nucleic acid denaturation

Summary

Summary: Disorganization of secondary structures of nucleic acids through cleavage of hydrogen bonds and hydrophobic linkages. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.

Top Publications

  1. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
  2. pmc Circular dichroism and conformational polymorphism of DNA
    Jaroslav Kypr
    Institute of Biophysics, vvi Academy of Sciences of the Czech Republic, Brno, Czech Republic
    Nucleic Acids Res 37:1713-25. 2009
  3. ncbi High-resolution DNA melting analysis for simple and efficient molecular diagnostics
    Gudrun H Reed
    Department of Pathology, University of Utah Medical Center, 5B418, 50 North Medical Drive, Salt Lake City, UT 84132, USA
    Pharmacogenomics 8:597-608. 2007
  4. ncbi High-resolution melting analysis (HRMA): more than just sequence variant screening
    Rolf H A M Vossen
    Leiden Genome Technology Center LGTC, Human and Clincal Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Hum Mutat 30:860-6. 2009
  5. pmc Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon
    S L Martin
    Department of Cellular and Structural Biology, University of Colorado School of Medicine, Denver, Colorado 80262, USA
    Mol Cell Biol 21:467-75. 2001
  6. pmc How long is too long? Effects of loop size on G-quadruplex stability
    Aurore Guédin
    INSERM, U869, European Institute of Chemistry and Biology, Bordeaux 2 University, 2 rue Robert Escarpit, Pessac F 33607, France
    Nucleic Acids Res 38:7858-68. 2010
  7. pmc A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    J SantaLucia
    Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
    Proc Natl Acad Sci U S A 95:1460-5. 1998
  8. pmc Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation
    Tomasz K Wojdacz
    Molecular Pathology Research Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
    Nucleic Acids Res 35:e41. 2007
  9. pmc Kinetics of tetramolecular quadruplexes
    Jean Louis Mergny
    Laboratoire de Biophysique, Muséum National d Histoire Naturelle USM503 INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris Cedex 05, France
    Nucleic Acids Res 33:81-94. 2005
  10. pmc The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression
    Daekyu Sun
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    J Med Chem 52:2863-74. 2009

Detail Information

Publications283 found, 100 shown here

  1. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    ..The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'...
  2. pmc Circular dichroism and conformational polymorphism of DNA
    Jaroslav Kypr
    Institute of Biophysics, vvi Academy of Sciences of the Czech Republic, Brno, Czech Republic
    Nucleic Acids Res 37:1713-25. 2009
    ..Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA...
  3. ncbi High-resolution DNA melting analysis for simple and efficient molecular diagnostics
    Gudrun H Reed
    Department of Pathology, University of Utah Medical Center, 5B418, 50 North Medical Drive, Salt Lake City, UT 84132, USA
    Pharmacogenomics 8:597-608. 2007
    ..Owing to its simplicity and speed, the method is a good fit for personalized medicine as a rapid, inexpensive method to predict therapeutic response...
  4. ncbi High-resolution melting analysis (HRMA): more than just sequence variant screening
    Rolf H A M Vossen
    Leiden Genome Technology Center LGTC, Human and Clincal Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Hum Mutat 30:860-6. 2009
    ..Together, these diverse applications make HRMA a multipurpose technology and a standard tool that should be present in any laboratory studying nucleic acids...
  5. pmc Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon
    S L Martin
    Department of Cellular and Structural Biology, University of Colorado School of Medicine, Denver, Colorado 80262, USA
    Mol Cell Biol 21:467-75. 2001
    ..These findings suggest a role for L1 ORF1p in mediating nucleic acid strand transfer steps during L1 reverse transcription...
  6. pmc How long is too long? Effects of loop size on G-quadruplex stability
    Aurore Guédin
    INSERM, U869, European Institute of Chemistry and Biology, Bordeaux 2 University, 2 rue Robert Escarpit, Pessac F 33607, France
    Nucleic Acids Res 38:7858-68. 2010
    ..This study will therefore extend the sequence repertoire of quadruplex-prone sequences, arguing for a modification of the widely used consensus (maximal loop size of 7 bases)...
  7. pmc A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    J SantaLucia
    Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
    Proc Natl Acad Sci U S A 95:1460-5. 1998
    ..Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics. Empirical salt dependencies are also derived for oligonucleotides and polymers...
  8. pmc Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation
    Tomasz K Wojdacz
    Molecular Pathology Research Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
    Nucleic Acids Res 35:e41. 2007
    ..The simplicity and high reproducibility of the MS-HRM protocol makes MS-HRM the method of choice for methylation assessment in many diagnostic and research applications...
  9. pmc Kinetics of tetramolecular quadruplexes
    Jean Louis Mergny
    Laboratoire de Biophysique, Muséum National d Histoire Naturelle USM503 INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris Cedex 05, France
    Nucleic Acids Res 33:81-94. 2005
    ..The data collected here allow us to predict the amount of time required for 50% (or 90%) quadruplex formation as a function of strand sequence and concentration, temperature and ionic strength...
  10. pmc The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression
    Daekyu Sun
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    J Med Chem 52:2863-74. 2009
    ....
  11. ncbi Methylation-sensitive high-resolution melting
    Tomasz K Wojdacz
    Institute of Human Genetics, University of Aarhus, The Bartholin Building, Wilhelm Meyers Alle, Bygn 1242, DK 8000 Aarhus C, Denmark
    Nat Protoc 3:1903-8. 2008
    ..Here, we provide a protocol for MS-HRM, which enables highly sensitive, labor- and cost-efficient single-locus methylation studies on the basis of DNA high-resolution melting technology...
  12. pmc KRAS mutation: comparison of testing methods and tissue sampling techniques in colon cancer
    Wilbur A Franklin
    Department of Pathology, University of Colorado Denver, Fitzsimons Campus, 12801 E 17 Ave, Aurora, CO 80045, USA
    J Mol Diagn 12:43-50. 2010
    ..We conclude that coring of the paraffin blocks and testing by ARMS/S is a sensitive, specific, and efficient method for KRAS testing...
  13. ncbi Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability
    Bernardo G Moreira
    Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
    Biochem Biophys Res Commun 327:473-84. 2005
    ..Depending on the dye/quencher combination employed, it can be important to include thermodynamic contributions from fluorophore and quencher when designing oligonucleotide probe assays...
  14. ncbi Genotyping of the protozoan pathogen Toxoplasma gondii using high-resolution melting analysis of the repeated B1 gene
    Jean Marc Costa
    groupe hospitalier Chenevier Mondor, APHP, Laboratoire de Parasitologie Mycologie, Creteil, France
    J Microbiol Methods 86:357-63. 2011
    ..Using HRM analysis, we obtained at least an equally good discrimination of the main lineages than that based on five microsatellite markers...
  15. ncbi CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone
    W Jiang
    Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    J Biol Chem 272:196-202. 1997
    ..Such a function may be crucial for efficient translation of mRNAs at low temperatures and may also have an effect on transcription...
  16. ncbi Formation of pearl-necklace monomorphic G-quadruplexes in the human CEB25 minisatellite
    Samir Amrane
    School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
    J Am Chem Soc 134:5807-16. 2012
    ..Further, we demonstrate that such a monomorphic structure is formed within longer sequence contexts folding into a pearl-necklace structure...
  17. pmc Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching using fluorescence microscopy
    Graeme A King
    LaserLaB Amsterdam and Department of Physics and Astronomy, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
    Proc Natl Acad Sci U S A 110:3859-64. 2013
    ..These findings enhance our knowledge of DNA mechanics and stability, which are of fundamental importance to understanding how proteins modify the physical state of DNA...
  18. pmc Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors
    Maxim Y Sheinin
    Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
    Phys Rev Lett 107:108102. 2011
    ..We have also discovered that at low forces melted DNA properties are highly dependent on DNA sequence. These results provide a more comprehensive picture of the global DNA force-torque phase diagram...
  19. pmc Design of LNA probes that improve mismatch discrimination
    Yong You
    Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
    Nucleic Acids Res 34:e60. 2006
    ..New guidelines are suggested for design of LNA probes, which significantly improve mismatch discrimination in comparison with unmodified DNA probes...
  20. pmc DNA overstretching in the presence of glyoxal: structural evidence of force-induced DNA melting
    Leila Shokri
    Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
    Biophys J 95:1248-55. 2008
    ..This result demonstrates that DNA overstretching is accompanied by a disruption of the DNA helical structure, including a loss of hydrogen bonding...
  21. pmc Modulation of the stability of the Salmonella fourU-type RNA thermometer
    Jörg Rinnenthal
    Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Max von Laue Strasse 7, D 60438 Frankfurt Main, Germany
    Nucleic Acids Res 39:8258-70. 2011
    ..Binding of the two Mg(2+) ions exhibits a positive cooperativity with a Hill coefficient of 1.47. Free energy values ΔG for Mg(2+) binding determined by NMR are in agreement with data determined from CD measurements...
  22. pmc Multiplex fluorescence melting curve analysis for mutation detection with dual-labeled, self-quenched probes
    Qiuying Huang
    Engineering Research Center of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences, School of Life Sciences, and Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, Xiamen University, Xiamen, Fujian, China
    PLoS ONE 6:e19206. 2011
    ....
  23. pmc Intercalating nucleic acids containing insertions of 1-O-(1-pyrenylmethyl)glycerol: stabilisation of dsDNA and discrimination of DNA over RNA
    Ulf B Christensen
    Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK 5230 Odense M, Denmark
    Nucleic Acids Res 30:4918-25. 2002
    ..Fluorescence measurements show a stronger interaction of the pyrene moiety with DNA than with RNA, indicating intercalation as the stabilising factor in DNA/INA duplexes...
  24. ncbi Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns
    N Fromin
    Microbiology Laboratory, University of Neuchatel, Switzerland
    Environ Microbiol 4:634-43. 2002
    ..As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non-ambiguous interpretation of the spatial and temporal functioning of microbial communities...
  25. pmc Determining the effectiveness of High Resolution Melting analysis for SNP genotyping and mutation scanning at the TP53 locus
    Sonia Garritano
    Department of Biology, Genetics via Derna 1, University of Pisa, Pisa, Italy
    BMC Genet 10:5. 2009
    ..Recently, the use of new fluorescent dyes allowed the high-resolution analysis of DNA melting curves (HRM)...
  26. ncbi Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.)
    Leo van Overbeek
    Plant Research International, Wageningen, The Netherlands
    FEMS Microbiol Ecol 64:283-96. 2008
    ..Its prevalence was affected by plant growth stage and experiment rather than by plant genotype. It was concluded that plant growth stage overwhelmed any effect of plant genotype on the bacterial communities associated with potato...
  27. ncbi Mutation scanning using high-resolution melting
    Claire F Taylor
    Cancer Research UK Genome Variation Service, St James s University Hospital, Leeds, UK
    Biochem Soc Trans 37:433-7. 2009
    ..Practical considerations for successful mutation scanning by high-resolution melting are also discussed in this review...
  28. pmc Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution
    Jörg Rinnenthal
    Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Max von Laue Strasse 7, D 60438 Frankfurt Main, Germany
    Nucleic Acids Res 38:3834-47. 2010
    ..Furthermore, remote effects of the A8C mutation affecting the stability of nucleobase G14 could be identified. According to our analysis we deduce that this effect is most probably transduced via the hydration shell of the RNA...
  29. pmc Tertiary interactions determine the accuracy of RNA folding
    Seema Chauhan
    Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
    J Am Chem Soc 130:1296-303. 2008
    ..Our results show that stable tertiary structure increases the flux through folding pathways that lead directly and rapidly to the native structure...
  30. pmc Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
    Peter Yakovchuk
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 34:564-74. 2006
    ..Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence...
  31. pmc Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure
    M H Hou
    Institute of Chemistry, Academia Sinica, Taipei, 115 Taiwan
    Nucleic Acids Res 29:5121-8. 2001
    ..Our results may suggest that the interconversion of various DNA structures can be accomplished readily in the presence of polyamine. This may be relevant in understanding the role of DNA polymorphism in cells...
  32. ncbi Heteronuclear NMR studies of the interaction of tRNA(Lys)3 with HIV-1 nucleocapsid protein
    C Tisne
    Laboratoire de Cristallographie et RMN Biologiques, EP 2075 CNRS Faculté de Pharmacie, 4 avenue de l Observatoire, Paris, 75006, France
    J Mol Biol 306:443-54. 2001
    ..It is interesting that for the biological role of the NC protein, these pairs could be the starting points of the tRNA melting required for the hybridisation to the viral RNA...
  33. pmc High-resolution melting analysis as a powerful tool to discriminate and genotype Pseudomonas savastanoi pathovars and strains
    Andrea Gori
    Laboratorio di Patologia Vegetale e Molecolare, Dipartimento di Biotecnologie Agrarie, Universita degli Studi di Firenze, Sesto Fiorentino, Firenze, Italy
    PLoS ONE 7:e30199. 2012
    ..Its application is particularly suitable for sanitary certification programs for P. savastanoi, aimed at avoiding the spreading of this phytopathogen through asymptomatic plants...
  34. ncbi Rapid detection of CFH (p.Y402H) and ARMS2 (p.A69S) polymorphisms in age-related macular degeneration using high-resolution melting analysis
    Enrica Mello
    Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University, Rome, Italy
    Clin Chem Lab Med 50:1031-4. 2012
    ..In order to perform the genetic screening of these single nucleotide polymorphisms (SNPs), we describe a high resolution melting analysis (HRM) as a rapid closed tube mutation scanning assay...
  35. pmc The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure
    B Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
    RNA 6:282-95. 2000
    ..The putative biological function of this conformational polymorphism as molecular RNA switch in the HIV-1 replication cycle is discussed...
  36. pmc G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA
    Soma Dhakal
    Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, USA
    Biophys J 102:2575-84. 2012
    ....
  37. pmc Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity
    Matthew M Cousins
    Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    J Clin Microbiol 50:3054-9. 2012
    ..The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution...
  38. ncbi Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase
    R K Saiki
    Cetus Corporation, Department of Human Genetics, Emeryville, CA 94608
    Science 239:487-91. 1988
    ..In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells...
  39. ncbi Denaturing RNA electrophoresis in TAE agarose gels
    Tomas Masek
    Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44, Prague, Czech Republic
    Anal Biochem 336:46-50. 2005
    ..Additionally, another benefit is the reduced exposure of laboratory personnel to hazardous chemicals...
  40. ncbi Overstretching and force-driven strand separation of double-helix DNA
    Simona Cocco
    Laboratoire de Dynamiques des Fluides Complexes, CNRS, 3 rue de l Université, Strasbourg, France
    Phys Rev E Stat Nonlin Soft Matter Phys 70:011910. 2004
    ..For long genomic sequences, these barriers to unpeeling cannot be kinetically crossed until force exceeds approximately 150 piconewtons...
  41. ncbi Mechanical measurement of single-molecule binding rates: kinetics of DNA helix-destabilization by T4 gene 32 protein
    Kiran Pant
    Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
    J Mol Biol 336:851-70. 2004
    ....
  42. ncbi Genotyping of Candida albicans using length fragment and high-resolution melting analyses together with minisequencing of a polymorphic microsatellite locus
    Jean Marc Costa
    groupe hospitalier Chenevier Mondor, APHP, Laboratoire de Parasitologie Mycologie, Creteil, France
    J Microbiol Methods 80:306-9. 2010
    ..88 in complete congruence with previous MLP typing (Mantel test R=0.99, P<10(-)(4)). HRM is a useful tool of adding resolving power to MLP genotyping in identifying SNPs...
  43. pmc Self-association of short DNA loops through minor groove C:G:G:C tetrads
    Júlia Viladoms
    Departament de Química Orgànica and IBUB, Universitat de Barcelona, C Martí i Franquès 1 11, 08028 Barcelona, Spain
    Nucleic Acids Res 37:3264-75. 2009
    ..We hypothesize that these quadruplex structures can be formed by many different DNA sequences, but its observation in linear oligonucleotides is usually hampered by competing Watson-Crick duplexes...
  44. pmc C-terminal domain modulates the nucleic acid chaperone activity of human T-cell leukemia virus type 1 nucleocapsid protein via an electrostatic mechanism
    Dominic F Qualley
    Department of Chemistry and Biochemistry, Center for Retrovirus Research, Ohio State University, Columbus, Ohio 43210, USA
    J Biol Chem 285:295-307. 2010
    ..The latter inhibits both NA/NC aggregation and rapid protein dissociation from single-stranded DNA. These features make HTLV-1 NC a poor NA chaperone, despite its robust duplex destabilizing capability...
  45. ncbi Assessing high-resolution melt curve analysis for accurate detection of gene variants in complex DNA fragments
    Elizabeth A Tindall
    Cancer Genetics Group, Children s Cancer Institute Australia for Medical Research, Sydney Children s Hospital, Randwick, Sydney, NSW, Australia
    Hum Mutat 30:876-83. 2009
    ..We demonstrate current limitations of the HRM method for the analysis of complex DNA regions and call for caution when using HRM as the sole method to make a clinical diagnosis based on genetic analysis...
  46. ncbi Monitoring the conformational fluctuations of DNA hairpins using single-pair fluorescence resonance energy transfer
    J R Grunwell
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    J Am Chem Soc 123:4295-303. 2001
    ..The surface immobilization chemistries and other experimental techniques described here should prove useful for studies of single-molecule populations and dynamics...
  47. ncbi High-resolution DNA melting analysis: advancements and limitations
    Carl T Wittwer
    Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
    Hum Mutat 30:857-9. 2009
    ....
  48. pmc Synthesis of 2'-O-methyl-RNAs incorporating a 3-deazaguanine, and UV melting and computational studies on its hybridization properties
    Kohji Seio
    Frontier Collaborative Research Center, Tokyo Institute of Technology, 4259 Nagatsuta cho, Midori ku, Yokohama, Japan
    Nucleic Acids Res 34:4324-34. 2006
    ..Computational studies based on ab initio calculations suggest that the weaker hydrogen bonding ability and larger dipole moment of c3G can be the origin of the lower T(m)...
  49. ncbi Development of high-resolution melting (HRM) analysis for population studies of Fascioloides magna (Trematoda: Fasciolidae), the giant liver fluke of ruminants
    Jan Radvansky
    Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina, 842 15 Bratislava, Slovakia
    Parasitol Res 108:201-9. 2011
    ..magna and promises its application as fast and cheap screening technique for phylogeography studies of the giant liver fluke on its original continent...
  50. ncbi Differentiation between vaccine and wild-type varicella-zoster virus genotypes by high-resolution melt analysis of single nucleotide polymorphisms
    Cheryl S Toi
    Clinical Virology, Centre for Infectious Diseases and Microbiology Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
    J Clin Virol 43:18-24. 2008
    ..The analysis of single nucleotide polymorphisms (SNPs) of varicella-zoster virus (VZV) has enabled differentiation between wild-type genotypes from the Oka vaccine strain (V-Oka)...
  51. ncbi Enhanced DNA binding of 9-ω-amino alkyl ether analogs from the plant alkaloid berberine
    Md Maidul Islam
    Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology CSIR, Kolkata, India
    DNA Cell Biol 30:123-33. 2011
    ..These results may be of potential use in the design of berberine derivatives and understanding of the structure-activity relationship for improved therapeutic applications...
  52. ncbi Quantitative PCR high-resolution melting (qPCR-HRM) curve analysis, a new approach to simultaneously screen point mutations and large rearrangements: application to MLH1 germline mutations in Lynch syndrome
    Etienne Rouleau
    Centre Rene Huguenin, Laboratoire d oncogénétique, Institut Nationale de la Santé et de la Recherche Médicale INSERM U735, Saint Cloud, France
    Hum Mutat 30:867-75. 2009
    ..In replicate, its reagent cost, sensitivity, and specificity are comparable to those of dHPLC+MLPA techniques. However, qPCR HRM outperformed the other techniques in terms of its rapidity and amount of data provided...
  53. ncbi Rapid, comprehensive screening of the human medium chain acyl-CoA dehydrogenase gene
    J T McKinney
    Idaho Technology, 390 Wakara Way, Salt Lake City, UT 84132, USA
    Mol Genet Metab 82:112-20. 2004
    ..The entire process is homogeneous requiring no post-PCR manipulation and is completed in under 3 h...
  54. pmc Enthalpy-entropy contribution to carcinogen-induced DNA conformational heterogeneity
    Fengting Liang
    Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA
    Biochemistry 49:259-66. 2010
    ..6 cal mol(-1) K(-1) in favor of the intercalated S conformer. These findings demonstrate that the favorable entropy of the S conformer over B conformer determines the S/B population ratios at physiological temperatures...
  55. ncbi BRAFV600E detection in melanoma is highly improved by COLD-PCR
    Pamela Pinzani
    Department of Clinical Physiopathology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy
    Clin Chim Acta 412:901-5. 2011
    ..Our aim was to investigate COLD-PCR (co-amplification at lower denaturation temperature-PCR) as a new approach for the pre-analytical enrichment of the BRAFV600E variant in formalin fixed paraffin embedded (FFPE) melanoma tissues...
  56. pmc Molecular beacons with intrinsically fluorescent nucleotides
    Angel A Marti
    Department of Chemistry, Columbia University, New York, NY 10027, USA
    Nucleic Acids Res 34:e50. 2006
    ..The thermal denaturation profile of MB-FB hybridized with its target shows a marked fluorescence reduction at 53 degrees C, consistent with a transition from double stranded helix to random coil DNA...
  57. pmc Temperature-tolerant COLD-PCR reduces temperature stringency and enables robust mutation enrichment
    E Castellanos-Rizaldos
    Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
    Clin Chem 58:1130-8. 2012
    ..We present a temperature-tolerant (TT) approach (TT-COLD-PCR) that reduces this obstacle...
  58. pmc Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators
    Matthias Bahr
    Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D 52056 Aachen, Germany
    Nucleic Acids Res 36:5000-12. 2008
    ..Altogether, our results demonstrate that macrocyclic distance-constrained bis-intercalators are efficient and selective mismatch-binding ligands that can interfere with mismatch-binding enzymes...
  59. pmc Kinetic barriers and the role of topology in protein and RNA folding
    Tobin R Sosnick
    University of Chicago, 929 East 57th Street, GCIS W107E, Chicago, IL 60637, USA
    Protein Sci 17:1308-18. 2008
    ....
  60. ncbi uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application
    Zachary Dwight
    School of Computing, University of Utah, Salt Lake City, UT 84112, USA
    Bioinformatics 27:1019-20. 2011
    ..uMelt provides a convenient platform for simulation and design of high-resolution melting assays...
  61. pmc Multiplex amplification coupled with COLD-PCR and high resolution melting enables identification of low-abundance mutations in cancer samples with low DNA content
    Coren A Milbury
    Department of Radiation Oncology, Dana Farber Brigham and Women s Cancer Center, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Mol Diagn 13:220-32. 2011
    ..In summary, we demonstrate an efficient approach to increase screening capabilities from limited DNA material via multiplex-PCR and improve mutation detection sensitivity via COLD-PCR amplification...
  62. ncbi Multiplex high resolution melting assay for estimation of Porcine Endogenous Retrovirus (PERV) relative gene dosage in pigs and detection of PERV infection in xenograft recipients
    Shaun Wynyard
    Molecular Diagnostic Laboratory, Living Cell Technologies, Manukau 2025, New Zealand
    J Virol Methods 175:95-100. 2011
    ..This assay can be used as both a screening tool for PERV proviral levels within donor pigs and as a diagnostic tool to examine PERV transmission in human patients treated with porcine xenotransplantation material...
  63. ncbi The Escherichia coli ibpA thermometer is comprised of stable and unstable structural elements
    Torsten Waldminghaus
    Lehrstuhl für Biologie der Mikroorganismen, Ruhr Universitat Bochum, Bochum, Germany
    RNA Biol 6:455-63. 2009
    ..Our study demonstrates how the combination of stable and unstable modules controls translation efficiency in a complete RNA thermometer...
  64. pmc Stability of intramolecular quadruplexes: sequence effects in the central loop
    Aurore Guédin
    INSERM, U565, Acides Nucléiques, Dynamique, ciblage et fonctions biologiques, Paris Cedex 05 F 75231, France
    Nucleic Acids Res 37:5559-67. 2009
    ..Finally, analysis of some of the sequences by microcalorimetry (DSC) confirmed the differences found between the sequence motifs...
  65. ncbi A DNA nanomachine induced by single-walled carbon nanotubes on gold surface
    Chao Zhao
    Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Jilin, China
    Biomaterials 30:1739-45. 2009
    ..Therefore our work will provide new insights into the design and application of SWNT-induced DNA nanodevice under physiological conditions...
  66. pmc In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form
    Graham L Randall
    Baylor College of Medicine, Houston, TX 77030 3498, USA
    Nucleic Acids Res 37:5568-77. 2009
    ..Finally, our data support a model in which base flipping can result from torsional stress...
  67. pmc New approaches toward recognition of nucleic acid triple helices
    Dev P Arya
    Department of Chemistry, Clemson University, USA
    Acc Chem Res 44:134-46. 2011
    ..These principles of dual recognition should be applicable to the design of ligands that can bind any given nucleic acid target with nanomolar affinities and with high selectivity...
  68. pmc Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: effect of mRNA target sequence and chimera design
    Dwaine A Braasch
    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9041, USA
    Nucleic Acids Res 30:5160-7. 2002
    ..Our data suggest that LNA bases can be used to develop antisense oligonucleotides and that their use is a versatile approach for efficiently inhibiting gene expression inside cells...
  69. pmc COLD-PCR-enhanced high-resolution melting enables rapid and selective identification of low-level unknown mutations
    Coren A Milbury
    Department of Radiation Oncology, Division of Medical Physics and Biophysics, and Division of Genome Stability and DNA Repair, Dana Farber Brigham and Women s Cancer Center, Harvard Medical School, Boston, MA, USA
    Clin Chem 55:2130-43. 2009
    ..To enable enrichment, quick scanning, and identification of low-level unknown mutations, we combined COLD-PCR with HRM mutation scanning, followed by sequencing of positive samples...
  70. pmc PCR-based methods for the enrichment of minority alleles and mutations
    Coren A Milbury
    Department of Radiation Oncology, Division of Medical Physics and Biophysics, and Division of DNA Repair and Genome Stability, Dana Farber Brigham and Women s Cancer Center, Harvard Medical School, Boston, MA 02115, USA
    Clin Chem 55:632-40. 2009
    ..Routine application in clinical and diagnostic settings requires that these techniques be accurate and cost-effective and require little effort to optimize, perform, and analyze...
  71. ncbi Activity and DNA contamination of commercial polymerase chain reaction reagents for the universal 16S rDNA real-time polymerase chain reaction detection of bacterial pathogens in blood
    Helge Mühl
    Institut für Angewandte Mikrobiologie und Biotechnologie, Hochschule Bremerhaven, An der Karlstadt 8, D 27568 Bremerhaven, Germany
    Diagn Microbiol Infect Dis 66:41-9. 2010
    ..The reagent was validated by the detection of pathogens at low titers using bacterial DNA extracted from blood that was spiked with various Gram-positive and Gram-negative bacteria...
  72. pmc The utility of high-resolution melting analysis of SNP nucleated PCR amplicons--an MLST based Staphylococcus aureus typing scheme
    Rachael A Lilliebridge
    Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
    PLoS ONE 6:e19749. 2011
    ..The MLST databases for all species tested contained abundant unlinked SNPs, thus suggesting that high resolving power is not dependent upon large numbers of SNPs...
  73. pmc Guanines are a quartet's best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes
    Julien Gros
    Laboratoire de Biophysique, Museum National d Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris Cedex 05, France
    Nucleic Acids Res 35:3064-75. 2007
    ..The thermodynamic and kinetic data compiled here are highly valuable for the design of DNA quadruplex assemblies with tunable association/dissociation properties...
  74. pmc The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site
    Audrey Tupin
    Universite de Montpellier 1, Centre d Etudes d Agents Pathogenes et Biotechnologies pour la Sante CPBS, CNRS, UMR 5236, CPBS, Montpellier, France
    EMBO J 29:2527-37. 2010
    ..2 is essential for promoter melting and for de novo initiation of RNA synthesis, and our results suggest that Lpm impedes this process...
  75. pmc Synthesis and properties of oligonucleotides containing 5-formyl-2'-deoxycytidine: in vitro DNA polymerase reactions on DNA templates containing 5-formyl-2'-deoxycytidine
    N Karino
    Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
    Nucleic Acids Res 29:2456-63. 2001
    ..These results suggest that fC may induce the transition mutation C.G-->T.A and the transversion mutation C.G-->A.T during DNA synthesis...
  76. ncbi RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloid coralyne
    Md Maidul Islam
    Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology Council of Scientific and Industrial Research, 4 Raja S C Mullick Road, Kolkata 700032, India
    Mol Biosyst 5:244-54. 2009
    ..Docking studies provided further insights into the partially intercalated state of coralyne inside the t-RNA structure. This study presents a complete binding and thermodynamic profile of coralyne interaction to t-RNA...
  77. ncbi Increased sensitivity of KRAS mutation detection by high-resolution melting analysis of COLD-PCR products
    Lasse S Kristensen
    Institute of Human Genetics, University of Aarhus, The Bartholin Building, Aarhus C, Denmark
    Hum Mutat 31:1366-73. 2010
    ..In conclusion, COLD-PCR combined with HRM, is a simple way of increasing the sensitivity of KRAS mutation detection without adding to the complexity and cost of the experiments...
  78. ncbi Validation of dye-binding/high-resolution thermal denaturation for the identification of mutations in the SLC22A5 gene
    Steven F Dobrowolski
    Idaho Technology, Salt Lake City, Utah, USA
    Hum Mutat 25:306-13. 2005
    ..These results expand the mutational spectrum in primary carnitine deficiency and indicate dye-binding/high-resolution thermal denaturation as an ideal system to screen for mutations in diseases with no prevalent molecular alteration...
  79. pmc Thermodynamic comparison of PNA/DNA and DNA/DNA hybridization reactions at ambient temperature
    F P Schwarz
    Center for Advanced Research in Biotechnology National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 27:4792-800. 1999
    ....
  80. ncbi Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR
    Ju Chien Cheng
    School of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, and Department of Pathology and Laboratory Medicine, Li Shin Hospital, Tao Yuan, Taiwan, Republic of China
    Clin Chem 52:1997-2004. 2006
    ..This study assesses the combined use of broad-range real-time PCR and high-resolution melting analysis for rapid detection and identification of clinically important bacteria...
  81. ncbi Simple fluorescent pyrimidine analogues detect the presence of DNA abasic sites
    Nicholas J Greco
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    J Am Chem Soc 127:10784-5. 2005
    ..The most responsive of the family was incorporated in DNA. This isosteric fluorescent DNA analogue monitors denaturation of a DNA duplex via fluorescence and positively detects the presence of abasic sites in DNA duplexes...
  82. ncbi Rapid, simple, and low-cost identification of Candida species using high-resolution melting analysis
    Silvia Arancia
    Mycoses Unit, Department of Infectious, Parasitic and Immune Mediated Disease, Istituto Superiore di Sanita, Viale Regina Elena, 299, 00161 Rome, Italy
    Diagn Microbiol Infect Dis 69:283-5. 2011
    ..albicans, C. glabrata, C. kefyr, C. parapsilosis, and C. guilliermondii). HRMA was able to differentiate clinical Candida species and resulted in being sensitive, reproducible, and inexpensive...
  83. ncbi Analysis of thermal melting curves
    Jean Louis Mergny
    Laboratoire de Biophysique, INSERM UR565, CNRS UMR 5153, Museum national d histoire naturelle, 75231 Paris, France
    Oligonucleotides 13:515-37. 2003
    ..We present the classic problems encountered during these experiments and try to demonstrate that a number of useful pieces of information can be extracted from these experimental curves...
  84. ncbi Natural and synthetic G-quadruplex interactive berberine derivatives
    Marco Franceschin
    Dipartimento di Chimica, Universita di Roma La Sapienza, Piazzale A Moro 5, 00185 Rome, Italy
    Bioorg Med Chem Lett 16:1707-11. 2006
    ..The results show that these molecules have selectivity for G-quadruplex compared to duplex DNA, and that their aromatic moieties play a dominant role in quadruplex binding...
  85. pmc High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer
    Michael Krypuy
    Molecular Pathology Research Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, A Beckett St, Melbourne, Victoria 8006, Australia
    BMC Cancer 6:295. 2006
    ..In non-small cell lung cancer, KRAS mutations have been shown to identify a group of patients that do not respond to EGFR targeted therapies and the identification of these mutations is thus clinically important...
  86. pmc Breathing dynamics in heteropolymer DNA
    Tobias Ambjörnsson
    NORDITA, Nordic Institute for Theoretical Physics, Copenhagen, Denmark
    Biophys J 92:2674-84. 2007
    ..The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs...
  87. pmc 8-methyl-2'-deoxyguanosine incorporation into parallel DNA quadruplex structures
    Antonella Virgilio
    Dipartimento di Chimica delle Sostanze Naturali, Universita degli Studi di Napoli Federico II, via D Montesano 49, I 80131 Napoli, Italy
    Nucleic Acids Res 33:6188-95. 2005
    ..As far as d(TGGG(Me)T) is concerned, NMR data indicate that at 25 degrees C it exists primarily as a single-strand conformation in equilibrium with minor amounts of a quadruplex structure...
  88. pmc High resolution melting applications for clinical laboratory medicine
    Maria Erali
    ARUP Institute for Clinical and Experimental Pathology, University of Utah, Salt Lake City, UT 84108, USA
    Exp Mol Pathol 85:50-8. 2008
    ..In the clinical laboratory, it is an ideal format for in-house testing, with minimal cost and time requirements for new assay development...
  89. ncbi Structural features of intra- and intermolecular G-quadruplexes derived from telomeric repeats
    Viktor Viglasky
    Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P J Safarik University, 04154 Kosice, Slovakia
    Biochemistry 49:2110-20. 2010
    ..Intermolecular G-quadruplex forms are more likely to form in a higher concentration of ions for sequences where G-runs are separated by only one or two nucleotides...
  90. ncbi Synthesis and biophysical properties of arabinonucleic acids (ANA): circular dichroic spectra, melting temperatures, and ribonuclease H susceptibility of ANA.RNA hybrid duplexes
    A M Noronha
    Department of Chemistry, McGill University, Montreal, Quebec, Canada
    Biochemistry 39:7050-62. 2000
    ..These features, combined with the fact that ara-2'OH groups project into the major groove of the helix (where they should not interfere with RNase H binding), help to explain the RNase H activity of ANA/RNA hybrids...
  91. ncbi Imino proton exchange and base-pair kinetics in RNA duplexes
    K Snoussi
    , Groupe de Biophysique, UMR 7643 du CNRS, Ecole Polytechnique 91128 Palaiseau, France
    Biochemistry 40:8898-904. 2001
    ..The r(A.U) opening and closing rates are much larger than those of the d(A.T) pairs, but the stabilities are comparable...
  92. ncbi A ligase-mediated gene detection technique
    U Landegren
    Division of Biology, California Institute of Technology, Pasadena 91125
    Science 241:1077-80. 1988
    ..Thus single nucleotide substitutions can be distinguished. This strategy permits the rapid and standardized identification of single-copy gene sequences in genomic DNA...
  93. ncbi Mutation scanning and genotyping by high-resolution DNA melting analysis in olive germplasm
    Rosario Muleo
    Department of Crop Production, Woody Plant Molecular Ecophysiology Laboratory, University of Tuscia Viterbo, Via S Camillo de Lellis, 01100 Viterbo, Italy
    Genome 52:252-60. 2009
    ..HRM analysis has a very high reproducibility and sensitivity for detecting SNPs and SSRs, allowing olive cultivar genotyping and resulting in an informative, easy, and low-cost method able to greatly reduce the operating time...
  94. pmc Coamplification at lower denaturation temperature-PCR increases mutation-detection selectivity of TaqMan-based real-time PCR
    Jin Li
    Department of Radiation Oncology, Divisions of Genomic Stability and DNA Repair, and Medical Physics, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
    Clin Chem 55:748-56. 2009
    ..We demonstrate that combining COLD-PCR with TaqMan technology provides TaqMan genotyping with the selectivity needed to detect low-level somatic mutations...
  95. pmc Description and validation of high-throughput simultaneous genotyping and mutation scanning by high-resolution melting curve analysis
    Tú Nguyen-Dumont
    International Agency for Research on Cancer IARC, Lyon, France
    Hum Mutat 30:884-90. 2009
    ..Hence, HR-melt is a rapid, efficient, and cost-effective tool that can be used for high-throughput mutation screening for research, as well as for molecular diagnostic and clinical purposes...
  96. pmc Force-induced denaturation of RNA
    U Gerland
    Department of Physics, University of California at San Diego, La Jolla, California 92093 0319 USA
    Biophys J 81:1324-32. 2001
    ..Our software is available to the public through an "RNA-pulling server."..
  97. pmc Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation
    Peter J Mikulecky
    Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA
    Nucleic Acids Res 32:3967-76. 2004
    ..We weigh the strengths and limitations of this method for determining DeltaC(P) values. Finally, we discuss the data in light of the physical origins of the DeltaC(P)s for RNA folding and consider their impact on biological function...
  98. pmc Novel RNA base pair with higher specificity using single selenium atom
    Huiyan Sun
    Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
    Nucleic Acids Res 40:5171-9. 2012
    ..This oxygen replacement with selenium offers a unique chemical strategy to enhance the base pairing specificity at the atomic level...
  99. pmc A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity
    Sandra L Martin
    Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Nucleic Acids Res 36:5845-54. 2008
    ....
  100. ncbi The mechanism of nucleic acid melting by a CspA family protein
    Sangita Phadtare
    Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA
    J Mol Biol 337:147-55. 2004
    ..The results allow us to orient a CspE molecule relative to the melting substrate and to put forward a mechanistic model of nucleic acid melting by Csps...
  101. ncbi Single-molecule study of the DNA denaturation phase transition in the force-torsion space
    D Salerno
    Dipartimento di Medicina Sperimentale, Universita degli Studi di Milano Bicocca, Via Cadore 48, Monza MB 20900, Italy
    Phys Rev Lett 109:118303. 2012
    ..The model correctly describes the position of the denaturation regions, the transition boundaries, and the measured values of the DNA extension fluctuations...

Research Grants66

  1. ALGORITHMS, THERMODYNAMICS AND STATISTICS FOR RNA FOLDIN
    Michael Zuker; Fiscal Year: 2003
    ..Partition function computations will be extended to allow folding constraints and to compute probabilities of foldings similar to a given one. ..
  2. Analysis of ATP7B in Screening for Wilson Disease
    Steven Dobrowolski; Fiscal Year: 2004
    ..Prospective screening for WD improves efficacy of treatment and quality of life for affected patients. Genotyping is the best option to confirm results based upon ceruloplasmin analysis in asymptomatic patients. ..
  3. Molecular Epidemiological Approach to Determine S. mutans
    Yihong Li; Fiscal Year: 2005
    ..Application of the new molecular tools will have a substantial impact on improving the oral health of children. ..
  4. Targeting Tumor Angiogenesis with G-Quadruplex Binders
    Daekyu Sun; Fiscal Year: 2010
    ..abstract_text> ..
  5. DNA LIGASE I AS A POTENTIAL TARGET FOR ANTICANCER DRUGS
    Daekyu Sun; Fiscal Year: 2002
    ..3) Test whether DNA ligase I inhibition produces antitumor activity using antisense strategy in preclinical in vitro and in vivo evaluation systems. 4) Develop a sensitive and reproducible assay for DNA ligase I. ..
  6. Newborn screening for PKU and BH4 responsiveness
    Steven Dobrowolski; Fiscal Year: 2008
    ..High resolution melt profiling will play a role to identify BH4 responsive PKU patients. ..
  7. Genotype Analysis for Diagnosis of Urea Cycle Disorders
    Steven Dobrowolski; Fiscal Year: 2007
    ..The proposed assay panels provide a means to readily assess gene that are well established to contribute to hyperammonemia. [unreadable] [unreadable] [unreadable]..
  8. FilmArray-A Closed System for Multi-Pathogen Screening
    Steven Dobrowolski; Fiscal Year: 2005
    ..Pouches are designed to assay for candidate infectious agents consistent with clinical presentation. ..
  9. A Novel Inhibitor of Stat3 for Prostate Cancer Therapy
    Naijie Jing; Fiscal Year: 2009
    ..abstract_text> ..
  10. CHIP BASED QTL MAPPING IN ARABIDOPSIS
    Peter Oefner; Fiscal Year: 2001
    ..It is anticipated that experience gained on the mapping of QTLs in Arabidopsis will be very valuable for similar efforts in other eukaryotes, including human. ..
  11. DEVELOPING A POTENT INHIBITOR OF HIV-I INTEGRASE
    Naijie Jing; Fiscal Year: 2001
    ....
  12. Functional Proteogenomics of Mitochondria
    Peter Oefner; Fiscal Year: 2005
    ..The concordance of protein data with those obtained by means of human mRNA expression arrays and the functional genomic findings from yeast will be assessed. ..
  13. Combinational Transcription Control in Bacteria
    Terence Hwa; Fiscal Year: 2005
    ..The information obtained could be of significant value to the diagnosis and treatment of complex diseases. ..
  14. Studies of Hematologic Malignancies by PNA Technology
    Maxim Frank Kamenetskii; Fiscal Year: 2004
    ..It will allow fool roof characterization of malignant samples by detecting viral DNA in a very low number of copies like in case of provirus. ..
  15. Targeted Assisted Combinational Synthesis
    Steven Benner; Fiscal Year: 2004
    ..abstract_text> ..
  16. Flexible Biochip for Highly Parallel Microbial Detection
    Syed Hashsham; Fiscal Year: 2005
    ..Ability to detect all microorganisms of interest in a given matrix together will significantly improve the management of health concerns related to microorganisms. ..
  17. Theoretical and MD Simulation Studies of U1A-RNA Binding and Specificity
    David Beveridge; Fiscal Year: 2006
    ....
  18. Effects of Formamidopyrimidine Lesions on DNA
    Marc Greenberg; Fiscal Year: 2006
    ..abstract_text> ..
  19. The Genetic Basis of a Disease Free Model of Aging
    Yvette Conley; Fiscal Year: 2006
    ..This is the first study to propose to use lens transparency as a continuous, quantitative measure of the human aging process that will be suitable for genetic linkage and gene identification. ..
  20. Plant Viruses as Platforms for Biomaterials
    John Johnson; Fiscal Year: 2006
    ....
  21. SNP Analysis by Surface Invasive Cleavage on DNA Arrays
    Lloyd Smith; Fiscal Year: 2007
    ....
  22. FASEB CONFERENCE: VIRUS ASSEMBLY
    John Johnson; Fiscal Year: 2002
    ..We also seek to encourage unconventional aspects of virology as represented at our last meeting by presentations describing plant viruses as bio materials and nano reaction vessels. ..
  23. EVOLUTION OF THE RIBONUCLEASE SUPERFAMILY
    Steven Benner; Fiscal Year: 2001
    ....
  24. Molecular Genetics of the HPA(I) Axis
    Phillip Danielson; Fiscal Year: 2002
    ....
  25. MECHANISM OF TERMINATION OF DNA REPLICATION
    Deepak Bastia; Fiscal Year: 2010
    ..Finally, we wish to uncover the mode of action of the Swi1 and Swi3 proteins to determine if these act as "antisweepases". ..
  26. Real-time and quantitative determination of biomolecules in living specimen
    Weihong Tan; Fiscal Year: 2010
    ..The study will focus on EGR1 and Synaptotagmin IV, both of which have been linked to different stages of learning and memory. ..
  27. TECHNOLOGY FOR MUTATION ANALYSIS OF CANCER
    G Makrigiorgos; Fiscal Year: 2002
    ..Further envisioned ALBUMS applications include genotyping and polymorphism studies and role of mutations in diseases other than cancer. ..
  28. HIGH RESOLUTION OF STRUCTURAL STUDIES OF INSECT VIRUSES
    John Johnson; Fiscal Year: 2001
    ....
  29. GLUTAMATE BIOANALYSIS: PRECISE DETERMINATION
    Weihong Tan; Fiscal Year: 2002
    ....
  30. Near Term Development of Reagents and Enzymes for Genome Sequencing
    Steven A Benner; Fiscal Year: 2010
    ..This proposal, from a laboratory with a track record of innovation in structures, reagents, and enzymes to manipulate nucleic acids, is focused on near term development of these to enable NHGRI cost-reduction sequencing goals. ..
  31. Chemistry to Improve Human Genomic Array Analysis Architectures
    Steven A Benner; Fiscal Year: 2010
    ..This proposal seeks funds to benchmark the improvements in array performance generated by these new technologies, improve them by a cycle of test and redesign, and provide them to the genomics community. ..
  32. Quantitative Characterization & Modeling of sRNA-Mediated Gene Regulation
    Terence Hwa; Fiscal Year: 2010
    ..Additionally, the silencing of endogenous target may lead to an effective tool to generate multiple gene knockdown strains which may be used for drug discover studies as well as gene- gene interaction studies at the genome-wide scale. ..
  33. ERROR-FREE DNA AMPLIFICATION FOR MUTATION DETECTION
    G Makrigiorgos; Fiscal Year: 2003
    ..abstract_text> ..
  34. Polymerases for Sequencing by Synthesis
    Steven Benner; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  35. DNA Sequencing using Nanopores
    Steven Benner; Fiscal Year: 2007
    ..These will then be targeted against specific sequences extracted from mammalian genomes. [unreadable] [unreadable]..
  36. Sequence Effects of Arylamine-DNA Adducts: Repair and Replication
    BONGSUP CHO; Fiscal Year: 2008
    ..Such knowledge will also be of help in the development of sensible prevention and risk assessment strategies. ..
  37. Modeling maternal-fetal gene interactions: preterm birth
    Vinod Misra; Fiscal Year: 2008
    ..The educational climate and resources of the University, the commitment of his Department, and the expertise of his mentor will prepare Dr. Misra for a career as an independent investigator. [unreadable] [unreadable]..
  38. Enrichment and Detection of Exfoliated Cancer Cells
    Weihong Tan; Fiscal Year: 2008
    ..If successful the proposed research could have a great impact in cancer detection in that the protocols developed will be applicable to nearly all exfoliated cancer cell types. [unreadable] [unreadable] [unreadable]..
  39. GENE CONTROL IN INFECTION AND LYSOGENY BY PHAGE LAMBDA
    Jeffrey Roberts; Fiscal Year: 2008
    ..We will investigate the mechanism of transcription termination and the manner in which regulatory proteins interfere with this process. ..
  40. Artificial Genetic Systems
    Steven A Benner; Fiscal Year: 2010
    ..Multiplexed PCR is the rate limiting step in many genomics analyses. Our long term, highly ambitious goal is to develop a "synthetic biology", a chemical system capable of Darwinian evolution, based on AEGIS components. ..
  41. Quantitative RT-PCR: Prediction Lymphoma Transformation
    Kojo Elenitoba Johnson; Fiscal Year: 2005
    ....
  42. THE EFFECT OF APOE ON OUTCOMES IN TBI ADULTS
    Yvette Conley; Fiscal Year: 2003
    ....
  43. DNA SEQUENCING BY CHARGE REDUCTION ESI-MS
    Lloyd Smith; Fiscal Year: 2004
    ..The use of this existing instrument will eliminate the need to design and build an entirely new mass spectrometer from scratch while permitting dramatic improvements in nmass spectrometric performance. ..
  44. TRAINING GRANT IN MOLECULAR BIOPHYSICS
    WILMA OLSON; Fiscal Year: 2003
    ..The requested funds help to attract a pool of outstanding predoctoral students, to unify existing graduate offerings, and to offer an independent graduate curriculum in molecular biophysics. ..
  45. Hybridization of Oligonucleotide Probes with Duplex DNA
    Maxim Frank Kamenetskii; Fiscal Year: 2005
    ..The implementation of the project will open totally new opportunities for DNA diagnostics of pathogens and for isolation and analysis of genes in an intact form. ..
  46. INFERRING CHROMOSOME ARCHITECTURE FROM GENOMIC SEQUENCE
    Craig Benham; Fiscal Year: 2002
    ..It will be used to develop a new generation of precisely targeted and regulated transfection vectors for gene therapy. ..
  47. Microsphere Array for Lung Cancer Mutation Scanning
    G Makrigiorgos; Fiscal Year: 2002
    ..If the engineering and application of the present array proves successful, future work will automate the production of microsphere-based DNA arrays in order to simultaneously screen for mutations/SNPs in the entire human genome. ..
  48. PEPTIDE NUCLEIC ACIDS (PNA)-MEDIATED GENE EXPRESSION
    Gan Wang; Fiscal Year: 2003
    ..To investigate parameters that affect PNA delivery efficiency and intracellular PNA binding. To explore the possibility of PNA binding-induced endogenous human gene expression. ..
  49. Fluorescence in situ detection of short DNA sequences
    Maxim Frank Kamenetskii; Fiscal Year: 2006
    ..The implementation of the project will yield a convenient fluorescent in situ technique with a great potential for reliable and highly sensitive diagnosis of cancer on the DNA level. [unreadable] [unreadable]..
  50. CIRCULATING DNA AMPLIFICATION & COLON CA DETECTION
    G Makrigiorgos; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  51. Supercritical Fluid Extraction for Membrane Proteomics
    Lloyd Smith; Fiscal Year: 2006
    ..The successful development of this new technology for membrane proteomics will address a critical gap in current proteomics efforts. [unreadable] [unreadable]..
  52. Dynamic combinatorial chemistry for nucleic acids
    Steven Benner; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  53. Molecular mechanism of antibiotic rifampicin action
    Irina Artsimovitch; Fiscal Year: 2006
    ..Finally a set of rules for design of more potent rifamycin-like antibiotics will be formulated to achieve the long-term goal of knowledge-based creation of the new generation of antibacterial drugs. ..
  54. GENETICS AND BIOCHEMISTRY OF A MURINE RETROPOSON
    Sandra Martin; Fiscal Year: 2009
    ....
  55. Hepatitis C VIrus NS3 Helicase Inhibitor Discovery
    David Frick; Fiscal Year: 2008
    ..The goal here is to find chemicals that prevent the virus from replicating in human cells. [unreadable] [unreadable] [unreadable]..
  56. Mitochondrial Genetics of Recovery After Brain Injury
    Yvette Conley; Fiscal Year: 2008
    ....
  57. MOLECULAR DYNAMICS SIMULATIONS OF DNA OLIGONUCLEOTIDES
    David Beveridge; Fiscal Year: 2003
    ..abstract_text> ..
  58. HOMOGENEOUS MULTIPLEX PCR BY FLUORESCENCE AND TM
    Carl Wittwer; Fiscal Year: 2002
    ..This will be the first real-time instrument compatible with all visible/near IR fluorescent probes and amplification techniques. Multiplexing by fluorescence and Tm greatly expands the power of real-time nucleic acid analysis. ..
  59. Massively Parallel Cloning and Sequencing of DNA
    Xiaohua Huang; Fiscal Year: 2007
    ..The personal genome project could be a reality. That will truly transform the nature of biomedical research and individual healthcare. [unreadable] [unreadable] [unreadable]..
  60. Genome Sequencing by Ligation Using Nano-Arrays of Single DNA Molecules
    Xiaohua Huang; Fiscal Year: 2007
    ..Once developed, this kind of technology will enable routine sequencing of individual human genomes, revolutionizing biomedical research and healthcare. ..
  61. Homogeneous Mutation Scanning
    Carl Wittwer; Fiscal Year: 2006
    ....
  62. A System for Rapid PCR, Mutation Scanning and Genotyping
    Carl Wittwer; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  63. Protein Structure Refinement Using a Novel Moveset
    Tobin Sosnick; Fiscal Year: 2009
    ..The proposed research involves a new, synergistic collaboration and novel computational techniques as indicated in the RFA. ..
  64. MECHANISM OF REPLICATION OF DRUG RESISTANCE FACTORS
    Deepak Bastia; Fiscal Year: 2008
    ..abstract_text> ..
  65. Molecular Diagnosis of pathogenic fungi
    Robert Akins; Fiscal Year: 2007
    ..We expect that the protocols and strategies developed here for fungi will extend to other, non-culturable organisms. ..