph) (Cu-Terph), with results being compared directly to Sigman’s reagent [Cu(phen)2]2+ throughout (phen = 1,10-phenanthroline; DPQ = dipyridoquinoxaline; DPPZ = dipyridophenazine). Oxidative DNA damage was identified at the minor groove through use of surface bound recognition elements of methyl green, netropsin, and [Co(NH3)6]Cl3 that functioned to control complex accessibility at selected regions. ROS-specific scavengers and stabilisers were employed to identify the cleavage process, the results of which infer hydrogen peroxide produced metal-hydroxo or free hydroxyl radicals (•OH) as the predominant species. The extent of DNA damage owing to these radicals was then quantified through 8-oxo-2'-deoxyguanosine (8-oxo-dG) lesion detection under ELISA protocol with the overall trend following Cu-DPQ-Phen > Cu-Terph > Cu-Phen > Cu-DPPZ. Finally, the effects of oxidative damage on DNA replication processes were investigated using the polymerase chain reaction (PCR) where amplification of 120 base pair DNA sequences of varying base content were inhibited - particularly along A-T rich chains - through oxidative damage of the template strands.

  3. The effect of chemical additives on the synthesis of ethanol

    Energy Technology Data Exchange (ETDEWEB)

    Chuang, S.S.C.

    1992-03-06

    The objective of this research was to investigate the reaction mechanism of higher alcohol and aldehyde synthesis from syngas and the role of additives in the synthesis. An in situ IR reaction system and probe molecule technique were developed to study adsorbed species, active sites, and reaction pathway during reaction. The catalysts used for this study included silica-supported Rh, Ru, and Ni. (VC)

  4. Chemically functionalized gold nanoparticles: Synthesis, characterization, and applications

    Science.gov (United States)

    Daniel, Weston Lewis

    This thesis focuses on the development and application of gold nanoparticle based detection systems and biomimetic structures. Each class of modified nanoparticle has properties that are defined by its chemical moieties that interface with solution and the gold nanoparticle core. In Chapter 2, a comparison of the biomolecular composition and binding properties of various preparations of antibody oligonucleotide gold nanoparticle conjugates is presented. These constructs differed significantly in terms of their structure and binding properties. Chapter 3 reports the use of electroless gold deposition as a light scattering signal enhancer in a multiplexed, microarray-based scanometric immunoassay using the gold nanoparticle probes evaluated in Chapter 2. The use of gold development results in greater signal enhancement than the typical silver development, and multiple rounds of metal development were found to increase the resulting signal compared to one development. Chapter 4 describes an amplified scanometric detection method for human telomerase activity. Gold nanoparticles functionalized with specific oligonucleotide sequences can efficiently capture telomerase enzymes and subsequently be elongated. Both the elongated and unmodified oligonucleotide sequences are simultaneously measured. At low telomerase concentrations, elongated strands cannot be detected, but the unmodified sequences, which come from the same probe particles, can be detected because their concentration is higher, providing a novel form of amplification. Chapter 5 reports the development of a novel colorimetric nitrite and nitrate ion assay based upon gold nanoparticle probes functionalized with Griess reaction reagents. This assay takes advantage of the distance-dependent plasmonic properties of the gold nanoparticles and the ability of nitrite ion to facilitate the cross coupling of novel nanoparticle probes. The assay works on the concept of a kinetic end point and can be triggered at the EPA

  5. Radioautographic DNA synthesis study on mice Mus musculus gingival epithelium

    International Nuclear Information System (INIS)

    The DNA-synthetizing cells frequency in the gingival epithelium basal layer of the first lower molar region in young and adult mice were studied. The 3H-thymidine and radioautography were used. The labeled cells frequency was determined by calculating their proportions. The data were statiscally analysed. (M.A.C.)

  6. Selective inhibition of influenza virus protein synthesis by inhibitors of DNA function

    International Nuclear Information System (INIS)

    Various known inhibitors of cellular DNA function were shown to inhibit cellular RNA synthesis and influenza (fowl plague) virus multiplication. The drugs were investigated for their effect upon the synthesis of influenza virus proteins. According to this effect they could be classified with previously studied compounds as follows: Group I (ethidium bromide, proflavine, and N-nitroquinoline-N-oxide) inhibited both viral and cellular protein synthesis; Group II (nogalomycin, daunomycin and α-amanitin) inhibited viral but not cellular protein synthesis, and all viral proteins were inhibited coordinately; Group III (mithramycin, echinomycin, and actinomycin D) inhibited all viral but not cellular protein synthesis at high concentrations, but at a lower critical concentration inhibited the synthesis of viral haemagglutinin, neuraminidase, and M protein preferentially; Group IV(uv irradiation and camptothecin) inhibited the synthesis of viral haemagglutinin, neuraminidase, and M protein, but not other viral proteins, even at high doses. The mode of action of these inhibitors is discussed in relation to the mechanism of the nuclear events upon which influenza virus multiplication is dependent

  7. Synthesis of DNA Oligodeoxynucleotides Containing Site-Specific 1,3-Butadiene- Deoxyadenosine Lesions

    Science.gov (United States)

    Wickramaratne, Susith; Seiler, Christopher L.

    2016-01-01

    Post-oligomerization synthesis is a useful technique for preparing site-specifically modified DNA oligomers. This approach involves site-specific incorporation of inherently reactive halogenated nucleobases into DNA strands using standard solid phase synthesis, followed by post-oligomerization nucleophilic aromatic substitution (SNAr) reactions with carcinogen-derived synthons. In these reactions, the inherent reactivities of DNA and carcinogen-derived species are reversed: the modified DNA nucleobase acts as an electrophile, while the carcinogen-derived species acts as a nucleophile. In the present protocol, we describe the use of the post-oligomerization approach to prepare DNA strands containing site- and stereospecific N6-adenine and N1, N6-adenine adducts induced by epoxide metabolites of the known human and animal carcinogen, 1,3-butadiene (BD). The resulting oligomers containing site specific, structurally defined DNA adducts can be used in structural and biological studies to reveal the roles of specific BD adducts in carcinogenesis and mutagenesis. PMID:26344227

  8. Epigallocatechin gallate inhibits HBV DNA synthesis in a viral replication - inducible cell line

    Institute of Scientific and Technical Information of China (English)

    Wei He; Li-Xia Li; Qing-Jiao Liao; Chun-Lan Liu; Xu-Lin Chen

    2011-01-01

    AIM: To analyze the antiviral mechanism of Epigallocatechin gallate (EGCG) against hepatitis B virus (HBV) replication. METHODS: In this research, the HBV-replicating cell line HepG2.117 was used to investigate the antiviral mechanism of EGCG. Cytotoxicity of EGCG was analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Hepatitis B virus e antigen (HBeAg) and hepatitis B virus surface antigen (HBsAg) in the supernatant were detected by enzyme-linked immunosorbent assay. Precore mRNA and pregenomic RNA (pgRNA) levels were determined by semi-quantitative reverse transcription polymerase chain reaction (PCR) assay. The effect of EGCG on HBV core promoter activity was measured by dual luciferase reporter assay. HBV covalently closed circular DNA and replicative intermediates of DNA were quantified by real-time PCR assay. RESULTS: When HepG2.117 cells were grown in the presence of EGCG, the expression of HBeAg was suppressed, however, the expression of HBsAg was not affected. HBV precore mRNA level was also downregulated by EGCG, while the transcription of precore mRNA was not impaired. The synthesis of both HBV covalently closed circular DNA and replicative intermediates of DNA were reduced by EGCG treatment to a similar extent, however, HBV pgRNA transcripted from chromosome-integrated HBV genome was not affected by EGCG treatment, indicating that EGCG targets only replicative intermediates of DNA synthesis. CONCLUSION: In HepG2.117 cells, EGCG inhibits HBV replication by impairing HBV replicative intermediates of DNA synthesis and such inhibition results in reduced production of HBV covalently closed circular DNA.

  9. Physico-Chemical and In-vitro Microbial Studies of Newly Synthesis Organometallic Complexes

    Directory of Open Access Journals (Sweden)

    Isam Hussain Al-Karkhi

    2014-05-01

    Full Text Available Drugs normally synthesized to use as medication to treat diseases like cancer and microbial infections, these synthesized drugs were interested more than naturally-derived drugs which have been shows low activity or not as efficient against diseases. A new ligand 3-methylbenzyl (2Z-2-[1-(pyridin-4-ylethylidene]hydrazine carbodithioate (PE3MBC and its Cd(II, Cu(II, Co(II and Zn(II metal complexes. The new ligand and metal complexes were characterized via various physico-chemical and spectroscopic techniques. Cd(II complex show more activity against microbes and against cancer cell line MCF-7, while other complexes does not shows activity like cadmium complex, all the complexes does not shows any activity against MDAMB-231 cell line. The fatal of the cancer and the microbes cell was due to inhibition of DNA synthesis which was probably due to chelating with metals complexes, or could be referred to lipophilicity, presence of hydrophobic moiety in the complex molecule, also could be due to steric effects and electronic effects.

  10. The effect of caffeine and adenine on radiation induced suppression of DNA synthesis, and cell survival

    International Nuclear Information System (INIS)

    Exposure of cultured mammalian cells to ionizing radiation or UV light results in a transient decrease in the rate of DNA synthesis. This depression in synthetic rate may be attenuated or deferred via a post-irradiation treatment with caffeine or adenine. It has been suggested that this attenuation may increase the fixation of damage and, therefore, increase radiation sensitivity. However, it has been previously reported that, for V79 cells treated with caffeine or adenine, no correlation exists between the extent of depression and cell survival. The present investigation expands upon these findings by examining the effect of caffeine or adenine post-irradiation treatment on two cell lines with normal UV sensitivity, mouse 3T3 and CHO AA8 cells, and one UV sensitive cell line, CHO UV5 cells. Both caffeine and adenine have been found to reduce, or delay, the suppression in DNA synthesis in all three cell lines. Surprisingly, caffeine appeared to induced even the UV5 cells to recover DNA synthetic ability. The amount of reduction in suppression of DNA synthesis, however, varies between the different cell lines and no consistent relationship with cell survival has emerged

  11. A new paradigm of DNA synthesis: three-metal-ion catalysis.

    Science.gov (United States)

    Yang, Wei; Weng, Peter J; Gao, Yang

    2016-01-01

    Enzyme catalysis has been studied for over a century. How it actually occurs has not been visualized until recently. By combining in crystallo reaction and X-ray diffraction analysis of reaction intermediates, we have obtained unprecedented atomic details of the DNA synthesis process. Contrary to the established theory that enzyme-substrate complexes and transition states have identical atomic composition and catalysis occurs by the two-metal-ion mechanism, we have discovered that an additional divalent cation has to be captured en route to product formation. Unlike the canonical two metal ions, which are coordinated by DNA polymerases, this third metal ion is free of enzyme coordination. Its location between the α- and β-phosphates of dNTP suggests that the third metal ion may drive the phosphoryltransfer from the leaving group opposite to the 3'-OH nucleophile. Experimental data indicate that binding of the third metal ion may be the rate-limiting step in DNA synthesis and the free energy associated with the metal-ion binding can overcome the activation barrier to the DNA synthesis reaction. PMID:27602203

  12. Amplifying the SERS signal of DNA bases via the chemical resonance

    Science.gov (United States)

    Freeman, Lindsay M.; Pang, Lin; Fainman, Yeshaiahu

    2015-03-01

    Label-free detection methods of DNA bases using surface-enhanced Raman spectroscopy (SERS) have yet to be successfully utilized due to inconsistent signal readouts. We have identified the primary reason for the discrepancies in the SERS signals of nucleic acids as being caused by the charge-transfer chemical resonance of the base silver system which is dependent on excitation wavelength. Time-dependent density functional theory (TD-DFT) methods to calculate the electronic transitions and resonance Raman spectra of base silver complexes are performed, and the optimal excitation wavelength for the charge-transfer electronic transition is found for each base silver complex. The enhancement caused by the chemical resonance is then experimentally measured for adenine, cytosine, guanine and thymine at multiple excitation wavelengths. The dependence of the Raman intensity on excitation wavelength shows good agreement with the TD-DFT calculations. In order to fully achieve the maximum Raman intensity, both the electromagnetic and chemical resonance must be enhanced by the appropriate wavelength selection. Based on the optimal chemical resonance Raman wavelength, we design a SERS substrate which has an electromagnetic maximum wavelength that matches the chemical resonance wavelength. By aligning both resonances, the highest Raman intensity can be found for each base silver system. We have proven that the variance in DNA bases' Raman intensities are caused by chemical enhancement. By incorporating the chemical resonance and optimizing both the chemical and electromagnetic resonance, we believe a label-free DNA SERS based detection method can be realized.

  13. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    Science.gov (United States)

    Gardner, Shea N.; Mariella, Jr., Raymond P.; Christian, Allen T.; Young, Jennifer A.; Clague, David S.

    2011-01-18

    A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

  14. Synthesis, Characterization, and DNA Binding Studies of Nanoplumbagin

    Directory of Open Access Journals (Sweden)

    Sheik Dawood Shahida Parveen

    2014-01-01

    Full Text Available The traditional anticancer medicine plumbagin (PLN was prepared as nanostructured material (nanoplumbagin, NPn1 from its commercial counterparts, simultaneously coencapsulating with cetyltrimethylammonium bromide or cyclodextrin as stabilizers using ultrasonication technique. Surface morphology of NPn analysed from atomic force microscopy (AFM indicates that NPn has tunable size between 75 nm and 100 nm with narrow particle size distribution. Its binding efficiency with herring sperm DNA was studied using spectral and electrochemical techniques and its efficiency was found to be more compared to the commercial microcrystalline plumbagin (PLN. DNA cleavage was also studied by gel electrophoresis. The observed results indicate that NPn1 has better solubility in aqueous medium and hence showed better bioavailability compared to its commercial counterparts.

  15. Synthesis and biological activity of benzamide DNA minor groove binders.

    Science.gov (United States)

    Khan, Gul Shahzada; Pilkington, Lisa I; Barker, David

    2016-02-01

    A range of di- and triaryl benzamides were synthesised to investigate the effect of the presence and nature of a polar sidechain, bonding and substitution patterns and functionalisation of benzylic substituents. These compounds were tested for their antiproliferative activity as well as their DNA binding activity. The most active compounds in all assays were unsymmetrical triaryl benzamides with a bulky or alkylating benzylic substituent and a polar amino sidechain.

  16. Simple Laboratory methods to measure cell proliferation using DNA synthesis property

    Directory of Open Access Journals (Sweden)

    Madhavan H N

    2007-01-01

    Full Text Available This is a mini-review on the techniques to measure proliferation of cells by estimation of DNA synthesis. This is not an exhaustive review of literature, but a bird’s eye view of a few selected articles which may provide the technical details to the readers.The nucleus of a cell occupies about 10-30% of the cells space, depends on the type of genetic material (DNA -DeoxyriboNucleic Acid. DNA is a long, double-stranded, helical molecule which carries the genetic information. Duplication of the DNA takes place by the phenomena of replication. One copy of double-stranded DNA molecule forms two double-stranded DNA molecules. DNA replication is the fundamental process used in all living organisms as it is the basis for biological inheritance. This process is known also as Mitosis in somatic cells. In Mitosis, the duplication process results in two genetically identical "daughter" cells from a single "parent" cell. The resulting double-stranded DNA molecules are identical; proof reading and error-checking mechanisms exist to ensure near perfect pair. Mitosis is divided into six phases: prophase, prometaphase, metaphase, anaphase, telophase, and cytokinesis.

  17. Regulation of chloroplast number and DNA synthesis in higher plants. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Mullet, J.E.

    1995-11-10

    The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailing description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.

  18. Regulation of chloroplast number and DNA synthesis in higher plants. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Mullet, J.E.

    1995-11-10

    The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.

  19. Studies on a Novel Minor-groove Targeting Artificial Nuclease: Synthesis and DNA Binding Behavior

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Nucleases play an important role in molecular biology, for example, in DNA sequencing. Synthetic polyamide conjugates can be considered as a novel tool for the selective inhibition of gene expressions and also as potential drugs in anticancer or antiviral chemotherapy. In this article, the synthesis of a novel minor-groove targeting artificial nuclease, an oligopyrrol-containing compound, has been reported. It was found that this novel compound can bind DNA in AT-rich minor groove with high affinity and site specificity. DNA binding behavior was determined by using UV-Vis and CD. It is indicated that compound 6 can enhance the Tm of DNA from 80. 4 C to 84. 4 ℃ and that it possesses a high binding constant value(Kb = 3.05×104 L/mol).

  20. New methods for toxicokinetic studies on chemicals carcinogens by means of analysis of DNA damage

    International Nuclear Information System (INIS)

    For investigating the potential carcinogenic properties of chemicals or for elucidating their mechanisms of activities, it is as important to determine their DNA damaging effects as it is to determine their mutagenicity. In the following, three methods will be presented which may be utilized to detect chemically induced DNA damage. These are the classical DNA filter elution procedure (AE), the in situ nick translation (NT), and the single cell microgel-electrophoresis (MGE) assay. Latter two methods have the advantage that they will allow genotoxic effects to be determined in many organs of the experimental animals, since only minute quantities of tissue are needed. Therefore it is possible to efficiently obtain data pertaining to the toxicokinetics of the test chemical which may be used for purposes of risk assessment. (orig.)

  1. Synthesis of a duplex oligonucleotide containing a nitrogen mustard interstrand DNA-DNA cross-link.

    Science.gov (United States)

    Ojwang, J O; Grueneberg, D A; Loechler, E L

    1989-12-01

    Many cancer chemotherapeutic agents react with DNA and give adducts that block DNA replication, which is thought to result in cytotoxicity, especially in rapidly proliferating cells such as cancer cells. One class of these agents is bifunctionally reactive (e.g., the nitrogen mustards) and forms DNA-DNA cross-links. It is unknown whether inter- or intrastrand cross-links are more effective at blocking DNA replication. To evaluate this, a DNA shuttle vector is being constructed with an interstrand cross-link at a unique site. In the first step of this project, a duplex oligonucleotide containing an interstrand cross-link is isolated by denaturing polyacrylamide gel electrophoresis from the reaction of nitrogen mustard with two partially complementary oligodeoxynucleotides. The purified oligonucleotide product is characterized and shown to be cross-linked in a 5'-GAC-3' 3'-CTG-5' sequence by a nitrogen mustard moiety that is bound at the N(7)-position of the guanines in the opposing strands; the glycosylic bonds of these guanine adducts are stabilized in their corresponding imidazole ring-opened form. Nitrogen mustard is shown to react with a variety of oligonucleotides and, based upon these results, its preferred targets for interstrand cross-linking are 5'-GXC-3' sequences, where X can be any of the four deoxyribonucleotide bases. PMID:2819709

  2. Solution-Chemical Synthesis of Cobalt and Iron:Zinc Oxide Nanocomposite Films

    OpenAIRE

    Lagerqvist, Ulrika

    2016-01-01

    The potentially most important challenges today are related to energy and the environment. New materials and methods are needed in order to, in a sustainable way, convert and store energy, reduce pollution, and clean the air and water from contaminations. In this, nanomaterials and nanocomposites play a key role, and hence knowledge about the relation between synthesis, structure, and properties of nanosystems is paramount. This thesis demonstrates that solution-chemical synthesis, using amin...

  3. Influence of nitroimidazole derivatives and irradiation on the DNA synthesis of L5178Y cells and human lymphocytes

    International Nuclear Information System (INIS)

    The radiosensitizing effect of 4-nitroimidazoles a further substance similar to the known 2-nitroderivative misonidazole was involved in the testing. The investigation with four different nitroimidazole derivatives carried out under the same conditions permit a good comparison of their effectiveness for the selected criteria. The influence of these substances on the DNA synthesis before and after irradiation was examined in vitro in L5178Y cells and human lymphocytes. Regarding their inhibitory effect on DNA synthesis, all substances in a radiotherapeutically relevant concentration are without effect for well oxygenated cells. This also applies to hypoxic cultures, except the 2-nitroimidazole. The radiation-induced inhibition of the DNA synthesis is considerably intensified by all derivatives only under hypoxia. The radiation-induced DNA synthesis in lymphocytes is not influenced. (author)

  4. The total chemical synthesis of polymer/graphene nanocomposite films.

    Science.gov (United States)

    Salvatierra, Rodrigo V; Cava, Carlos E; Roman, Lucimara S; Oliveira, Marcela M; Zarbin, Aldo J G

    2016-01-28

    A versatile and room temperature synthesis of thin films of polymer/graphene is reported. Drastically differing from other methods, not only the polymer but also the graphene are completely built from their simplest monomers (thiophene and benzene) in a one-pot polymerization reaction at a liquid-liquid interface. The materials were characterized and electronic properties are presented. PMID:26658554

  5. Direct synthesis of nanocrystalline oxide powders by wet-chemical techniques

    Directory of Open Access Journals (Sweden)

    Vladimir V. Srdić

    2010-09-01

    Full Text Available In a recent period there is a great need for increasing the knowledge of tailoring the innovative procedures for the synthesis of electroceramic nanopowders and materials with improved quality for specific application. In order to produce electroceramics with desirable microstructure and properties, synthesis of stoichiometric, ultra-fine and agglomerate free powders with narrow size distributions is one of the most important steps. Within this scope, in the present paper we summarize our recent results on direct synthesis of some important perovskites and ferrites nanopowders by wet-chemical techniques.

  6. Solution-phase synthesis of inorganic nanostructures by chemical transformation from reactive templates

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The solution-phase synthesis by chemical transformation from reactive templates has proved to be very effective in morphology-controlled synthesis of inorganic nanostructures. This review paper summarizes the recent progress in solution-phase synthesis of one-dimensional and hollow inorganic nanostructures via reactive templates, focusing on the approaches developed in our lab. The formation mechanisms based on reactive templates are discussed in depth to show the general concepts for the preparation processes. An outlook on the future development in this area is also presented.

  7. Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA.

    Science.gov (United States)

    Schinn, Song-Min; Broadbent, Andrew; Bradley, William T; Bundy, Bradley C

    2016-06-25

    A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems. PMID:27085957

  8. N-Methylcysteine-Mediated Total Chemical Synthesis of Ubiquitin Thioester

    OpenAIRE

    Erlich, Lesly A.; Ajish Kumar, K. S.; Haj-Yahya, Mahmood; Dawson, Philip E.; Brik, Ashraf

    2010-01-01

    Ubiquitin thioester is a key intermediate in the ubiquitylation of proteins and is formed enzymatically through the activation of α-COOH of ubiquitin in an ATP dependent manner using the E1 enzyme. The current methods used for the preparation of ubiquitin thioester rely on either the enzymatic machinery or on expressed protein ligation technology. In this article, we report a new chemical strategy, combining native chemical ligation and N-methylcysteine containing peptides, to chemically prep...

  9. Phospholipase C-gamma 1 can induce DNA synthesis by a mechanism independent of its lipase activity.

    OpenAIRE

    Smith, M. R.; Liu, Y.L.; Matthews, N T; Rhee, S G; Sung, W K; Kung, H F

    1994-01-01

    Inositol phospholipid-specific phospholipase C (PLC) is involved in several signaling pathways leading to cellular growth and differentiation. Our previous studies reported the induction of DNA synthesis in quiescent NIH 3T3 cells after microinjection of PLC and the inhibition of serum- or Ras-stimulated DNA synthesis by a mixture of monoclonal antibodies to PLC-gamma 1. In the course of our investigation of anti-PLC-gamma 1 monoclonal antibodies, we found that each antibody exerts different ...

  10. The Foundry: the DNA synthesis and construction Foundry at Imperial College.

    Science.gov (United States)

    Chambers, Stephen; Kitney, Richard; Freemont, Paul

    2016-06-15

    The establishment of a DNA synthesis and construction foundry at Imperial College in London heralds a new chapter in the development of synthetic biology to meet new global challenges. The Foundry employs the latest technology to make the process of engineering biology easier, faster and scalable. The integration of advanced software, automation and analytics allows the rapid design, build and testing of engineered organisms. PMID:27284027

  11. The Foundry: the DNA synthesis and construction Foundry at Imperial College

    Science.gov (United States)

    Chambers, Stephen; Kitney, Richard; Freemont, Paul

    2016-01-01

    The establishment of a DNA synthesis and construction foundry at Imperial College in London heralds a new chapter in the development of synthetic biology to meet new global challenges. The Foundry employs the latest technology to make the process of engineering biology easier, faster and scalable. The integration of advanced software, automation and analytics allows the rapid design, build and testing of engineered organisms. PMID:27284027

  12. Polyanionic Carboxyethyl Peptide Nucleic Acids (ce-PNAs: Synthesis and DNA Binding.

    Directory of Open Access Journals (Sweden)

    Yuliya Kirillova

    Full Text Available New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral α- and γ-monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified γ-S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA.

  13. Divalent cation ionophores stimulate resorption and inhibit DNA synthesis in cultured fetal rat bone

    Energy Technology Data Exchange (ETDEWEB)

    Lorenzo, J.A.; Raisz, L.G.

    1981-06-01

    Two divalent cation ionophores, A23187 and Ionomycin, which are selective for calcium, stimulated the resorption of fetal rat long bones in organ culture at 0.1 to 1 micromolar but not at higher concentrations. Both agents inhibited DNA synthesis at concentrations that stimulated resorption. These results might explain the differences in ionophore effects on bone previously reported, and they imply that cell replication is not required for osteoclast formation in fetal rat long bone cultures.

  14. [DNA synthesis inhibition test of INAH by cultured human fibroblasts].

    Science.gov (United States)

    Nishio, K; Yanagisawa, K

    1986-03-20

    The most commonly used screening test of carcinogens is the Ames test. But this system occasionally shows false positive and false negative. Painter's method is one which has been developed to minimize false results. Now we test by Painter's method isonicotinic acid hydrazide, which shows negative in the Ames test but positive in an animal test. INAH showed positive by Painter's method. More chemicals are now under study for their carcinogenicity by Painter's method.

  15. Mechanism of ultraviolet-induced mutagenesis: extent and fidelity of in vitro DNA synthesis on irradiated templates

    International Nuclear Information System (INIS)

    The effect of uv irradiation on the extent and fidelity of DNA synthesis in vitro was studied by using homopolymers and primed single-stranded phi X174 phage DNA as substrates. Unfractionated and fractionated cell-free extracts from Escherichia coli pol+ and polA1 mutants as well as purified DNA polymerase I were used as sources of enzymatic activity. (DNA polymerases, as used here, refer to deoxynucleosidetriphosphate : DNA deoxynucleotidyltransferase, EC 2.7.7.7.) The extent of inhibition of DNA synthesis on uv-irradiated phi X174 DNA suggested that pyrimidine dimers act as an absolute block for chain elongation by DNA polymerases I and III. Experiments with an irradiated poly(dC) template failed to detect incorporation of noncomplementary bases due to pyrimidine dimers. A large increase in the turnover of nucleoside triphosphates to free monophosphates during synthesis by DNA polymerase I on irradiated phi X174 DNA has been observed. We propose that this nucleotide turnover is due to idling by DNA polymerase (i.e., incorporation and subsequent excision of nucleotides opposite uv photolesions, by the 3' to 5' ''proofreading'' exonuclease) thus preventing replication past pyrimidine dimers and the potentially mutagenic event that should result

  16. Novel pattern of post-γ ray de novo DNA synthesis in a radioresistant human strain

    International Nuclear Information System (INIS)

    Enhanced resistance to radiation cytotoxicity in a fibroblast strain from an afflicted member of a Li-Fraumeni syndrome family may be largely ascribable to a change in the pattern of DNA replicative synthesis following γ ray exposure. That is, the extent of the initial radiogenic inhibition of replicative synthesis and the time interval before its subsequent recovery were both found to be greater in radioresistant (RR) compared to normal cells. In addition, the post-recovery replication rates in the RR cells were both higher and longer lasting than those in the control cells. A similar differential pattern was also seen following treatment with 4NQO, another DNA-damaging agent to which this RR strain displays enhanced resistance. Moreover, several conventional DNA repair assays indicated that the RR cells repair radiogenic damage at normal rates. The authors therefore suggest that the increased inhibition and prolonged lag in resumption of replicative synthesis seen in the RR strain upon exposure to certain genotoxic agents may enhance cellular recovery by ''buying additional time'' for processing of potentially lethal lesions

  17. Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis

    International Nuclear Information System (INIS)

    Completion of DNA replication needs to be ensured even when challenged with fork progression problems or DNA damage. PCNA and its modifications constitute a molecular switch to control distinct repair pathways. In yeast, SUMOylated PCNA (S-PCNA) recruits Srs2 to sites of replication where Srs2 can disrupt Rad51 filaments and prevent homologous recombination (HR). We report here an unexpected additional mechanism by which S-PCNA and Srs2 block the synthesis-dependent extension of a recombination intermediate, thus limiting its potentially hazardous resolution in association with a cross-over. This new Srs2 activity requires the SUMO interaction motif at its C-terminus, but neither its translocase activity nor its interaction with Rad51. Srs2 binding to S-PCNA dissociates Polδ and Polη from the repair synthesis machinery, thus revealing a novel regulatory mechanism controlling spontaneous genome rearrangements. Our results suggest that cycling cells use the Siz1-dependent SUMOylation of PCNA to limit the extension of repair synthesis during template switch or HR and attenuate reciprocal DNA strand exchanges to maintain genome stability. (authors)

  18. DNA-Bank of the Siberian Group Chemical Enterprises workers and Seversk city residents

    International Nuclear Information System (INIS)

    According to the mostr common definition a DNA-bank is a system of a genetic material storage. Applying to nuclear-chemical plant workers, DNA-bank creation is determined by the necessity to preserve a hereditary material of these people and their descendants for the further evaluation of consequences fo technogenic factors action on human genome using a contemporary conceptual and applied advances of genetics. In the frameworks of the study of technogenic factors indluence on human genome and genetic-caused disorders development the Seversk Biophysical Research Center is being created DNA-bank of Siberian Group of Chemical Enterprises workers exposed to radiation, their descendants, and ZATO Seversk and Tomsk city inhabitants. The DNA-bank will be a basis for all major research laboratory projects: analysis of molecular basis of individual radiosensitivity; analysis of technogenic factors role in congenital malformations and hereditary diseases development in nuclear-chemical plant workers offspring; elaboration of genotype-specific tes-systems of cancer prognosis and development of cardiovascular and other common disorders connected with the effect of technogenic factors. The DNA-bank creation is a technological issue aggravated by ethical problems. Whereas the DNA isolation is not a problem today, ethical complication id debated widely in the world. These questions strongly arise in a view of advances of Human Genome Project. Information consent on DNA usage is imperative today. Also questions on DNA property (who is its owner a doner or a banker) and of a confidentiality, which maintenance is a doubtable question in a case of multiple genetic testing, are not solved today. At present, the Genomic Medicine Laboratory disposes the DNA samples of more than 400 Sevesk and Tomsk inhabitants affected with breast and lung cancer. More than 800 blood samples of main manufacture of the Siberian Group of Chemical Enterprises workers are collected. About 1500 DNA samples

  19. DNA repair after ultraviolet irradiation of ICR 2A frog cells: pyrimidine dimers are long acting blocks to nascent DNA synthesis

    International Nuclear Information System (INIS)

    The ability of ICR 2A frog cells to repair DNA damage induced by ultraviolet irradiation was examined. These cells are capable of photoreactivation but are nearly totally deficient in excision repair. They have the ability to convert the small molecular weight DNA made after irradiation into large molecules but do not show an enhancement in this process when the UV dose is delivered in two separate exposures separated by a 3- or 24-h incubation. Total DNA synthesis is depressed and low molecular weight DNA continues to be synthesized during pulse-labeling as long as 48 h after irradiation. The effects of pyrimidine dimer removal through exposure of UV irradiated cells to photoreactivating light indicate that dimers act as the critical lesions blocking DNA synthesis

  20. DNA synthesis and cell division in the adult primate brain

    International Nuclear Information System (INIS)

    It is generally accepted that the adult human brain is incapable of producing new neuron. Even cursory examination of neurologic, neuropathologic, or neurobiological textbooks published during the past 50 years will testify that this belief is deeply entrenched. In his classification of cell populations on the basis of their proliferative behavior, Leblond regarded neurons of the central nervous system as belonging to a category of static, nonrenewing epithelial tissue incapable of expanding or replenishing itself. This belief, however needs to re reexamined for two major reasons: First, as reviewed below, a number of reports have provided evidence of neurogenesis in adult brain of several vertebrate species. Second, the capacity for neurogenesis in the adult primate central nervous system has never been examined by modern methods. In this article the author described recent results from an extensive autoradiographic analysis performed on twelve rhesus monkeys injected with the specific DNA precursor [3H] thymidine at ages ranging from 6 postnatal months to 17 years

  1. Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine.

    OpenAIRE

    Eritja, R.; Kaplan, B E; Mhaskar, D; Sowers, L C; Petruska, J; Goodman, M F

    1986-01-01

    DNA heptamers containing the mutagenic base analogue 2-aminopurine (AP) have been chemically synthesized and physically characterized. We report on the relative stabilities of base pairs between AP and each of the common DNA bases, as determined from heptamer duplex melts at 275 and 330 nm. Base pairs are ranked in order of decreasing stability: AP.T greater than AP.A greater than AP.C greater than AP.G. It is of interest that AP.A is more stable than AP.C even though DNA polymerase strongly ...

  2. Recent Applications of Alkene Metathesis in Fine Chemical Synthesis

    Science.gov (United States)

    Bicchielli, Dario; Borguet, Yannick; Delaude, Lionel; Demonceau, Albert; Dragutan, Ileana; Dragutan, Valerian; Jossifov, Christo; Kalinova, Radostina; Nicks, François; Sauvage, Xavier

    During the last decade or so, the emergence of the metathesis reaction in organic synthesis has revolutionised the strategies used for the construction of complex molecular structures. Olefin metathesis is indeed particularly suited for the construction of small open-chain molecules and macrocycles using crossmetathesis and ring-closing metathesis, respectively. These reactions serve, inter alia, as key steps in the synthesis of various agrochemicals and pharmaceuticals such as macrocyclic peptides, cyclic sulfonamides, novel macrolides, or insect pheromones. The present chapter is aiming at illustrating the great synthetic potential of metathesis reactions. Shortcomings, such as the control of olefin geometry and the unpredictable effect of substituents on the reacting olefins, will also be addressed. Examples to be presented include epothilones, amphidinolides, spirofungin A, and archazolid. Synthetic approaches involving silicon-tethered ring-closing metathesis, relay ring-closing metathesis, sequential reactions, domino as well as tandem metathesis reactions will also be illustrated.

  3. Electrophoretic mobility of PM2 DNA treated with ultimate chemical carcinogens or with ultraviolet light

    International Nuclear Information System (INIS)

    Superhelical DNA of the Pseudomonas phage PM2 was irradiated with UV-light or reacted with covalently binding carcinogens, such as 7-bromomethyl-benz[a]anthracene, (Ac)2ONFln, K-region epoxides, and alkylating agents. Migration velocity of the DNA products was determined using agarose gel electrophoresis. In gels of more than 1.3%-1.9% agarose, modified PM2 DNA exhibited a dose-(concentration-)dependent decrease of migration velocity. This phenomenon is probably due to a decrease in superhelix density which caused the compact DNA coil to assume eventually an open-circular conformation. Comparison of the extent of DNA modification with the decrease of migration velocity revealed that the superhelical structure sensitively reflected the chemical DNA alterations. DNA species exhibiting in 1.6% agarose gels, a migration velocity of up to 30% of that of control DNA showed an increase of velocity in 0.4% agarose. Therefore, in 1.3%-1.9% agarose gels, the decrease of superhelix density is accompanied by an increase of the frictional coefficient, whereas in 0.4%-0.9% agarose gels the same decrease of superhelix density apparently led to a higher degree of flexibility of the macromolecule and/or exposure of additional electric charges. (orig.)

  4. Defect in UV-induced unscheduled DNA synthesis in cultured epidermal keratinocytes from xeroderma pigmentosum

    International Nuclear Information System (INIS)

    DNA repair synthesis in 8 explant-outgrowth cultures of epidermal cells isolated from variant and complementation groups A and E of xeroderma pigmentosum (XP) was examined by measuring unscheduled DNA synthesis (UDS) on autoradiographs. The extents of UDS in XP epidermal cells were compared with those in normal epidermal cells obtained from 26 subjects. In both normal and XP epidermal cells, UDS was induced dose-dependently by radiation at doses of 5-20 J/m2. XP epidermal cells showed various extents of defect in DNA repair depending on the type of XP. In XP-A, the extent of UDS in epidermal cells was very low, being seen in only 3-10% of the normal epidermal cells. But epidermal cells isolated from XP-E and XP-variants exhibited relatively high levels of residual DNA repair; i.e., 69-84% of the control in XP-E and 67-85% in XP-variant. The extents of UDS in XP epidermal cells were almost the same as those in fibroblastic cells isolated from the same specimens. (Auth.)

  5. A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis.

    Science.gov (United States)

    Zhang, Yu; Yu, Hao; Qin, Jianhua; Lin, Bingcheng

    2009-11-06

    Boolean logic performs a logical operation on one or more logic input and produces a single logic output. Here, we describe a microfluidic DNA computing processor performing Boolean logic operations for gene expression analysis and gene drug synthesis. Multiple cancer-related genes were used as input molecules. Their expression levels were identified by interacting with the computing related DNA strands, which were designed according to the sequences of cancer-related genes and the suicide gene. When all the expressions of the cancer-related genes fit in with the diagnostic criteria, positive diagnosis would be confirmed and then a complete suicide gene (gene drug) could be synthesized as an output molecule. Microfluidic chip was employed as an effective platform to realize the computing process by integrating multistep biochemical reactions involving hybridization, displacement, denaturalization, and ligation. By combining the specific design of the computing related molecules and the integrated functions of the microfluidics, the microfluidic DNA computing processor is able to analyze the multiple gene expressions simultaneously and realize the corresponding gene drug synthesis with simplicity and fast speed, which demonstrates the potential of this platform for DNA computing in biomedical applications.

  6. Biomarkers of DNA and cytogenetic damages induced by environmental chemicals or radiation

    International Nuclear Information System (INIS)

    This paper presents and discusses results from the studies on various biomarkers of the DNA and cytogenetic damages induced by environmental chemicals or radiation. Results of the biomonitoring studies have shown that particularly in the condition of Poland, health hazard from radiation exposure is overestimated in contradistinction to the environmental hazard

  7. Induction of DNA repair synthesis in human monocytes/B-lymphocytes compared with T-lymphocytes after exposure to N-acetoxy-N-acetylaminofluorene and dimethylsulfate in vitro

    DEFF Research Database (Denmark)

    Knudsen, Lisbeth E.; Ryder, L P; Wassermann, K

    1992-01-01

    We have explored the induction of DNA repair synthesis in monocyte/B- and T-lymphocyte enriched cell fractions from 12 different human mononuclear blood cell populations. Unscheduled DNA synthesis was measured in monocyte/B- and T-cells after exposure to the DNA-damaging agents dimethylsulfate (D...

  8. Inhibitor of DNA synthesis is present in normal chicken serum

    International Nuclear Information System (INIS)

    The authors have found that heat-inactivated serum (570C for 1 hour) from normal chickens reduces the proliferation of mitogen-stimulated chicken and murine splenocytes as well as some transformed mammalian lymphoblastoid cell lines. Greater than a 50% reduction in 3H-thymidine incorporation was observed when concanavalin A (Con A)-activated chicken splenocytes that were cultured in the presence of 10% autologous or heterologous serum were compared to mitogen-stimulated cells cultured in the absence of serum. Normal chicken serum (10%) also caused greater than 95% suppression of 3H-thymidine incorporation by bovine (EBL-1 and BL-3) and gibbon ape (MLA 144) transformed lymphoblastoid cell lines. The only cell line tested that was not inhibited by chicken serum was an IL-2-dependent, murine cell line. Chicken serum also inhibited both 3H-thymidine incorporation and IL-2 synthesis by Con A-activated murine splenocytes. Suppression was caused by actions other than cytotoxicity because viability of chicken splenocytes was unaffected by increasing levels of chicken serum. Furthermore, dialyzed serum retained its activity, which suggested that thymidine in the serum was not inhibiting uptake of radiolabeled thymidine. Suppressive activity was not due to adrenal glucocorticoids circulating in plasma because neither physiologic nor pharmacologic doses of corticosterone had inhibitory effects on mitogen-stimulated chicken splenocytes. These data demonstrate that an endogenous factor that is found in normal chicken serum inhibits proliferation of T-cells from chickens and mice as well as some transformed mammalian lymphoblastoid cell lines

  9. Synthesis and Crystal Structure of 2’-Se-modified guanosine Containing DNA

    Energy Technology Data Exchange (ETDEWEB)

    Salon, J.; Sheng, J; Gan, J; Huang, Z

    2010-01-01

    Selenium modification of nucleic acids is of great importance in X-ray crystal structure determination and functional study of nucleic acids. Herein, we describe a convenient synthesis of a new building block, the 2{prime}-SeMe-modified guanosine (G{sub Se}) phosphoramidite, and report the first incorporation of the 2{prime}-Se-G moiety into DNA. The X-ray crystal structure of the 2{prime}-Se-modified octamer DNA (5{prime}-GTG{sub Se}TACAC-3{prime}) was determined at a resolution of 1.20 {angstrom}. We also found that the 2{prime}-Se modification points to the minor groove and that the modified and native structures are virtually identical. Furthermore, we observed that the 2{prime}-Se-G modification can significantly facilitate the crystal growth with respect to the corresponding native DNA.

  10. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases

    Institute of Scientific and Technical Information of China (English)

    Scott D McCulloch; Thomas A Kunkel

    2008-01-01

    In their seminal publication describing the structure of the DNA double helix [1], Watson and Crick wrote what may be one of the greatest understatements in the scientific literature, namely that "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Half a century later, we more fully appreciate what a huge challenge it is to replicate six billion nucleotides with the accuracy needed to stably maintain the human genome over many generations. This challenge is perhaps greater than was realized 50 years ago, because subsequent studies have revealed that the genome can be destabilized not only by environmental stresses that generate a large number and variety of potentially cytotoxic and mutagenic lesions in DNA but also by various sequence motifs of normal DNA that present challenges to replication. Towards a better understanding of the many determinants of genome stability, this chapter reviews the fidelity with which undamaged and damaged DNA is copied, with a focus on the eukaryotic B- and Y-family DNA polymerases, and considers how this fidelity is achieved.

  11. Energy-dependent existence of soliton in the synthesis of chemical elements

    OpenAIRE

    Iwata, Yoritaka

    2014-01-01

    Light chemical elements are, for instance, produced through ion collisions taking place in the core of stars, where fusion is particularly important to the synthesis of chemical elements. Meanwhile soliton provides non-interacting transparency leading to the hindrance of fusion cross section. In order to explain high fusion cross section actually observed in low incident energies, it is necessary to discover the suppression mechanism of soliton propagation. In this paper, based on a systemati...

  12. Phosphorus-containing cyclodextrins. Characteristics of the synthesis and chemical behaviour

    Science.gov (United States)

    Grachev, M. K.

    2013-11-01

    Published data on the preparation of phosphorus-containing cyclodextrins are summarized. It is demonstrated that some significant features of their synthesis and chemical behaviour are caused by specific supramolecular interactions involving the inner chiral cavity of cyclodextrins capable of incorporating various guests, which often leads to alteration of customary routes of chemical transformations. The possibilities of practical applications of phosphorus-containing cyclodextrins are briefly analyzed. The bibliography includes 89 references.

  13. Parallel combinatorial chemical synthesis using single-layer poly(dimethylsiloxane) microfluidic devices

    OpenAIRE

    Dexter, Joseph P.; Parker, William

    2009-01-01

    Improving methods for high-throughput combinatorial chemistry has emerged as a major area of research because of the importance of rapidly synthesizing large numbers of chemical compounds for drug discovery and other applications. In this investigation, a novel microfluidic chip for performing parallel combinatorial chemical synthesis was developed. Unlike past microfluidic systems designed for parallel combinatorial chemistry, the chip is a single-layer device made of poly(dimethylsiloxane) ...

  14. Automated screening for small organic ligands using DNA-encoded chemical libraries.

    Science.gov (United States)

    Decurtins, Willy; Wichert, Moreno; Franzini, Raphael M; Buller, Fabian; Stravs, Michael A; Zhang, Yixin; Neri, Dario; Scheuermann, Jörg

    2016-04-01

    DNA-encoded chemical libraries (DECLs) are collections of organic compounds that are individually linked to different oligonucleotides, serving as amplifiable identification barcodes. As all compounds in the library can be identified by their DNA tags, they can be mixed and used in affinity-capture experiments on target proteins of interest. In this protocol, we describe the screening process that allows the identification of the few binding molecules within the multiplicity of library members. First, the automated affinity selection process physically isolates binding library members. Second, the DNA codes of the isolated binders are PCR-amplified and subjected to high-throughput DNA sequencing. Third, the obtained sequencing data are evaluated using a C++ program and the results are displayed using MATLAB software. The resulting selection fingerprints facilitate the discrimination of binding from nonbinding library members. The described procedures allow the identification of small organic ligands to biological targets from a DECL within 10 d. PMID:26985574

  15. Green chemical synthesis of silver nanomaterials with maltodextrin.

    Energy Technology Data Exchange (ETDEWEB)

    Tallant, David Robert; Lu, Ping; Lambert, Timothy N.; Bell, Nelson Simmons

    2010-11-01

    Silver nanomaterials have significant application resulting from their optical properties related to surface enhanced Raman spectroscopy, high electrical conductivity, and anti-microbial impact. A 'green chemistry' synthetic approach for silver nanomaterials minimizes the environmental impact of silver synthesis, as well as lowers the toxicity of the reactive agents. Biopolymers have long been used for stabilization of silver nanomaterials during synthesis, and include gum Arabic, heparin, and common starch. Maltodextrin is a processed derivative of starch with lower molecular weight and an increase in the number of reactive reducing aldehyde groups, and serves as a suitable single reactant for the formation of metallic silver. Silver nanomaterials can be formed under either a thermal route at neutral pH in water or by reaction at room temperature under more alkaline conditions. Deposited silver materials are formed on substrates from near neutral pH solutions at low temperatures near 50 C. Experimental conditions based on material concentrations, pH and reaction time are investigated for development of deposited films. Deposit morphology and optical properties are characterized using SEM and UV-vis techniques. Silver nanoparticles are generated under alkaline conditions by a dissolution-reduction method from precipitated silver (II) oxide. Synthesis conditions were explored for the rapid development of stable silver nanoparticle dispersions. UV-vis absorption spectra, powder X-ray diffraction (PXRD), dynamic light scattering (DLS), and transmission electron microscopy (TEM) techniques were used to characterize the nanoparticle formation kinetics and the influence of reaction conditions. The adsorbed content of the maltodextrin was characterized using thermogravimetric analysis (TGA).

  16. Structural diversity and chemical synthesis of peroxide and peroxide-derived polyketide metabolites from marine sponges.

    Science.gov (United States)

    Norris, Matthew D; Perkins, Michael V

    2016-07-28

    Covering: up to early 2016Marine sponges are widely known as a rich source of natural products, especially of polyketide origin, with a wealth of chemical diversity. Within this vast collection, peroxide and peroxide-derived secondary metabolites have attracted significant interest in the fields of natural product isolation and chemical synthesis for their structural distinction and promising in vitro antimicrobial and anticancer properties. In this review, peroxide and peroxide-derived polyketide metabolites isolated from marine sponges in the past 35 years are summarised. Efforts toward their synthesis are detailed with a focus on methods that utilise or attempt to elucidate the complex biosynthetic interrelationships of these compounds beyond enzymatic polyketide synthesis. Recent isolations, advances in synthetic methodology and theories of biogenesis are highlighted and critically evaluated. PMID:27163115

  17. Activation of aluminum as an effective reducing agent by pitting corrosion for wet-chemical synthesis.

    Science.gov (United States)

    Li, Wei; Cochell, Thomas; Manthiram, Arumugam

    2013-01-01

    Metallic aluminum (Al) is of interest as a reducing agent because of its low standard reduction potential. However, its surface is invariably covered with a dense aluminum oxide film, which prevents its effective use as a reducing agent in wet-chemical synthesis. Pitting corrosion, known as an undesired reaction destroying Al and is enhanced by anions such as F⁻, Cl⁻, and Br⁻ in aqueous solutions, is applied here for the first time to activate Al as a reducing agent for wet-chemical synthesis of a diverse array of metals and alloys. Specifically, we demonstrate the synthesis of highly dispersed palladium nanoparticles on carbon black with stabilizers and the intermetallic Cu₂Sb/C, which are promising candidates, respectively, for fuel cell catalysts and lithium-ion battery anodes. Atomic hydrogen, an intermediate during the pitting corrosion of Al in protonic solvents (e.g., water and ethylene glycol), is validated as the actual reducing agent. PMID:23390579

  18. Parallel combinatorial chemical synthesis using single-layer poly(dimethylsiloxane) microfluidic devices

    Science.gov (United States)

    Dexter, Joseph P.; Parker, William

    2009-01-01

    Improving methods for high-throughput combinatorial chemistry has emerged as a major area of research because of the importance of rapidly synthesizing large numbers of chemical compounds for drug discovery and other applications. In this investigation, a novel microfluidic chip for performing parallel combinatorial chemical synthesis was developed. Unlike past microfluidic systems designed for parallel combinatorial chemistry, the chip is a single-layer device made of poly(dimethylsiloxane) that is extremely easy and inexpensive to fabricate. Using the chip, a 2×2 combinatorial series of amide-formation reactions was performed. The results of this combinatorial synthesis indicate that the new device is an effective platform for running parallel organic syntheses at significantly higher throughput than with past methodologies. Additionally, a design algorithm for scaling up the 2×2 combinatorial synthesis chip to address more complex cases was developed. PMID:20216962

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-11-03

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

  20. Iron may induce both DNA synthesis and repair in rat hepatocytes stimulated by EGF/pyruvate

    Energy Technology Data Exchange (ETDEWEB)

    Chenoufi, N.; Loreal, O.; Cariou, S.; Hubert, N.; Lescoat, G. [Univ. Hospital Pontchaillou, Unite de Recherches Hepatologiques, INSERM U 49, Rennes (France); Drenou, B. [Univ. Hospital Pontchaillou, Lab. d`Hematologie et d`Immunologie, Rennes (France); Leroyer, P.; Brissot, P. [Univ. Hospital Pontchaillou, Clinique des Maladies du Foie, Rennes (France)

    1997-03-01

    Background/Aims: Hepatocellular carcinoma develops frequently in the course of genetic hemochromatosis, and a role of iron overload in hepatic carcinogenesis is strongly suggested. Methods: The aim of our study was to investigate the effect of iron exposure on DNA synthesis of adult rat hepatocytes maintained in primary culture stimulated or not by EGF/pyruvate and exposed to iron-citrate complex. Results: In EGF/pyruvate-stimulated cultures, the level of [{sup 3}H] methyl thymidine incorporation was strongly increased as compared to unstimulated cultures. The addition of iron to stimulated cultures increased [{sup 3}H] methyl thymidine incorporation. The mitotic index was also significantly higher at 72 h. However,the number of cells found in the cell layer was not significantly different from iron-citrate free culture. By flow cytometry, no difference in cell ploidy was found between iron-treated and untreated EGF/pyruvate-stimulated cultures. A significant increase in LDH leakage reflecting a toxic effect of iron was found in the cell medium 48 h after cell seeding. In addition, [{sup 3}H] methyl thymidine incorporation in the presence of hydroxyurea was increased in iron-treated compared to untreated cultures. Conclusions: Our results show that DNA synthesis is increased in the presence of iron in rat hepatocyte cultures stimulated by EGF/pyruvate, and they suggest that DNA synthesis is likely to be related both to cell proliferation and to DNA repair. These observations may allow better understanding of the role of iron overload in the development of hepatocellular carcinoma. (au) 61 refs.

  1. Modeling and Experimental Studies on Phase and Chemical Equilibria in High-Pressure Methanol Synthesis

    NARCIS (Netherlands)

    van Bennekom, Joost G.; Winkelman, Jozef G. M.; Venderbosch, Robertus H.; Nieland, Sebastiaan D. G. B.; Heeres, Hero J.

    2012-01-01

    A solution method was developed to calculate the simultaneous phase and chemical equilibria in high-pressure methanol synthesis (P = 20 MPa, 463

  2. Synthesis of chemicals and polymers: towards cleaner processes and atom economy, session 5

    Energy Technology Data Exchange (ETDEWEB)

    Razavi, A.; Thivolle-Cazat, J.; Hutchings, G.; Murata, K.; Leininger, S.; Sorokin, A.; Angelis, A. de; Apesteguia, C.I.; Mayoral, J.A.; Hardacre, C.; Jeon, J.; Tominaga, K.; Plasseraud, L.; Kervennal, J.; Souza, R.F. de; Ciardelli, F.; Dominguez, J.M.

    2004-07-01

    The abstracts of all the presentations (1 plenary session, 2 keynotes, 16 oral communications, 151 posters) of the thematic session 5 'synthesis of chemicals and polymers: towards cleaner processes and atom economy' are gathered in the CD-Rom of the conference. (O.M.)

  3. A wet-chemical approach to perovskite and fluorite-type nanoceramics: synthesis and processing

    NARCIS (Netherlands)

    Veldhuis, Sjoerd Antonius

    2015-01-01

    In thesis the low-temperature, wet-chemical approach to various functional inorganic oxide materials is described. The main focus of this research is to control the material’s synthesis from liquid precursor to metal oxide powder or thin film; while understanding its formation mechanism. In addition

  4. Interdisciplinary Learning for Chemical Engineering Students from Organic Chemistry Synthesis Lab to Reactor Design to Separation

    Science.gov (United States)

    Armstrong, Matt; Comitz, Richard L.; Biaglow, Andrew; Lachance, Russ; Sloop, Joseph

    2008-01-01

    A novel approach to the Chemical Engineering curriculum sequence of courses at West Point enabled our students to experience a much more realistic design process, which more closely replicated a real world scenario. Students conduct the synthesis in the organic chemistry lab, then conduct computer modeling of the reaction with ChemCad and…

  5. Effects of gastrin, epidermal growth factor, and somatostatin on DNA synthesis in a small intestinal crypt cell line (IEC-6)

    International Nuclear Information System (INIS)

    Exposure of IEC-6 cells for 24 hr to either gastrin (50-500 ng/ml) or EGF (100-500 ng/ml) significantly (100-165%) the rate of [3H]thymidine incorporation into DNA (referred to as DNA synthesis) when compared with the corresponding basal levels. Somatostatin (10-500 ng/ml) produced no apparent change in DNA synthesis in IEC cells. On the other hand, somatostatin completely inhibited the EGF-induced rise in DNA synthesis. The gastrin-mediated stimulation in DNA synthesis was not affected by somatostatin. The rate of DNA synthesis in IEC cells in the presence of both gastrin and EGF was found to be greater (additive) than that caused by either of the peptides alone. A similar but less dramatic change in the actual number of cells (assessment of cell replication) was observed when the IEC cells were exposed for 24 hr to gastrin, EGF, and somatostatin, either alone or in combination. Whereas gastrin (250 ng/ml) and EGF (250 ng/ml) by themselves increased the number of cells significantly by 29 and 37%, respectively, together they caused a 72% stimulation, when compared with the basal levels. Somatostatin by itself caused no apparent change in IEC cell population, but it significantly inhibited the EGF- but not the gastrin-induced stimulation in IEC cell replication. It is concluded that both gastrin and EGF exert a direct proliferative effect on IEC cells, and the EGF action is regulated by somatostatin

  6. STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis

    Science.gov (United States)

    Hla, Saw-Wai; Rieder, Karl-Heinz

    2003-10-01

    The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.

  7. Trophic magnification of organic chemicals: A global synthesis

    Science.gov (United States)

    Walters, David; Jardine, T.D.; Cade, Brian S.; Kidd, K.A.; Muir, D.C.G.; Leipzig-Scott, Peter C.

    2016-01-01

    Production of organic chemicals (OCs) is increasing exponentially, and some OCs biomagnify through food webs to potentially toxic levels. Biomagnification under field conditions is best described by trophic magnification factors (TMFs; per trophic level change in log-concentration of a chemical) which have been measured for more than two decades. Syntheses of TMF behavior relative to chemical traits and ecosystem properties are lacking. We analyzed >1500 TMFs to identify OCs predisposed to biomagnify and to assess ecosystem vulnerability. The highest TMFs were for OCs that are slowly metabolized by animals (metabolic rate kM  0.2 day–1). This probabilistic model provides a new global tool for screening existing and new OCs for their biomagnification potential.

  8. Synthesis and chemical etching of Te/C nanocables

    Indian Academy of Sciences (India)

    Guang Sheng Cao; Yong Gang Liu; Wen Wu Yang; Chang Tan; Hui Li; Xiao Juan Zhang

    2011-10-01

    In this paper, Te/C nanocables were fabricated by a hydrothermal method in the presence of cetyltrimethylammonium bromide (CTAB). The products were characterized in detail by multiform techniques: transmission electron microscopy, X-ray diffraction, energy-dispersive X-ray analysis and Fourier transform infrared (FTIR) spectroscopy. The results showed that the products were nanocables with lengths of several microns, core about 20 nm in diameter, and a surrounding sheath of about 60–80 nm in thickness. Te/C nanocables were tailored freely by chemical etching. Carbonaceous nanotubes and Te/C nanocables with fragmentary Te core were obtained by adjusting time of chemical etching.

  9. Chemical synthesis and cloning of a gene for human beta-urogastrone.

    OpenAIRE

    J. Smith; Cook, E.; Fotheringham, I; Pheby, S; Derbyshire, R; Eaton, M A; Doel, M; Lilley, D M; Pardon', J.F.; T Patel; Lewis, H.; Bell, L. D.

    1982-01-01

    A DNA duplex coding for the 53 amino acids of human beta-urogastrone has been synthesised. Computer assisted design of the gene included restriction endonuclease sites for plasmid insertion, a termination codon and two triplets coding for lysine at the 5'-end of the structural gene. The synthesis involved preparation of 23 oligodeoxyribonucleotides by phosphotriester procedures coupled to rapid HPLC techniques. The gene was constructed in two halves by enzymatic ligation of the oligonucleotid...

  10. Synthesis of chiral polyaniline films via chemical vapor phase polymerization

    DEFF Research Database (Denmark)

    Chen, J.; Winther-Jensen, B.; Pornputtkul, Y.;

    2006-01-01

    Electrically and optically active polyaniline films doped with (1)-(-)-10- camphorsulfonic acid were successfully deposited on nonconductive substrates via chemical vapor phase polymerization. The above polyaniline/ R- camphorsulfonate films were characterized by electrochemical and physical...... and Raman spectrum, but also exhibited optical activity corresponding to the polymer chains as observed by circular dichroism spectra. (c) 2005 The Electrochemical Society....

  11. Total chemical synthesis of human proinsulin†‡

    OpenAIRE

    Luisier, Samuel; Avital-Shmilovici, Michal; Weiss, Michael A.; Kent, Stephen B H

    2010-01-01

    A convergent synthetic strategy based on modern chemical ligation methods was used to make human proinsulin. The synthetic protein was characterized by LCMS, CD spectroscopy, and by 1D- and 2D-NMR spectroscopy. Synthetic human proinsulin had full biochemical activity in a receptor-binding assay.

  12. Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

    Science.gov (United States)

    Swasey, Steven M.; Gwinn, Elisabeth G.

    2016-04-01

    The thermal and chemical fragility of DNA nanomaterials assembled by Watson–Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag+, as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag+–DNA nanostructures. Our studies of Ag+-induced assembly of non-complementary DNA oligomers employ strands of 2–24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag+ can be achieved by optimizing solution conditions. These Ag+-mediated duplexes are stable to at least 60 mM Mg2+, higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag+-mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag+-mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’.

  13. Capturing Biological Activity in Natural Product Fragments by Chemical Synthesis.

    Science.gov (United States)

    Crane, Erika A; Gademann, Karl

    2016-03-14

    Natural products have had an immense influence on science and have directly led to the introduction of many drugs. Organic chemistry, and its unique ability to tailor natural products through synthesis, provides an extraordinary approach to unlock the full potential of natural products. In this Review, an approach based on natural product derived fragments is presented that can successfully address some of the current challenges in drug discovery. These fragments often display significantly reduced molecular weights, reduced structural complexity, a reduced number of synthetic steps, while retaining or even improving key biological parameters such as potency or selectivity. Examples from various stages of the drug development process up to the clinic are presented. In addition, this process can be leveraged by recent developments such as genome mining, antibody-drug conjugates, and computational approaches. All these concepts have the potential to identify the next generation of drug candidates inspired by natural products.

  14. Studies on the Synthesis, Characterization, DNA Binding, Cytotoxicity and Antioxidant activity of 2-methyl-4-nitrophenylferrocene

    International Nuclear Information System (INIS)

    We report herein the synthesis, structural characterization, DNA binding, BamH1 digestion, cytotoxicity and antioxidant activity of 2-methyl-4-nitrophenylferrocene. Structural characterization is based on multinuclear (1H and 13C) NMR, FT-IR spectroscopy and elemental analysis. Interaction of 2-methyl-4-nitrophenylferrocene with pBR322 plasmid DNA shows noncovalent interactions however these noncovalent interactions reveal the prevention of BamH1 restriction site (g/ggtcc). In the voltammogram, a negative shift in peak potential has been observed on addition of increasing concentration of CT-DNA, which shows electrostatic interaction for 2-methyl-4-nitrophenylferro with negatively charged phosphate of DNA backbone. The binding ratio, binding constant, binding free energy and diffusion coefficient of free and bound drug were calculated to understand the mechanism. The high negative value of -delta G signifies the spontaneity and high conformational stability of 2-methyl-4-nitrophenylferro with CT-DNA. The compound has the ability to scavenge free radicals as have been revealed by DPPH findings. (author)

  15. Inhibition by 2-deoxy-D-ribose of DNA synthesis and growth in Raji cells

    International Nuclear Information System (INIS)

    When Raji cells were cultured for 3 days in serum-free medium, addition of 2-deoxy-D-ribose at the start of culture inhibited incorporation of [3H]thymidine and cell division. At deoxyribose concentrations between 1 and 5 mM, viability was 80% or greater after 3 days of culture even though 5 mM deoxyribose inhibited thymidine incorporation 95-99%. Inhibition by deoxyribose could be completely reversed if the culture medium was replaced with fresh medium up to 8 hr after the start of culture. The inhibition was specific for deoxyribose since other monosaccharides had no effect. Inhibition of DNA synthesis did not appear to be due to depletion of essential nutrients in the medium since the percentage inhibition of thymidine incorporation by cells cultured either in suboptimal serum-free media or in media supplemented with 0.025-5% human AB serum was similar. When DNA repair synthesis was measured as hydroxyurea-resistant thymidine incorporation, addition of deoxyribose to Raji cultures caused increased thymidine incorporation. These results, together with data from others,suggest that deoxyribose damages DNA

  16. Arsenic Trioxide Modulates DNA Synthesis and Apoptosis in Lung Carcinoma Cells

    Directory of Open Access Journals (Sweden)

    Kenneth Ndebele

    2010-04-01

    Full Text Available Arsenic trioxide, the trade name Trisenox, is a drug used to treat acute promyleocytic leukemia (APL. Studies have demonstrated that arsenic trioxide slows cancer cells growth. Although arsenic influences numerous signal-transduction pathways, cell-cycle progression, and/or apoptosis, its apoptotic mechanisms are complex and not entirely delineated. The primary objective of this research was to evaluate the effects of arsenic trioxide on DNA synthesis and to determine whether arsenic-induced apoptosis is mediated via caspase activation, p38 mitogen–activated protein kinase (MAPK, and cell cycle arrest. To achieve this goal, lung cancer cells (A549 were exposed to various concentrations (0, 2, 4, 6, 8, and 10 µg/mL of arsenic trioxide for 48 h. The effect of arsenic trioxide on DNA synthesis was determined by the [3H]thymidine incorporation assay. Apoptosis was determined by the caspase-3 fluorescein isothiocyanate (FITC assay, p38 MAP kinase activity was determined by an immunoblot assay, and cell-cycle analysis was evaluated by the propidium iodide assay. The [3H]thymidine-incorporation assay revealed a dose-related cytotoxic response at high levels of exposure. Furthermore, arsenic trioxide modulated caspase 3 activity and induced p38 MAP kinase activation in A549 cells. However, cell-cycle studies showed no statistically significant differences in DNA content at subG1 check point between control and arsenic trioxide treated cells.

  17. Chemical synthesis of erythropoietin glycoforms for insights into the relationship between glycosylation pattern and bioactivity.

    Science.gov (United States)

    Murakami, Masumi; Kiuchi, Tatsuto; Nishihara, Mika; Tezuka, Katsunari; Okamoto, Ryo; Izumi, Masayuki; Kajihara, Yasuhiro

    2016-01-01

    The role of sialyloligosaccharides on the surface of secreted glycoproteins is still unclear because of the difficulty in the preparation of sialylglycoproteins in a homogeneous form. We selected erythropoietin (EPO) as a target molecule and designed an efficient synthetic strategy for the chemical synthesis of a homogeneous form of five EPO glycoforms varying in glycosylation position and the number of human-type biantennary sialyloligosaccharides. A segment coupling strategy performed by native chemical ligation using six peptide segments including glycopeptides yielded homogeneous EPO glycopeptides, and folding experiments of these glycopeptides afforded the correctly folded EPO glycoforms. In an in vivo erythropoiesis assay in mice, all of the EPO glycoforms displayed biological activity, in particular the EPO bearing three sialyloligosaccharides, which exhibited the highest activity. Furthermore, we observed that the hydrophilicity and biological activity of the EPO glycoforms varied depending on the glycosylation pattern. This knowledge will pave the way for the development of homogeneous biologics by chemical synthesis.

  18. A Comparison between Chemical Synthesis Magnetite Nanoparticles and Biosynthesis Magnetite

    Directory of Open Access Journals (Sweden)

    Seyed Abolghasem Kahani

    2014-01-01

    Full Text Available The preparation of Fe3O4 from ferrous salt by air in alkaline aqueous solution at various temperatures was proposed. The synthetic magnetites have different particle size distributions. We studied the properties of the magnetite prepared by chemical methods compared with magnetotactic bacterial nanoparticles. The results show that crystallite size, morphology, and particle size distribution of chemically prepared magnetite at 293 K are similar to biosynthesis of magnetite. The new preparation of Fe3O4 helps to explain the mechanism of formation of magnetosomes in magnetotactic bacteria. The products are characterized by X-ray powder diffraction (XRD, infrared (IR spectra, vibrating sample magnetometry (VSM, and scanning electron microscopy (SEM.

  19. Assembly fabrication of linkers on glass surface and their effect on DNA synthesis and hybridization

    Institute of Scientific and Technical Information of China (English)

    ShenJiayao; XiaoPengfeng; HouPeng; JiMeiju; SunXiao; HeNongyue

    2003-01-01

    Linkers were assembled on a glass surface based on the hydrolysis and condensation of 3-glycidoxy-propyltrimethoxysilane (GPS). After the assembly of GPS, four approaches were tried to open the ending epoxide group of GPS or to further elongate the linkers. The effect of these approaches on DNA in situ synthesis and hybridization was investigated. For the spacing of the synthesis initiation sites, the wettability of the support and the length of the linking group that attaches the initiation site to the surface have direct influences on the yield of coupling reactions and the subsequent hybridization events. X-ray photoelectron spectroscopy (XPS) and mean contact angles of deionized water of the above slides were measured to assess the linker's characteristics in each procedure. It was proved that the glass slides were successfully modified and became excellent supports for the oligonucleotides synthesis. In addition, it proved best for the in situ oligonueleotides synthesis that a glass slide was in turn treated with ethylenediamine, glutaradehyde, ethanolamine and sodium borohydride solution at ambient temperature after silanized with GPS.

  20. Synthesis of Colloidal Ruthenium Nanocatalyst by Chemical Reduction Method

    OpenAIRE

    Patharkar, R. G.; S. U. Nandanwar; Chakraborty, M.

    2013-01-01

    Colloidal ruthenium nanoparticles were prepared by chemical reduction of ruthenium trichloride (RuCl3) using sodium borohydrate (NaBH4) as reducing agent and sodium dodecyl sulfate (SDS) as a stabilizer. Size and size distribution of synthesized colloidal Ru nanoparticles were studied by varying different parameters such as molar ratio (MR) of SDS/RuCl3, NaBH4/RuCl3, effects of different stabilizers, and reducing agents. Prepared nanoparticles were characterized by transmission electron micro...

  1. Synthesis, chemical modification, and surface assembly of carbon nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Amma, A.; St. Angelo, S.K.; Mallouk, T.E. [Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 (United States); Razavi, B.; Mayer, T.S. [Electrical Engineering, The Pennsylvania State University, University Park, PA 16802 (United States)

    2003-05-01

    Carbon nanotubules and nanowires were synthesized by pyrolysis of polymer precursors in the pores of alumina membranes. The nanowires were released by dissolving the membranes, and were then made hydrophobic or hydrophilic by chemical surface derivatization. These nanowires could be placed into lithographically defined wells on surfaces by means of electrostatic interactions with monolayers at the bottoms of the wells. (Abstract Copyright [2003], Wiley Periodicals, Inc.)

  2. Generation of synthesis gas for fuels and chemicals production

    OpenAIRE

    Tunå, Per

    2013-01-01

    Many scientists believe that the oil production will peak in the near future, if the peak has not already occurred. Peak oil theories and uncertain future oil deliveries have stimulated interest in alternative sources of fuel and chemicals. This interest has been enhanced by concerns about energy security and about the climate change caused by emissions of carbon dioxide. The result has been increased interest in substituting fossil fuels with renewable energy sources such as wind, solar and ...

  3. Green Chemical Synthesis of II-VI Semiconductor Quantum Dots

    OpenAIRE

    Shahid, Robina

    2012-01-01

    Nanotechnology is the science and technology of manipulating materials at atomic and molecular scale with properties different from bulk. Semiconductor QDs are important class of nanomaterials with unique physical and chemical properties owing to the quantum confinement effect. Size dependent optical properties make research on semiconductor QDs more attractive in the field of nanotechnology. Semiconductor QDs are usually composed of combination of elements from groups II–VI, III–V, or IV–VI ...

  4. Bioinspired greigite magnetic nanocrystals: chemical synthesis and biomedicine applications

    OpenAIRE

    Mei Feng; Yang Lu; Yuan Yang; Meng Zhang; Yun-Jun Xu; Huai-Ling Gao; Liang Dong; Wei-Ping Xu; Shu-Hong Yu

    2013-01-01

    Large scale greigite with uniform dimensions has stimulated significant demands for applications such as hyperthermia, photovoltaics, medicine and cell separation, etc. However, the inhomogeneity and hydrophobicity for most of the as prepared greigite crystals has limited their applications in biomedicine. Herein, we report a green chemical method utilizing β-cyclodextrin (β-CD) and polyethylene glycol (PEG) to synthesize bioinspired greigite (Fe3S4) magnetic nanocrystals (GMNCs) with similar...

  5. Nanostructured conjugated polymers in chemical sensors: synthesis, properties and applications.

    Science.gov (United States)

    Correa, D S; Medeiros, E S; Oliveira, J E; Paterno, L G; Mattoso, Luiz C

    2014-09-01

    Conjugated polymers are organic materials endowed with a π-electron conjugation along the polymer backbone that present appealing electrical and optical properties for technological applications. By using conjugated polymeric materials in the nanoscale, such properties can be further enhanced. In addition, the use of nanostructured materials makes possible miniaturize devices at the micro/nano scale. The applications of conjugated nanostructured polymers include sensors, actuators, flexible displays, discrete electronic devices, and smart fabric, to name a few. In particular, the use of conjugated polymers in chemical and biological sensors is made feasible owning to their sensitivity to the physicochemical conditions of its surrounding environment, such as chemical composition, pH, dielectric constant, humidity or even temperature. Subtle changes in these conditions bring about variations on the electrical (resistivity and capacitance), optical (absorptivity, luminescence, etc.), and mechanical properties of the conjugated polymer, which can be precisely measured by different experimental methods and ultimately associated with a specific analyte and its concentration. The present review article highlights the main features of conjugated polymers that make them suitable for chemical sensors. An especial emphasis is given to nanostructured sensors systems, which present high sensitivity and selectivity, and find application in beverage and food quality control, pharmaceutical industries, medical diagnosis, environmental monitoring, and homeland security, and other applications as discussed throughout this review.

  6. Plasma-chemical Synthesis and Regeneration of Catalysts for CH4 Steam Conversion

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    We carried out experimental studies concerning the plasma-chemical synthesis(PCS) of a catalyst for CH4 steam conversion and designed and built the equipment for PCS and/ or regeneration of spent catalyst for CH4 steam conversion. Under the conditions of an electric-arc low-temperature plasma (LTP), we studied the Ni-O-Al system and performed a comprehensive physicochemical analysis of the ultradispersed product obtained. It's the first time worldwide when the conditions of plasma-chemical synthesis and/ or regeneration of CH4 steam conversion catalysts under the conditions of electric-arc LTP are investigated depending on the plasma-chemical process (PCP) parameters and the plasma-chemical reactor (PCP) type (with CW-"cold walls" Tw = 500 K or WW-"warm walls" Tw = 1500 K), samples with a specific surface of 120 m2/g are obtained. Plasma-chemically synthesized and/ or regenerated samples have a homogenous chemical composition similar to that the Girdller (USA) conventional industrial catalyst. It is empirically established that the optimal temperature range in PCR for synthesis of samples with maximum dispersity is (2000 ~ 3000) K. Results from investigation on dynamics and kinetics of plasma-chemically synthesized and / or regenerated catalysts for CH4 steam conversion show that under LTP conditions premises for the formation of catalyst compositions are established. They are reduced 3 to 4 times faster than their industrial analogues. High specific surface of the samples, homogenous composition, high rate of active chemical surface formed by reduction, faulty crystal lattice of catalytically active phases and mostly high catalytic activity make them a potential competitor with their industrial analogues for their probable production in catalyst shops.

  7. DNA-Conjugated Organic Chromophores in DNA Stacking Interactions

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V.; Pedersen, Erik Bjerregaard

    2009-01-01

    Since the discovery of the intercalation of acridine derivatives into DNA (1961), chemists have synthesized many intercalators tethered to DNA. Advances in the chemical synthesis of modified nucleosides along with progress in oligonucleotide synthesis have made it possible to introduce organic...... review presents those efforts in the design of intercalators/organic chromophores as oligonucleotide conjugates that form a foundation for the generation of novel nucleic acid architectures...

  8. Assessment of DNA synthesis in Islet-1+ cells in the adult murine heart

    International Nuclear Information System (INIS)

    Highlights: • Islet-1 was expressed in the adult heart. • Islet-1-positive cells did not proliferate in the adult heart. • Sinoatrial node cells did not proliferate in the adult heart. - Abstract: Rationale: Islet-1 positive (Islet-1+) cardiac progenitor cells give rise to the right ventricle, atria and outflow tract during murine cardiac development. In the adult heart Islet-1 expression is limited to parasympathetic neurons, few cardiomyocytes, smooth muscle cells, within the proximal aorta and pulmonary artery and sinoatrial node cells. Its role in these cells is unknown. Here we tested the hypothesis that Islet-1+ cells retain proliferative activity and may therefore play a role in regenerating specialized regions in the heart. Methods and results: DNA synthesis was analyzed by the incorporation of tritiated thymidine (3H-thymidine) in Isl-1-nLacZ mice, a transgenic model with an insertion of a nuclear beta-galactosidase in the Islet-1 locus. Mice received daily injections of 3H-thymidine for 5 days. DNA synthesis was visualized throughout the heart by dipping autoradiography of cryosections. Colocalization of an nLacZ-signal and silver grains would indicate DNA synthesis in Islet-1+ cells. Whereas Islet− non-myocyte nuclei were regularly marked by accumulation of silver grains, colocalization with nLacZ-signals was not detected in >25,000 cells analyzed. Conclusions: Islet-1+ cells are quiescent in the adult heart, suggesting that, under normal conditions, even pacemaking cells do not proliferate at higher rates than normal cardiac myocytes

  9. Assessment of DNA synthesis in Islet-1{sup +} cells in the adult murine heart

    Energy Technology Data Exchange (ETDEWEB)

    Weinberger, Florian, E-mail: f.weinberger@uke.de; Mehrkens, Dennis, E-mail: dennis.mehrkens@uk-koeln.de; Starbatty, Jutta, E-mail: starbatty@uke.uni-hamburg.de; Nicol, Philipp, E-mail: Philipp.Nicol@gmx.de; Eschenhagen, Thomas, E-mail: t.eschenhagen@uke.de

    2015-01-02

    Highlights: • Islet-1 was expressed in the adult heart. • Islet-1-positive cells did not proliferate in the adult heart. • Sinoatrial node cells did not proliferate in the adult heart. - Abstract: Rationale: Islet-1 positive (Islet-1{sup +}) cardiac progenitor cells give rise to the right ventricle, atria and outflow tract during murine cardiac development. In the adult heart Islet-1 expression is limited to parasympathetic neurons, few cardiomyocytes, smooth muscle cells, within the proximal aorta and pulmonary artery and sinoatrial node cells. Its role in these cells is unknown. Here we tested the hypothesis that Islet-1{sup +} cells retain proliferative activity and may therefore play a role in regenerating specialized regions in the heart. Methods and results: DNA synthesis was analyzed by the incorporation of tritiated thymidine ({sup 3}H-thymidine) in Isl-1-nLacZ mice, a transgenic model with an insertion of a nuclear beta-galactosidase in the Islet-1 locus. Mice received daily injections of {sup 3}H-thymidine for 5 days. DNA synthesis was visualized throughout the heart by dipping autoradiography of cryosections. Colocalization of an nLacZ-signal and silver grains would indicate DNA synthesis in Islet-1{sup +} cells. Whereas Islet{sup −} non-myocyte nuclei were regularly marked by accumulation of silver grains, colocalization with nLacZ-signals was not detected in >25,000 cells analyzed. Conclusions: Islet-1{sup +} cells are quiescent in the adult heart, suggesting that, under normal conditions, even pacemaking cells do not proliferate at higher rates than normal cardiac myocytes.

  10. Advances in chemical synthesis and application of metal-metalloid amorphous alloy nanoparticulate catalysts

    Institute of Scientific and Technical Information of China (English)

    WU Zhijie; LI Wei; ZHANG Minghui; TAO Keyi

    2007-01-01

    This paper reviews the advances in the chemical synthesis and application of metal-metalloid amorphous alloy nanoparticles consisting of transition metal (M) and metalloid elements (B,P).After a brief introduction on the history of amorphous alloy catalysts,the paper focuses on the properties and characterization of amorphous alloy catalysts,and recent developments in the solution-phase synthesis of amorphous alloy nanoparticles.This paper further outlines the applications of amorphous alloys,with special emphasis on the problems and strategies for the application of amorphous alloy nanoparticles in catalytic reactions.

  11. Micro-chemical synthesis of molecular probes on an electronic microfluidic device

    OpenAIRE

    Keng, Pei Yuin; Chen, Supin; Ding, Huijiang; Sadeghi, Saman; Shah, Gaurav J.; Dooraghi, Alex; Michael E. Phelps; Satyamurthy, Nagichettiar; Chatziioannou, Arion F; Kim, Chang-Jin “CJ”; van Dam, R. Michael

    2011-01-01

    We have developed an all-electronic digital microfluidic device for microscale chemical synthesis in organic solvents, operated by electrowetting-on-dielectric (EWOD). As an example of the principles, we demonstrate the multistep synthesis of [18F]FDG, the most common radiotracer for positron emission tomography (PET), with high and reliable radio-fluorination efficiency of [18F]FTAG (88 ± 7%, n = 11) and quantitative hydrolysis to [18F]FDG (> 95%, n = 11). We furthermore show that batches of...

  12. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS. FINAL QUARTERLY STATUS REPORT

    Energy Technology Data Exchange (ETDEWEB)

    None

    1999-04-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  13. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS. FINAL QUARTERLY STATUS REPORT NO. 10

    Energy Technology Data Exchange (ETDEWEB)

    None

    1998-11-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  14. Alternative fuels and chemicals from synthesis gas. Fourth quarterly report, 1994

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-10-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE`s LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  15. Synthesis and analysis in studies of chemical evolution

    Science.gov (United States)

    Ponnamperuma, C.; Hobish, M. K.; Kobayashi, K.; Hua, L. L.; Senaratne, N.

    1986-01-01

    Studies of the various processes that may have given rise to life on the Earth have demonstrated the appropriateness of an approach that makes use of analysis and synthesis. Analysis of extraterrestrial samples in the form of meteorites has demonstrated the presence of several precursors of biomolecules, most notably a full suite of nucleic acid bases and nucleotides of biological significance. These species were determined after exhaustive extraction of the sample and subsequent analysis using HPLC, GC, MS, and GC-MS. Procedural blanks indicate that these molecules are likely not the result of contamination during the extraction and analysis process. Similar species were found as products of spark discharge experiments in atmospheres thought to mimic primitive Earth conditions. These results indicate that the basic chemistry underlying these syntheses is common, and that life may not be unique to the Earth. Studies underway in the laboratory make use of proton nuclear magnetic resonance spectroscopy as a probe to assess associations between selected amino acids and any of several nucleotides comprising their genetic code and genetic anticode sequences. These studies demonstrate a clear selectivity by the anticode sequences, thus confirming the hydrophobicity studies performed by Lacey et al. These studies further support the contention that life is likely a natural result of the physics and chemistry of the universe.

  16. Determination of radioinduced delay in DNA synthesis in two-garlic-clones cells (Allium Sativum L.)

    International Nuclear Information System (INIS)

    To contribute to tech improvement of the use of ionizing radiations as an auxiliary tool in the fitoimprovement, dose-effect curves for the 'Martinez' and 'Sancti Spiritus-3' clones were stablished by using as effect the delay induced by radiations in DNA synthesis determined by the 'Martinez' clone which induces a delay of 50% in reference to the control is approximately 11 Gy, while the dose value for the 'Sancti Spiritus-3' clone is 18 Gy, thus the 'Martinez' clones has a higher sensitivity to radiations than the other clone, therefore it coincides with what we found for these clones other indexes are used as radiosensitivity criteria

  17. AlkB recognition of a bulky DNA base adduct stabilized by chemical cross-linking

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    E.coli AlkB is a direct DNA/RNA repair protein that oxidatively reverses N1 alkylated purines and N3 alkylated pyrimidines to regular bases.Previous crystal structures have revealed N1-methyl adenine(1-meA) recognition by AlkB and a unique base flipping mechanism,but how the AlkB active site can accommodate bulky base adducts is largely unknown.Employing a previously developed chemical cross-linking technique,we crystallized AlkB with a duplex DNA containing a caged thymine base(cagedT).The structure revealed a flexible hairpin lid and a reorganized substrate recognition loop used by AlkB to accommodate cagedT.These observations demonstrate,at the molecular level,how bulky DNA adducts may be recognized and processed by AlkB.

  18. Fabrication of polyurethane molecular stamps for the synthesis of DNA microarray

    Science.gov (United States)

    Liu, Zhengchun; He, Quanguo; Xiao, Pengfeng; He, Nongyao; Lu, Zuhong; Bo, Liang

    2001-10-01

    Polyurethane based on polypropylene glycol (PPG) and Toluene diisocyanate (TDI) using 3,3'-dichloride-4,4'- methylenedianiline (MOCA) as the crosslinker is presented for the first time to fabricate molecular stamps (PU stamps) for the synthesis of DNA microarray with contact procedure. The predictability of the process is achieved by utilizing commercially available starting materials. SEM analysis of the morphology of PU stamps and master showed that PU elastometer could replicate subtly the motherboard's patterns with high fidelity. It was proved from the contact angle measurement that PU stamps surface has good affinity with acetonitrile, which guarantee the well-distribution of DNA monomers on patterned stamps. Laser confocal fluorescence microscopy images of oligonucleotide arrays confirmed polyurethane is an excellent material for molecular stamps.

  19. Estimations of the DNA Synthesis Rate of Bone Marrow Cells after Administration of Labelled Thymidine In Vitro

    International Nuclear Information System (INIS)

    Bone marrow cells are incubated with labelled thymidine under varying in vitro conditions. The incorporation rate of labelled thymidine into DNA is influenced by the condition and duration of. the in vitro incubation. Similar influences operate on the pool size of labelled thymidine phosphates. Up to concentrations of 10-6 M thymidine in the incubation medium there is a linear relation of thymidine concentration and thymidine incorporation into DNA. Concentrations of thymidine exceeding 10-6 M lead to increasing inhibition of the thymidine kinase. The endogenous formation of thymidylate cannot be inhibited entirely by exogenous thymidine supply. Consequently, determinations of the DNA synthesis rate from the incorporated amount of labelled thymidine have to be corrected for the respective endogenous thymidylate contribution. A better procedure is to block the formation of endogenous thymidylate by means of amethopterin. Standard conditions are described, under which an undisturbed synthesis of DNA thymine from exogenous thymidine only takes place. Determinations can be performed by means of autoradiographic or biochemical techniques. By application of the semi-automatic grain counting technique, after sufficient autoradiographic standardization, evaluations of DNA synthesis rates and DNA synthesis times of different cell types in the bone marrow become practicable. (author)

  20. DNA-Based Identification and Chemical Characteristics of Hypnea musciformis from Coastal Sites in Ghana

    OpenAIRE

    Marcel Tutor Ale; Kristian Barrett; Gloria Naa Dzama Addico; Nanna Rhein-Knudsen; Amoako Atta deGraft-Johnson; Meyer, Anne S.

    2016-01-01

    This work reveals new, important insights about the influence of broad spatial variations on the phylogenetic relationship and chemical characteristics of Ghanaian Hypnea musciformis—a carrageenan-containing red seaweed. DNA barcoding techniques alleviate the difficulty for accurate morphological identification. COI barcode sequences of the Ghanaian H. musciformis showed <0.7% intraspecies divergence, indicating no distinct phylogenetic variation, suggesting that they actually belong to th...

  1. Microwave-irradiation-assisted hybrid chemical approach for titanium dioxide nanoparticle synthesis: microbial and cytotoxicological evaluation.

    Science.gov (United States)

    Ranjan, Shivendu; Dasgupta, Nandita; Rajendran, Bhavapriya; Avadhani, Ganesh S; Ramalingam, Chidambaram; Kumar, Ashutosh

    2016-06-01

    Titanium dioxide nanoparticles (TNPs) are widely used in the pharmaceutical and cosmetics industries. It is used for protection against UV exposure due to its light-scattering properties and high refractive index. Though TNPs are increasingly used, the synthesis of TNPs is tedious and time consuming; therefore, in the present study, microwave-assisted hybrid chemical approach was used for TNP synthesis. In the present study, we demonstrated that TNPs can be synthesized only in 2.5 h; however, the commonly used chemical approach using muffle furnace takes 5 h. The activity of TNP depends on the synthetic protocol; therefore, the present study also determined the effect of microwave-assisted hybrid chemical approach synthetic protocol on microbial and cytotoxicity. The results showed that TNP has the best antibacterial activity in decreasing order from Escherichia coli, Bacillus subtilis, and Staphylococcus aureus. The IC50 values of TNP for HCT116 and A549 were found to be 6.43 and 6.04 ppm, respectively. Cell death was also confirmed from trypan blue exclusion assay and membrane integrity loss was observed. Therefore, the study determines that the microwave-assisted hybrid chemical approach is time-saving; hence, this technique can be upgraded from lab scale to industrial scale via pilot plant scale. Moreover, it is necessary to find the mechanism of action at the molecular level to establish the reason for greater bacterial and cytotoxicological toxicity. Graphical abstract A graphical representation of TNP synthesis.

  2. Microwave-irradiation-assisted hybrid chemical approach for titanium dioxide nanoparticle synthesis: microbial and cytotoxicological evaluation.

    Science.gov (United States)

    Ranjan, Shivendu; Dasgupta, Nandita; Rajendran, Bhavapriya; Avadhani, Ganesh S; Ramalingam, Chidambaram; Kumar, Ashutosh

    2016-06-01

    Titanium dioxide nanoparticles (TNPs) are widely used in the pharmaceutical and cosmetics industries. It is used for protection against UV exposure due to its light-scattering properties and high refractive index. Though TNPs are increasingly used, the synthesis of TNPs is tedious and time consuming; therefore, in the present study, microwave-assisted hybrid chemical approach was used for TNP synthesis. In the present study, we demonstrated that TNPs can be synthesized only in 2.5 h; however, the commonly used chemical approach using muffle furnace takes 5 h. The activity of TNP depends on the synthetic protocol; therefore, the present study also determined the effect of microwave-assisted hybrid chemical approach synthetic protocol on microbial and cytotoxicity. The results showed that TNP has the best antibacterial activity in decreasing order from Escherichia coli, Bacillus subtilis, and Staphylococcus aureus. The IC50 values of TNP for HCT116 and A549 were found to be 6.43 and 6.04 ppm, respectively. Cell death was also confirmed from trypan blue exclusion assay and membrane integrity loss was observed. Therefore, the study determines that the microwave-assisted hybrid chemical approach is time-saving; hence, this technique can be upgraded from lab scale to industrial scale via pilot plant scale. Moreover, it is necessary to find the mechanism of action at the molecular level to establish the reason for greater bacterial and cytotoxicological toxicity. Graphical abstract A graphical representation of TNP synthesis. PMID:26976013

  3. Protein synthesis by native chemical ligation: expanded scope by using straightforward methodology.

    Science.gov (United States)

    Hackeng, T M; Griffin, J H; Dawson, P E

    1999-08-31

    The total chemical synthesis of proteins has great potential for increasing our understanding of the molecular basis of protein function. The introduction of native chemical ligation techniques to join unprotected peptides next to a cysteine residue has greatly facilitated the synthesis of proteins of moderate size. Here, we describe a straightforward methodology that has enabled us to rapidly analyze the compatibility of the native chemical ligation strategy for X-Cys ligation sites, where X is any of the 20 naturally occurring amino acids. The simplified methodology avoids the necessity of specific amino acid thioester linkers or alkylation of C-terminal thioacid peptides. Experiments using matrix-assisted laser-desorption ionization MS analysis of combinatorial ligations of LYRAX-C-terminal thioester peptides to the peptide CRANK show that all 20 amino acids are suitable for ligation, with Val, Ile, and Pro representing less favorable choices because of slow ligation rates. To illustrate the method's utility, two 124-aa proteins were manually synthesized by using a three-step, four-piece ligation to yield a fully active human secretory phospholipase A(2) and a catalytically inactive analog. The combination of flexibility in design with general access because of simplified methodology broadens the applicability and versatility of chemical protein synthesis. PMID:10468563

  4. Use of Modern Chemical Protein Synthesis and Advanced Fluorescent Assay Techniques to Experimentally Validate the Functional Annotation of Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kent, Stephen [University of Chicago

    2012-07-20

    The objective of this research program was to prototype methods for the chemical synthesis of predicted protein molecules in annotated microbial genomes. High throughput chemical methods were to be used to make large numbers of predicted proteins and protein domains, based on microbial genome sequences. Microscale chemical synthesis methods for the parallel preparation of peptide-thioester building blocks were developed; these peptide segments are used for the parallel chemical synthesis of proteins and protein domains. Ultimately, it is envisaged that these synthetic molecules would be ‘printed’ in spatially addressable arrays. The unique ability of total synthesis to precision label protein molecules with dyes and with chemical or biochemical ‘tags’ can be used to facilitate novel assay technologies adapted from state-of-the art single molecule fluorescence detection techniques. In the future, in conjunction with modern laboratory automation this integrated set of techniques will enable high throughput experimental validation of the functional annotation of microbial genomes.

  5. Synthesis and crystal chemical evolution of fresnoite powders

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Chui L., E-mail: wong0233@e.ntu.edu.sg [School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore); Madhavi, S. [School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore); Phonthammachai, N. [Institute of Materials Science and Engineering, 3 Research Link, Singapore 117602 (Singapore); White, Timothy J., E-mail: tjwhite@ntu.edu.sg [School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore); Centre for Advanced Microscopy, Australian National University, RN Robertson Building, Sullivan' s Creek Road, Canberra, 0200 ACT (Australia)

    2012-03-15

    (Ba,Sr){sub 2}TiSi{sub 2}O{sub 8} fresnoite powders were prepared via a Pechini process in which citric acid and ethylene glycol were used as complexing agents. The resulting gel contained a homogeneous distribution of the metal ions that suppressed the formation of (Ba,Sr)TiO{sub 3} perovskite as a secondary phase during calcination. Phase development was examined as by isochronal and isothermal reaction analysis. A combination of thermo- and differential gravimetric analysis (TGA-DGA), quantitative X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) confirmed that calcination at 900 Degree-Sign C/12 h yielded finely crystalline ({approx}70 nm) Ba{sub 2}TiSi{sub 2}O{sub 8} (BTS) and Sr{sub 2}TiSi{sub 2}O{sub 8} (STS). The endmembers and compositional intermediates crystallized directly from the Pechini resin and indirectly through reaction of (Ba,Sr)CO{sub 3}, (Ba,Sr)TiO{sub 3} and a silica-rich glass intermediates. This new method for preparing fresnoite yields materials suitable for consolidation as dense monolithic dielectrics or for use as high surface area catalytic powders. - Graphical abstract: The Pechini synthesis of (Ba, Sr){sub 2}TiSi{sub 2}O{sub 8} titano-silicate fresnoites delivers finely divided precursors for applications as diverse as solid electrolytes and photocatalysis that exploit the unique Ti-O and Si-O bonding and structural morphology of these materials. Highlights: Black-Right-Pointing-Pointer A Pechini method for synthesizing (Ba,Sr){sub 2}TiSi{sub 2}O{sub 8} fresnoites is demonstrated. Black-Right-Pointing-Pointer The method minimizes a persistent glassy intermediate phase. Black-Right-Pointing-Pointer The Pechini process is generally applicable for tailoring fresnoites as functional materials.

  6. Wet chemical synthesis of quantum dots for medical applications

    Science.gov (United States)

    Cepeda-Pérez, E. I.; López-Luke, T.; Pérez-Mayen, L.; Hidalgo, Alberto; de la Rosa, E.; Torres-Castro, Alejandro; Ceja-Fdez, Andrea; Vivero-Escoto, Juan; Gonzalez-Yebra, Ana L.

    2015-07-01

    In recent years the use of nanoparticles in medical applications has boomed. This is because the various applications that provide these materials like drug delivery, cancer cell diagnostics and therapeutics [1-5]. Biomedical applications of Quantum Dots (QDs) are focused on molecular imaging and biological sensing due to its optical properties. The size of QDs can be continuously tuned from 2 to 10 nm in diameter, which, after polymer encapsulation, generally increases to 5 - 20 nm diminishing the toxicity. The QDs prepared in our lab have a diameter between 2 to 7 nm. Particles smaller than 5 nm can interact with the cells [2]. Some of the characteristics that distinguish QDs from the commonly used fluorophores are wider range of emission, narrow and more sharply defined emission peak, brighter emission and a higher signal to noise ratio compared with organic dyes [6]. In this paper we will show our progress in the study of the interaction of quantum dots in live cells for image and Raman spectroscopy applications. We will also show the results of the interaction of quantum dots with genomic DNA for diagnostic purposes.

  7. Stability of the human polymerase δ holoenzyme and its implications in lagging strand DNA synthesis.

    Science.gov (United States)

    Hedglin, Mark; Pandey, Binod; Benkovic, Stephen J

    2016-03-29

    In eukaryotes, DNA polymerase δ (pol δ) is responsible for replicating the lagging strand template and anchors to the proliferating cell nuclear antigen (PCNA) sliding clamp to form a holoenzyme. The stability of this complex is integral to every aspect of lagging strand replication. Most of our understanding comes from Saccharomyces cerevisae where the extreme stability of the pol δ holoenzyme ensures that every nucleobase within an Okazaki fragment is faithfully duplicated before dissociation but also necessitates an active displacement mechanism for polymerase recycling and exchange. However, the stability of the human pol δ holoenzyme is unknown. We designed unique kinetic assays to analyze the processivity and stability of the pol δ holoenzyme. Surprisingly, the results indicate that human pol δ maintains a loose association with PCNA while replicating DNA. Such behavior has profound implications on Okazaki fragment synthesis in humans as it limits the processivity of pol δ on undamaged DNA and promotes the rapid dissociation of pol δ from PCNA on stalling at a DNA lesion.

  8. Synthesis of Colloidal Ruthenium Nanocatalyst by Chemical Reduction Method

    Directory of Open Access Journals (Sweden)

    R. G. Patharkar

    2013-01-01

    Full Text Available Colloidal ruthenium nanoparticles were prepared by chemical reduction of ruthenium trichloride (RuCl3 using sodium borohydrate (NaBH4 as reducing agent and sodium dodecyl sulfate (SDS as a stabilizer. Size and size distribution of synthesized colloidal Ru nanoparticles were studied by varying different parameters such as molar ratio (MR of SDS/RuCl3, NaBH4/RuCl3, effects of different stabilizers, and reducing agents. Prepared nanoparticles were characterized by transmission electron microscope (TEM and dynamic light scattering (DLS. Stability of colloidal nanoparticles was detected by Turbiscan. Stable Ru nanoparticles were dispersed on γ-Al2O3 to prepare Ru/γ-Al2O3 catalyst. This catalyst was characterized by X-ray Diffraction (XRD and transmission electron microscope (TEM.

  9. Synthesis of Aligned Carbon Nanotubes by Thermal Chemical Vapor Deposition

    Institute of Scientific and Technical Information of China (English)

    LI Gang; ZHOU Ming; MA Weiwei; CAI Lan

    2009-01-01

    Single crystal silicon was found to be very beneficial to the growth of aligned carbon nanotubes by chemical vapor deposition with C2H2 as carbon source. A thin film of Ni served as catalyst was deposited on the Si substrate by the K575X Peltier Cooled High Resolution Sputter Coater before growth. The growth properties of carbon nanotubes were studied as a function of the Ni catalyst layer thickness. The diameter, growth rate and areal density of the carbon nanotubes were controlled by the initial thickness of the catalyst layer. Steric hindrance between nanotubes forces them to grow in well-aligned manner at an initial stage of growth. Transmission electron microscope analysis revealed that nanotubes grew by a tip growth mechanism.

  10. Accelerated Chemical Reactions and Organic Synthesis in Leidenfrost Droplets.

    Science.gov (United States)

    Bain, Ryan M; Pulliam, Christopher J; Thery, Fabien; Cooks, R Graham

    2016-08-22

    Leidenfrost levitated droplets can be used to accelerate chemical reactions in processes that appear similar to reaction acceleration in charged microdroplets produced by electrospray ionization. Reaction acceleration in Leidenfrost droplets is demonstrated for a base-catalyzed Claisen-Schmidt condensation, hydrazone formation from precharged and neutral ketones, and for the Katritzky pyrylium into pyridinium conversion under various reaction conditions. Comparisons with bulk reactions gave intermediate acceleration factors (2-50). By keeping the volume of the Leidenfrost droplets constant, it was shown that interfacial effects contribute to acceleration; this was confirmed by decreased reaction rates in the presence of a surfactant. The ability to multiplex Leidenfrost microreactors, to extract product into an immiscible solvent during reaction, and to use Leidenfrost droplets as reaction vessels to synthesize milligram quantities of product is also demonstrated.

  11. Synthesis of mullite coatings by chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Mulpuri, R.P.; Auger, M.; Sarin, V.K. [Boston Univ., MA (United States)

    1996-08-01

    Formation of mullite on ceramic substrates via chemical vapor deposition was investigated. Mullite is a solid solution of Al{sub 2}O{sub 3} and SiO{sub 2} with a composition of 3Al{sub 2}O{sub 3}{circ}2SiO{sub 2}. Thermodynamic calculations performed on the AlCl{sub 3}-SiCl{sub 4}-CO{sub 2}-H{sub 2} system were used to construct equilibrium CVD phase diagrams. With the aid of these diagrams and consideration of kinetic rate limiting factors, initial process parameters were determined. Through process optimization, crystalline CVD mullite coatings have been successfully grown on SiC and Si{sub 3}N{sub 4} substrates. Results from the thermodynamic analysis, process optimization, and effect of various process parameters on deposition rate and coating morphology are discussed.

  12. Alternative fuels and chemicals from synthesis gas. Quarterly report, April 1--June 30, 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE`s LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts. The paper reports the progress on the following tasks: engineering and modifications: AFDU shakedown, operations, deactivation and disposal; and research and development on new processes for DME, chemistry and catalyst development, and oxygenates via synthesis gas.

  13. EFFECT OF ASCORBIC ACID ON DNA SYNTHESIS, INTRACELLULAR ACCUMULATION OF ADM AND ADM RESISTANCE OF TUMOR CELL LINES

    Institute of Scientific and Technical Information of China (English)

    Xie Zuofu; Lin Xiandong; Zhou Dongmei; Lin Sheng

    1998-01-01

    Objective: To determine the effect of ascorbic acid (AA) on DNA synthesis, intracellular accumulation of ADM and ADM resistance of tumor cell lines.Methods: K562, K562/ADM and KB cell lines were used to study the effect of ascorbic acid on DNA synthesis,intracellular accumulation of ADM and ADM resistance by fluid scintillometry, MTT method, spectrofluorophotometry and immunocytochemistry. Results: Results showed that AA was capable of inhibiting DNA synthesis of K562 and K562/ADM in a dose-dependence fashion,but not KB cell line, and significantly reducing ADM sensitivity in K562 and KB cell lines, as well as potentiating obviously ADM resistance in K562/ADM cell line. Conclusion: These effects of AA may be closely correlated with significant elevation of intracellular accumulation of ADM in KB cell line, and significant reduction of that in K562 and K562/ADM cell lines but possibly not correlated with the expression of Pglycoprotein.

  14. DNA hybridization as a guide to phylogeny: chemical and physical limits.

    Science.gov (United States)

    Schmid, C W; Marks, J

    1990-03-01

    The technique of forming interspecific DNA heteroduplexes and estimating phylogenetic distances from the depression in their duplex melting temperature has several physical and chemical constraints. These constraints determine the maximum phylogenetic distance that may be estimated by this technique and the most appropriate method of analyzing that distance. Melting curves of self-renatured single copy primate DNAs reveal the presence of components absent from the renaturation products of exactly paired sequences. This observation, which confirms existing literature, challenges a fundamental assumption: that orthologous (i.e., corresponding) DNA sequences in the divergent species are being compared in DNA heteroduplex melting experiments. As a model system, the thermal stabilities of heteroduplexes formed between a human alpha-globin cDNA and four alpha-like globin genes isolated from chimpanzee are qualitatively compared. The results of this comparison show that the cross-hybrids of imperfectly matched gene duplicates from divergent species can contribute to the additional components that are present in renatured single copy DNAs. Single copy DNA, as usually defined, includes sequence duplicates that will obscure phylogenetic comparisons in a mass hybridization of genomes. PMID:2109086

  15. Error-prone translesion synthesis past DNA-peptide cross-links conjugated to the major groove of DNA via C5 of thymidine.

    Science.gov (United States)

    Wickramaratne, Susith; Boldry, Emily J; Buehler, Charles; Wang, Yen-Chih; Distefano, Mark D; Tretyakova, Natalia Y

    2015-01-01

    DNA-protein cross-links (DPCs) are exceptionally bulky, structurally diverse DNA adducts formed in cells upon exposure to endogenous and exogenous bis-electrophiles, reactive oxygen species, and ionizing radiation. If not repaired, DPCs can induce toxicity and mutations. It has been proposed that the protein component of a DPC is proteolytically degraded, giving rise to smaller DNA-peptide conjugates, which can be subject to nucleotide excision repair and replication bypass. In this study, polymerase bypass of model DNA-peptide conjugates structurally analogous to the lesions induced by reactive oxygen species and DNA methyltransferase inhibitors was examined. DNA oligomers containing site-specific DNA-peptide conjugates were generated by copper-catalyzed [3 + 2] Huisgen cyclo-addition between an alkyne-functionalized C5-thymidine in DNA and an azide-containing 10-mer peptide. The resulting DNA-peptide conjugates were subjected to steady-state kinetic experiments in the presence of recombinant human lesion bypass polymerases κ and η, followed by PAGE-based assays to determine the catalytic efficiency and the misinsertion frequency opposite the lesion. We found that human polymerase κ and η can incorporate A, G, C, or T opposite the C5-dT-conjugated DNA-peptide conjugates, whereas human polymerase η preferentially inserts G opposite the lesion. Furthermore, HPLC-ESI(-)-MS/MS sequencing of the extension products has revealed that post-lesion synthesis was highly error-prone, resulting in mutations opposite the adducted site or at the +1 position from the adduct and multiple deletions. Collectively, our results indicate that replication bypass of peptides conjugated to the C5 position of thymine by human translesion synthesis polymerases leads to large numbers of base substitution and frameshift mutations.

  16. Effect of different BNCT protocols on DNA synthesis in precancerous and normal tissues in an experimental model of oral cancer

    International Nuclear Information System (INIS)

    We previously reported the therapeutic success of different BNCT protocols in the treatment of oral cancer, employing the hamster cheek pouch model. The aim of the present study was to evaluate the effect of these BNCT protocols on DNA synthesis in precancerous and normal tissue in this model and assess the potential lag in the development of second primary tumors in precancerous tissue. The data are relevant to potential control of field cancerized tissue and tolerance of normal tissue. We evaluated DNA synthesis in precancerous and normal pouch tissue 1-30 days post-BNCT mediated by BPA, GB-10 or BPA + GB-10 employing incorporation of bromo-deoxyuridine as an end-point. The BNCT-induced potential lag in the development of second primary tumors in precancerous tissue was monitored. A drastic, statistically significant reduction in DNA synthesis occurred in pacancerous tissue as early as 1 day post-BNCT and was sustained at virtually all time points until 30 days post-BNCT for all protocols. The histological categories evaluated individually within precancerous tissue (dysplasia, hyperplasia and NUMF [no unusual microscopic features]) responded similarly. DNA synthesis in normal tissue treated with BNCT oscillated around the very low pre-treatment values. A BNCT-induced lag in the development of second primary tumors was observed. BNCT induced a drastic fall in DNA synthesis in precancerous tissue that would be associated to the observed lag in the development of second primary tumors. The minimum variations in DNA synthesis in BNCT-treated normal tissue would correlate with the absence of normal tissue radiotoxicity. The present data would contribute to optimize therapeutic efficacy in the treatment of field-cancerized areas. (author)

  17. Synthesis and chemical modification of carbon nanostructures for materials applications

    Science.gov (United States)

    Higginbotham, Amanda Lynn

    This dissertation explores the structure, chemical reactivities, electromagnetic response, and materials properties of various carbon nanostructures, including single-walled carbon nanotubes (SWCNTs), multi-walled carbon nanotubes (MWCNTs), graphite, and graphene nanoribbons (GNRs). Efficient production and modification of these unique structures, each with their own distinct properties, will make them more accessible for applications in electronics, materials, and biology. A method is reported for controlling the permittivity from 1--1000 MHz of SWCNT-polymer composites (0.5 wt%) for radio frequency applications including passive RF antenna structures and EMI shielding. The magnitude of the real permittivity varied between 20 and 3.3, decreasing as higher fractions of functionalized-SWCNTs were added. The microwave absorbing properties and subsequent heating of carbon nanotubes were used to rapidly cure ceramic composites. With less than 1 wt% carbon nanotube additives and 30--40 W of directed microwave power (2.45 GHz), bulk composite samples reached temperatures above 500°C within 1 min. Graphite oxide (GO) polymer nanocomposites were developed at 1, 5, and 10 wt% for the purpose of evaluating the flammability reduction and materials properties of the resulting systems. Microscale oxygen consumption calorimetry revealed that addition of GO reduced the total heat release in all systems, and GO-polycarbonate composites demonstrated very fast self-extinguishing times in vertical open flame tests. A simple solution-based oxidative process using potassium permanganate in sulfuric acid was developed for producing nearly 100% yield of graphene nanoribbons (GNRs) by lengthwise cutting and unraveling of MWCNT sidewalls. Subsequent chemical reduction of the GNRs resulted in restoration of electrical conductivity. The GNR synthetic conditions were investigated in further depth, and an improved method which utilized a two-acid reaction medium was found to produce GNRs with

  18. Alternate fuels and chemicals from synthesis gas: Vinyl acetate monomer. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Richard D. Colberg; Nick A. Collins; Edwin F. Holcombe; Gerald C. Tustin; Joseph R. Zoeller

    1999-01-01

    There has been a long-standing desire on the part of industry and the U.S. Department of Energy to replace the existing ethylene-based vinyl acetate monomer (VAM) process with an entirely synthesis gas-based process. Although there are a large number of process options for the conversion of synthesis gas to VAM, Eastman Chemical Company undertook an analytical approach, based on known chemical and economic principles, to reduce the potential candidate processes to a select group of eight processes. The critical technologies that would be required for these routes were: (1) the esterification of acetaldehyde (AcH) with ketene to generate VAM, (2) the hydrogenation of ketene to acetaldehyde, (3) the hydrogenation of acetic acid to acetaldehyde, and (4) the reductive carbonylation of methanol to acetaldehyde. This report describes the selection process for the candidate processes, the successful development of the key technologies, and the economic assessments for the preferred routes. In addition, improvements in the conversion of acetic anhydride and acetaldehyde to VAM are discussed. The conclusion from this study is that, with the technology developed in this study, VAM may be produced from synthesis gas, but the cost of production is about 15% higher than the conventional oxidative acetoxylation of ethylene, primarily due to higher capital associated with the synthesis gas-based processes.

  19. Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

    Science.gov (United States)

    Whitesides, George M.; Mathias, John P.; Seto, Christopher T.

    1991-12-01

    Molecular self assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by non-covalent bonds. Molecular self-assembly is ubiquitous in biological systems, and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated non-covalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating non-biological structures having dimensions of 1-10(exp 2) nanometers. Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

  20. Chemical vs. biotechnological synthesis of C13-apocarotenoids: current methods, applications and perspectives.

    Science.gov (United States)

    Cataldo, Vicente F; López, Javiera; Cárcamo, Martín; Agosin, Eduardo

    2016-07-01

    Apocarotenoids are natural compounds derived from the oxidative cleavage of carotenoids. Particularly, C13-apocarotenoids are volatile compounds that contribute to the aromas of different flowers and fruits and are highly valued by the Flavor and Fragrance industry. So far, the chemical synthesis of these terpenoids has dominated the industry. Nonetheless, the increasing consumer demand for more natural and sustainable processes raises an interesting opportunity for bio-production alternatives. In this regard, enzymatic biocatalysis and metabolically engineered microorganisms emerge as attractive biotechnological options. The present review summarizes promising bioengineering approaches with regard to chemical production methods for the synthesis of two families of C13-apocarotenoids: ionones/dihydroionones and damascones/damascenone. We discuss each method and its applicability, with a thorough comparative analysis for ionones, focusing on the production process, regulatory aspects, and sustainability. PMID:27154347

  1. The impact of the chemical synthesis on the magnetic properties of intermetallic PdFe nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Castellanos-Rubio, I.; Insausti, M.; Muro, I. Gil de [Universidad del País Vasco, UPV/EHU, Dpto. de Química Inorgánica (Spain); Arias-Duque, D. Carolina; Hernández-Garrido, Juan Carlos [Universidad de Cadiz, Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias (Spain); Rojo, T.; Lezama, L., E-mail: luis.lezama@ehu.es [Universidad del País Vasco, UPV/EHU, Dpto. de Química Inorgánica (Spain)

    2015-05-15

    Palladium-rich Iron nanoparticles in the 4–8 nm range have been produced by a combination of two methods: the thermal decomposition of organometallic precursors and the reduction of metallic salts by a polyol. Herein, it is shown how the details of the synthesis have a striking impact on the magnetic and morphological properties of the final products. In the synthesis of these bimetallic nanoparticles, the use of high reaction temperatures plays an essential role in attaining good chemical homogeneity, which has proved to have a key influence on the magnetic properties. Magnetic characterization has been performed by electron magnetic resonance and magnetization measurements, which have confirmed the superparamagnetic-like behavior at room temperature. No clear traces of magnetic polarization in palladium atoms have been detected. The combination of long-term stability and homogeneous chemical and magnetic properties makes these particles very suitable for a wide range of applications in nanotechnology.

  2. The in vitro unscheduled DNA synthesis (UDS) assay in rat primary hepatocytes

    International Nuclear Information System (INIS)

    The in vitro unscheduled DNA synthesis (UDS) assay was evaluated for inclusion in a battery of assays used at The Upjohn Company for evaluation of lead compounds in the development of new and existing drug entities. This evaluation process uncompassed aspects of the isolation of hepatocytes and tests of reference mutagens and genotoxins. The flow rate of perfusion solutions and their temperatures were critical in the isolation of high viability hepatocytes in good yield. The attachment of freshly isolated hepatocytes to coverslips was greatly enhanced by coating the coverslips with type III colagen. Results of testing 12 known genotoxic agents (UV light, cyclophosphamide, 7,12-dimethylbenzanthracene, dimethylnitrosamine, diethylnitrosamine, 2-acetylaminofluorene, benzo[a]pyrene, methyl methanesulfonate, ethyl methanesulfonate, N-propyl-N'-nitro-N-nitrosoguanidine, benzidine and 4-aminobiphenyl) were in agreement with the literature. The use of X-ray did not induce unscheduled DNA synthesis in hepatocytes. This latter finding draws attention to the inability of this assay to detect agents which result in 'short-patch' repair of damage. (author). 35 refs.; 8 tabs

  3. Uranium complexes with macrosyclic polyethers. Synthesis and structural chemical analysis

    International Nuclear Information System (INIS)

    This dissertation reports about studies on the chemical coordination behaviour of uranium of oxidation stages IV and VI with regard to twelve different macrocyclic ligands. For the preparation of the complexes, for every system a different method has been developed. The elementary analysis of the various complexes including the uranium had been done by X-ray fluorescence analysis, and the structural characterization proceeded via vibrational, uv-vis and emission spectroscopy as well as 1H-NMR and 13C-spin-lattice relaxation time studies. Conformational analysis of the polyethers used allowed the structural changes in the complexes to be observed. The structural analysis of the hydrous uranium VI crown ether complexes yielded information of characteristic features of these types of complexes. The first coordination sphere of the uranyl ion with covalently bonded anion remains unchanged. As to the water content, there is a certain range. Depending upon the solvent used, the complexes have two or four H2O molecules per formula unit. (orig./EF)

  4. Bioinspired greigite magnetic nanocrystals: chemical synthesis and biomedicine applications

    Science.gov (United States)

    Feng, Mei; Lu, Yang; Yang, Yuan; Zhang, Meng; Xu, Yun-Jun; Gao, Huai-Ling; Dong, Liang; Xu, Wei-Ping; Yu, Shu-Hong

    2013-10-01

    Large scale greigite with uniform dimensions has stimulated significant demands for applications such as hyperthermia, photovoltaics, medicine and cell separation, etc. However, the inhomogeneity and hydrophobicity for most of the as prepared greigite crystals has limited their applications in biomedicine. Herein, we report a green chemical method utilizing β-cyclodextrin (β-CD) and polyethylene glycol (PEG) to synthesize bioinspired greigite (Fe3S4) magnetic nanocrystals (GMNCs) with similar structure and magnetic property of magnetosome in a large scale. β-CD and PEG is responsible to control the crystal phase and morphology, as well as to bound onto the surface of nanocrystals and form polymer layers. The GMNCs exhibit a transverse relaxivity of 94.8 mM-1s-1 which is as high as iron oxide nanocrystals, and an entrapment efficiency of 58.7% for magnetic guided delivery of chemotherapeutic drug doxorubicin. Moreover, enhanced chemotherapeutic treatment of mice tumor was obtained via intravenous injection of doxorubicin loaded GMNCs.

  5. Amino acids attached to 2'-amino-LNA: Synthesis of DNA mixmer oligonucleotides with increased duplex stability

    DEFF Research Database (Denmark)

    Johannsen, Marie Willaing; Wengel, Jesper; Wamberg, Michael Chr.;

    2010-01-01

    The synthesis of 2'-amino-LNA (locked nucleic acid) opens up exciting possibilities for modification of nucleic acids by conjugation to the 2'-nitrogen. Incorporation of unmodified and N-functionalized 2'-amino-LNA nucleotides improve duplex stability compared to unmodified DNA. 2'-Amino......-LNA nucleosides derivatized with amino acids have been synthesized and incorporated into DNA oligonucleotides. Following oligonucleotide synthesis, peptides have been added using solid phase peptide coupling chem. Modification of oligonucleotides with pos. charged residues greatly improves thermal stability....

  6. A Library of Fluorinated Electrophiles for Chemical Tagging and Materials Synthesis.

    Science.gov (United States)

    Kasper, Jonathan J; Hitro, Jamie E; Fitzgerald, Sabrina R; Schnitter, Joseph M; Rutowski, James J; Heck, John A; Steinbacher, Jeremy L

    2016-09-01

    Various applications could benefit from new fluorinated molecules that offer chemical handles for quickly functionalizing reactive surfaces and molecules. Herein, we report the synthesis of a library of fluorinated molecules that contain nonafluoro-tert-butyl groups and electrophilic handles, mostly acrylates and acrylamides. Featuring a variety of hydrophobic and hydrophilic linkers, these molecules could find use in polymer chemistry, biomaterials, biomedical imaging, and protein tagging. PMID:27467082

  7. Biomimetic, Mild Chemical Synthesis of CdTe-GSH Quantum Dots with Improved Biocompatibility

    OpenAIRE

    Pérez-Donoso, José M.; Monrás, Juan P; Denisse Bravo; Adam Aguirre; Quest, Andrew F.; Igor O Osorio-Román; Aroca, Ricardo F.; Chasteen, Thomas G.; Vásquez, Claudio C.

    2012-01-01

    Multiple applications of nanotechnology, especially those involving highly fluorescent nanoparticles (NPs) or quantum dots (QDs) have stimulated the research to develop simple, rapid and environmentally friendly protocols for synthesizing NPs exhibiting novel properties and increased biocompatibility. In this study, a simple protocol for the chemical synthesis of glutathione (GSH)-capped CdTe QDs (CdTe-GSH) resembling conditions found in biological systems is described. Using only CdCl(2), K(...

  8. Low-temperature synthesis of graphene on nickel foil by microwave plasma chemical vapor deposition

    OpenAIRE

    Kim, Y.; Song, W.; Lee, S. Y.; Jeon, C; Jung, W.; Kim, M.; Park, C. -Y.

    2011-01-01

    Microwave plasma chemical vapor deposition (MPCVD) was employed to synthesize high quality centimeter scale graphene film at low temperatures. Monolayer graphene was obtained by varying the gas mixing ratio of hydrogen and methane to 80:1. Using advantages of MPCVD, the synthesis temperature was decreased from 750 °C down to 450 °C. Optical microscopy and Raman mapping images exhibited that a large area monolayer graphene was synthesized regardless of the temperatures. Since the overall trans...

  9. Some chemical synthesis of 14C labelled compounds of pharmaceutical or biological interest

    International Nuclear Information System (INIS)

    The recent discovery of the tuberculostatic properties of the hydrazide of isonicotinic acid (so-called 'Isoniazide', 'Rimifon') has raised considerably its interest, as for metabolic studies which it is more interesting to have it labelled with 14C. We describe in this report the chemical synthesis of 14C carboxyl labelled isoniazide which were done in the pyridine ring to highlight his metabolic function on the Koch's bacillus. (M.B.)

  10. Some chemical synthesis of {sup 14}C labelled compounds of pharmaceutical or biological interest

    Energy Technology Data Exchange (ETDEWEB)

    Pichat, I.; Baret, C.; Audinot, M.; Herbert, M.; Lambin, J. [Commissariat a l' Energie Atomique, Lab. du Fort de Chatillon, Fontenay-aux-Roses (France). Centre d' Etudes Nucleaires

    1955-07-01

    The recent discovery of the tuberculostatic properties of the hydrazide of isonicotinic acid (so-called 'Isoniazide', 'Rimifon') has raised considerably its interest, as for metabolic studies which it is more interesting to have it labelled with {sup 14}C. We describe in this report the chemical synthesis of {sup 14}C carboxyl labelled isoniazide which were done in the pyridine ring to highlight his metabolic function on the Koch's bacillus. (M.B.)

  11. The past, present and potential for microfluidic reactor technology in chemical synthesis.

    Science.gov (United States)

    Elvira, Katherine S; Casadevall i Solvas, Xavier; Wootton, Robert C R; deMello, Andrew J

    2013-11-01

    The past two decades have seen far-reaching progress in the development of microfluidic systems for use in the chemical and biological sciences. Here we assess the utility of microfluidic reactor technology as a tool in chemical synthesis in both academic research and industrial applications. We highlight the successes and failures of past research in the field and provide a catalogue of chemistries performed in a microfluidic reactor. We then assess the current roadblocks hindering the widespread use of microfluidic reactors from the perspectives of both synthetic chemistry and industrial application. Finally, we set out seven challenges that we hope will inspire future research in this field.

  12. Phospholipase C-delta1 expression is linked to proliferation, DNA synthesis, and cyclin E levels.

    Science.gov (United States)

    Stallings, Jonathan D; Zeng, Yue X; Narvaez, Francisco; Rebecchi, Mario J

    2008-05-16

    We previously reported that phospholipase C-delta1 (PLC-delta1) accumulates in the nucleus at the G1/S transition, which is largely dependent on its binding to phosphatidylinositol 4,5-bisphosphate ( Stallings, J. D., Tall, E. G., Pentyala, S., and Rebecchi, M. J. (2005) J. Biol. Chem. 280, 22060-22069 ). Here, using small interfering RNA (siRNA) that specifically targets rat PLC-delta1, we investigated whether this enzyme plays a role in cell cycle control. Inhibiting expression of PLC-delta1 significantly decreased proliferation of rat C6 glioma cells and altered S phase progression. [3H]Thymidine labeling and fluorescence-activated cell sorting analysis indicated that the rates of G1/S transition and DNA synthesis were enhanced. On the other hand, knockdown cultures released from the G1/S boundary were slower to reach full G2/M DNA content, consistent with a delay in S phase. The levels of cyclin E, a key regulator of the G1/S transition and DNA synthesis, were elevated in asynchronous cultures as well as those blocked at the G1/S boundary. Epifluorescence imaging showed that transient expression of human phospholipase C-delta1, resistant to these siRNA, suppressed expression of cyclin E at the G1/S boundary despite treatment of cultures with rat-specific siRNA. Although whole cell levels of phosphatidylinositol 4,5-bisphosphate were unchanged, suppression of PLC-delta1 led to a significant rise in the nuclear levels of this phospholipid at the G1/S boundary. These results support a role for PLC-delta1 and nuclear phospholipid metabolism in regulating cell cycle progression.

  13. Synthesis of a multibranched porphyrin-oligonucleotide scaffold for the construction of DNA-based nano-architectures.

    Science.gov (United States)

    Clavé, Guillaume; Chatelain, Grégory; Filoramo, Arianna; Gasparutto, Didier; Saint-Pierre, Christine; Le Cam, Eric; Piétrement, Olivier; Guérineau, Vincent; Campidelli, Stéphane

    2014-05-01

    The interest in the functionalization of oligonucleotides with organic molecules has grown considerably over the last decade. In this work, we report on the synthesis and characterization of porphyrin-oligonucleotide hybrids containing one to four DNA strands (P1-P4). The hybrid P4, which inserts one porphyrin and four DNA fragments, was combined with gold nanoparticles and imaged by transmission electron microscopy.

  14. DNA-Based Identification and Chemical Characteristics of Hypnea musciformis from Coastal Sites in Ghana

    DEFF Research Database (Denmark)

    Ale, Marcel Tutor; Barrett, Kristian; Addico, Gloria;

    2016-01-01

    This work reveals new, important insights about the influence of broad spatial variationson the phylogenetic relationship and chemical characteristics of Ghanaian Hypnea musciformis—acarrageenan-containing red seaweed. DNA barcoding techniques alleviate the difficulty for accurate morphological i...

  15. Production of thymine glycols in DNA by radiation and chemical carcinogens as detected by a monoclonal antibody.

    OpenAIRE

    Leadon, S A

    1987-01-01

    In order to understand the role in carcinogenesis of damage indirectly induced by chemical carcinogens, it is important to identify the primary DNA lesions. We have measured the formation and repair of one type of DNA modification, 5,6-dihydroxydihydrothymine (thymine glycol), following exposure of cultured human cells to the carcinogens N-hydroxy-2-naphthylamine or benzo(a)pyrene. The efficiency of production of thymine glycols in DNA by these carcinogens was compared to that by ionizing rad...

  16. Antiproliferative activity of bicyclic benzimidazole nucleosides: synthesis, DNA-binding and cell cycle analysis.

    Science.gov (United States)

    Sontakke, Vyankat A; Lawande, Pravin P; Kate, Anup N; Khan, Ayesha; Joshi, Rakesh; Kumbhar, Anupa A; Shinde, Vaishali S

    2016-04-26

    An efficient route was developed for synthesis of bicyclic benzimidazole nucleosides from readily available d-glucose. The key reactions were Vörbruggen glycosylation and ring closing metathesis (RCM). Primarily, to understand the mode of DNA binding, we performed a molecular docking study and the binding was found to be in the minor groove region. Based on the proposed binding model, UV-visible and fluorescence spectroscopic techniques using calf thymus DNA (CT-DNA) demonstrated a non-intercalative mode of binding. Antiproliferative activity of nucleosides was tested against MCF-7 and MDA-MB-231 breast cancer cell lines and found to be active at low micromolar concentrations. Compounds and displayed significant antiproliferative activity as compared to and with the reference anticancer drug, doxorubicin. Cell cycle analysis showed that nucleoside induced cell cycle arrest at the S-phase. Confocal microscopy has been performed to validate the induction of cellular apoptosis. Based on these findings, such modified bicyclic benzimidazole nucleosides will make a significant contribution to the development of anticancer drugs. PMID:27074628

  17. Enzymatic synthesis of modified oligonucleotides by PEAR using Phusion and KOD DNA polymerases.

    Science.gov (United States)

    Wang, Xuxiang; Zhang, Jianye; Li, Yingjia; Chen, Gang; Wang, Xiaolong

    2015-02-01

    Antisense synthetic oligonucleotides have been developed as potential gene-targeted therapeutics. We previously reported polymerase-endonuclease amplification reaction (PEAR) for amplification of natural and 5'-O-(1-thiotriphosphate) (S)-modified oligonucleotides. Here, we extended the PEAR technique for enzymatic preparation of 2'-deoxy-2'-fluoro-(2'-F) and 2'-F/S double-modified oligonucleotides. The result showed that KOD and Phusion DNA polymerase could synthesize oligonucleotides with one or two modified nucleotides, and KOD DNA polymerase is more suitable than Phusion DNA polymerase for PEAR amplification of 2'-F and 2'-F/S double modified oligonucleotides. The composition of PEAR products were analyzed by electrospray ionization liquid chromatography mass spectrometry (ESI/LC/MS) detection and showed that the sequence of the PEAR products are maintained at an extremely high accuracy (>99.9%), and after digestion the area percent of full-length modified oligonucleotides reaches 89.24%. PEAR is suitable for synthesis of modified oligonucleotides efficiently and with high purity. PMID:25517220

  18. Synthesis of full length and truncated microcin B17 analogues as DNA gyrase poisons.

    Science.gov (United States)

    Thompson, Robert E; Collin, Frédéric; Maxwell, Anthony; Jolliffe, Katrina A; Payne, Richard J

    2014-03-14

    Microcin B17 (MccB17) is a post-translationally modified peptide containing thiazole and oxazole heterocycles that interrupt the peptide backbone. MccB17 is capable of poisoning DNA gyrase through stabilization of the gyrase-DNA cleavage complex and has therefore attracted significant attention. Using a combination of Fmoc-strategy solid-phase peptide synthesis and solution-phase fragment assembly we have prepared a library of full-length and truncated MccB17 analogues to investigate key structural requirements for gyrase-poisoning activity. Synthetic peptides lacking the glycine-rich N-terminal portion of the full-length sequence showed strong stabilization of the gyrase-DNA cleavage complex with increased potency relative to the full-length sequences. This truncation, however, led to a decrease in antibacterial activity of these analogues relative to their full-length counterparts indicating a potential role of the N-terminal region of the natural product for cellular uptake.

  19. Eukaryotic DNA damage tolerance and translesion synthesis through covalent modifications of PCNA

    Institute of Scientific and Technical Information of China (English)

    Parker L Andersen; Fang Xu; Wei Xiao

    2008-01-01

    In addition to well-defined DNA repair pathways, all living organisms have evolved mechanisms to avoid cell death caused by replication fork collapse at a site where replication is blocked due to disruptive covalent modi-fications of DNA. The term DNA damage tolerance (DDT) has been employed loosely to include a collection of mechanisms by which cells survive replication-blocking lesions with or without associated genomic instability. Recent genetic analyses indicate that DDT in eukaryotes, from yeast to human, consists of two parallel pathways with one being error-free and another highly mutagenic. Interestingly, in budding yeast, these two pathways are mediated by sequential modifications of the proliferating cell nuclear antigen (PCNA) by two ubiquitination complexes Rad6-Rad18 and Mms2-Ubcl3-Rad5. Damage-induced monoubiquitination of PCNA by Rad6-Rad18 promotes translesion synthesis (TLS) with increased mutagenesis, while subsequent polyubiquitination of PCNA at the same Ki64 residue by Mms2-Ubcl3-Rad5 promotes error-free lesion bypass. Data obtained from recent studies suggest that the above mechanisms are conserved in higher eukaryotes. In particular, mammals contain multiple specialized TLS polymerases. Defects in one of the TLS polymerases have been linked to genomic insta-bility and cancer.

  20. [DNA and chemical analyses of commercial fly agaric-related products].

    Science.gov (United States)

    Maruyama, Takuro; Kawahara, Nobuo; Fukiharu, Toshimitsu; Yokoyama, Kazumasa; Makino, Yukiko; Goda, Yukihiro

    2005-04-01

    Since June 6, 2002, psilocin and psilocybin-containing fungi (commonly called "magic mushrooms") have been regulated by the Narcotics and Psychotropics Control Law in Japan. However, various fly agaric-related products are now entering the Japanese market via the internet. In this study, fly agaric-related products available in this way were investigated for raw materials by DNA analysis and for additives by chemical analysis. Nucleotide sequence analysis of the mitochondrial 12S rDNA region suggested that these fly agaric-related products originate from A. muscaria or A. muscaria var. persicina. Furthermore, they were classified into three strains based on the ITS2-LSU nucleotide sequence. Harmine derivatives and/or tryptamine derivatives were detected in some of these products by LC/MS analysis. In accordance with this, the matK gene of Peganum harmala was found in all of the harmine derivative-containing samples. PMID:16018591

  1. Dose-Dependent AMPK-Dependent and Independent Mechanisms of Berberine and Metformin Inhibition of mTORC1, ERK, DNA Synthesis and Proliferation in Pancreatic Cancer Cells.

    Directory of Open Access Journals (Sweden)

    Ming Ming

    Full Text Available Natural products represent a rich reservoir of potential small chemical molecules exhibiting anti-proliferative and chemopreventive properties. Here, we show that treatment of pancreatic ductal adenocarcinoma (PDAC cells (PANC-1, MiaPaCa-2 with the isoquinoline alkaloid berberine (0.3-6 µM inhibited DNA synthesis and proliferation of these cells and delay the progression of their cell cycle in G1. Berberine treatment also reduced (by 70% the growth of MiaPaCa-2 cell growth when implanted into the flanks of nu/nu mice. Mechanistic studies revealed that berberine decreased mitochondrial membrane potential and intracellular ATP levels and induced potent AMPK activation, as shown by phosphorylation of AMPK α subunit at Thr-172 and acetyl-CoA carboxylase (ACC at Ser79. Furthermore, berberine dose-dependently inhibited mTORC1 (phosphorylation of S6K at Thr389 and S6 at Ser240/244 and ERK activation in PDAC cells stimulated by insulin and neurotensin or fetal bovine serum. Knockdown of α1 and α2 catalytic subunit expression of AMPK reversed the inhibitory effect produced by treatment with low concentrations of berberine on mTORC1, ERK and DNA synthesis in PDAC cells. However, at higher concentrations, berberine inhibited mitogenic signaling (mTORC1 and ERK and DNA synthesis through an AMPK-independent mechanism. Similar results were obtained with metformin used at doses that induced either modest or pronounced reductions in intracellular ATP levels, which were virtually identical to the decreases in ATP levels obtained in response to berberine. We propose that berberine and metformin inhibit mitogenic signaling in PDAC cells through dose-dependent AMPK-dependent and independent pathways.

  2. A derivative of an ataxia-telangiectasia (A-T) cell line with normal radiosensitivity but A-T-like inhibition of DNA synthesis

    International Nuclear Information System (INIS)

    Ataxia-telangiectasia (A-T) cells are hypersensitive to the lethal effects of ionizing radiation and fail to inhibit DNA synthesis following radiation exposure. A cell line derived from an A-T line following DNA-mediated gene transfer has normal radiation sensitivity, but the kinetics of DNA synthesis after γ-irradiation are similar to those of A-T cells. (author)

  3. Dictyostelium discoideum, a lower eukaryote model for the study of DNA repair: Implications for the role of DNA-damaging chemicals in the evolution of repair proficient cells

    Science.gov (United States)

    Deering, R. A.

    1994-10-01

    The evolution of the ability of living cells to cope with stress is crucial for the maintenance of their genetic integrity. Yet low levels of mutation must remain to allow adaptation to environmental changes. The cellular slime mold D. discoideum is a good system for studying molecular aspects of the repair of lethal and mutagenic damage to DNA by radiation and chemicals. The wild-type strains of this soil microorganism are extremely resistant to DNA damaging agents. In nature the amoeboid cells in their replicative stage feed on soil bacteria and are exposed to numerous DNA-damaging chemicals produced by various soil microorganisms. It is probable that the evolution of repair systems in this organism and perhaps in others is a consequence of the necessity to cope with chemical damage which also confers resistance to radiation.

  4. Defective recovery of semi-conservative DNA synthesis in xeroderma pigmentosum cells following split-dose ultraviolet irradiation

    International Nuclear Information System (INIS)

    In normal human fibroblasts the authors observe an enhancement of the recovery of the rate of semi-conservative DNA synthesis after split-dose UV-irradation relative to a single total UV dose. The enhanced recovery is totally absent in both a xeroderma pigmentosum variant line and two xeroderma pigmentosum lines belonging to complementation groups A and C. (Auth.)

  5. Synthesis of DNA templated trifunctional electrically conducting, optical, and magnetic nanochain of Nicore-Aushell for biodevice

    Science.gov (United States)

    Mandal, Madhuri; Mandal, Kalyan

    2009-07-01

    Synthesis of trifunctional, e.g., electrically conducting, optical, and magnetic nanochains of Nicore-Aushell, has been discussed here. Properties of the materials were investigated from the view of its application in bionanodevice. Our investigation indicates that such material attached to biomolecule "DNA chain" and having three main properties in one material will have great potentiality in medical instrumentation and biocomputer device.

  6. Neuropeptide Y stimulates DNA synthesis in human vascular smooth muscle cells through neuropeptide Y Y1 receptors

    DEFF Research Database (Denmark)

    Nilsson, T; Edvinsson, L

    2000-01-01

    We investigated the mitogenic effect, measured as [3H]thymidine incorporation, of neuropeptide Y (NPY) on smooth muscle cells (SMCs) from human subcutaneous arteries (diameter: 0.4 mm). NPY stimulated DNA synthesis in a concentration-dependent manner, Emax 32 +/- 5% relative to control. The effec...

  7. ENHANCEMENT OF DNA SYNTHESIS IN CULTURED ADULT RAT HEPATOCYTES BY 5-HT THROUGH STIMULATION OF 5-HT2 RECEPTOR

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Hepatocytes were isolated from livers of adult male Sprague-Dawley rats and cultured in Williams'E Medium with [3 H] thymidine. The effect of 5-hydroxytryptamine (5-HT) was investigated through adding various concentrations (10-8~10-3 mol/L) of 5-HT to the hepatocyte cultures in the presence or absence of epidermal growth factor (EGF) and insulin. The involvement of 5-HT2 receptor was examined by adding a 5-HT2 receptor antagonist, ketanserin (10-6 mol/L), to some of the cultures containing 5-HT. The increment of DNA synthesis was measured by [3 H] thymidine incorporation. The results showed that 5-HT2 (≥10-6 mol/L) significantly (P<0.05) increased the amount of DNA synthesis induced by EGF and insulin in the cultured adult rat hepaptocytes. The effect of 5-HT in enhancing DNA synthesis began to appear at a concentration between 10-7 and 10-6 mol/L and reached maximum at concentrations of ≥10-4 mol/L. The enhancement of DNA synthesis by 5-HT was significantly (P<0.05) antagonized by ketanserin, suggesting that this effect of 5-HT was mediated by 5-HT2 receptor subtype.

  8. Synthesis and spectroscopic studies of the aminoglycoside (neomycin)--perylene conjugate binding to human telomeric DNA.

    Science.gov (United States)

    Xue, Liang; Ranjan, Nihar; Arya, Dev P

    2011-04-12

    Synthesis of a novel perylene-neomycin conjugate (3) and the properties of its binding to human telomeric G-quadruplex DNA, 5'-d[AG3(T2AG3)3] (4), are reported. Various spectroscopic techniques were employed to characterize the binding of conjugate 3 to 4. A competition dialysis assay revealed that 3 preferentially binds to 4, in the presence of other nucleic acids, including DNA, RNA, DNA-RNA hybrids, and other higher-order structures (single strands, duplexes, triplexes, other G-quadruplexes, and the i-motif). UV thermal denaturation studies showed that thermal stabilization of 4 increases as a function of the increasing concentration of 3. The fluorescence intercalator displacement (FID) assay displayed a significantly tighter binding of 3 with 4 as compared to its parent constituents [220-fold stronger than neomycin (1) and 4.5-fold stronger than perylene diamine (2), respectively]. The binding of 3 with 4 resulted in pronounced changes in the molar ellipticity of the DNA absorption region as confirmed by circular dichroism. The UV-vis absorption studies of the binding of 3 to 4 resulted in a red shift in the spectrum of 3 as well as a marked hypochromic change in the perylene absorption region, suggesting that the ligand-quadruplex interaction involves stacking of the perylene moiety. Docking studies suggest that the perylene moiety serves as a bridge that end stacks on 4, making contacts with two thymine bases in the loop, while the two neomycin moieties branch into the grooves of 4.

  9. Rational design, synthesis, and DNA binding properties of novel sequence-selective peptidyl congeners of ametantrone.

    Science.gov (United States)

    Gianoncelli, Alessandra; Basili, Serena; Scalabrin, Matteo; Sosic, Alice; Moro, Stefano; Zagotto, Giuseppe; Palumbo, Manlio; Gresh, Nohad; Gatto, Barbara

    2010-07-01

    Natural and synthetic compounds characterized by an anthraquinone nucleus represent an important class of anti-neoplastic agents, the mechanism of action of which is related to intercalation into DNA. Ametantrone (AM) is a synthetic 9,10-anthracenedione bearing two (hydroxyethylamino)ethylamino residues at positions 1 and 4; along with other anthraquinones and anthracyclines, it shares a polycyclic intercalating moiety and charged side chains that stabilize DNA binding. All these drugs elicit adverse side effects, which represent a challenge for antitumor chemotherapy. In the present work the structure of AM was augmented with appropriate groups that target well-defined base pairs in the major groove. These should endow AM with DNA sequence selectivity. We describe the rationale for the synthesis and the evaluation of activity of a new series of compounds in which the planar anthraquinone is conjugated at positions 1 and 4 through the side chains of AM or other bioisosteric linkers to appropriate dipeptides. The designed novel AM derivatives were shown to selectively stabilize two oligonucleotide duplexes that both have a palindromic GC-rich hexanucleotide core, but their stabilizing effects on a random DNA sequence was negligible. In the case of the most effective compound, the 1,4-bis-[Gly-(L-Lys)] derivative of AM, the experimental results confirm the predictions of earlier theoretical computations. In contrast, AM had equal stabilizing effects on all three sequences and showed no preferential binding. This novel peptide derivative can be classified as a strong binder regarding the sequences that it selectively targets, possibly opening the exploitation of less cytotoxic conjugates of AM to the targeted treatment of oncological and viral diseases. PMID:20458714

  10. Contiguous 2,2,4-triamino-5(2H)-oxazolone obstructs DNA synthesis by DNA polymerases α, β, η, ι, κ, REV1 and Klenow Fragment exo-, but not by DNA polymerase ζ.

    Science.gov (United States)

    Suzuki, Masayo; Kino, Katsuhito; Kawada, Taishu; Oyoshi, Takanori; Morikawa, Masayuki; Kobayashi, Takanobu; Miyazawa, Hiroshi

    2016-03-01

    Guanine is the most easily oxidized of the four DNA bases, and contiguous guanines (GG) in a sequence are more readily oxidized than a single guanine in a sequence. Continued oxidation of GGs results in a contiguous oxidized guanine lesion. Two contiguous 2,5-diamino-4H-imidazol-4-ones, an oxidized form of guanine that hydrolyses to 2,2,4-triamino-5(2H)-oxazolone (Oz), are detected following the oxidation of GG. In this study, we analysed translesion synthesis (TLS) across two contiguous Oz molecules (OzOz) using Klenow Fragment exo(-) (KF exo(-)) and DNA polymerases (Pols) α, β, ζ, η, ι, κ and REV1. We found that KF exo(-) and Pols α, β, ι and REV1 inserted one nucleotide opposite the 3' Oz of OzOz and stalled at the subsequent extension, and that Pol κ incorporated no nucleotide. Pol η only inefficiently elongated the primer up to full-length across OzOz; the synthesis of most DNA strands stalled at the 3' or 5' Oz of OzOz. Surprisingly, however, Pol ζ efficiently extended the primer up to full-length across OzOz, unlike the other DNA polymerases, but catalysed error-prone nucleotide incorporation. We therefore believe that Pol ζ is required for efficient TLS of OzOz. These results show that OzOz obstructs DNA synthesis by DNA polymerases except Pol ζ.

  11. Serine Metabolism Supports the Methionine Cycle and DNA/RNA Methylation through De Novo ATP Synthesis in Cancer Cells.

    Science.gov (United States)

    Maddocks, Oliver D K; Labuschagne, Christiaan F; Adams, Peter D; Vousden, Karen H

    2016-01-21

    Crosstalk between cellular metabolism and the epigenome regulates epigenetic and metabolic homeostasis and normal cell behavior. Changes in cancer cell metabolism can directly impact epigenetic regulation and promote transformation. Here we analyzed the contribution of methionine and serine metabolism to methylation of DNA and RNA. Serine can contribute to this pathway by providing one-carbon units to regenerate methionine from homocysteine. While we observed this contribution under methionine-depleted conditions, unexpectedly, we found that serine supported the methionine cycle in the presence and absence of methionine through de novo ATP synthesis. Serine starvation increased the methionine/S-adenosyl methionine ratio, decreasing the transfer of methyl groups to DNA and RNA. While serine starvation dramatically decreased ATP levels, this was accompanied by lower AMP and did not activate AMPK. This work highlights the difference between ATP turnover and new ATP synthesis and defines a vital function of nucleotide synthesis beyond making nucleic acids.

  12. Interaction between Escherichia coli DNA polymerase IV and single-stranded DNA-binding protein is required for DNA synthesis on SSB-coated DNA.

    Science.gov (United States)

    Furukohri, Asako; Nishikawa, Yoshito; Akiyama, Masahiro Tatsumi; Maki, Hisaji

    2012-07-01

    DNA polymerase IV (Pol IV) is one of three translesion polymerases in Escherichia coli. A mass spectrometry study revealed that single-stranded DNA-binding protein (SSB) in lysates prepared from exponentially-growing cells has a strong affinity for column-immobilized Pol IV. We found that purified SSB binds directly to Pol IV in a pull-down assay, whereas SSBΔC8, a mutant protein lacking the C-terminal tail, failed to interact with Pol IV. These results show that the interaction between Pol IV and SSB is mediated by the C-terminal tail of SSB. When polymerase activity was tested on an SSBΔC8-coated template, we observed a strong inhibition of Pol IV activity. Competition experiments using a synthetic peptide containing the amino acid sequence of SSB tail revealed that the chain-elongating capacity of Pol IV was greatly impaired when the interaction between Pol IV and SSB tail was inhibited. These results demonstrate that Pol IV requires the interaction with the C-terminal tail of SSB to replicate DNA efficiently when the template ssDNA is covered with SSB. We speculate that at the primer/template junction, Pol IV interacts with the tail of the nearest SSB tetramer on the template, and that this interaction allows the polymerase to travel along the template while disassembling SSB.

  13. Design, Synthesis, and Mechanistic Evaluation of Iron-Based Catalysis for Synthesis Gas Conversion to Fuels and Chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Akio Ishikawa; Manuel Ojeda; Enrique Iglesia

    2005-09-30

    This project extends previously discovered Fe-based catalysts to hydrogen-poor synthesis gas streams derived from coal and biomass sources. These catalysts have shown unprecedented Fischer-Tropsch synthesis rate, selectivity for feedstocks consisting of synthesis gas derived from methane. During the first reporting period, we certified a microreactor, installed required analytical equipment, and reproduced synthetic protocols and catalytic results previously reported. During the second reporting period, we prepared several Fe-based compositions for Fischer-Tropsch synthesis and tested the effects of product recycle under both subcritical and supercritical conditions. During the third reporting period, we improved the catalysts preparation method, which led to Fe-based FT catalysts with the highest FTS reaction rates and selectivities so far reported, a finding that allowed their operation at lower temperatures and pressures with high selectivity to desired products (C{sub 5+}, olefins). During this fourth reporting period, we have determined the effects of different promoters on catalytic performance. More specifically, we have found that the sequence in which promoters are introduced has a marked positive impact on rates and selectivities. Cu or Ru chemical promoters should be impregnated before K to achieve higher Fischer-Tropsch synthesis rates. The catalyst prepared in this way was evaluated for 240 h, showing a high catalytic activity and stability after an initial period of time necessary for the formation of the active phases. Concurrently, we are studying optimal activation procedures, which involve the reduction and carburization of oxide precursors during the early stages of contact with synthesis gas. Activation at low temperatures (523 K), made possible by optimal introduction of Cu or Ru, leads to lower catalyst surface area than higher activation temperatures, but to higher reaction rates, because such low temperatures avoid concurrent deactivation

  14. Synthesis of Novel Metal Ion Sensors Based on DNA-Metal Interactions

    Institute of Scientific and Technical Information of China (English)

    Akira Ono; Shiqi Cao; Humika Togashi; Yoko Miyake

    2005-01-01

    @@ 1Introduction The interactions of metal ions with nucleic acids, nucleosides, and nucleo-bases have been extensively investigated[1,2]. We have reported that thymine-thymine (T-T) and cytosine-cytosine (C- C) miss base pairs in DNA duplexes highly selectively capture HgⅡ ion and Ag Ⅰ ion, which result in formations of metal-mediated base pairs, T-HgⅡ -T and C-AgⅠ -C, in duplexes[3]. The phenomenon is expected to be useful for a variety of studies such as synthesis of nano-wires containing metal ions, developing metal-ion sensing methods, etc.Here, we report novel oligodeoxyribonucleotide (ODN)-based sensors that detect HgⅡ ions and AgⅠ ions in aqueous solutions.

  15. Recovery of DNA synthesis after ultraviolet irradiation of xeroderma pigmentosum cells depends on excision repair and is blocked by caffeine

    International Nuclear Information System (INIS)

    Normal human and xeroderma pigmentosum (XP, excision-defective group A) cells (both SV40-transformed) pulse-labeled with [3H] thymidine at various times after irradiation with ultraviolet light showed a decline and recovery of both the molecular weights of newly synthesized DNA and the rated of synthesis per cell. At the same ultraviolet dose, both molecular weights and rates of synthesis were inhibited more in XP than in normal cells. This indicates that excision repair plays a role in minimizing the inhibition of chain growth, possibly by excision of dimers ahead of the growing point. The ability to synthesize normal-sized DNA recovered more rapidly than rates of synthesis in normal cells, but both parameters recovered in phase in XP cells. During recovery in normal cells there are therefore fewer actively replicating clusters of replicons because the single-strand breaks involved in the excision of dimers inhibit replicon initiation. XP cells have few excision repair events and therefore fewer breaks to interfere with initiation, but chain growth is blocked by unexcised dimers. In both cell types recovery of the ability to synthesize normal-sized DNA was prevented by growing cells in caffeine after irradiation, possibly because of competition between the DNA binding properties of caffeine and replication proteins. These observations imply that excision repair and semiconservative replication interact strongly in irradiated cells to produce a complex spectrum of changes in DNA replication which may be confused with parts of alternative systems such as post-replication repair. (author)

  16. Peptide Nucleic Acid with a Lysine Side Chain at the β-Position: Synthesis and Application for DNA Cleavage.

    Science.gov (United States)

    Sugiyama, Toru; Kuwata, Keiko; Imamura, Yasutada; Demizu, Yosuke; Kurihara, Masaaki; Takano, Masashi; Kittaka, Atsushi

    2016-01-01

    This paper reports the synthesis of new β-Lys peptide nucleic acid (PNA) monomers and their incorporation into a 10-residue PNA sequence. PNA containing β-Lys PNA units formed a stable hybrid duplex with DNA. However, incorporation of β-Lys PNA units caused destabilization of PNA-DNA duplexes to some extent. Electrostatic attractions between β-PNA and DNA could reduce this destabilization effect. Subsequently, bipyridine-conjugated β-Lys PNA was prepared and exhibited sequence selective cleavage of DNA. Based on the structures of the cleavage products and molecular modeling, we reasoned that bipyridine moiety locates within the minor groove of the PNA-DNA duplexes. The lysine side chain of β-PNA is a versatile handle for attaching various functional molecules. PMID:27373637

  17. Synthesis and crystal structure study of 2′-Se-adenosine-derivatized DNA

    Institute of Scientific and Technical Information of China (English)

    SALON; Jozef

    2010-01-01

    The selenium derivatization of nucleic acids is a novel and promising strategy for 3D structure determination of nucleic acids.Selenium can serve as an excellent anomalous scattering center to solve the phase problem,which is one of the two major bottlenecks in macromolecule X-ray crystallography.The other major bottleneck is crystallization.It has been demonstrated that the incorporated selenium functionality at the 2′-positions of the nucleosides and nucleotides is stable and does not cause significant structure perturbation.Furthermore,it was observed that the 2′-Se-derivatization could facilitate crystallization of oligonucleotides with fast crystal growth and high diffraction quality.Herein,we describe a convenient synthesis of the 2′-Se-adenosine phosphoramidite,and report the first synthesis and X-ray crystal structure determination of the DNA containing the 2′-Se-A derivatization.The 3D structure of 2′-Se-A-DNA decamer 5′-GTACGCGT(2′-Se-A)C-3′2 was determined at 1.75 ? resolution,the 2′-Se-functionality points to the minor groove,and the Se-modified and native structures are virtually identical.Moreover,we have observed that the 2′-Se-A modification can greatly facilitate the crystal growth with high diffraction quality.In conjunction with the crystallization facilitation by the 2′-Se-U and 2′-Se-T,this novel observation on the 2′-Se-A functionality suggests that the 2′-Se moiety is sole responsible for the crystallization facilitation and the identity of nucleobases does not influence the crystal growth significantly.

  18. The effect of human milk on DNA synthesis of neonatal rat hepatocytes in primary culture.

    Science.gov (United States)

    Kohno, Y; Shiraki, K; Mura, T

    1991-03-01

    We studied the effect of human milk on DNA synthesis of neonatal hepatocytes to elucidate the physiologic role of human milk in growth of the liver. Neonatal hepatocytes were isolated from 5-d-old rats and cultured in serum-free medium. Human milk stimulated DNA synthesis of these hepatocytes in a concentration-dependent manner. The stimulatory activity of 7.5% (vol/vol) human milk plus 0.1 mumol/L insulin was five times that of control and was almost the same as that of 20 micrograms/L human epidermal growth factor (hEGF) plus insulin. The effect of human milk was additive with treatment with hEGF and insulin. The milk associated with prolonged jaundice of infants was significantly more active than the milk that was not associated with jaundice, although the concentration of hEGF was not different between the two types of milk. The mitogenic activity of milk was heat-labile, inactivated by DTT and stable after treatment with trypsin. Three peaks of the activity were detected in milk by gel filtration and the fraction containing proteins of molecular weight between 36,000 and 76,000 showed the highest activity. Anti-hEGF antibody did not inhibit this activity completely. These results suggested the presence of mitogens other than hEGF or a more active form of hEGF in human milk. The milk associated with breast-milk jaundice exerts a different influence on cell growth and may affect maturation of the liver function related to bilirubin metabolism. The mitogenic activity of milk might be important for growth and development of the liver in infants.

  19. Chemical synthesis and characterization of highly soluble conducting polyaniline in the mixtures of common solvents

    Directory of Open Access Journals (Sweden)

    Zeghioud Hichem

    2015-01-01

    Full Text Available This work presents the synthesis and characterization of soluble and conducting polyaniline PANI-PIA according to chemical polymerization route. This polymerization pathway leads to the formation of poly(itaconic acid doped polyaniline salts, which are highly soluble in a number of mixtures between organic common polar solvents and water, the solubility reaches 4 mg mL-1. The effect of synthesis parameters such as doping level on the conductivity and the study of solubility and other properties of the resulting PANI salts were also undertaken. The maximum of conductivity was found equal to 2.48×10-4 S cm-1 for fully protonated PANI-EB. In addition, various characterizations of the synthesized materials were also done with the help of viscosity measurements, UV-vis spectroscopy, XRD, FTIR and finally TGA for the thermal properties behaviour.

  20. Low-temperature synthesis of graphene on nickel foil by microwave plasma chemical vapor deposition

    Science.gov (United States)

    Kim, Y.; Song, W.; Lee, S. Y.; Jeon, C.; Jung, W.; Kim, M.; Park, C.-Y.

    2011-06-01

    Microwave plasma chemical vapor deposition (MPCVD) was employed to synthesize high quality centimeter scale graphene film at low temperatures. Monolayer graphene was obtained by varying the gas mixing ratio of hydrogen and methane to 80:1. Using advantages of MPCVD, the synthesis temperature was decreased from 750 °C down to 450 °C. Optical microscopy and Raman mapping images exhibited that a large area monolayer graphene was synthesized regardless of the temperatures. Since the overall transparency of 89% and low sheet resistances ranging from 590 to 1855 Ω/sq of graphene films were achieved at considerably low synthesis temperatures, MPCVD can be adopted in manufacturing future large-area electronic devices based on graphene film.

  1. Synthesis of low leakage current chemical vapour deposited (CVD) diamond films for particle detection

    International Nuclear Information System (INIS)

    We report on synthesis of diamond films by direct current glow discharge chemical vapour deposition (CVD) prepared at different deposition conditions, for application in high energy physics. The synthesis apparatus is briefly described. Continuous undoped diamond samples have been grown onto Mo substrates with a deposition area up to 1 cm2 and an electrical resistivity as high as 1013 Ωcm. The deposition parameters are related to the material properties of the diamonds, investigated by optical spectroscopy, electron microscopy and diffraction analysis. Decreasing the linear growth rate results in good quality films with small remnants of graphite-like phases. The high crystalline quality and phase purity of the films are related to very low values of leakage currents. The particle induced conductivity of these samples is also studied and preliminary results on charge collection efficiency are presented. (orig.)

  2. Synthesis of 5-(hydroxymethyl)furfural in Ionic Liquids - Paving the Way to Renewable Chemicals

    DEFF Research Database (Denmark)

    Ståhlberg, Tim; Fu, Wenjing; Woodley, John;

    2011-01-01

    The synthesis of 5-(hydroxymethyl)furfural (HMF) in ionic liquids is a field that has grown rapidly in recent years. Unique dissolving properties for crude biomass in combination with a high selectivity for HMF formation from hexose sugars make ionic liquids attractive reaction media...... for the production of chemicals from renewable resources. A wide range of new catalytic systems that are unique for the transformation of glucose and fructose to HMF in ionic liquids has been found. However, literature examples of scale-up and process development are still scarce, and future research needs...... to complement the new chemistry with studies on larger scales in order to find economically and environmentally feasible processes for HMF production in ionic liquids. This Minireview surveys important progress made in catalyst development for the synthesis of HMF in ionic liquids, and proposes future research...

  3. Evaluation of [methyl- 14C]4'-thio-thymidine for DNA synthesis imaging in vivo

    International Nuclear Information System (INIS)

    Objective: In order to obtain a thymidine analog that might prove simpler to use for imaging DNA synthesis and follow the same biochemistry of thymidine in vivo, we evaluated [methyl- 11C]4'-thio-thymidine ([methyl- 11C]S-dThd) by using the [14C]-labeled counterpart ([methyl- 14C]S-dThd). Methods: [methyl-14C]S-dThd was synthesized by rapid methylation of 5-trimethyl-stannyl-4' -thio-2' -deoxyuridine via a palladium mediated Stille-coupling reaction with [14C]methyl iodide. Degradation of [methyl- 14C]S-dThd when incubated in human blood was analyzed by HPLC. The in vivo potential of [methyl- 14C]S-dThd was evaluated by distribution study of EMT-6 mammary carcinoma-bearing mice. Gemcitabine, a potent inhibitor of DNA synthesis, was used to modulate cell proliferation. Tissue extraction was also performed to investigate the incorporation of [methyl-14C]S-dThd into DNA. Results: [methyl- 14C]S-dThd was obtained in 31-41% radiochemical yield (calculated from [14C]methyl iodide) at 130, 5 min reaction in N,N-dimethylforamide. After semi-preparative HPLC purification, radiochemical purity of [methyl- 14C]S-dThd was >99% and the specific activity was 2.04 GBq/mmol (according to the specific activity of [14C]methyl iodide). Incubation with human blood demonstrated rapid degradation of [2- 14C]thymidine. In contrast, [methyl- 14C]S-dThd was stable with less than 3% degradation at 60 min. In vivo distribution study showed progressive accumulation of radioactivity in proliferating tissues (spleen, thymus, duodenum and tumor). On the other hand, the washout of radioactivity by the non-proliferating tissues (lung, liver, kidney and muscle) appeared nearly exponential. The tumor uptake of [methyl- 14C]S-dThd was high (8.8%ID/g at 60 min) and selective (Tumor to blood ratio: 12.2 at 60 min). Gemicitabine pretreatment significantly reduced the tumor uptake of [methyl- 14C]S-dThd. Relative blood flow as measured by the uptake 4-[N-Methyl- 14C]iodoantipyrine was similar in the

  4. Translesion Synthesis DNA Polymerase: A Novel DNA Polymerase%跨损伤合成的DNA聚合酶——一类新的DNA聚合酶

    Institute of Scientific and Technical Information of China (English)

    陈建明; 余应年

    2001-01-01

    although there are many repair pathways in cells, some lesions still escape repair inevitably and remain in genome. In cells, the molecular mechanism of translesion DNA synthesis has been one of the major unsolved problems in DNA repair for a long time. Recently, it was found that the members of a structurally related UmuC/DinB protein superfarnily have DNA polyrnerase function. Unlike the classical replicative DNA polymerases, these newly identified DNA polymerases can carry out translesion DNA synthesis in both error prone/mutagenic and/or error-free ways. It was also found that their functions are conserved from bacteria to human.%细胞虽然拥有多种修复途径,但有些DNA损伤仍不可避免地会逃避修复而在基因组上保留下来,细胞跨 损伤DNA合成的分子机制一直是DNA修复中主要的未解决问题之一.最近通过对一类结构相关性UmuC/DinB 蛋白质超家族成员的研究发现它们具有DNA聚合酶功能.这类新发现的DNA聚合酶不同于经典的复制性DNA 聚合酶,它们能以易误/突变(error-prone/mutagenic)或无误(error-free)方式进行跨损伤(translesion)DNA合 成,并且从细菌到人在进化上功能保守.

  5. DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization.

    Science.gov (United States)

    Addamiano, Claudia; Gerland, Béatrice; Payrastre, Corinne; Escudier, Jean-Marc

    2016-01-01

    Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5'-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxyl- or carboxyl-azide. Structural impacts of 5'-C(S)-functionalization were investigated to evaluate how 3WJ flexibility/stability is affected. PMID:27563857

  6. DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization

    Directory of Open Access Journals (Sweden)

    Claudia Addamiano

    2016-08-01

    Full Text Available Construction and physico-chemical behavior of DNA three way junction (3WJ functionalized by protein-like residues (imidazole, alcohol and carboxylic acid at unpaired positions at the core is described. One 5′-C(S-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxyl- or carboxyl-azide. Structural impacts of 5′-C(S-functionalization were investigated to evaluate how 3WJ flexibility/stability is affected.

  7. Polyurethane Molecular Stamps for the in situ Synthesis of DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Fabrication of polyurethane molecular stamps (PU stamps) based on polypropylene glycol (PPG) and toluene diisocyanate (TDI), using 3, 3(-dichloro-4, 4(-methylenedianiline (MOCA) as the crosslinker, is reported. It was shown from the contact angle measurement that PU stamps surface has good affinity with acetonitrile, guaranteeing the well distribution of DNA monomers on patterned stamps. Laser confocal fluorescence microscopy images of oligonucleotide arrays after hybridization confirmed polyurethane is an excellent material for molecular stamps when transferring polar chemicals and conducting reactions on interfaces by stamping.

  8. Biomimetic, mild chemical synthesis of CdTe-GSH quantum dots with improved biocompatibility.

    Directory of Open Access Journals (Sweden)

    José M Pérez-Donoso

    Full Text Available Multiple applications of nanotechnology, especially those involving highly fluorescent nanoparticles (NPs or quantum dots (QDs have stimulated the research to develop simple, rapid and environmentally friendly protocols for synthesizing NPs exhibiting novel properties and increased biocompatibility. In this study, a simple protocol for the chemical synthesis of glutathione (GSH-capped CdTe QDs (CdTe-GSH resembling conditions found in biological systems is described. Using only CdCl(2, K(2TeO(3 and GSH, highly fluorescent QDs were obtained under pH, temperature, buffer and oxygen conditions that allow microorganisms growth. These CdTe-GSH NPs displayed similar size, chemical composition, absorbance and fluorescence spectra and quantum yields as QDs synthesized using more complicated and expensive methods.CdTe QDs were not freely incorporated into eukaryotic cells thus favoring their biocompatibility and potential applications in biomedicine. In addition, NPs entry was facilitated by lipofectamine, resulting in intracellular fluorescence and a slight increase in cell death by necrosis. Toxicity of the as prepared CdTe QDs was lower than that observed with QDs produced by other chemical methods, probably as consequence of decreased levels of Cd(+2 and higher amounts of GSH. We present here the simplest, fast and economical method for CdTe QDs synthesis described to date. Also, this biomimetic protocol favors NPs biocompatibility and helps to establish the basis for the development of new, "greener" methods to synthesize cadmium-containing QDs.

  9. Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif

    International Nuclear Information System (INIS)

    The DNA i-motif is a quadruplex structure formed in tandem cytosine-rich sequences in slightly acidic conditions. Besides being considered as a building block of DNA nano-devices, it may also play potential roles in regulating chromosome stability and gene transcriptions. The stability of i-motif is crucial for these functions. In this work, we investigated the mechanical stability of a single i-motif formed in the human telomeric sequence 5'-(CCCTAA)3CCC, which revealed a novel pH and loading rate-dependent bimodal unfolding force distribution. Although the cause of the bimodal unfolding force species is not clear, we proposed a phenomenological model involving a direct unfolding favored at lower loading rate or higher pH value, which is subject to competition with another unfolding pathway through a mechanically stable intermediate state whose nature is yet to be determined. Overall, the unique mechano—chemical responses of i-motif-provide a new perspective to its stability, which may be useful to guide designing new i-motif-based DNA mechanical nano-devices

  10. Synthesis of a drug delivery vehicle for cancer treatment utilizing DNA-functionalized gold nanoparticles

    Science.gov (United States)

    Brann, Tyler

    The treatment of cancer with chemotherapeutic agents has made great strides in the last few decades but still introduces major systemic side effects. The potent drugs needed to kill cancer cells often cause irreparable damage to otherwise healthy organs leading to further morbidity and mortality. A therapy with intrinsic selective properties and/or an inducible activation has the potential to change the way cancer can be treated. Gold nanoparticles (GNPs) are biocompatible and chemically versatile tools that can be readily functionalized to serve as molecular vehicles. The ability of these particles to strongly absorb light with wavelengths in the therapeutic window combined with the heating effect of surface plasmon resonance makes them uniquely suited for noninvasive heating in biologic applications. Specially designed DNA aptamers have shown their ability to serve as drug carriers through intercalation as well as directly acting as therapeutic agents. By combining these separate molecules a multifaceted drug delivery vehicle can be created with great potential as a selective and controllable treatment for cancer. Oligonucleotide-coated GNPs have been created using spherical GNPs but little work has been reported using gold nanoplates in this way. Using the Diasynth method gold nanoplates were produced to absorb strongly in the therapeutic near infrared (nIR) window. These particles were functionalized with two DNA oligonucleotides: one serving as an intercalation site for doxorubicin, and another, AS1411, serving directly as an anticancer targeting/therapeutic agent. These functional particles were fully synthesized and processed along with confirmation of DNA functionalization and doxorubicin intercalation. Doxorubicin is released via denaturation of the DNA structure into which doxorubicin is intercalated upon the heating of the gold nanoplate well above the DNA melting temperature. This temperature increase, due to light stimulation of surface plasmon

  11. Colloidal chemical synthesis and formation kinetics of uniformly sized nanocrystals of metals, oxides, and chalcogenides.

    Science.gov (United States)

    Kwon, Soon Gu; Hyeon, Taeghwan

    2008-12-01

    Nanocrystals exhibit interesting electrical, optical, magnetic, and chemical properties not achieved by their bulk counterparts. Consequently, to fully exploit the potential of nanocrystals, the synthesis of nanocrystals must focus on producing materials with uniform size and shape. Top-down physical processes can produce large quantities of nanocrystals, but controlling the size is difficult with these methods. On the other hand, colloidal chemical synthetic methods can produce uniform nanocrystals with a controlled particle size. In this Account, we present our synthesis of uniform nanocrystals of various shapes and materials, and we discuss the kinetics of nanocrystal formation. We employed four different synthetic approaches including thermal decomposition, nonhydrolytic sol-gel reactions, thermal reduction, and use of reactive chalcogen reagents. We synthesized uniform oxide nanocrystals via heat-up methods. This method involved slowly heat-up reaction mixtures composed of metal precursors, surfactants, and solvents from room temperature to high temperature. We then held reaction mixtures at an aging temperature for a few minutes to a few hours. Kinetics studies revealed a three-step mechanism for the synthesis of nanocrystals through the heat-up method with size distribution control. First, as metal precursors thermally decompose, monomers accumulate. At the aging temperature, burst nucleation occurs rapidly; at the end of this second phase, nucleation stops, but continued diffusion-controlled growth leads to size focusing to produce uniform nanocrystals. We used nonhydrolytic sol-gel reactions to synthesize various transition metal oxide nanocrystals. We employed ester elimination reactions for the synthesis of ZnO and TiO(2) nanocrystals. Uniform Pd nanoparticles were synthesized via a thermal reduction reaction induced by heating up a mixture of Pd(acac)(2), tri-n-octylphosphine, and oleylamine to the aging temperature. Similarly, we synthesized

  12. Inhibition of semiconservative DNA synthesis in ICR 2A frog cells exposed to monochromatic uv wavelengths (252-313 nm) and photoreactivating light

    International Nuclear Information System (INIS)

    Exposure of ICR 2A frog cells to monochromatic uv wavelengths in the range 252-313 nm caused an inhibition of semiconservative DNA synthesis which was partially relieved in cells receiving a post irradiation treatment with photoreactivating light (>350 nm). Hence pyrimidine dimers acted as lesions blocking DNA synthesis in uv-irradiated cells based upon the specificity of photoreactivating enzyme for the light-dependent monomerization of dimers in DNA. Compared with the shorter wavelengths tested, however, this recovery of DNA synthesis was not as great in cells exposed to 302-nm radiation and was nearly absent in 313-nm-irradiated cells up to 12 hr after treatment. These results suggest that nondimer photoproducts also play an important role in causing DNA synthesis inhibition in cells exposed to wavelengths greater than 300 nm

  13. Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

    Science.gov (United States)

    Srinivas, Niranjan

    Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for

  14. Epidermal DNA synthesis in organ culture explants. A study of hairless mouse ear epidermis.

    Science.gov (United States)

    Hansteen, I L; Iversen, O H; Refsum, S B

    1979-10-01

    Explants of split mouse ear were incubated in organ culture for up to 48 h, and the cell proliferation was studied by the addition of Thymidine-methyl-3-H (3HTdR) to the medium during different time periods, mainly for the first 14 h of incubation. Cultures were started at 0900, 2130 and 2300. In all cases the labelling index remained stable for 6-8 h, and then increased. The mean grain count, however, was falling and so was the epidermal DNA-specific uptake of 3HTdR. Based on the experimental results, calculations can be made of the flux of cells through S. It is concluded that the increasing LI is not due to inherent diurnal variation in cell proliferation, and is not a sign of real growth but caused instead by a complete block of the cell exit from S, probably combined with periods of an increased entrance rate into S. Other methodological factors, however, may also contribute to the increasing LI. Hence, this system is not suited for the measurement of factors that influence epidermal DNA synthesis.

  15. Delay in maturation of the submandibular gland in Chagas disease correlates with lower DNA synthesis

    Directory of Open Access Journals (Sweden)

    José B Alves

    2008-09-01

    Full Text Available It has been demonstrated that the acute phase of Trypanosoma cruzi infection promotes several changes in the oral glands. The present study examined whether T. cruzi modulates the expression of host cell apoptotic or mitotic pathway genes. Rats were infected with T. cruzi then sacrificed after 18, 32, 64 or 97 days, after which the submandibular glands were analyzed by immunohistochemistry. Immunohistochemical analyses using an anti-bromodeoxyuridine antibody showed that, during acute T. cruzi infection, DNA synthesizing cells in rat submandibular glands were lower than in non-infected animals (p < 0.05. However, after 64 days of infection (chronic phase, the number of immunolabeled cells are similar in both groups. However, immunohistochemical analysis of Fas and Bcl-2 expression did not find any difference between infected and non-infected animals in both the acute and chronic stages. These findings suggest that the delay in ductal maturation observed at the acute phase of Chagas disease is correlated with lower expression of DNA synthesis genes, but not apoptotic genes.

  16. Polycationic ligands of different chemical classes stimulate DNA strand displacement between short oligonucleotides in a protein-free system.

    Science.gov (United States)

    Volodin, Alexander A; Bocharova, Tatiana N; Smirnova, Elena A

    2016-09-01

    The ability of polycationic ligands to stimulate DNA strand displacement between short oligonucleotides in a protein-free system is demonstrated. We show that two ligands, tetracationic aliphatic amine (spermine) and a dicationic intercalating drug (chloroquine), promote strand displacement in a concentration-dependent manner. At low concentrations both ligands decelerate spontaneous strand displacement because of their impact on the stability of the DNA duplex. At elevated concentrations they accelerate strand displacement via formation of intermediate structures containing three DNA strands. The rate of the last process does not correlate with the thermal dissociation rate of the entire DNA duplex. It indicates that, possibly, the action of these agents cannot be explained by their influence on the stability of the DNA duplex. In general, our results suggest that the ability to stimulate DNA strand displacement appears to be a common feature of polycations of different chemical and structural classes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 633-641, 2016. PMID:27106951

  17. Chemical Capping Synthesis of Nickel Oxide Nanoparticles and their Characterizations Studies

    CERN Document Server

    rifaya, M Nowsath; Alagar, M; 10.5923/j.nn.20120205.01

    2012-01-01

    This work reports aspect related to chemical capping synthesis of nano-sized particles of nickel oxide. It is a simple, novel and cost effective method. The average particle size, specific surface area, crystallinity index are estimated from XRD analysis. The structural, functional groups and optical characters are analyzed with using of SEM, FTIR and UV- visible techniques. XRD studies confirm the presence of high degree of crystallinity nature of nickel oxide nanoparticles. Their particle size is found to be 12 nm and specific surface area (SSA) is 74m2 g-1. The optical band gap energy value 3.83ev has also been determined from UV-vis spectrum.

  18. Synthesis and oxidation behavior of boron-substituted carbon powders by hot filament chemical vapor deposition

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Boron-substituted carbon powder, BxC1-x with x up to 0.17, has been successfully synthesized by hot filament chemical vapor deposition. The boron concentration in prepared BxC1-x samples can be controlled by varying the relative proportions of methane and diborane. X-ray diffraction, transmission electron microscopy, and electron energy loss spectrum confirm the successful synthesis of an amorphous BC5 compound, which consists of 10―20 nm particles with disk-like morphology. Thermogravimetry measurement shows that BC5 compound starts to oxidize ap-proximately at 620℃ and has a higher oxidation resistance than carbon.

  19. Synthesis and Characterization of Tin(IV) Oxide Obtained by Chemical Vapor Deposition Method

    Science.gov (United States)

    Nagirnyak, Svitlana V.; Lutz, Victoriya A.; Dontsova, Tatiana A.; Astrelin, Igor M.

    2016-07-01

    The effect of precursors on the characteristics of tin oxide obtained by chemical vapor deposition (CVD) method was investigated. The synthesis of nanosized tin(IV) oxide was carried out with the use of two different precursors: tin(II) oxalate obtained using tin chloride(II) and oxalic acid; tin(II) oxalate obtained using tin chloride(II); and ammonium oxalate. The synthesized tin(IV) oxide samples were studied by electron microscopy, X-ray diffraction and optical spectra. The lattice parameters of tin(IV) oxide samples were defined, the bandgap of samples were calculated.

  20. Involvement of sulfoquinovosyl diacylglycerol in DNA synthesis in Synechocystis sp. PCC 6803

    Directory of Open Access Journals (Sweden)

    Aoki Motohide

    2012-02-01

    Full Text Available Abstract Background Sulfoquinovosyl diacylglycerol (SQDG is present in the membranes of cyanobacteria and their postulated progeny, plastids, in plants. A cyanobacterium, Synechocystis sp. PCC 6803, requires SQDG for growth: its mutant (SD1 with the sqdB gene for SQDG synthesis disrupted can grow with external supplementation of SQDG. However, upon removal of SQDG from the medium, its growth is retarded, with a decrease in the cellular content of SQDG throughout cell division, and finally ceases. Concomitantly with the decrease in SQDG, the maximal activity of photosynthesis at high-light intensity is repressed by 40%. Findings We investigated effects of SQDG-defect on physiological aspects in Synechocystis with the use of SD1. SD1 cells defective in SQDG exhibited normal photosynthesis at low-light intensity as on culturing. Meanwhile, SD1 cells defective in SQDG were impaired in light-activated heterotrophic growth as well as in photoautotrophic growth. Flow cytometric analysis of the photoautotrophically growing cells gave similar cell size histograms for the wild type and SD1 supplemented with SQDG. However, the profile of SD1 defective in SQDG changed such that large part of the cell population was increased in size. Of particular interest was the microscopic observation that the mitotic index, i.e., population of dumbbell-like cells with a septum, increased from 14 to 29% in the SD1 culture without SQDG. Flow cytometric analysis also showed that the enlarged cells of SD1 defective in SQDG contained high levels of Chl, however, the DNA content was low. Conclusions Our experiments strongly support the idea that photosynthesis is not the limiting factor for the growth of SD1 defective in SQDG, and that SQDG is responsible for some physiologically fundamental process common to both photoautotrophic and light-activated heterotrophic growth. Our findings suggest that the SQDG-defect allows construction of the photosynthetic machinery at an

  1. Detection of short repeated genomic sequences on metaphase chromosomes using padlock probes and target primed rolling circle DNA synthesis

    Directory of Open Access Journals (Sweden)

    Stougaard Magnus

    2007-11-01

    Full Text Available Abstract Background In situ detection of short sequence elements in genomic DNA requires short probes with high molecular resolution and powerful specific signal amplification. Padlock probes can differentiate single base variations. Ligated padlock probes can be amplified in situ by rolling circle DNA synthesis and detected by fluorescence microscopy, thus enhancing PRINS type reactions, where localized DNA synthesis reports on the position of hybridization targets, to potentially reveal the binding of single oligonucleotide-size probe molecules. Such a system has been presented for the detection of mitochondrial DNA in fixed cells, whereas attempts to apply rolling circle detection to metaphase chromosomes have previously failed, according to the literature. Methods Synchronized cultured cells were fixed with methanol/acetic acid to prepare chromosome spreads in teflon-coated diagnostic well-slides. Apart from the slide format and the chromosome spreading everything was done essentially according to standard protocols. Hybridization targets were detected in situ with padlock probes, which were ligated and amplified using target primed rolling circle DNA synthesis, and detected by fluorescence labeling. Results An optimized protocol for the spreading of condensed metaphase chromosomes in teflon-coated diagnostic well-slides was developed. Applying this protocol we generated specimens for target primed rolling circle DNA synthesis of padlock probes recognizing a 40 nucleotide sequence in the male specific repetitive satellite I sequence (DYZ1 on the Y-chromosome and a 32 nucleotide sequence in the repetitive kringle IV domain in the apolipoprotein(a gene positioned on the long arm of chromosome 6. These targets were detected with good efficiency, but the efficiency on other target sites was unsatisfactory. Conclusion Our aim was to test the applicability of the method used on mitochondrial DNA to the analysis of nuclear genomes, in particular as

  2. Protein-DNA chimeras: synthesis of two-arm chimeras and non-mechanical effects of the DNA spring

    International Nuclear Information System (INIS)

    DNA molecular springs have recently been used to control the activity of enzymes and ribozymes. In this approach, the mechanical stress exerted by the molecular spring alters the enzyme's conformation and thus the enzymatic activity. Here we describe a method alternative to our previous one to attach DNA molecular springs to proteins, where two separate DNA 'arms' are coupled to the protein and subsequently ligated. We report certain non-mechanical effects associated with the DNA spring observed in some chimeras with specific DNA sequences and the nucleotide binding enzyme guanylate kinase. If a ssDNA 'arm' is attached to the protein by one end only, we find that in some cases (depending on the DNA sequence and attachment point on the protein's surface) the unhybridized DNA arm inhibits the enzyme, while hybridization of the DNA arm leads to an apparent activation of the enzyme. One interpretation is that, in these cases, hybridization of the DNA arm removes it from the vicinity of the active site of the enzyme. We show how mechanical and non-mechanical effects of the DNA spring can be distinguished. This is important if one wants to use the protein-DNA chimeras to quantitatively study the response of the enzyme to mechanical perturbations.

  3. Effects of Pulsed Electric Fields on DNA Synthesis in an Osteoblast-Like Cell Line (UMR-106)

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The study of the bioeffects of electromagnetic fields (EMFs) is an important national task in biological physics. Using EMFs to treat bone diseases involves electrical technology, biology, and medicine. But the effects of EMFs are still controversial and the mechanisms are not yet clear. Therefore, more effect is needed to detect the effects at the cellular and molecular levels. This paper investigates the effects of low-energy, low-frequency pulsed capacitively coupled electric fields (PCCEFs) on DNA synthesis in UMR-106 osteoblast-like cells. The equipment can generate 25250Hz frequency, 0300V amplitude and 0.2ms pulse width signal. DNA synthesis is judged by the uptake of 3H-thymidine (3H-TdR). The results showed that the response of UMR-106 cells to electric field exposure are characterized by: (a) a frequency window for increased DNA synthesis, with a peak near 125Hz; (b) decreased synthesis with increasing electric intensity with repression at 100V/cm and 25Hz.

  4. Inhibition of semiconservative DNA synthesis in ICR 2A frog cells by pyrimidine dimers and nondimer photoproducts induced by ultraviolet radiation

    International Nuclear Information System (INIS)

    DNA synthesis was examined in ultraviolet (uv)-irradiated ICR 2A frog cells in which either pyrimidine dimers or nondimer photoproducts represented the major class of DNA lesions. In addition, cells were exposed to 60Co γ rays. The cultures were pulse-labeled and the size distribution of the DNA synthesized was estimated using both sucrose gradient sedimentation and alkaline step elution. Using either of these techniques, it was found that the presence of dimers resulted in a reduction principally in the synthesis of high molecular weight (MW) DNA. In contrast, nondimer photoproducts caused a strong inhibition in the synthesis of low MW DNA, as was also observed in γ-irradiated cells. Hence the induction of pyrimidine dimers in DNA mainly affected the elongation of replicons, whereas nondimer lesions primarily caused an inhibition of replicon initiation

  5. The inhibition of DNA synthesis in vitamin-E-depleted lymphosarcoma cells by X-rays and cytostatics

    International Nuclear Information System (INIS)

    Since there is evidence that the lipid-soluble anti-oxidant vitamin E may protect the polyunsaturated fatty acids of cellular membranes from free-radical attack, a shortage of vitamin E should increase the radiosensitivity of the membranes. An investigation has been carried out into the in vivo incorporation of 3H-thymidine in spleen lymphosarcomas growing in X-irradiated (500 rad) normal and vitamin-E-deficient C57BL mice. The results showed that DNA synthesis was significantly more radiosensitive in the vitamin-E-depleted lymphosarcoma cells, and that the effect was most pronounced 3 to 5 hours post irradiation. Studied of the effects of intraperitoneal injections of the cancer therapeutic agents 1-β-D-Arabinofuranosylcytosine (ARA-C) and Adriamycin on the inhibition of thymidine incorporation into DNA showed no significant differences between normal and vitamin-E deficient lymphosarcoma cells. The inhibition of DNA synthesis by these drugs does not involve free radicals. The vitamin E deficient tumour cells had a higher lipid peroxidation rate at 370C (0.5 +- 0.1 nmoles/mg protein per hour) than the normal cells (0.2 +- 0.1 nmoles/mg protein per hour). The higher lipid peroxidation capacity corresponded with the enhanced radiosensitivity. The results provide indirect evidence for the involvement of cellular membranes in the mechanism of radiation-induced inhibition of DNA synthesis. (U.K.)

  6. Energy-dependent existence of soliton in the synthesis of chemical elements

    Science.gov (United States)

    Iwata, Yoritaka

    2015-05-01

    Light chemical elements are, for instance, produced through ion collisions taking place in the core of stars, where fusion is particularly important to the synthesis of chemical elements. Meanwhile soliton provides transparency leading to the hindrance of fusion cross-section. In order to explain high fusion cross-section actually observed in low incident energies, it is necessary to discover the suppression mechanism of soliton propagation. In this paper, based on a systematic three-dimensional time-dependent density functional calculation, the existence of soliton is examined for ion collisions with some incident energies, impact parameters, and nuclear force parameter sets. As a result, solitons are suggested to exist highly depending on the energy. The suppression of soliton is consequently due to the spin-orbit force and the momentum-dependent components of the nuclear force.

  7. Energy-dependent existence of soliton in the synthesis of chemical elements

    CERN Document Server

    Iwata, Yoritaka

    2014-01-01

    Light chemical elements are, for instance, produced through ion collisions taking place in the core of stars, where fusion is particularly important to the synthesis of chemical elements. Meanwhile soliton provides non-interacting transparency leading to the hindrance of fusion cross section. In order to explain high fusion cross section actually observed in low incident energies, it is necessary to discover the suppression mechanism of soliton propagation. In this paper, based on a systematic three-dimensional time-dependent density functional calculation, the existence of soliton is examined for ion collisions with some incident energies, impact parameters, and nuclear force parameter sets. As a result solitons are suggested to exist highly depending on the energy. The suppression of soliton is consequently due to the spin-orbit force and the momentum-dependent components of the nuclear force.

  8. Synthesis, interaction with DNA, cytotoxicity, cell cycle arrest and apoptotic inducing properties of ruthenium(II) molecular "light switch" complexes.

    Science.gov (United States)

    Shobha Devi, C; Anil Kumar, D; Singh, Surya S; Gabra, Nazar; Deepika, N; Kumar, Y Praveen; Satyanarayana, S

    2013-06-01

    In an endeavor toward the development of metal-based anticancer drugs, we present here the design, synthesis and characterization of three ruthenium(II) functionalized phenanthroline complexes with extended π-conjugation. These complexes have been shown to act as promising CT-DNA intercalators as evidenced by UV-visible, luminescence, emission quenching by [Fe(CN)6](4-), DNA competitive binding with ethidium bromide and salt dependent studies. All three complexes [Ru(Hdpa)2PPIP](2+) (1), [Ru(Hdpa)2PIP](2+) (2), [Ru(Hdpa)24HEPIP](2+) (3) clearly demonstrated that they can bind to DNA through the intercalation mode. Cell viability experiments indicated that all complexes showed significant dose dependent cytotoxicity in selected cell lines. The apoptosis and cell cycle arrest were also investigated. The complexes were docked into DNA-base-pairs using the 'GOLD' (Genetic Optimization for Ligand Docking), docking program. PMID:23665797

  9. Synthesis and Characterization of Carbon nanofibers on Co and Cu Catalysts by Chemical Vapor Deposition

    Energy Technology Data Exchange (ETDEWEB)

    Park, Eunsil; Kim, Jongwon; Lee, Changseop [Keimyung Univ., Daegu (Korea, Republic of)

    2014-06-15

    This study reports on the synthesis of carbon nanofibers via chemical vapor deposition using Co and Cu as catalysts. In order to investigate the suitability of their catalytic activity for the growth of nanofibers, we prepared catalysts for the synthesis of carbon nanofibers with Cobalt nitrate and Copper nitrate, and found the optimum concentration of each respective catalyst. Then we made them react with Aluminum nitrate and Ammonium Molybdate to form precipitates. The precipitates were dried at a temperature of 110 .deg. C in order to be prepared into catalyst powder. The catalyst was sparsely and thinly spread on a quartz tube boat to grow carbon nanofibers via thermal chemical vapor deposition. The characteristics of the synthesized carbon nanofibers were analyzed through SEM, EDS, XRD, Raman, XPS, and TG/DTA, and the specific surface area was measured via BET. Consequently, the characteristics of the synthesized carbon nanofibers were greatly influenced by the concentration ratio of metal catalysts. In particular, uniform carbon nanofibers of 27 nm in diameter grew when the concentration ratio of Co and Cu was 6:4 at 700 .deg. C of calcination temperature; carbon nanofibers synthesized under such conditions showed the best crystallizability, compared to carbon nanofibers synthesized with metal catalysts under different concentration ratios, and revealed 1.26 high amorphicity as well as 292 m{sup 2}g{sup -1} high specific surface area.

  10. Five Decades with Polyunsaturated Fatty Acids: Chemical Synthesis, Enzymatic Formation, Lipid Peroxidation and Its Biological Effects

    Science.gov (United States)

    Catalá, Angel

    2013-01-01

    I have been involved in research on polyunsaturated fatty acids since 1964 and this review is intended to cover some of the most important aspects of this work. Polyunsaturated fatty acids have followed me during my whole scientific career and I have published a number of studies concerned with different aspects of them such as chemical synthesis, enzymatic formation, metabolism, transport, physical, chemical, and catalytic properties of a reconstructed desaturase system in liposomes, lipid peroxidation, and their effects. The first project I became involved in was the organic synthesis of [1-14C] eicosa-11,14-dienoic acid, with the aim of demonstrating the participation of that compound as a possible intermediary in the biosynthesis of arachidonic acid “in vivo.” From 1966 to 1982, I was involved in several projects that study the metabolism of polyunsaturated fatty acids. In the eighties, we studied fatty acid binding protein. From 1990 up to now, our laboratory has been interested in the lipid peroxidation of biological membranes from various tissues and different species as well as liposomes prepared with phospholipids rich in PUFAs. We tested the effect of many antioxidants such as alpha tocopherol, vitamin A, melatonin and its structural analogues, and conjugated linoleic acid, among others. PMID:24490074

  11. A Helping Hand to Overcome Solubility Challenges in Chemical Protein Synthesis.

    Science.gov (United States)

    Jacobsen, Michael T; Petersen, Mark E; Ye, Xiang; Galibert, Mathieu; Lorimer, George H; Aucagne, Vincent; Kay, Michael S

    2016-09-14

    Although native chemical ligation (NCL) and related chemoselective ligation approaches provide an elegant method to stitch together unprotected peptides, the handling and purification of insoluble and aggregation-prone peptides and assembly intermediates create a bottleneck to routinely preparing large proteins by completely synthetic means. In this work, we introduce a new general tool, Fmoc-Ddae-OH, N-Fmoc-1-(4,4-dimethyl-2,6-dioxocyclo-hexylidene)-3-[2-(2-aminoethoxy)ethoxy]-propan-1-ol, a heterobifunctional traceless linker for temporarily attaching highly solubilizing peptide sequences ("helping hands") onto insoluble peptides. This tool is implemented in three simple and nearly quantitative steps: (i) on-resin incorporation of the linker at a Lys residue ε-amine, (ii) Fmoc-SPPS elongation of a desired solubilizing sequence, and (iii) in-solution removal of the solubilizing sequence using mild aqueous hydrazine to cleave the Ddae linker after NCL-based assembly. Successful introduction and removal of a Lys6 helping hand is first demonstrated in two model systems (Ebola virus C20 peptide and the 70-residue ribosomal protein L31). It is then applied to the challenging chemical synthesis of the 97-residue co-chaperonin GroES, which contains a highly insoluble C-terminal segment that is rescued by a helping hand. Importantly, the Ddae linker can be cleaved in one pot following NCL or desulfurization. The purity, structure, and chaperone activity of synthetic l-GroES were validated with respect to a recombinant control. Additionally, the helping hand enabled synthesis of d-GroES, which was inactive in a heterochiral mixture with recombinant GroEL, providing additional insight into chaperone specificity. Ultimately, this simple, robust, and easy-to-use tool is expected to be broadly applicable for the synthesis of challenging peptides and proteins. PMID:27532670

  12. Synthesis and characterization of chemically functionalized shape memory nanofoams for unattended sensing applications

    Science.gov (United States)

    Soliani, Anna Paola

    The work in this dissertation is devoted to the synthesis and characterization of novel materials for off-line unattended sensing: shape-memory grafted nanofoams. The fabrication process and characterization of highly efficient, polymeric nanosensor element with the ability to selectively detect analytes and retain memory of specific exposure events is reported. These shape memory nanofoams could potentially act as efficient and highly sensitive coatings for evanescent waveguide-based optical monitoring systems. On exposure to specific analytes, the polymeric coatings locally change their internal structure irreversibly at the nanolevel, affecting the local optical properties such as refractive index. Currently, enrichment polymer layers (EPLs) are currently being used to detect of chemical vapors. EPLs are thin polymer films that can increase signal of an analyte through absorption. These films are designed to interact with analytes via chemical interactions while this analyte is present in the environment. Once the analyte is removed from the environment surrounding the EPL, these EPLs have no residual memory of the interaction(s). This dissertation will address this limitation in the field of chemical unattended sensing through the use of functionalized polymeric films that possess ability to retain memory of analyte exposure. Specifically, we will use chemically cross-linked gradient nanofoam as a material with built-in analyte-specific sensing properties. A novel method has been created to fabricate chemically functionalized shape memory nanofoams. First, a polymer film containing epoxy groups is deposited onto a substrate. Then, the film is cross-linked via reaction of the epoxy groups to create a non-soluble, yet swellable coating. This film is then treated with specific chemical substances capable of reacting with the epoxy functionalities. This procedure is necessary to convert the epoxy groups into various functional moieties. This process generates a

  13. Rectangular Coordination Polymer Nanoplates: Large-Scale, Rapid Synthesis and Their Application as a Fluorescent Sensing Platform for DNA Detection

    OpenAIRE

    Yingwei Zhang; Yonglan Luo; Jingqi Tian; Asiri, Abdullah M.; Al-Youbi, Abdulrahman O.; Xuping Sun

    2012-01-01

    In this paper, we report on the large-scale, rapid synthesis of uniform rectangular coordination polymer nanoplates (RCPNs) assembled from Cu(II) and 4,4'-bipyridine for the first time. We further demonstrate that such RCPNs can be used as a very effective fluorescent sensing platform for multiple DNA detection with a detection limit as low as 30 pM and a high selectivity down to single-base mismatch. The DNA detection is accomplished by the following two steps: (1) RCPN binds dye-labeled sin...

  14. DNA aptamers for selective identification and separation of flame retardant chemicals.

    Science.gov (United States)

    Kim, Un-Jung; Kim, Byoung Chan

    2016-09-14

    Polybrominated diphenyl ethers (PBDEs) are group of chemicals which are representative persistent organic pollutants (POPs) and used as brominated flame retardants for many consumer products. PBDEs were phased out since 2009 but are still frequently observed in various environmental matrices and human body. Here, we report ssDNA aptamers which bind to BDE47, one of the PBDE congeners commonly found in various environmental matrices, and show affinity to other major tri-to hepta- BDE congeners. The PBDE specific aptamers were isolated from random library of ssDNA using Mag-SELEX. Two out of 15 sequences, based on their alignment and hairpin loop structures, were chosen to determine dissociation constant with BDE47 and showed from picomolar to nanomolar affinities (200 pM and 1.53 nM). The aptamers displayed high selectivity to the original target, BDE47, and implying general specificity to PBDE backbone with varying affinities to other congeners. Further, we showed that the use of two aptamers together could enhance the separation efficiency of BDE47 and other BDE congeners when dissolved in a solvent compared to use of single aptamer. These aptamers are expected to provide a tool for preliminary screening or quick separation of PBDEs in environmental samples prior to trace quantitative analysis. PMID:27566357

  15. DNA aptamers for selective identification and separation of flame retardant chemicals.

    Science.gov (United States)

    Kim, Un-Jung; Kim, Byoung Chan

    2016-09-14

    Polybrominated diphenyl ethers (PBDEs) are group of chemicals which are representative persistent organic pollutants (POPs) and used as brominated flame retardants for many consumer products. PBDEs were phased out since 2009 but are still frequently observed in various environmental matrices and human body. Here, we report ssDNA aptamers which bind to BDE47, one of the PBDE congeners commonly found in various environmental matrices, and show affinity to other major tri-to hepta- BDE congeners. The PBDE specific aptamers were isolated from random library of ssDNA using Mag-SELEX. Two out of 15 sequences, based on their alignment and hairpin loop structures, were chosen to determine dissociation constant with BDE47 and showed from picomolar to nanomolar affinities (200 pM and 1.53 nM). The aptamers displayed high selectivity to the original target, BDE47, and implying general specificity to PBDE backbone with varying affinities to other congeners. Further, we showed that the use of two aptamers together could enhance the separation efficiency of BDE47 and other BDE congeners when dissolved in a solvent compared to use of single aptamer. These aptamers are expected to provide a tool for preliminary screening or quick separation of PBDEs in environmental samples prior to trace quantitative analysis.

  16. Chemical elemental distribution and soil DNA fingerprints provide the critical evidence in murder case investigation.

    Directory of Open Access Journals (Sweden)

    Giuseppe Concheri

    Full Text Available BACKGROUND: The scientific contribution to the solution of crime cases, or throughout the consequent forensic trials, is a crucial aspect of the justice system. The possibility to extract meaningful information from trace amounts of samples, and to match and validate evidences with robust and unambiguous statistical tests, are the key points of such process. The present report is the authorized disclosure of an investigation, carried out by Attorney General appointment, on a murder case in northern Italy, which yielded the critical supporting evidence for the judicial trial. METHODOLOGY/PRINCIPAL FINDINGS: The proportional distribution of 54 chemical elements and the bacterial community DNA fingerprints were used as signature markers to prove the similarity of two soil samples. The first soil was collected on the crime scene, along a corn field, while the second was found in trace amounts on the carpet of a car impounded from the main suspect in a distant location. The matching similarity of the two soils was proven by crossing the results of two independent techniques: a elemental analysis via inductively coupled plasma mass spectrometry (ICP-MS and optical emission spectrometry (ICP-OES approaches, and b amplified ribosomal DNA restriction analysis by gel electrophoresis (ARDRA. CONCLUSIONS: Besides introducing the novel application of these methods to forensic disciplines, the highly accurate level of resolution observed, opens new possibilities also in the fields of soil typing and tracking, historical analyses, geochemical surveys and global land mapping.

  17. Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex.

    Science.gov (United States)

    Loth, Karine; Landon, Céline; Paquet, Françoise

    2015-04-01

    MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.

  18. DNA damage and autophagy

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States); Panayiotidis, Mihalis I. [School of Community Health Sciences, University of Nevada, Reno, NV 89557 (United States); Franco, Rodrigo, E-mail: rfrancocruz2@unl.edu [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States)

    2011-06-03

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  19. EFFECT OF HYPOXIA ON DNA SYNTHESIS AND C-MYC GENE EXPRESSION OF PULMONARY ARTERY SMOOTH MUSCLE CELLS

    Institute of Scientific and Technical Information of China (English)

    罗兰; 李世强; 蔡英年

    1996-01-01

    The neonate is particularly susceptible to the development of hypoxie pulmonary hypertension. The present study was undertaken to observe the effect of hypoxia on DNA synthesis and c-mye gene expressionbetween newborn calf and adult bovine PASMC in vitro DNA synthesis measured by 3H-TdR incorporation was increased after hypoxie challenge for 24h. Hypoxia enhanced the increment in 3H-TdR incorporationinduced by EGF. Northern blot analysis revealed that PASMC cultured in both normoxia and hypoxia expressed c-mye gene transcript of 2.2Kb ,but there is a higher 2.2Kb mRNA expression in hypoxie PASMC than that in normoxia. We speculate that newborn calf PASMC exhibited potential response to hypoxia than adult,which was augmented by EGF. Enhanced c-myc gene expression may lead to a great understanding of the mechanism of PASMC growth in the development of pulmonary hypertension.

  20. Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA

    Science.gov (United States)

    Price, Nathan E.; Catalano, Michael J.; Liu, Shuo; Wang, Yinsheng; Gates, Kent S.

    2015-01-01

    A new type of interstrand DNA–DNA cross-link between abasic (Ap) sites and 2′-deoxyadenosine (dA) residues was recently reported, but the chemical structure and properties of this lesion were not rigorously established. Here we characterized the nucleoside cross-link remnant released by enzymatic digestion of duplex DNA containing the dA-Ap cross-link. A synthetic standard was prepared for the putative nucleoside cross-link remnant 6 in which the anomeric carbon of the 2-deoxyribose residue was connected to the exocyclic N6-amino group of dA. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that the synthetic material 6 matched the authentic cross-link remnant released by enzymatic digestion of cross-linked DNA. These findings establish the chemical structure of the dA-Ap cross-link released from duplex DNA and may provide methods for the detection of this lesion in cellular DNA. Both the nucleoside cross-link remnant 6 and the cross-link in duplex DNA were quite stable at pH 7 and 37°C, suggesting that the dA-Ap cross-link could be a persistent lesion with the potential to block the action of various DNA processing enzymes. PMID:25779045

  1. DNA Synthesis in the Giant Nuclei of Insects - Control Machinery and Structures Observed in the Silk-Producing Gland of Bombyx Mori

    International Nuclear Information System (INIS)

    The existence in many insect organs of giant nuclei without visible chromosomes raises the question of possible homologies between the chromatin structures of these nuclei and those of polytene nuclei or common euploid cells. Studies have been made of the nuclei in the silk-producing gland of Bombyx mori. The DNA synthesis is cyclic. During the third stage there are three successive synthesis cycles, which appear to be relatively autonomous in the individual nuclei. For more than 24 hours after moulting, however, synthesis is greatly reduced; moulting factors thus cause synchronization of all the nuclei. This leads to the conclusion that the triggering of a synthesis cycle is controlled by general factors external to the cell. At the end of larval development, DNA synthesis is suspended at the moment when large-scale secretion of silk begins. Evaluation of the pool of endogenic precursors of DNA shows that it is considerably reduced at the end of the DNA synthesis period. The hypothesis proposed is that large-scale synthesis of fibroin requires polarization of the metabolism, hence the depletion of the nucleotide pool and the end of DNA synthesis. DNA synthesis within a single nucleus is to some extent asynchronic. In particular, a well-defined, delayed-synthesis structure visible only in the female seems to be a possible homologue of a sex chromosome. Other asynchronisms are also apparent, though less clearly. Functional studies thus allow the supposition that in the giant nucleus replication units retain an individuality comparable to that of a polytene chromosome. These observations together lead to the conclusion that a nucleus in the silk-producing gland has physiological and structural characteristics similar to those of a polytene nucleus, differing from it essentially in the lesser degree of condensation of its structures. (author)

  2. Chemical synthesis of porous web-structured CdS thin films for photosensor applications

    International Nuclear Information System (INIS)

    The photo-activity of chemically deposited cadmium sulphide (CdS) thin film has been studied. The simple chemical route nucleates the CdS films with size up to the mean free path of the electron. Growth Kinematics of crystalline hexagonal CdS phase in the thin film form was monitored using X-ray diffraction. The time limitation set for the formation of the amorphous/nano-crystalline material is 40 and 60 min. Thereafter enhancement of the crystalline orientation along the desired plane was identified. Web-like porous structured surface morphology of CdS thin film over the entire area is observed. With decrease in synthesis time, increase of band gap energy i.e., a blue spectral shift was seen. The activation energy of CdS thin film at low and high temperature region was examined. It is considered that this activation energy corresponds to the donor levels associated with shallow traps or surface states of CdS thin film. The photo-electrochemical performance of CdS thin films in polysulphide electrolyte showed diode-like characteristics. Exposure of light on the CdS electrode increases the photocurrent. This suggests the possibility of production of free carriers via excited ions and also the light harvesting mechanism due to porous web-structured morphology. These studies hint that the obtained CdS films can work as a photosensor. - Highlights: • Photoactivity of chemically synthesized cadmium sulphide (CdS) thin films was studied. • Web-like porous structured surface morphology of CdS thin film over the entire area was observed. • Blue spectral shift with lowering of the synthesis time suggests films can act as a window layer over the absorber layer. • Porous web-structured CdS thin films can be useful in light harvesting

  3. Complementation of the xeroderma pigmentosum DNA repair synthesis defect with Escherichia coli UvrABC proteins in a cell-free system.

    OpenAIRE

    Hansson, J; Grossman, L; Lindahl, T; Wood, R D

    1990-01-01

    A newly developed cell-free system was used to study DNA repair synthesis carried out by extracts from human cell lines in vitro. Extracts from a normal human lymphoid cell line and from cell lines established from individuals with hereditary dysplastic nevus syndrome perform damage-dependent repair synthesis in plasmid DNA treated with cis- or trans-diamminedichloro-platinum(II) or irradiated with ultraviolet light. Cell extracts of xeroderma pigmentosum origin (complementation groups A, C, ...

  4. Rectangular coordination polymer nanoplates: large-scale, rapid synthesis and their application as a fluorescent sensing platform for DNA detection.

    Directory of Open Access Journals (Sweden)

    Yingwei Zhang

    Full Text Available In this paper, we report on the large-scale, rapid synthesis of uniform rectangular coordination polymer nanoplates (RCPNs assembled from Cu(II and 4,4'-bipyridine for the first time. We further demonstrate that such RCPNs can be used as a very effective fluorescent sensing platform for multiple DNA detection with a detection limit as low as 30 pM and a high selectivity down to single-base mismatch. The DNA detection is accomplished by the following two steps: (1 RCPN binds dye-labeled single-stranded DNA (ssDNA probe, which brings dye and RCPN into close proximity, leading to fluorescence quenching; (2 Specific hybridization of the probe with its target generates a double-stranded DNA (dsDNA which detaches from RCPN, leading to fluorescence recovery. It suggests that this sensing system can well discriminate complementary and mismatched DNA sequences. The exact mechanism of fluorescence quenching involved is elucidated experimentally and its use in a human blood serum system is also demonstrated successfully.

  5. Poly(ADP-ribose)--a unique natural polymer structural features, biological role and approaches to the chemical synthesis.

    Science.gov (United States)

    Drenichev, Mikhail S; Mikhailov, Sergey N

    2015-01-01

    Poly(ADP-ribose) (PAR) is a natural polymer, taking part in numerous important cellular processes. Several enzymes are involved in biosynthesis and degradation of PAR. One of them, poly(ADP-ribose)polymerase-1 (PARP-1) is considered to be a perspective target for the design of new drugs, affecting PAR metabolism. The structure of PAR was established by enzymatic hydrolysis and further analysis of the products, but total chemical synthesis of PAR hasn't been described yet. Several approaches have been developed on the way to chemical synthesis of this unique biopolymer.

  6. DNA synthesis time in germinating rice and pattern of diethylsulphate induced mutations in pre-soaked seeds

    International Nuclear Information System (INIS)

    DNA synthesis pattern in germinating rice seeds, pre-soaked in water for varying periods upto 48 hr, was determined by following the pulse incorporation of 3H-thymidine into the TCA-insoluble nucleoprotein. Synthesis of DNA commenced at 24 hr, progressively increased to a first peak at about 38 hr, thereafter showed a 1/3rd drop and subsequently increased to a 2nd and still higher peak at 46 to 48 hr of pre-soaking. Treatments of diethylsulphate (dES) at a low concentration (0.2%-2hr) administered at various progressing stages of DNA synthesis resulted in decrease in seedling height and survival, and increase in mutation frequency at 45 hr. pre-soaking, maximum mutation frequencies of 20, 10 and 2% on M1 plants, M1 spikes and M2 seedling bases, respectively were observed. Higher dES concentration (0.3%-2hr) given at later periods of pre-soaking showed near lethal effects and consequently decreased mutation frequencies. Treatments of sodium fluoride given singly or in combination with dES did not show any substantially different results as compared to those of the respective controls. Mutation spectra observed after dES treatments to germinating seeds, at different pre-soaking periods, were quite dissimilar. Specific mutations of economic importance like semi-dwarf mutants were isolated from the treatment of germinating seeds pre-soaked for 37.5 hr or more when shoot apex cells were undergoing DNA synthesis. (author)

  7. DNA repair in lymphocytes from patients with secondary leukemia as measured by strand rejoining and unscheduled DNA synthesis

    DEFF Research Database (Denmark)

    Bohr, V; Køber, L

    1985-01-01

    The ability to repair damage to DNA was compared in 2 groups of patients having undergone treatment for leukemia, one of which developed secondary leukemia (SL), and the other without signs of secondary malignancy (treated controls). Both were related to normal controls. DNA repair was assessed...

  8. Comparison of protein and DNA synthesis assays of guinea pig spleen lymphocytes after stimulation with influenza virus antigen and phytohemagglutinin

    International Nuclear Information System (INIS)

    Two in vitro methods for the demonstration of cell-mediated immune response are compared: Protein and DNA synthesis for detection of in vitro influenza virus antigen- and mitogen-induced lymphocyte stimulation. Guinea pig spleen lymphocytes sensitized with influenza virus antigen were tested in a microadaptation of the lymphocyte transformation test using 14C- or 3H-leucine and 3H-thymidine. As a positive control for T-cell stimulation phytohemagglutinin (PHA)-induced lymphocyte stimulation was measured. The following results were obtained: 1. Kinetics of the incorporation of 14C-leucine and 3H-thymidine in lymphocytes incubated with optimal and suboptimal PHA-doses respectively are quantitatively similar but different in time. 2. The results of the protein and DNA synthesis stimulation assays were correlated against influenza virus antigens. 3. The administration of influenza virus antigens in complete Freund's adjuvant induced a more intensive cell-mediated reaction than injections of antigens in aqueous suspensions, but the results of both methods of cell-mediated immune response (CMI) were correlated. 4. The optimal CMI under the experimental cinditions described is induced by an administration of 30 to 50 μg virus protein per animal and by a combined intramuscular - intraperitoneal immunization procedure. 5. The measurement of the early stimulation of protein synthesis in the protein synthesis stimulation test is substantially more rapid than for the classical lymphocyte transformation test. (author)

  9. Synthesis of a Hoechst 32258 analogue amino acid building block for direct incorporation of a fluorescent, high-affinity DNA binding motif into peptides

    DEFF Research Database (Denmark)

    Behrens, C; Harrit, N; Nielsen, P E

    2001-01-01

    The synthesis of a new versatile "Hoechst 33258-like" Boc-protected amino acid building block for peptide synthesis is described. It is demonstrated that this new ligand is an effective mimic of Hoechst 33258 in terms of DNA affinity and sequence specificity. Furthermore, this minor groove binder...

  10. Synthesis, spectroscopic characterization, biological screenings, DNA binding study and POM analyses of transition metal carboxylates

    Science.gov (United States)

    Uddin, Noor; Sirajuddin, Muhammad; Uddin, Nizam; Tariq, Muhammad; Ullah, Hameed; Ali, Saqib; Tirmizi, Syed Ahmed; Khan, Abdur Rehman

    2015-04-01

    This article contains the synthesis of a novel carboxylic acid derivative, its transition metal complexes and evaluation of biological applications. Six carboxylate complexes of transition metals, Zn(II) and Hg(II), have been successfully synthesized and characterized by FT-IR and NMR (1H, 13C). The ligand, HL, (4-[(2,6-Diethylphenyl)amino]-4-oxobutanoic acid) was also characterized by single crystal X-ray analysis. The complexation occurs via oxygen atoms of the carboxylate moiety. FT-IR date show the bidentate nature of the carboxylate moiety of the ligand as the Δν value in all complexes is less than that of the free ligand. The ligand and its complexes were screened for antifungal and antileishmanial activities. The results showed that the ligand and its complexes are active with few exceptions. UV-visible spectroscopy and viscometry results reveal that the ligand and its complexes interact with the DNA via intercalative mode of interaction. A new and efficient strategy to identify the pharmacophores and anti-pharmacophores sites in carboxylate derivatives for the antibacterial/antifungal activity using Petra, Osiris and Molinspiration (POM) analyses was also carried out.

  11. The DNA methylation inhibitor 5-azacytidine decreases melanin synthesis by inhibiting CREB phosphorylation.

    Science.gov (United States)

    Shin, Jun Seob; Jeong, Hyo-Soon; Kim, Myo-Kyoung; Yun, Hye-Young; Baek, Kwang Jin; Kwon, Nyoun Soo; Kim, Dong-Seok

    2015-10-01

    Here we examined the effects of a DNA methylation inhibitor, 5-azacytidine, on melanogenesis in Mel-Ab cells. We found that 5-azacytidine decreased the melanin content and tyrosinase activity in these cells in a dose-dependent manner; importantly, 5-azacytidine was not cytotoxic at the concentrations used in these experiments. On the other hand, 5-azacytidine did not affect tyrosinase activity in a cell-free system, indicating that 5-azacytidine is not a direct tyrosinase inhibitor. Instead, 5-azacytidine decreased the protein levels of microphthalmia-associated transcription factor (MITF) and tyrosinase. Thus, we investigated the effects of 5-azacytidine on signal transduction pathways related to melanogenesis. However, 5-azacytidine did not have any effect on either Akt or glycogen synthase kinase 3β (GSK3β) phosphorylation. The phosphorylation of cAMP response element-binding protein (CREB) is well known to regulate MITF expression, thereby also regulating tyrosinase expression. We found that 5-azacytidine decreased the phosphorylation of CREB. Therefore, we propose that 5-azacytidine may decrease melanin synthesis by downregulating MITF and tyrosinase via CREB inactivation. PMID:26601420

  12. Candida famata (Debaryomyces hansenii) DNA sequences containing genes involved in riboflavin synthesis.

    Science.gov (United States)

    Voronovsky, Andriy Y; Abbas, Charles A; Dmytruk, Kostyantyn V; Ishchuk, Olena P; Kshanovska, Barbara V; Sybirna, Kateryna A; Gaillardin, Claude; Sibirny, Andriy A

    2004-11-01

    Previously cloned Candida famata (Debaryomyces hansenii) strain VKM Y-9 genomic DNA fragments containing genes RIB1 (codes for GTP cyclohydrolase II), RIB2 (encodes specific reductase), RIB5 (codes for dimethylribityllumazine synthase), RIB6 (encodes dihydroxybutanone phosphate synthase) and RIB7 (codes for riboflavin synthase) were sequenced. The derived amino acid sequences of C. famata RIB genes showed extensive homology to the corresponding sequences of riboflavin synthesis enzymes of other yeast species. The highest identity was observed to homologues of D. hansenii CBS767, as C. famata is the anamorph of this hemiascomycetous yeast. The D. hansenii CBS767 RIB3 gene encoding specific deaminase was cloned. This gene successfully complemented riboflavin auxotrophy of the rib3 mutant of flavinogenic yeast, Pichia guilliermondii. Putative iron-responsive elements (potential sites for binding of the transcription factors Fep1p or Aft1p and Aft2p) were found in the upstream regions of some C. famata and D. hansenii RIB genes. The sequences of C. famata RIB genes have been submitted to the EMBL data library under Accession Nos AJ810169-AJ810173. PMID:15543522

  13. Harnessing DNA Synthesis to Develop Rapid Responses to Emerging and Pandemic Pathogens

    Directory of Open Access Journals (Sweden)

    Lisa M. Runco

    2011-01-01

    Full Text Available Given the interconnected nature of our world today, emerging pathogens and pandemic outbreaks are an ever-growing threat to the health and economic stability of the global community. This is evident by the recent 2009 Influenza A (H1N1 pandemic, the SARS outbreak, as well as the ever-present threat of global bioterrorism. Fortunately, the biomedical community has been able to rapidly generate sequence data so these pathogens can be readily identified. To date, however, the utilization of this sequence data to rapidly produce relevant experimental results or actionable treatments is lagging in spite of obtained sequence data. Thus, a pathogenic threat that has emerged and/or developed into a pandemic can be rapidly identified; however, translating this identification into a targeted therapeutic or treatment that is rapidly available has not yet materialized. This commentary suggests that the growing technology of DNA synthesis should be fully implemented as a means to rapidly generate in vivo data and possibly actionable therapeutics soon after sequence data becomes available.

  14. Candida famata (Debaryomyces hansenii) DNA sequences containing genes involved in riboflavin synthesis.

    Science.gov (United States)

    Voronovsky, Andriy Y; Abbas, Charles A; Dmytruk, Kostyantyn V; Ishchuk, Olena P; Kshanovska, Barbara V; Sybirna, Kateryna A; Gaillardin, Claude; Sibirny, Andriy A

    2004-11-01

    Previously cloned Candida famata (Debaryomyces hansenii) strain VKM Y-9 genomic DNA fragments containing genes RIB1 (codes for GTP cyclohydrolase II), RIB2 (encodes specific reductase), RIB5 (codes for dimethylribityllumazine synthase), RIB6 (encodes dihydroxybutanone phosphate synthase) and RIB7 (codes for riboflavin synthase) were sequenced. The derived amino acid sequences of C. famata RIB genes showed extensive homology to the corresponding sequences of riboflavin synthesis enzymes of other yeast species. The highest identity was observed to homologues of D. hansenii CBS767, as C. famata is the anamorph of this hemiascomycetous yeast. The D. hansenii CBS767 RIB3 gene encoding specific deaminase was cloned. This gene successfully complemented riboflavin auxotrophy of the rib3 mutant of flavinogenic yeast, Pichia guilliermondii. Putative iron-responsive elements (potential sites for binding of the transcription factors Fep1p or Aft1p and Aft2p) were found in the upstream regions of some C. famata and D. hansenii RIB genes. The sequences of C. famata RIB genes have been submitted to the EMBL data library under Accession Nos AJ810169-AJ810173.

  15. Production of thymine glycols in DNA by radiation and chemical carcinogens as detected by a monoclonal antibody.

    Science.gov (United States)

    Leadon, S A

    1987-06-01

    In order to understand the role in carcinogenesis of damage indirectly induced by chemical carcinogens, it is important to identify the primary DNA lesions. We have measured the formation and repair of one type of DNA modification, 5,6-dihydroxydihydrothymine (thymine glycol), following exposure of cultured human cells to the carcinogens N-hydroxy-2-naphthylamine or benzo(a)pyrene. The efficiency of production of thymine glycols in DNA by these carcinogens was compared to that by ionizing radiation and ultraviolet light. Thymine glycols were detected using a monoclonal antibody against this product in a sensitive immunoassay. We found that thymine glycols were produced in DNA in a dose dependent manner after exposure to the carcinogens and that their production was reduced if either catalase or superoxide dismutase or both were present at the time of treatment. The efficiency of thymine glycol production following exposure to the chemical carcinogens was greater than that following equi-toxic doses of radiation. Thymine glycols were efficiently removed from the DNA of human cells following treatment with either the chemical carcinogens, ionizing radiation or ultraviolet light. PMID:3477281

  16. Post-irradiation chemical processing of DNA damage generates double-strand breaks in cells already engaged in repair

    Science.gov (United States)

    Singh, Satyendra K.; Wang, Minli; Staudt, Christian; Iliakis, George

    2011-01-01

    In cells exposed to ionizing radiation (IR), double-strand breaks (DSBs) form within clustered-damage sites from lesions disrupting the DNA sugar–phosphate backbone. It is commonly assumed that these DSBs form promptly and are immediately detected and processed by the cellular DNA damage response (DDR) apparatus. This assumption is questioned by the observation that after irradiation of naked DNA, a fraction of DSBs forms minutes to hours after exposure as a result of temperature dependent, chemical processing of labile sugar lesions. Excess DSBs also form when IR-exposed cells are processed at 50°C, but have been hitherto considered method-related artifact. Thus, it remains unknown whether DSBs actually develop in cells after IR exposure from chemically labile damage. Here, we show that irradiation of ‘naked’ or chromatin-organized mammalian DNA produces lesions, which evolve to DSBs and add to those promptly induced, after 8–24 h in vitro incubation at 37°C or 50°C. The conversion is more efficient in chromatin-associated DNA, completed within 1 h in cells and delayed in a reducing environment. We conclude that IR generates sugar lesions within clustered-damage sites contributing to DSB formation only after chemical processing, which occurs efficiently at 37°C. This subset of delayed DSBs may challenge DDR, may affect the perceived repair kinetics and requires further characterization. PMID:21745815

  17. Electric Current Activated Combustion Synthesis and Chemical Ovens Under Terrestrial and Reduced Gravity Conditions

    Science.gov (United States)

    Unuvar, C.; Fredrick, D.; Anselmi-Tamburini, U.; Manerbino, A.; Guigne, J. Y.; Munir, Z. A.; Shaw, B. D.

    2004-01-01

    Combustion synthesis (CS) generally involves mixing reactants together (e.g., metal powders) and igniting the mixture. Typically, a reaction wave will pass through the sample. In field activated combustion synthesis (FACS), the addition of an electric field has a marked effect on the dynamics of wave propagation and on the nature, composition, and homogeneity of the product as well as capillary flow, mass-transport in porous media, and Marangoni flows, which are influenced by gravity. The objective is to understand the role of an electric field in CS reactions under conditions where gravity-related effects are suppressed or altered. The systems being studied are Ti+Al and Ti+3Al. Two different ignition orientations have been used to observe effects of gravity when one of the reactants becomes molten. This consequentially influences the position and concentration of the electric current, which in turn influences the entire process. Experiments have also been performed in microgravity conditions. This process has been named Microgravity Field Activated Combustion Synthesis (MFACS). Effects of gravity have been demonstrated, where the reaction wave temperature and velocity demonstrate considerable differences besides the changes of combustion mechanisms with the different high currents applied. Also the threshold for the formation of a stable reaction wave is increased under zero gravity conditions. Electric current was also utilized with a chemical oven technique, where inserts of aluminum with minute amounts of tungsten and tantalum were used to allow observation of effects of settling of the higher density solid particles in liquid aluminum at the present temperature profile and wave velocity of the reaction.

  18. The PCNA-associated protein PARI negatively regulates homologous recombination via the inhibition of DNA repair synthesis.

    Science.gov (United States)

    Burkovics, Peter; Dome, Lili; Juhasz, Szilvia; Altmannova, Veronika; Sebesta, Marek; Pacesa, Martin; Fugger, Kasper; Sorensen, Claus Storgaard; Lee, Marietta Y W T; Haracska, Lajos; Krejci, Lumir

    2016-04-20

    Successful and accurate completion of the replication of damage-containing DNA requires mainly recombination and RAD18-dependent DNA damage tolerance pathways. RAD18 governs at least two distinct mechanisms: translesion synthesis (TLS) and template switching (TS)-dependent pathways. Whereas TS is mainly error-free, TLS can work in an error-prone manner and, as such, the regulation of these pathways requires tight control to prevent DNA errors and potentially oncogenic transformation and tumorigenesis. In humans, the PCNA-associated recombination inhibitor (PARI) protein has recently been shown to inhibit homologous recombination (HR) events. Here, we describe a biochemical mechanism in which PARI functions as an HR regulator after replication fork stalling and during double-strand break repair. In our reconstituted biochemical system, we show that PARI inhibits DNA repair synthesis during recombination events in a PCNA interaction-dependent way but independently of its UvrD-like helicase domain. In accordance, we demonstrate that PARI inhibits HRin vivo, and its knockdown suppresses the UV sensitivity of RAD18-depleted cells. Our data reveal a novel human regulatory mechanism that limits the extent of HR and represents a new potential target for anticancer therapy. PMID:26792895

  19. Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop DNA synthesis.

    OpenAIRE

    Foran, D R; Hixson, J E; Brown, W. M.

    1988-01-01

    The mitochondrial DNA (mtDNA) control regions for common chimpanzee, pygmy chimpanzee and gorilla were sequenced and the lengths and termini of their D-loop DNA's characterized. In these and all other species for which there are data, 5' termini map to sequences that contain the trinucleotide YAY. 3' termini are 25-51 nucleotides downstream from a sequence that is moderately conserved among vertebrates. Substitutions were greater than 1.5 times more frequent in the control region than in regi...

  20. The application of zero-current potentiometry in chemical synthesis and characterization of polypyrrole using electrochemical sensors

    Energy Technology Data Exchange (ETDEWEB)

    Budimir, M.V. (Faculty of Agriculture, Univ. of Osijek (Yugoslavia)); Sak-Bosnar, M. (Pedagogical Faculty, Univ. of Osijek (Yugoslavia)); Kovac, S. (Faculty of Food Tech., Univ. of Osijek (Yugoslavia)); Duic, L. (Faculty of Tech., Inst. of Electrochemistry, Univ. of Zagreb (Yugoslavia))

    1991-01-01

    The chemical polymerization of pyrrole to highly conducting polypyrrole in aqueous and acetonitrile solutions using various oxidizing agents was studied. The course of synthesis was followed using zero-current potentiometry with a platinum reference electrode as redox sensor. The obtained results can be used for a better understanding of pyrrole polymerization kinetics. In addition, the halogenide-ion content as counter ion can be determined potentiometrically after chemical degradation of polypyrrole using a chloride-selective electrode as sensor. (orig.).

  1. Early evaluation of potential environmental impacts of carbon nanotube synthesis by chemical vapor deposition.

    Science.gov (United States)

    Plata, Desirée L; Hart, A John; Reddy, Christopher M; Gschwend, Philip M

    2009-11-01

    The carbon nanotube (CNT) industry is expanding rapidly, yet little is known about the potential environmental impacts of CNT manufacture. Here, we evaluate the effluent composition of a representative multiwalled CNT synthesis by catalytic chemical vapor deposition (CVD) in order to provide data needed to design strategies for mitigating any unacceptable emissions. During thermal pretreatment of the reactant gases (ethene and H(2)), we found over 45 side-products were formed, including methane, volatile organic compounds (VOCs), and polycyclic aromatic hydrocarbons (PAHs). This finding suggests several environmental concerns with the existing process, including potential discharges of the potent greenhouse gas, methane (up to 1.7%), and toxic compounds such as benzene and 1,3-butadiene (up to 36000 ppmv). Extrapolating these laboratory-scale data to future industrial CNT production, we estimate that (1) contributions of atmospheric methane will be negligible compared to other existing sources and (2) VOC and PAH emissions may become important on local scales but will be small when compared to national industrial sources. As a first step toward reducing such unwanted emissions, we used continuous in situ measures of CNT length during growth and sought to identify which thermally generated compounds correlated with CNT growth rate. The results suggested that, in future CNT production approaches, key reaction intermediates could be delivered to the catalyst without thermal treatment. This would eliminate the most energetically expensive component of CVD synthesis (heating reactant gases), while reducing the formation of unintended byproducts. PMID:19924971

  2. Bio-electrochemical synthesis of commodity chemicals by autotrophic acetogens utilizing CO_{2} for environmental remediation

    Indian Academy of Sciences (India)

    GUGAN JABEEN; ROBINA FAROOQ

    2016-09-01

    Bio-electrochemical synthesis (BES) is a technique in which electro-autotrophic bacteria such as Clostridiumljungdahlii utilize electric currents as an electron source from the cathode to reduce CO_{2} to extracellular, multicarbon,exquisite products through autotrophic conversion. The BES of volatile fatty acids and alcohols directly fromCO_{2} is a sustainable alternative for non-renewable, petroleum-based polymer production. This conversion ofCO_{2} implies reduction of greenhouse gas emissions. The synthesis of heptanoic acid, heptanol, hexanoic acidand hexanol, for the first time, by Clostridium ljungdahlii was a remarkable achievement of BES. In ourstudy, these microorganisms were cultivated on the cathode of a bio-electrochemical cell at −400 mV by aDC power supply at 37°C, pH 6.8, and was studied for both batch and continuous systems. Pre-enrichment ofbio-cathode enhanced the electroactivity of cells and resulted in maximizing extracellular products in lesstime. The main aim of the research was to investigate the impact of low-cost substrate CO_{2}, and the longercathode recovery range was due to bacterial reduction of CO_{2} to multicarbon chemical commodities withelectrons driven from the cathode. Reactor design was simplified for cost-effectiveness and to enhance energyefficiencies. The Columbic recovery of ethanoic acid, ethanol, ethyl butyrate, hexanoic acid, heptanoic acidand hexanol being in excess of 80% proved that BES was a remarkable technology.

  3. Bio-electrochemical synthesis of commodity chemicals by autotrophic acetogens utilizing CO2 for environmental remediation.

    Science.gov (United States)

    Jabeen, Gugan; Farooq, Robina

    2016-09-01

    Bio-electrochemical synthesis (BES) is a technique in which electro-autotrophic bacteria such as Clostridium ljungdahlii utilize electric currents as an electron source from the cathode to reduce CO2 to extracellular, multicarbon, exquisite products through autotrophic conversion. The BES of volatile fatty acids and alcohols directly from CO2 is a sustainable alternative for non-renewable, petroleum-based polymer production. This conversion of CO2 implies reduction of greenhouse gas emissions. The synthesis of heptanoic acid, heptanol, hexanoic acid and hexanol, for the first time, by Clostridium ljungdahlii was a remarkable achievement of BES. In our study, these microorganisms were cultivated on the cathode of a bio-electrochemical cell at -400 mV by a DC power supply at 37 degree Centrigrade, pH 6.8, and was studied for both batch and continuous systems. Pre-enrichment of bio-cathode enhanced the electroactivity of cells and resulted in maximizing extracellular products in less time. The main aim of the research was to investigate the impact of low-cost substrate CO2, and the longer cathode recovery range was due to bacterial reduction of CO2 to multicarbon chemical commodities with electrons driven from the cathode. Reactor design was simplified for cost-effectiveness and to enhance energy efficiencies. The Columbic recovery of ethanoic acid, ethanol, ethyl butyrate, hexanoic acid, heptanoic acid and hexanol being in excess of 80 percent proved that BES was a remarkable technology. PMID:27581929

  4. Copper Nanoparticles Mediated by Chitosan: Synthesis and Characterization via Chemical Methods

    Directory of Open Access Journals (Sweden)

    Muhammad Sani Usman

    2012-12-01

    Full Text Available Herein we report a synthesis of copper nanoparticles (Cu-NPs in chitosan (Cts media via a chemical reaction method. The nanoparticles were synthesized in an aqueous solution in the presence of Cts as stabilizer and CuSO4·5H2O precursor. The synthesis proceeded with addition of NaOH as pH moderator, ascorbic acid as antioxidant and hydrazine as the reducing agent. The characterization of the prepared NPs was done using ultraviolet-visible spectroscopy, which showed a 593 nm copper band. The Field Emission Scanning Electron Microscope (FESEM images were also observed, and found to be in agreement with the UV-Vis result, confirming the formation of metallic Cu-NPs. The mean size of the Cu-NPs was estimated to be in the range of 35–75 nm using X-ray diffraction. XRD was also used in analysis of the crystal structure of the NPs. The interaction between the chitosan and the synthesized NPs was studied using Fourier transform infrared (FT-IR spectroscopy, which showed the capping of the NPs by Cts.

  5. Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis.

    Science.gov (United States)

    Suyama, Takashi L; Gerwick, William H; McPhail, Kerry L

    2011-11-15

    The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable 'detective work' remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques.

  6. Synthesis of high performance ceramic fibers by chemical vapor deposition for advanced metallics reinforcing

    Science.gov (United States)

    Revankar, Vithal; Hlavacek, Vladimir

    1991-01-01

    The chemical vapor deposition (CVD) synthesis of fibers capable of effectively reinforcing intermetallic matrices at elevated temperatures which can be used for potential applications in high temperature composite materials is described. This process was used due to its advantage over other fiber synthesis processes. It is extremely important to produce these fibers with good reproducible and controlled growth rates. However, the complex interplay of mass and energy transfer, blended with the fluid dynamics makes this a formidable task. The design and development of CVD reactor assembly and system to synthesize TiB2, CrB, B4C, and TiC fibers was performed. Residual thermal analysis for estimating stresses arising form thermal expansion mismatch were determined. Various techniques to improve the mechanical properties were also performed. Various techniques for improving the fiber properties were elaborated. The crystal structure and its orientation for TiB2 fiber is discussed. An overall view of the CVD process to develop CrB2, TiB2, and other high performance ceramic fibers is presented.

  7. Bio-electrochemical synthesis of commodity chemicals by autotrophic acetogens utilizing CO2 for environmental remediation.

    Science.gov (United States)

    Jabeen, Gugan; Farooq, Robina

    2016-09-01

    Bio-electrochemical synthesis (BES) is a technique in which electro-autotrophic bacteria such as Clostridium ljungdahlii utilize electric currents as an electron source from the cathode to reduce CO2 to extracellular, multicarbon, exquisite products through autotrophic conversion. The BES of volatile fatty acids and alcohols directly from CO2 is a sustainable alternative for non-renewable, petroleum-based polymer production. This conversion of CO2 implies reduction of greenhouse gas emissions. The synthesis of heptanoic acid, heptanol, hexanoic acid and hexanol, for the first time, by Clostridium ljungdahlii was a remarkable achievement of BES. In our study, these microorganisms were cultivated on the cathode of a bio-electrochemical cell at -400 mV by a DC power supply at 37 degree Centrigrade, pH 6.8, and was studied for both batch and continuous systems. Pre-enrichment of bio-cathode enhanced the electroactivity of cells and resulted in maximizing extracellular products in less time. The main aim of the research was to investigate the impact of low-cost substrate CO2, and the longer cathode recovery range was due to bacterial reduction of CO2 to multicarbon chemical commodities with electrons driven from the cathode. Reactor design was simplified for cost-effectiveness and to enhance energy efficiencies. The Columbic recovery of ethanoic acid, ethanol, ethyl butyrate, hexanoic acid, heptanoic acid and hexanol being in excess of 80 percent proved that BES was a remarkable technology.

  8. Magnetite Fe3O4 nanoparticles synthesis by wet chemical reduction and their characterization

    Science.gov (United States)

    Chaki, S. H.; Malek, Tasmira J.; Chaudhary, M. D.; Tailor, J. P.; Deshpande, M. P.

    2015-09-01

    The authors report the synthesis of Fe3O4 nanoparticles by wet chemical reduction technique at ambient temperature and its characterization. Ferric chloride hexa-hydrate (FeCl3 · 6H2O) and sodium boro-hydrate (NaBH4) were used for synthesis of Fe3O4 nanoparticles at ambient temperature. The elemental composition of the synthesized Fe3O4 nanoparticles was determined by energy dispersive analysis of x-rays technique. The x-ray diffraction (XRD) technique was used for structural characterization of the nanoparticles. The crystallite size of the nanoparticles was determined using XRD data employing Scherrer’s formula and Hall-Williamson’s plot. Surface morphology of as-synthesized Fe3O4 nanoparticles was studied by scanning electron microscopy. High resolution transmission electron microscopy analysis of the as-synthesized Fe3O4 nanoparticles showed narrow range of particles size distribution. The optical absorption of the synthesized Fe3O4 nanoparticles was studied by UV-vis-NIR spectroscopy. The as-synthesized nanoparticles were analyzed by Fourier transform infrared spectroscopy technique for absorption band study in the infrared region. The magnetic properties of the as-synthesized Fe3O4 nanoparticles were evaluated by vibrating sample magnetometer technique. The thermal stability of the as-synthesized Fe3O4 nanoparticles was studied by thermogravimetric technique. The obtained results are elaborated and discussed in details in this paper.

  9. Synthesis and chemical reactions of the steroidal hormone 17α-methyltestosterone.

    Science.gov (United States)

    El-Desoky, El-Sayed Ibrahim; Reyad, Mahmoud; Afsah, Elsayed Mohammed; Dawidar, Abdel-Aziz Mahmoud

    2016-01-01

    Structural modifications of natural products with complex structures like steroids require great synthetic effort. A review of literature is presented on the chemistry of the steroidal hormone 17α-methyltestosterone that is approved by Food and Drug Administration (FDA) in the United States as an androgen for estrogen-androgen hormone replacement therapy treatment. The analog also offers special possibilities for the prevention/treatment of hormone-sensitive cancers. The testosterone skeleton has important functionalities in the molecule that can act as a carbonyl component, an active methylene compound, α,β-unsaturated enone and tertiary hydroxyl group in various chemical reactions to access stereoisomeric steroidal compounds with potent activity. In addition, microbiological methods of synthesis and transformation of this hormone are presented.

  10. [Emission characteristics and hazard assessment analysis of volatile organic compounds from chemical synthesis pharmaceutical industry].

    Science.gov (United States)

    Li, Yan; Wang, Zhe-Ming; Song, Shuang; Xu, Zhi-Rong; Xu, Ming-Zhu; Xu, Wei-Li

    2014-10-01

    In this study, volatile organic compounds (VOCs) released from chemical synthesis pharmaceutical industry in Taizhou, Zhejiang province were analyzed quantitatively and qualitatively. The total volatile organic compounds (TVOCs) was in the range of 14.9-308.6 mg · m(-3). Evaluation models of ozone formation potentials (OFP) and health risk assessment were adopted to preliminarily assess the environmental impact and health risk of VOCs. The results showed that the values of OFP of VOCs were in the range of 3.1-315.1 mg · m(-3), based on the maximum incremental reactivity, the main principal contribution was toluene, tetrahydrofuran (THF), acetic ether etc. The non-carcinogenic risk and the carcinogen risk fell in the ranges of 9.48 x 10(-7)-4.98 x 10(-4) a(-1) and 3.17 x 10(-5)- 6.33 x 10(-3). The principal contribution of VOCs was benzene, formaldehyde and methylene chloride.

  11. Physico-chemical investigation of synthesis of lead salts from sulfide lead concentrate

    Directory of Open Access Journals (Sweden)

    ALEXANDER G. KHOLMOGOROV

    2005-06-01

    Full Text Available The leaching of lead from lead–zinc concentrates by iron(III salt solutins in the absence, as well as in the presence of mineral acids (HCl, H2SO4, HNO3 has been investigated. It was shown that the leaching of lead by means of 0.3 M Fe(NO33 at (22 ± 1 ºC leads to practically complete recovery of lead during 1 h. This conclusion was confirmed by data obtained using chemical, thermographical and X-ray photographical methods. Atechnological scheme for the synthesis of lead salts and oxides without the production of metal lead has been developed as a result of the present investigation.

  12. Design and synthesis of four steroid-oxirane derivatives using some chemical tools.

    Science.gov (United States)

    Lauro, Figueroa-Valverde; Francisco, Díaz-Cedillo; Otto, Ortega-Morales; Elodia, García-Cervera; Marcela, Rosas-Nexticapa; Eduardo, Pool-Gómez; Maria, Lopéz-Ramos; Fernanda, Rodriguez-Hurtado; Marissa, Chan-Salvador

    2016-08-01

    This study involved the synthesis of several new derivatives of progesterone, 11a-hydroxyprogesterone, 11a-t-butyldimethylsilanyloxyprogesterone, and andrenosterone. The new derivatives were prepared by condensation of the 4-en-3-one moiety of the four steroids with 2-hydroxy-1-naphthaldehyde to afford a series of 4-(R)-hydroxy-(2-hydroxynaphtalen-1-yl) adducts. These adducts were further modified by cyclization reactions of the dihydroxynaphthalenyl moieties with succinic acid, and the resulting cyclic succinates were then condensed with ethylenediamine to form imine derivatives at all available carbonyl groups. These compounds were then derivatized by N-acylation of the 11- and 17-imine nitrogens with chloroacetyl chloride and the resulting chloroacetamides were then condensed with 2-hydroxy-1-napthaldehyde in Darzens-type reactions forming the corresponding epoxy acetamides in the side chains. In addition, the chemical structure of steroid derivatives was confirmed by NMR spectroscopic data. PMID:27154751

  13. Synthesis and chemical reactions of the steroidal hormone 17α-methyltestosterone.

    Science.gov (United States)

    El-Desoky, El-Sayed Ibrahim; Reyad, Mahmoud; Afsah, Elsayed Mohammed; Dawidar, Abdel-Aziz Mahmoud

    2016-01-01

    Structural modifications of natural products with complex structures like steroids require great synthetic effort. A review of literature is presented on the chemistry of the steroidal hormone 17α-methyltestosterone that is approved by Food and Drug Administration (FDA) in the United States as an androgen for estrogen-androgen hormone replacement therapy treatment. The analog also offers special possibilities for the prevention/treatment of hormone-sensitive cancers. The testosterone skeleton has important functionalities in the molecule that can act as a carbonyl component, an active methylene compound, α,β-unsaturated enone and tertiary hydroxyl group in various chemical reactions to access stereoisomeric steroidal compounds with potent activity. In addition, microbiological methods of synthesis and transformation of this hormone are presented. PMID:26639430

  14. The validity of the autoradiographic method for detecting DNA repair synthesis in rat hepatocytes in primary culture

    International Nuclear Information System (INIS)

    The autoradiographic detection of unscheduled DNA synthesis (UDS) in primary cultures of rat hepatocytes (HPC) was used to measure excision repair of DNA lesions induced by genotoxic agents. Both directly and indirectly acting agents were tested. The HPC/DNA repair test has been claimed to have advantages over screening tests based on non-metabolizing cells in combination with a system for bio-activation. The experiments reported here, however, show that its advantages are greatly reduced by the difficulty of obtaining cell preparations of reliable and reproducible quality. The reproducibility of the system is affected by the large variations in the functional state of the isolated cells and by other factors. For some of these variations a correction is possible. For instance, differences due to the size of the nuclei can be eliminated by reporting the grains counted above the nucleus in proportion to the size of the nuclear area scored. (orig./AJ)

  15. Exploration of cellular DNA lesion, DNA-binding and biocidal ordeal of novel curcumin based Knoevenagel Schiff base complexes incorporating tryptophan: Synthesis and structural validation

    Science.gov (United States)

    Chandrasekar, Thiravidamani; Raman, Natarajan

    2016-07-01

    A few novel Schiff base transition metal complexes of general formula [MLCl] (where, L = Schiff base, obtained by the condensation reaction of Knoevenagel condensate of curcumin, L-tryptophan and M = Cu(II), Ni(II), Co(II), and Zn(II)), were prepared by stencil synthesis. They were typified using UV-vis, IR, EPR spectral techniques, micro analytical techniques, magnetic susceptibility and molar conductivity. Geometry of the metal complexes was examined and recognized as square planar. DNA binding and viscosity studies revealed that the metal(II) complexes powerfully bound via an intercalation mechanism with the calf thymus DNA. Gel-electrophoresis technique was used to investigate the DNA cleavage competence of the complexes and they establish to approve the cleavage of pBR322 DNA in presence of oxidant H2O2. This outcome inferred that the synthesized complexes showed better nuclease activity. Moreover, the complexes were monitored for antimicrobial activities. The results exposed that the synthesized compounds were forceful against all the microbes under exploration.

  16. Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword.

    Science.gov (United States)

    Jaszczur, Malgorzata; Bertram, Jeffrey G; Robinson, Andrew; van Oijen, Antoine M; Woodgate, Roger; Cox, Michael M; Goodman, Myron F

    2016-04-26

    1953, the year of Watson and Crick, bore witness to a less acclaimed yet highly influential discovery. Jean Weigle demonstrated that upon infection of Escherichia coli, λ phage deactivated by UV radiation, and thus unable to form progeny, could be reactivated by irradiation of the bacterial host. Evelyn Witkin and Miroslav Radman later revealed the presence of the SOS regulon. The more than 40 regulon genes are repressed by LexA protein and induced by the coproteolytic cleavage of LexA, catalyzed by RecA protein bound to single-stranded DNA, the RecA* nucleoprotein filament. Several SOS-induced proteins are engaged in repairing both cellular and extracellular damaged DNA. There's no "free lunch", however, because error-free repair is accompanied by error-prone translesion DNA synthesis (TLS), involving E. coli DNA polymerase V (UmuD'2C) and RecA*. This review describes the biochemical mechanisms of pol V-mediated TLS. pol V is active only as a mutasomal complex, pol V Mut = UmuD'2C-RecA-ATP. RecA* donates a single RecA subunit to pol V. We highlight three recent insights. (1) pol V Mut has an intrinsic DNA-dependent ATPase activity that governs polymerase binding and dissociation from DNA. (2) Active and inactive states of pol V Mut are determined at least in part by the distinct interactions between RecA and UmuC. (3) pol V is activated by RecA*, not at a blocked replisome, but at the inner cell membrane.

  17. Synthesis of carbon nanotubes using the cobalt nanocatalyst by thermal chemical vapor deposition technique

    Energy Technology Data Exchange (ETDEWEB)

    Madani, S.S. [Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Zare, K. [Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Department of Chemistry, Shahid Beheshti University, Tehran (Iran, Islamic Republic of); Ghoranneviss, M. [Plasma Physics Research Center, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Salar Elahi, A., E-mail: Salari_phy@yahoo.com [Plasma Physics Research Center, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of)

    2015-11-05

    The three main synthesis methods of Carbon nanotubes (CNTs) are the arc discharge, the laser ablation and the chemical vapour deposition (CVD) with a special regard to the latter one. CNTs were produced on a silicon wafer by Thermal Chemical Vapor Deposition (TCVD) using acetylene as a carbon source, cobalt as a catalyst and ammonia as a reactive gas. The DC-sputtering system was used to prepare cobalt thin films on Si substrates. A series of experiments was carried out to investigate the effects of reaction temperature and deposition time on the synthesis of the nanotubes. The deposition time was selected as 15 and 25 min for all growth temperatures. Energy Dispersive X-ray (EDX) measurements were used to investigate the elemental composition of the Co nanocatalyst deposited on Si substrates. Atomic Force Microscopy (AFM) was used to characterize the surface topography of the Co nanocatalyst deposited on Si substrates. The as-grown CNTs were characterized under Field Emission Scanning Electron Microscopy (FESEM) to study the morphological properties of CNTs. Also, the grown CNTs have been investigated by High Resolution Transmission Electron Microscopy (HRTEM) and Raman spectroscopy. The results demonstrated that increasing the temperature leads to increasing the diameter of CNTs. The ideal reaction temperature was 850 °C and the deposition time was 15 min. - Graphical abstract: FESEM images of CNTs grown on the cobalt catalyst at growth temperatures of (a) 850 °C, (b) 900 °C, (c) 950 °C and (d) 1000 °C during the deposition time of 15 min. - Highlights: • Carbon nanotubes (CNTs) were produced on a silicon wafer by TCVD technique. • EDX and AFM were used to investigate the elemental composition and surface topography. • FESEM was used to study the morphological properties of CNTs. • The grown CNTs have been investigated by HRTEM and Raman spectroscopy.

  18. On-line monitoring of continuous flow chemical synthesis using a portable, small footprint mass spectrometer.

    Science.gov (United States)

    Bristow, Tony W T; Ray, Andrew D; O'Kearney-McMullan, Anne; Lim, Louise; McCullough, Bryan; Zammataro, Alessio

    2014-10-01

    For on-line monitoring of chemical reactions (batch or continuous flow), mass spectrometry (MS) can provide data to (1) determine the fate of starting materials and reagents, (2) confirm the presence of the desired product, (3) identify intermediates and impurities, (4) determine steady state conditions and point of completion, and (5) speed up process optimization. Recent developments in small footprint atmospheric pressure ionization portable mass spectrometers further enable this coupling, as the mass spectrometer can be easily positioned with the reaction system to be studied. A major issue for this combination is the transfer of a sample that is representative of the reaction and also compatible with the mass spectrometer. This is particularly challenging as high concentrations of reagents and products can be encountered in organic synthesis. The application of a portable mass spectrometer for on-line characterization of flow chemical synthesis has been evaluated by coupling a Microsaic 4000 MiD to the Future Chemistry Flow Start EVO chemistry system. Specifically, the Hofmann rearrangement has been studied using the on-line mass spectrometry approach. Sample transfer from the flow reactor is achieved using a mass rate attenuator (MRA) and a sampling make-up flow from a high pressure pump. This enables the appropriate sample dilution, transfer, and preparation for electrospray ionization. The capability of this approach to provide process understanding is described using an industrial pharmaceutical process that is currently under development. The effect of a number of key experimental parameters, such as the composition of the sampling make-up flow and the dilution factor on the mass spectrometry data, is also discussed. PMID:25106707

  19. Synthesis of Si/SiO2/ZnO nanoporous materials using chemical and electrochemical deposition techniques

    Science.gov (United States)

    Dauletbekova, A. K.; Alzhanova, A. Ye.; Akilbekov, A. T.; Mashentseva, A. A.; Zdorovets, M. V.; Balabekov, K. N.

    2016-09-01

    The work represents the results of forming Zn-based nanoprecipitates in nanoporous amorphous silicon dioxide on silicon substrate by the template synthesis method. SEM and AFM images of the surface after chemical and electrochemical deposition of zinc were obtained. The analysis of photoluminescence of the precipitated samples resulted in the assumption of formation of nanoclusters of zinc oxide.

  20. [New biological active derivatives of indomethacin and acetylsalicylic acid. Synthesis, physico-chemical characterisation and structure validation].

    Science.gov (United States)

    Stan, Catalina; Stefanache, Alina; Dumitrache, M

    2006-01-01

    It is well known that niflumic acid glycinamide has a good antiinflammatory action useful in gum inflammatory diseases. The objective of this study was to obtain new glycinamides of acetylsalicylic acid and indomethacin, which could have a better antiinflammatory action than niflumic acid glycinamide. The study presents the synthesis, physico-chemical characterisation and structure validation of these glycinamides.

  1. Discovery of TNF inhibitors from a DNA-encoded chemical library based on diels-alder cycloaddition.

    Science.gov (United States)

    Buller, Fabian; Zhang, Yixin; Scheuermann, Jörg; Schäfer, Juliane; Bühlmann, Peter; Neri, Dario

    2009-10-30

    DNA-encoded chemical libraries are promising tools for the discovery of ligands toward protein targets of pharmaceutical relevance. DNA-encoded small molecules can be enriched in affinity-based selections and their unique DNA "barcode" allows the amplification and identification by high-throughput sequencing. We describe selection experiments using a DNA-encoded 4000-compound library generated by Diels-Alder cycloadditions. High-throughput sequencing enabled the identification and relative quantification of library members before and after selection. Sequence enrichment profiles corresponding to the "bar-coded" library members were validated by affinity measurements of single compounds. We were able to affinity mature trypsin inhibitors and identify a series of albumin binders for the conjugation of pharmaceuticals. Furthermore, we discovered a ligand for the antiapoptotic Bcl-xL protein and a class of tumor necrosis factor (TNF) binders that completely inhibited TNF-mediated killing of L-M fibroblasts in vitro.

  2. Dithiocarbamate/piperazine bridged pyrrolobenzodiazepines as DNA-minor groove binders: synthesis, DNA-binding affinity and cytotoxic activity.

    Science.gov (United States)

    Kamal, Ahmed; Sreekanth, Kokkonda; Shankaraiah, Nagula; Sathish, Manda; Nekkanti, Shalini; Srinivasulu, Vunnam

    2015-04-01

    A new series of C8-linked dithiocarbamate/piperazine bridged pyrrolo[2,1-c][1,4]benzodiazepine conjugates (5a-c, 6a,b) have been synthesized and evaluated for their cytotoxic potential and DNA-binding ability. The representative conjugates 5a and 5b have been screened for their cytotoxicity against a panel of 60 human cancer cell lines. Compound 5a has shown promising cytotoxic activity on selected cancer cell lines that display melanoma, leukemia, CNS, ovarian, breast and renal cancer phenotypes. The consequence of further replacement of the 3-cyano-3,3-diphenylpropyl 1-piperazinecarbodithioate in 5b and 5c with 4-methylpiperazine-1-carbodithioate yielded new conjugates 6a and 6b respectively. In addition, the compounds 5c and 6a,b have been evaluated for their in vitro cytotoxicity on some of the selected human cancer cell lines and these conjugates have exhibited significant cytotoxic activity. Further, the DNA-binding ability of these new conjugates has been evaluated by using thermal denaturation (ΔTm) studies. The correlation between structure and DNA-binding ability has been investigated by molecular modeling studies which predicted that 6b exhibits superior DNA-binding ability and these are in agreement with the experimental DNA-binding studies. PMID:25665519

  3. [Overgrowth and DNA synthesis of neuroepithelium in embryonic stages of induced Long-Evans rat myeloschisis].

    Science.gov (United States)

    Chono, Y

    1993-01-01

    Overgrowth of the myeloschisis, namely the excessive amount of the neural plate tissue, has been reported in the human myeloschisis. However, it is still debatable how the overgrowth develops and whether the overgrowth is the cause, or the secondary effect of spinal dysraphism. The author induced myeloschisis in the fetuses of Long-Evans rats by the administration of ethylenethiourea (ETU) to pregnant rats on day 10 of gestation. The fetuses were removed 1 hour after the treatment with bromodeoxyuridine (BrdU) to the dams on day 14 and 21. The fetuses were fixed in alcohol and embedded in paraffin. H-E staining and the immunohistologic examination were performed on the staining patterns to anti-neurofilament (NFP), anti-glial fibrillary acidic protein (GFAP) and anti-BrdU antibody by ABC method. On day 14, the lateral portion of everted neural plate showed a loose arrangement of cells and there was rosette formation in the mesoderm. On day 21, cell necrosis was observed at the dorsolateral portion of myeloschisis, although the ventral portion showed almost normal cytoarchitecture and was positive to NFP and GFAP. The cause of myeloschisis in this model is supposed to be the local and direct cytotoxic effect of ETU to neuro-ectodermal junction. On day 14, control animals contained few BrdU-incorporated cells at the basal plate of neural tube. In contrast, everted neural plate showed an active uptake of BrdU diffusely in the subependymal matrix layer cells. Overgrowth was not yet identified. On day 21, overgrowth of myeloschisis was found in spite of a few positive cells to BrdU which was identical to the control animals. These findings seem to suggest that cells in the myeloschisis retain their ability of DNA synthesis for longer periods of development and overgrowth found on day 21 is possibly a secondary effect of spinal dysraphism in this model.

  4. Gas temperature measurements inside a hot wall chemical vapor synthesis reactor.

    Science.gov (United States)

    Notthoff, Christian; Schilling, Carolin; Winterer, Markus

    2012-11-01

    One key but complex parameter in the chemical vapor synthesis (CVS) of nanoparticles is the time temperature profile of the gas phase, which determines particle characteristics such as size (distribution), morphology, microstructure, crystal, and local structure. Relevant for the CVS process and for the corresponding particle characteristics is, however, not the T(t)-profile generated by an external energy source such as a hot wall or microwave reactor but the temperature of the gas carrying reactants and products (particles). Due to a complex feedback of the thermodynamic and chemical processes in the reaction volume with the external energy source, it is very difficult to predict the real gas phase temperature field from the externally applied T(t)-profile. Therefore, a measurement technique capable to determine the temperature distribution of the gas phase under process conditions is needed. In this contribution, we demonstrate with three proof of principle experiments the use of laser induced fluorescence thermometry to investigate the CVS process under realistic conditions.

  5. Repair of DNA treated with γ-irradiation and chemical carcinogens. Progress report, 1980-1983

    International Nuclear Information System (INIS)

    We have studied in vitro DNA repair with the isolation and characterization of DNA glycosylases active in the removable of 3-methyladenine and the problem of repair of DNA in chromatin. The second area of focus has been on transposable elements and carcinogen action. The work on DNA adducts with β-propiolactone was done to define potential new substrates useful in a search for new glycosylases

  6. A Novel Cobalt(Ⅲ) Mixed-polypyridyl Complex: Synthesis,Characterization and DNA Binding

    Institute of Scientific and Technical Information of China (English)

    CHEN,Hui-Li(陈绘丽); YANG,Pin(杨频)

    2002-01-01

    A novel complex[Co(phen)2HPIP]Cl3[phen=phenanethroline,HPIP=2-(2-hydroxyphenyl)imidazo[4,5-f][1,10]phenanethroline]has been synthesized and structurally characterized by elemental analysis,UV,IR and 1H NMR spectroscopies. The interaction of the complex with calf thymus DNA(CT DNA)has been studied using absorption and emission spectroscopy, DNA melting techniques and cyclic voltammetry. The compound shows absorption hypochromicity, fluorescence enhancement and DNA melting temperature increment when binding to CT DNA. CV measurement shows a shift in reduction potential and a change in peak current with addition of DNA.These results prove that the compound inserts into DNA base pairs. The shift of peak potential indicates the ion interaction mode between the complex and DNA. The binding constant of the compound to DNA is 4.37×104. The complex also seems to be an efficient photocleavage reagent.

  7. Mechanism of Translesion Synthesis Past an Equine Estrogen-DNA Adduct by Y-Family DNA Polymerases

    OpenAIRE

    Yasui, Manabu; Suzuki, Naomi; Liu, Xiaoping; Kim, Yoshinori Okamoto Sung Yeon; Laxmi, Y. R. Santosh; Shibutani, Shinya

    2007-01-01

    4-Hydroxyequilenin (4-OHEN)-dC is a major, potentially mutagenic DNA adduct induced by equine estrogens used for hormone replacement therapy. To study the miscoding property of 4-OHEN-dC and the involvement of Y-family human DNA polymerases (pols) η, κ and ι in that process, we incorporated 4-OHEN-dC into oligodeoxynucleotides and used them as templates in primer extension reactions catalyzed by pol η, κ and ι. Pol η inserted dAMP opposite 4-OHEN-dC, accompanied by lesser amounts of dCMP and ...

  8. Replication of cloned DNA containing the Alu family sequence during cell extract-promoting simian virus 40 DNA synthesis.

    OpenAIRE

    Ariga, H

    1984-01-01

    The replicating activity of several cloned DNAs containing putative origin sequences was examined in a cell-free extract that absolutely depends on simian virus 40 (SV40) T antigen promoting initiation of SV40 DNA replication in vitro. Of the three DNAs containing the human Alu family sequence (BLUR8), the origin of (Saccharomyces cerevisiae plasmid 2 micron DNA (pJD29), and the yeast autonomous replicating sequence (YRp7), only BLUR8 was active as a template. Replication in a reaction mixtur...

  9. Radiation chemical and photochemical study of Z-DNA modified by 2-aminopurine and 8- bromodeoxyguanosine

    International Nuclear Information System (INIS)

    DNA is able to take a number of local conformations. (CG) n repeats have the highest potential to Z-DNA which has a left-handed zig-zag backbone and unusual syn-conformation purine base. Because of the polymorphic nature of dinucleotide repeats, it seems possible that Z-DNA forming sequences may provide a source of genetic variation if they occur in regions that are important for the regulation of gene activity. Here, we investigated structural properties of Z-DNA compared with those of B-DNA with respects to one-electron attachment reaction of 8-bromodeoxyguanosine (dBrG) and fluorescence properties of 2-aminopurine (Ap). To investigate one-electron attachment reaction of Z-DNA, we synthesized oligodeoxynucleotides modified by dBrG in which syn-conformation deoxyguanosine was stabilized by steric repulsion between 8-bromo group of dBrG and sugar moiety in Z-DNA. Debromination from the dBrG modified oligodeoxynucleotides occurred from the one-electron attachment during the gamma-ray irradiation. The structural dependence of B- and Z-DNA was observed in the one-electron attachment reaction. Interestingly, the higher conversion of dBrG were observed in the Z-DNA than in the B-DNA. Since the solvent accessibility to purine base in Z-DNA increases compared with that in B-DNA, it is suggested that the electron attachment is enhanced in Z-DNA than in B-DNA. Next we studied the fluorescence properties of Ap in left-handed Z-DNA and compared with those in B-DNA. Since photoexcited adenine analogue Ap can serve as a sensitive probe of DNA structural dynamics, we synthesized Ap- and dBrG-modified oligodeoxynucleotides. Higher intensity was observed in the steady-state fluorescence of Ap in Z-DNA than in B-DNA. A new peak at 275 nm was observed in the excitation spectrum measured at the Ap emission wavelength 370 nm in Z-DNA. This has been explained by the energy transfer from the excited nucleobases to Ap. It is found that Ap is a useful fluorescence probe of Z-DNA

  10. DNA binding, cytotoxicity and inhibitory effect on RNA synthesis of two new 1-nitro-9-aminoacridine dimers.

    Science.gov (United States)

    Markovits, J; Wilmańska, D; Lescot, E; Studzian, K; Szmigiero, L; Gniazdowski, M

    1989-01-01

    Two 1-nitro-9-aminoacridine dimers were prepared: one bearing a spermine flexible linking chain, compound 4, the other a rigid dipiperidine-type linker, compound 7. Both dimers elicited a higher affinity constant for DNA than the parent monomeric drug nitracrine 2. This affinity was several orders lower than what was found for other dimeric compounds having the same linkers and no nitro group on the acridine ring (3, 5, 6 and 8). Bisintercalation was evidenced for compound 4 by viscosimetric measurements. In the absence of dithiothreitol, an inhibitory effect of RNA synthesis in vitro was observed for all the tested compounds except 2 and 7. In the presence of dithiothreitol, 4 and 7 formed irreversible complexes with DNA of decreased template properties. The level of the dimers binding was lower than that of the parent compound 2. Cross-links were detected by means of hydroxylapatite chromatography in a complex of the dimer bearing a flexible linking chain, compound 4 with DNA, while the compound 7-DNA complex eluted in the single-stranded DNA region. The extent of cytotoxicity of the two 1-nitro-9-aminoacridine dimers against L1210 cultured cells was different. PMID:2472225

  11. Synthesis of titanium oxide nanoparticles using DNA-complex as template for solution-processable hybrid dielectric composites

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, J.C. [Center for Sustainable Materials Chemistry, 153 Gilbert Hall, Oregon State University, Corvallis, OR (United States); Mejia, I.; Murphy, J.; Quevedo, M. [Department of Materials Science and Engineering, University of Texas at Dallas, Dallas, TX (United States); Garcia, P.; Martinez, C.A. [Engineering and Technology Institute, Autonomous University of Ciudad Juarez, Ciudad Juarez, Chihuahua (Mexico)

    2015-09-15

    Highlights: • We developed a synthesis method to produce TiO{sub 2} nanoparticles using a DNA complex. • The nanoparticles were anatase phase (~6 nm diameter), and stable in alcohols. • Composites showed a k of 13.4, 4.6 times larger than the k of polycarbonate. • Maximum processing temperature was 90 °C. • Low temperature enables their use in low-voltage, low-cost, flexible electronics. - Abstract: We report the synthesis of TiO{sub 2} nanoparticles prepared by the hydrolysis of titanium isopropoxide (TTIP) in the presence of a DNA complex for solution processable dielectric composites. The nanoparticles were incorporated as fillers in polycarbonate at low concentrations (1.5, 5 and 7 wt%) to produce hybrid dielectric films with dielectric constant higher than thermally grown silicon oxide. It was found that the DNA complex plays an important role as capping agent in the formation and suspension stability of nanocrystalline anatase phase TiO{sub 2} at room temperature with uniform size (∼6 nm) and narrow distribution. The effective dielectric constant of spin-cast polycarbonate thin-films increased from 2.84 to 13.43 with the incorporation of TiO{sub 2} nanoparticles into the polymer host. These composites can be solution processed with a maximum temperature of 90 °C and could be potential candidates for its application in low-cost macro-electronics.

  12. SIMILARITY ANALYSIS OF DNA SEQUENCES BASED ON THE CHEMICAL PROPERTIES OF NUCLEOTIDE BASES, FREQUENCY AND POSITION OF GROUP MUTATIONS

    Directory of Open Access Journals (Sweden)

    Fatima KABLI

    2016-01-01

    Full Text Available The DNA sequences similarity analysis approaches have been based on the representation and the frequency of sequences components; however, the position inside sequence is important information for the sequence data. Whereas, insufficient information in sequences representations is important reason that causes poor similarity results. Based on three classifications of the DNA bases according to their chemical properties, the frequencies and average positions of group mutations have been grouped into two twelve-components vectors, the Euclidean distances among introduced vectors applied to compare the coding sequences of the first exon of beta globin gene of 11 species.

  13. Simple synthesis of carbon-11-labeled chromen-4-one derivatives as new potential PET agents for imaging of DNA-dependent protein kinase (DNA-PK) in cancer

    International Nuclear Information System (INIS)

    Carbon-11-labeled chromen-4-one derivatives were synthesized as new potential PET agents for imaging of DNA repair enzyme DNA-dependent protein kinase (DNA-PK) in cancer. The target tracers, X-[11C]methoxy-2-morpholino-4H-chromen-4-ones (X=8, 7, 6, 5; [11C]4a–d), were prepared from their corresponding precursors, X-hydroxy-2-morpholino-4H-chromen-4-ones (X=8, 7, 6, 5; 5a–d), with [11C]CH3OTf through O-[11C]methylation and isolated by a simplified solid-phase extraction (SPE) method using a C-18 Sep-Pak Plus cartridge. The radiochemical yields decay corrected to end of bombardment (EOB), from [11C]CO2, were 40–60%. The specific activity at end of synthesis (EOS) was 185–370 GBq/μmol. - Highlights: ► New chromen-4-one derivatives were synthesized. ► New carbon-11-labeled chromen-4-one derivatives were synthesized. ► Simple solid-phase extraction (SPE) method was employed in radiosynthesis.

  14. Pure magnetic hard fct FePt nanoparticles: Chemical synthesis, structural and magnetic properties correlations

    Energy Technology Data Exchange (ETDEWEB)

    Suber, L., E-mail: lorenza.suber@ism.cnr.it [ISM-CNR, Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo Scalo, RM (Italy); Marchegiani, G. [ISM-CNR, Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo Scalo, RM (Italy); Olivetti, E.S.; Celegato, F.; Coïsson, M.; Tiberto, P. [INRIM, Electromagnetism Division, Strada delle Cacce 91, 10135 Torino (Italy); Allia, P. [DISAT Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Barrera, G. [Dipartimento di Chimica, Università di Torino, Via Pietro Giuria 7, 10125 Torino (Italy); Pilloni, L. [UTTMAT-CHI, Via Anguillarese 10, 00123 S. Maria di Galeria, Roma (Italy); Barba, L. [IC-CNR, Area Science Park, SS 14 Km 163.5 Basovizza, 34149 Trieste (Italy); Padella, F. [UTTMAT-CHI, Via Anguillarese 10, 00123 S. Maria di Galeria, Roma (Italy); Cossari, P. [IGAG-CNR, Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo Scalo, RM (Italy); Chiolerio, A. [Istituto Italiano di Tecnologia, Center for Space Human Robotics, Corso Trento 21, 10129 Torino (Italy)

    2014-03-01

    FePt nanoparticles, containing a near-equal atomic percentage of Fe and Pt, with a face centered tetragonal structure (fct), are challenging for potential applications in high performance permanent magnets and high density data storage. In this study, we report on the chemical synthesis, carried out both solvothermally and hydrothermally in autoclave reacting iron (III) acetylacetonate and platinum (II) acetylacetonate with tri- or tetra-ethylene glycol, these employed as solvents, reducers and particle surface protecting agents as well. In both methods, a subsequent thermal treatment at high temperatures is necessary to transform the magnetic soft face centered cubic (fcc) phase to the hard fct one. Organic low-weight molecules, generally used to protect the nanoparticle surface and avoid particle aggregation, are decomposed by the thermal treatment resulting in particle aggregation and coalescence phenomena; on the contrary, in this case, a polymer matrix is formed as particle protecting agent and, by thermally treating the hydrothermally prepared nanoparticles up to 750 °C for 1 h, the pure magnetic hard fct phase is obtained while preserving the nanostructure. A detailed study is carried out on FePt nanoparticle structure (fcc and fct phases) and correlated to the magnetic properties of the system. - Highlights: • fct FePt nanoparticles for hard magnetic nanotechnology applications. • Influence of synthesis parameters on the precursor fcc FePt nanoparticle structure. • Easy hydrothermal method for preparing pure fct FePt nanoparticles. • Monitoring the role of temperature and time on the FePt fcc–fct phase transformation. • Correlation between FePt nanoparticle structural and magnetic properties.

  15. DNA strand breaks detected in embryos of the adult snails, Potamopyrgus antipodarum, and in neonates exposed to genotoxic chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Vincent-Hubert, Francoise, E-mail: francoise.vincent-hubert@irstea.fr [Unite de Recherche Hydrosystemes et Bioprocedes, equipe BELCA, IRSTEA/CEMAGREF, 1 rue Pierre-Gilles de Gennes, CS10030, 92761 Antony cedex, 92163 Antony (France); Revel, Messika [Unite de Recherche Hydrosystemes et Bioprocedes, equipe BELCA, IRSTEA/CEMAGREF, 1 rue Pierre-Gilles de Gennes, CS10030, 92761 Antony cedex, 92163 Antony (France); Garric, Jeanne [MALY Laboratoire d' ecotoxicologie, IRSTEA/CEMAGREF, 23 bis Quai Chauveau, 69006 Lyon (France)

    2012-10-15

    We tested the freshwater mudsnail Potamopyrgus antipodarum, which is a species that has already been used for endocrine-disrupting compounds (EDCs) to determine whether early life stages of aquatic organisms are sensitive to genotoxic chemicals. For this purpose, we first developed the alkaline comet assay on adults, embryos, and neonates. The comet assay protocol was validated on both embryonic cells exposed in vitro to hydrogen peroxide and adult snails in the reproducing stage exposed to methyl methane sulfonate. During the latter experiment, DNA strand breaks were investigated on both embryonic cells and on adult gill cells. The second part of this study investigated the stability of DNA strand breaks in adult reproducing snails and neonates exposed to cadmium (Cd) and bisphenol A for 8 days. Hydrogen peroxide-induced DNA strand breaks in vitro in isolated embryonic cells. Exposure of adult reproducing snails to methyl methane sulfonate for 24 h induced DNA strand breaks in embryos. Bisphenol A induced a significant increase in the DNA strand-break level in whole embryonic cells and whole neonate cells. Cd was genotoxic for both embryos and neonates during the exposure time and also after 7 days of depuration, suggesting that Cd could inhibit DNA repair enzymes. These preliminary results on this original model have encouraged us to consider the impact of genotoxic environmental contaminants on the F1 generation.

  16. Precision synthesis of functional materials via RAFT polymerization and click-type chemical reactions

    Science.gov (United States)

    Flores, Joel Diez

    2011-12-01

    The need to tailor polymeric architectures with specific physico-chemical properties via the simplest, cleanest, and most efficient synthetic route possible has become the ultimate goal in polymer synthesis. Recent progress in macromolecular science, such as the discoveries of controlled/"living" free radical polymerization (CRP) methods, has brought about synthetic capabilities to prepare (co)polymers with advanced topologies, predetermined molecular weights, narrow molecular weight distributions, and precisely located functional groups. In addition, the establishment of click chemistry has redefined the selected few highly efficient chemical reactions that become highly useful in post-polymerization modification strategies. Hence, the ability to make well-defined topologies afforded by controlled polymerization techniques and the facile incorporation of functionalities along the chain via click-type reactions have yielded complex architectures, allowing the investigation of physical phenomena which otherwise could not be studied with systems prepared via conventional methods. The overarching theme of the research work described in this dissertation is the fusion of the excellent attributes of reversible addition-fragmentation chain transfer (RAFT) polymerization method, which is one of the CRP techniques, and click-type chemical reactions in the precision of synthesis of advanced functional materials. Chapter IV is divided into three sections. In Section I, the direct RAFT homopolymerization of 2-(acryloyloxy)ethyl isocyanate (AOI) and subsequent post-polymerization modifications are described. The polymerization conditions were optimized in terms of the choice of RAFT chain transfer agent (CTA), polymerization temperature and the reaction medium. Direct RAFT polymerization of AOI requires a neutral CTA, and relatively low reaction temperature to yield AOI homopolymers with low polydispersities. Efficient side-chain functionalization of PAOI homopolymers was

  17. DNA photobinding of 7-methylpyrido[3,4-c]psoralen and 8-methoxypsoralen. Effects on macromolecular synthesis, repair and survival in cultured human cells

    International Nuclear Information System (INIS)

    The photobinding to DNA of tritiated 7-methylpyrido[3,4-c]psoralen (MPP), a recently synthesized monofunctional compound of therapeutical interest, and of 8-methoxypsoralen (8-MOP) was determined in cultured normal human fibroblasts. Employing compounds at 10-6 M, MPP photobinds approximately 11 times more efficiently than 8-MOP. For equivalent photobinding MPP ad 8-MOP induce similar inhibitions of DNA synthesis. However, the recovery of DNA synthesis during post-treatment incubation is lower after photoaddition of MPP than after that of 8-MOP. MPP also exerts a much higher lethal effect than 8-MOP. Alkaline elution experiments confirmed the monofunctional nature of MPP and indicated that in MPP-damaged cells DNA breaks accumulate with time of post-treatment incubation. In 8-MOP-treated cells, DNA cross-links appear to be partially repaired. In conclusion, MPP monoadducts turn out to constitute more cytotoxic lesions than 8-MOP mono- and bi-adducts. (Auth.)

  18. Effect of exogenous surfactants on viability and DNA synthesis in A549, immortalized mouse type II and isolated rat alveolar type II cells

    Directory of Open Access Journals (Sweden)

    Haller Thomas

    2011-02-01

    Full Text Available Abstract Background In mechanically ventilated preterm infants with respiratory distress syndrome (RDS, exogenous surfactant application has been demonstrated both to decrease DNA-synthesis but also and paradoxically to increase epithelial cell proliferation. However, the effect of exogenous surfactant has not been studied directly on alveolar type II cells (ATII cells, a key cell type responsible for alveolar function and repair. Objective The aim of this study was to investigate the effects of two commercially available surfactant preparations on ATII cell viability and DNA synthesis. Methods Curosurf® and Alveofact® were applied to two ATII cell lines (human A549 and mouse iMATII cells and to primary rat ATII cells for periods of up to 24 h. Cell viability was measured using the redox indicator resazurin and DNA synthesis was measured using BrdU incorporation. Results Curosurf® resulted in slightly decreased cell viability in all cell culture models. However, DNA synthesis was increased in A549 and rat ATII cells but decreased in iMATII cells. Alveofact® exhibited the opposite effects on A549 cells and had very mild effects on the other two cell models. Conclusion This study showed that commercially available exogenous surfactants used to treat preterm infants with RDS can have profound effects on cell viability and DNA synthesis.

  19. Down-regulation of SMT3A gene expression in association with DNA synthesis induction after X-ray irradiation in nevoid basal cell carcinoma syndrome (NBCCS) cells

    Energy Technology Data Exchange (ETDEWEB)

    Sugaya, Shigeru [Department of Environmental Biochemistry, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Nakanishi, Hiroshi [Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Tanzawa, Hideki [Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Sugita, Katsuo [Department of Clinical Medicine, Faculty of Education, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522 (Japan); Kita, Kazuko [Department of Environmental Biochemistry, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Suzuki, Nobuo [Department of Environmental Biochemistry, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan)]. E-mail: nobuo@faculty.chiba-u.jp

    2005-10-15

    Fibroblast cells derived from nevoid basal carcinoma syndrome (NBCCS) patients show increased levels of DNA synthesis after X-ray irradiation. Genes, whose expression is modulated in association with the DNA synthesis induction, were searched by using PCR-based mRNA differential display analysis in one of the NBCCS cell lines, NBCCS1 cells. Decreased levels of SMT3A gene expression were found in X-ray-irradiated NBCCS1 cells. This decrease was also shown by RT-PCR analysis in another cell line, NBCCS3 cells. In addition to NBCCS cells, normal fibroblast cells showed the DNA synthesis induction after X-ray irradiation when they were treated with antisense oligonucleotides (AO) for SMT3A. However, treatment of normal fibroblasts with the random oligonucleotides (RO) resulted in decreased levels of DNA synthesis after X-ray irradiation. Thus, down-regulation of SMT3A gene expression may be involved in the DNA synthesis induction after X-ray irradiation in the NBCCS cells at least tested.

  20. Medicinal plants recommended by the world health organization: DNA barcode identification associated with chemical analyses guarantees their quality.

    Directory of Open Access Journals (Sweden)

    Rafael Melo Palhares

    Full Text Available Medicinal plants are used throughout the world, and the regulations defining their proper use, such as identification of the correct species and verification of the presence, purity and concentration of the required chemical compounds, are widely recognized. Herbal medicines are made from vegetal drugs, the processed products of medicinal species. These processed materials present a number of challenges in terms of botanical identification, and according to the World Health Organization (WHO, the use of incorrect species is a threat to consumer safety. The samples used in this study consisted of the dried leaves, flowers and roots of 257 samples from 8 distinct species approved by the WHO for the production of medicinal herbs and sold in Brazilian markets. Identification of the samples in this study using DNA barcoding (matK, rbcL and ITS2 regions revealed that the level of substitutions may be as high as 71%. Using qualitative and quantitative chemical analyses, this study identified situations in which the correct species was being sold, but the chemical compounds were not present. Even more troubling, some samples identified as substitutions using DNA barcoding contained the chemical compounds from the correct species at the minimum required concentration. This last situation may lead to the use of unknown species or species whose safety for human consumption remains unknown. This study concludes that DNA barcoding should be used in a complementary manner for species identification with chemical analyses to detect and quantify the required chemical compounds, thus improving the quality of this class of medicines.