base pair mismatch

Summary

Summary: The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).

Top Publications

  1. ncbi Functional siRNAs and miRNAs exhibit strand bias
    Anastasia Khvorova
    Amgen, Inc, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
    Cell 115:209-16. 2003
  2. ncbi Asymmetry in the assembly of the RNAi enzyme complex
    Dianne S Schwarz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Worcester, MA 01605, USA
    Cell 115:199-208. 2003
  3. ncbi DNA mismatch repair
    Thomas A Kunkel
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Annu Rev Biochem 74:681-710. 2005
  4. ncbi The multifaceted mismatch-repair system
    Josef Jiricny
    Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Nat Rev Mol Cell Biol 7:335-46. 2006
  5. pmc Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    David H Mathews
    Center for Human Genetics and Molecular Pediatric Disease, The Aab Institute of Biomedical Sciences, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 703, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 101:7287-92. 2004
  6. pmc Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:921-6. 2008
  7. ncbi Systematic identification of abundant A-to-I editing sites in the human transcriptome
    Erez Y Levanon
    Compugen Ltd, 72 Pinchas Rosen St, Tel Aviv 69512, Israel
    Nat Biotechnol 22:1001-5. 2004
  8. ncbi Endonucleolytic function of MutLalpha in human mismatch repair
    Farid A Kadyrov
    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
    Cell 126:297-308. 2006
  9. ncbi DNA replication fidelity
    Thomas A Kunkel
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    J Biol Chem 279:16895-8. 2004
  10. pmc Tumor microsatellite-instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer
    Christine M Ribic
    Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto
    N Engl J Med 349:247-57. 2003

Research Grants

Detail Information

Publications296 found, 100 shown here

  1. ncbi Functional siRNAs and miRNAs exhibit strand bias
    Anastasia Khvorova
    Amgen, Inc, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
    Cell 115:209-16. 2003
    ..Together, these results suggest that the thermodynamic properties of siRNA play a critical role in determining the molecule's function and longevity, possibly biasing the steps involved in duplex unwinding and strand retention by RISC...
  2. ncbi Asymmetry in the assembly of the RNAi enzyme complex
    Dianne S Schwarz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Worcester, MA 01605, USA
    Cell 115:199-208. 2003
    ..Thus, the common step of RISC assembly is an unexpected source of asymmetry for both siRNA function and miRNA biogenesis...
  3. ncbi DNA mismatch repair
    Thomas A Kunkel
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Annu Rev Biochem 74:681-710. 2005
    ..Emphasis is on structure-function studies of MMR proteins, on how mismatches are recognized, on the process by which the newly replicated strand is identified, and on excision of the replication error...
  4. ncbi The multifaceted mismatch-repair system
    Josef Jiricny
    Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Nat Rev Mol Cell Biol 7:335-46. 2006
    ..This article reviews our current understanding of this multifaceted DNA-repair system in human cells...
  5. pmc Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    David H Mathews
    Center for Human Genetics and Molecular Pediatric Disease, The Aab Institute of Biomedical Sciences, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 703, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 101:7287-92. 2004
    ..For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs...
  6. pmc Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:921-6. 2008
    ..Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active...
  7. ncbi Systematic identification of abundant A-to-I editing sites in the human transcriptome
    Erez Y Levanon
    Compugen Ltd, 72 Pinchas Rosen St, Tel Aviv 69512, Israel
    Nat Biotechnol 22:1001-5. 2004
    ..A-to-I editing in humans primarily occurs in noncoding regions of the RNA, typically in Alu repeats. Analysis of the large set of editing sites indicates the role of editing in controlling dsRNA stability...
  8. ncbi Endonucleolytic function of MutLalpha in human mismatch repair
    Farid A Kadyrov
    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
    Cell 126:297-308. 2006
    ..Therefore, the mode of excision initiation may differ in these organisms...
  9. ncbi DNA replication fidelity
    Thomas A Kunkel
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    J Biol Chem 279:16895-8. 2004
  10. pmc Tumor microsatellite-instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer
    Christine M Ribic
    Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto
    N Engl J Med 349:247-57. 2003
    ..We investigated the usefulness of microsatellite-instability status as a predictor of the benefit of adjuvant chemotherapy with fluorouracil in stage II and stage III colon cancer...
  11. pmc Cadmium is a mutagen that acts by inhibiting mismatch repair
    Yong Hwan Jin
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Nat Genet 34:326-9. 2003
    ..In extracts of human cells, cadmium inhibited at least one step leading to mismatch removal. Together, our data show that a high level of genetic instability can result from environmental impediment of a mutation-avoidance system...
  12. pmc Allele-selective inhibition of huntingtin expression by switching to an miRNA-like RNAi mechanism
    Jiaxin Hu
    The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390 9041, USA
    Chem Biol 17:1183-8. 2010
    ..Potent, allele selective inhibition of HTT by mismatched RNAs provides a new option for developing HD therapeutics...
  13. ncbi Single-mismatch detection using gold-quenched fluorescent oligonucleotides
    B Dubertret
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nat Biotechnol 19:365-70. 2001
    ..In competitive hybridization assays, the ability to detect single mismatch is eightfold greater with this probe than with other molecular beacons...
  14. pmc Differential correction of lagging-strand replication errors made by DNA polymerases {alpha} and {delta}
    Stephanie A Nick McElhinny
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 107:21070-5. 2010
    ....
  15. pmc Sorting of Drosophila small silencing RNAs
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Cell 130:299-308. 2007
    ..Thus, in flies small-RNA duplexes are actively sorted into Argonaute-containing complexes according to their intrinsic structures...
  16. ncbi Mismatch repair proteins, meiosis, and mice: understanding the complexities of mammalian meiosis
    Anton Svetlanov
    Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Exp Cell Res 296:71-9. 2004
    ..This review will focus on the studies involving these mutant mouse models, with occasional comparison to the function of these proteins in other organisms...
  17. ncbi DNA sequence detection using selective fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles
    Huixiang Li
    Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
    Anal Chem 76:5414-7. 2004
    ..Subfemtomole amounts of untagged target are detected in minutes using commercially available materials. Target sequences in complex mixtures of DNA and single-base mismatches in DNA sequences are easily detected...
  18. pmc Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition
    Atanu Maiti
    Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 105:8890-5. 2008
    ..We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity...
  19. pmc Yeast DNA polymerase epsilon participates in leading-strand DNA replication
    Zachary F Pursell
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
    Science 317:127-30. 2007
    ....
  20. ncbi 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets
    Amanda Birmingham
    Dharmacon Research, 2650 Crescent Drive, 100, Lafayette, Colorado 80026, USA
    Nat Methods 3:199-204. 2006
    ..These findings have strong implications for future siRNA design and the application of RNAi in high-throughput screening and therapeutic development...
  21. pmc Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
    Alekos Athanasiadis
    Department of Biological Sciences, Lehigh University Bethlehem, Pennsylvania, USA
    PLoS Biol 2:e391. 2004
    ..The analysis suggests that modification of repetitive elements is a predominant activity for RNA editing with significant implications for cellular gene expression...
  22. pmc Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D
    Maarit Jokela
    Biocenter Oulu and Department of Biochemistry, PO Box 3000, FIN 90014 University of Oulu, Finland
    Nucleic Acids Res 32:2430-40. 2004
    ..MjaDP1 acts as a unidirectional, non-processive exonuclease preferring mispaired nucleotides and single-stranded DNA, suggesting that MjaDP1 functions as the proofreading exonuclease of archaeal family D DNA polymerase...
  23. ncbi MLH3: a DNA mismatch repair gene associated with mammalian microsatellite instability
    S M Lipkin
    Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
    Nat Genet 24:27-35. 2000
    ..Functional redundancy among Mlh3, Pms1 and Pms2 may explain why neither Pms1 nor Pms2 mutant mice develop colon cancer, and why PMS1 and PMS2 mutations are only rarely found in HNPCC families...
  24. pmc Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA
    Michele Cristovao
    Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 40:5448-64. 2012
    ..These findings shed light on prerequisites for MutS interactions with other MMR proteins for repairing the appropriate DNA strand...
  25. ncbi MutSalpha binds to and promotes synapsis of transcriptionally activated immunoglobulin switch regions
    Erik D Larson
    Department of Immunology, Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, 1959 N E Pacific Street, Box 357650, Seattle, WA 98195, USA
    Curr Biol 15:470-4. 2005
    ..G mismatches, initial products of DNA deamination by AID. These results suggest that MutSalpha interacts with the S regions in switching B cells to promote DNA synapsis and recombination...
  26. pmc Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs
    Atanu Maiti
    Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, School of Medicine, University of Maryland, Baltimore, 21201, USA
    DNA Repair (Amst) 10:545-53. 2011
    ..Our findings provide important insight into catalysis by TDG, particularly for mutagenic G·T mispairs...
  27. ncbi Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates
    William A Beard
    Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    J Biol Chem 279:31921-9. 2004
    ....
  28. ncbi Mechanism of 5'-directed excision in human mismatch repair
    Jochen Genschel
    Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, NC 27710, USA
    Mol Cell 12:1077-86. 2003
    ..As observed in the purified system, excision directed by a 5' strand break in HeLa nuclear extract can proceed in the absence of MutLalpha or PCNA, although 3' excision in the extract system requires both proteins...
  29. 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...
  30. pmc DNA bending and unbending by MutS govern mismatch recognition and specificity
    Hong Wang
    Department of Chemistry and Curriculum in Applied and Materials Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
    Proc Natl Acad Sci U S A 100:14822-7. 2003
    ..Our results provide a structural explanation for the long-standing question of how MutS achieves mismatch repair specificity...
  31. pmc Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS
    Maria Chiara Monti
    Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Nucleic Acids Res 39:8052-64. 2011
    ..PNP cofactor. This is the first direct evidence for such a postulated mismatch repair intermediate, and showcases the potential of native MS analysis in detecting mechanistically relevant reaction intermediates...
  32. ncbi Mammalian MutS homologue 5 is required for chromosome pairing in meiosis
    W Edelmann
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Nat Genet 21:123-7. 1999
    ..We found that this meiotic failure leads to a diminution in testicular size and a complete loss of ovarian structures. Our results show that normal Msh5 function is essential for meiotic progression and, in females, gonadal maintenance...
  33. pmc The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes
    Elzbieta Kierzek
    Department of Chemistry, University of Rochester RC Box 270216, Rochester, NY 14627 0216, USA
    Nucleic Acids Res 33:5082-93. 2005
    ..Internal mismatches with LNA nucleotides significantly destabilize duplexes with RNA...
  34. pmc In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair
    V Burdett
    Department of Biochemistry and Howard Hughes Medical Institute, Box 3711, Duke University Medical Center, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 98:6765-70. 2001
    ....
  35. ncbi Mutational specificity of mice defective in the MTH1 and/or the MSH2 genes
    Akinori Egashira
    Department of Medical Biophysics and Radiation Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
    DNA Repair (Amst) 1:881-93. 2002
    ..These results suggest a possible involvement of multiple anti-mutagenic pathways, including the MTH1 protein and other repair system(s), in mutagenesis caused by the oxidized nucleotides...
  36. pmc The UvrD helicase and its modulation by the mismatch repair protein MutL
    Steven W Matson
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Nucleic Acids Res 34:4089-97. 2006
    ..Here we present a brief summary of recent studies directed toward arriving at a better understanding of the interaction between MutL and UvrD, and the impact of this interaction on the activity of UvrD and its role in mismatch repair...
  37. ncbi Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H
    Ying Shen
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
    Nat Struct Mol Biol 19:98-104. 2012
    ..In the absence of mismatch repair and RNases H, ribonucleotide-driven gene modification increased by a factor of 47 in yeast and 77,000 in E. coli...
  38. ncbi Structure and specificity of the vertebrate anti-mutator uracil-DNA glycosylase SMUG1
    Jane E A Wibley
    Cancer Research UK DNA Repair Enzyme Group, Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, United Kingdom
    Mol Cell 11:1647-59. 2003
    ..This structure indicates a more invasive interaction with dsDNA than observed with other UDGs and reveals an elegant water displacement/replacement mechanism that allows SMUG1 to exclude thymine from its active site while accepting HmU...
  39. pmc Different mutator phenotypes in Mlh1- versus Pms2-deficient mice
    X Yao
    Molecular Biology Program, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 96:6850-5. 1999
    ..Alternatively, this strain difference in tumor spectra also may be related to the consequences of the absence of Pms2p compared with the absence of both Pms2p and Mlh1p on as yet little understood cellular processes...
  40. ncbi Sequence specific fluorescence detection of double strand DNA
    Victor C Rucker
    The Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
    J Am Chem Soc 125:1195-202. 2003
    ..We find that Im/Im is an energetically favorable ring pair for minor groove recognition of the T.G base pair...
  41. pmc Methylation-induced G(2)/M arrest requires a full complement of the mismatch repair protein hMLH1
    Petr Cejka
    Institute of Molecular Cancer Research, University of Zurich, August Forel Strasse 7, CH 8008 Zürich Switzerland
    EMBO J 22:2245-54. 2003
    ....
  42. pmc Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation
    J Majewski
    Department of Biology, Wesleyan University, Middletown, Connecticut 06459, USA
    J Bacteriol 182:1016-23. 2000
    ..We discuss the possible additional mechanisms of sexual isolation, in view of earlier findings from Bacillus, Escherichia, and Streptococcus...
  43. pmc Fitness evolution and the rise of mutator alleles in experimental Escherichia coli populations
    Aaron C Shaver
    Department of Biology, University of Pennsylvania, Philadelphia 19104, USA
    Genetics 162:557-66. 2002
    ..We found little evidence that the evolution of high mutation rates accelerated adaptation in these populations...
  44. pmc Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example
    D Bru
    INRA, University of Burgundy, Soil and Environmental Microbiology, CMSE, 17 rue Sully, B P 86510, 21065 Dijon Cedex, France
    Appl Environ Microbiol 74:1660-3. 2008
    ..We observed that the presence of a single mismatch in the second half of the primer extension sequence can result in an underestimation of up to 1,000-fold of the gene copy number, depending on the primer and position of the mismatch...
  45. pmc Excision of deaminated cytosine from the vertebrate genome: role of the SMUG1 uracil-DNA glycosylase
    H Nilsen
    Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, EN6 3LD, UK
    EMBO J 20:4278-86. 2001
    ....
  46. pmc Mechanisms in eukaryotic mismatch repair
    Paul Modrich
    Department of Biochemistry and Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA
    J Biol Chem 281:30305-9. 2006
  47. ncbi The tyrosine kinase c-Abl regulates p73 in apoptotic response to cisplatin-induced DNA damage
    J G Gong
    Department of Biology, University of California, San Diego, La Jolla 92093 0322, USA
    Nature 399:806-9. 1999
    ..Our results indicate that c-Abl and p73 are components of a mismatch-repair-dependent apoptosis pathway which contributes to cisplatin-induced cytotoxicity...
  48. ncbi DNA mismatch repair: functions and mechanisms
    Ravi R Iyer
    Department of Biochemistry and Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA
    Chem Rev 106:302-23. 2006
  49. pmc Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles
    Huixiang Li
    Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
    Proc Natl Acad Sci U S A 101:14036-9. 2004
    ..The assay is complete within 5 min, and <100 femtomoles of target produces color changes observable without instrumentation. Single-base-pair mismatches are easily detected...
  50. ncbi HNPCC-like cancer predisposition in mice through simultaneous loss of Msh3 and Msh6 mismatch-repair protein functions
    N de Wind
    Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
    Nat Genet 23:359-62. 1999
    ..Thus, loss of MMR functions specific to Msh2/Msh6 is sufficient for lymphoma development in mice, whereas predisposition to intestinal cancer requires loss of function of both Msh2/Msh6 and Msh2/Msh3...
  51. pmc Coordinating the initial steps of base excision repair. Apurinic/apyrimidinic endonuclease 1 actively stimulates thymine DNA glycosylase by disrupting the product complex
    Megan E Fitzgerald
    Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Biol Chem 283:32680-90. 2008
    ..Potential mechanisms for hAPE1 disruption of the of hTDG product complex are discussed...
  52. pmc Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli
    Xin tian Li
    Department of Biochemistry, The University of Hong Kong, 3 F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, PR China
    Nucleic Acids Res 31:6674-87. 2003
    ..These results demonstrate for the first time that the interplay between DNA replication and MMR has a major effect on the efficiency and strand bias of Red/SSO-mediated recombination in E.coli...
  53. ncbi Human thymine DNA glycosylase binds to apurinic sites in DNA but is displaced by human apurinic endonuclease 1
    T R Waters
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
    J Biol Chem 274:67-74. 1999
    ..The other proteins involved in base excision repair, polymerase beta, XRCC1, and DNA ligase III, do not affect the dissociation of thymine DNA glycosylase from the apurinic site...
  54. ncbi Investigation of the substrate spectrum of the human mismatch-specific DNA N-glycosylase MED1 (MBD4): fundamental role of the catalytic domain
    F Petronzelli
    Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    J Cell Physiol 185:473-80. 2000
    ..This suggests that the catalytic domain is fundamental, and the 5-methylcytosine binding domain dispensable, in determining the substrate spectrum of MED1...
  55. pmc Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs
    Huang Huang
    Institute of Molecular Medicine, Peking University, Beijing 100871, China
    Nucleic Acids Res 37:7560-9. 2009
    ..In summary, these findings could dramatically simplify the design of allele-specific siRNAs and might also provide guide to increase the specificity of therapeutic siRNAs...
  56. pmc Crystal structure of a thwarted mismatch glycosylase DNA repair complex
    T E Barrett
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT
    EMBO J 18:6599-609. 1999
    ....
  57. ncbi Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes
    N Sugimoto
    Department of Chemistry, Faculty of Science, and High Technology Research Center, Konan University, 8 9 1 Okamoto, Higashinada ku, Kobe 658 8501, Japan
    Biochemistry 39:11270-81. 2000
    ..These results would be useful for the design of antisense oligonucleotides...
  58. pmc Examination of Msh6- and Msh3-deficient mice in class switching reveals overlapping and distinct roles of MutS homologues in antibody diversification
    Ziqiang Li
    Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Chanin 403, Bronx, NY 10461, USA
    J Exp Med 200:47-59. 2004
    ..Together, our data suggest that MutS homologues Msh2, Msh3, and Msh6 play overlapping and distinct roles during antibody diversification processes...
  59. ncbi Cancer, cadmium and genome integrity
    Cynthia T McMurray
    Nat Genet 34:239-41. 2003
  60. ncbi Structural determinants of miRNAs for RISC loading and slicer-independent unwinding
    Tomoko Kawamata
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan
    Nat Struct Mol Biol 16:953-60. 2009
    ..Our findings show that unwinding of miRNAs is a precise mirror-image process of target recognition, and both processes reflect the unique geometry of RNAs in Ago proteins...
  61. pmc Direct visualization of asymmetric adenine-nucleotide-induced conformational changes in MutL alpha
    Elizabeth J Sacho
    Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Mol Cell 29:112-21. 2008
    ..These data reveal an ATPase cycle in which sequential nucleotide binding, hydrolysis, and release modulate the conformational states of MutL alpha...
  62. pmc Affinity of mismatch-binding protein MutS for heteroduplexes containing different mismatches
    J Brown
    Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton S016 7PX, UK
    Biochem J 354:627-33. 2001
    ..Studies with base analogues show good binding to phiT (where phi represents 1',2'-dideoxyribose), but much weaker binding to Gphi...
  63. ncbi The DNA mismatch repair genes Msh3 and Msh6 cooperate in intestinal tumor suppression
    W Edelmann
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Cancer Res 60:803-7. 2000
    ..When the Msh3-/- and Msh6-/- mutations are combined, the tumor predisposition phenotype is indistinguishable from Msh2-/- or Mlh1-/- mice. These results suggest that MSH3 cooperates with MSH6 in tumor suppression...
  64. pmc The adaptive imbalance in base excision-repair enzymes generates microsatellite instability in chronic inflammation
    Lorne J Hofseth
    Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 4255, USA
    J Clin Invest 112:1887-94. 2003
    ....
  65. pmc Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates
    Ganesh Natrajan
    Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
    Nucleic Acids Res 31:4814-21. 2003
    ..This hydrogen bond involves the N7 if the base stacking on Phe 36 is a purine and the N3 if it is a pyrimidine (thymine). Thus, MutS uses a common binding mode to recognize a wide range of mismatches...
  66. ncbi An Msh2 point mutation uncouples DNA mismatch repair and apoptosis
    Diana P Lin
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
    Cancer Res 64:517-22. 2004
    ....
  67. ncbi Genome maintenance mechanisms for preventing cancer
    J H Hoeijmakers
    MGC Department of Cell Biology and Genetics, Centre for Biomedical Genetics, Erasmus University, PO Box 1738, 3000DR Rotterdam, The Netherlands
    Nature 411:366-74. 2001
    ..This review summarizes the main DNA caretaking systems and their impact on genome stability and carcinogenesis...
  68. ncbi Progress and prospects: targeted gene alteration (TGA)
    H Parekh-Olmedo
    Department of Biological Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Gene Ther 14:1675-80. 2007
    ..We highlight the important advances over the last two to three years, some of which have moved the technology closer to the clinic while some others have introduced new reasons for caution...
  69. ncbi DNA: a programmable force sensor
    Christian Albrecht
    Nanotype GmbH, Lochhamer Schlag 12, 82166 Gräfelfing, Germany
    Science 301:367-70. 2003
    ..This option was exploited to overcome cross-reactions of antibodies in a protein biochip application...
  70. ncbi Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus
    Linjing Yang
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer Street, 10012, New York, NY, USA
    J Mol Biol 321:459-78. 2002
    ....
  71. pmc Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution
    Susana Lima
    Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee 32306, USA
    RNA 8:924-32. 2002
    ..C mismatch may reveal a unique structural motif required for the function of Com...
  72. ncbi Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1, and yOGG2
    Michael D Leipold
    Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
    Biochemistry 42:11373-81. 2003
    ..Indeed, the greater efficiency of the yOGG proteins for removal of the further oxidized products, Gh and Sp, over their 8-oxoguanine parent, suggests that these lesions may be the preferred substrates in vivo...
  73. ncbi Involvement of nucleotide-excision repair in msh2 pms1-independent mismatch repair
    O Fleck
    Institute of General Microbiology, University of Bern, Switzerland
    Nat Genet 21:314-7. 1999
    ..We identify here the NER genes rhpl4, swi10 and rad16 as components of this repair pathway and show that they act independently of msh2 and pms1...
  74. ncbi The role of MutS oligomers on Pseudomonas aeruginosa mismatch repair system activity
    Virginia Miguel
    Centro de Investigaciones en Química Biológica de Córdoba CIQUIBIC, CONICET, Departamento de Quimica Biologica, Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Ciudad Universitaria, 5000 Cordoba, Argentina
    DNA Repair (Amst) 7:1799-808. 2008
    ..aeruginosa...
  75. ncbi Initiation of repair of A/G mismatches is modulated by sequence context
    Ana M Sanchez
    Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, TX 77555 1071, USA
    DNA Repair (Amst) 2:863-78. 2003
    ..These data established that the relative syn/anti conformation did not correlate with the excision efficiency, as well as there being a lack of correlation between kinetics and thermal stability of these DNAs...
  76. pmc HU binds and folds single-stranded DNA
    Dmitri Kamashev
    Laboratoire de Physiologie Bacterienne, CNRS UPR 9073, Laboratoire de Biochimie Theorique, CNRS UPR 9080, Paris, France
    Nucleic Acids Res 36:1026-36. 2008
    ..Furthermore HU has a strong preference for poly(dG), while binding to poly(dA) is the weakest. HU binding to ssDNA is probably important for its capacity to cover and protect bacterial DNA both intact and carrying lesions...
  77. ncbi Cutting edge: the G-U mismatch glycosylase methyl-CpG binding domain 4 is dispensable for somatic hypermutation and class switch recombination
    Philip D Bardwell
    Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin 403, Bronx, NY 10461, USA
    J Immunol 170:1620-4. 2003
    ..These data indicate that the Mbd4 glycosylase does not significantly contribute to mechanisms of Ab diversification...
  78. pmc Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis
    Alexandra Vaisman
    Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 24:2957-67. 2005
    ..The correct incoming nucleotide allows DNA synthesis to overcome pyrophosphorolysis, but an incorrect incoming nucleotide does not...
  79. pmc Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays
    Shingo Suzuki
    Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    BMC Genomics 8:373. 2007
    ..Thus, pairs of PM and MM probes with greater specificity for single nucleotide mismatches are desirable for accurate analysis...
  80. pmc Enhanced activity of adenine-DNA glycosylase (Myh) by apurinic/apyrimidinic endonuclease (Ape1) in mammalian base excision repair of an A/GO mismatch
    H Yang
    Department of Microbiology and Molecular Genetics and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA and Department of Cancer Cell Biology, Harvard School of Public Health, Boston, MA 02115, USA
    Nucleic Acids Res 29:743-52. 2001
    ..Consequently, Ape1 preserves the Myh preference for A/GO over A/G and improves overall glycosylase efficiency. Our study suggests that protein-protein interactions may occur in vivo to achieve efficient BER of A/GO...
  81. ncbi Combined triplex/duplex invasion of double-stranded DNA by "tail-clamp" peptide nucleic acid
    Thomas Bentin
    Center for Biomolecular Recognition, IMBG, Department B, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Biochemistry 42:13987-95. 2003
    ..The results validate the tail-clamp PNA concept and expand the applications of the P-loop technology...
  82. pmc Discrimination against purine-pyrimidine mispairs in the polymerase active site of DNA polymerase I: a structural explanation
    Dana T Minnick
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 99:1194-9. 2002
    ..Moreover, this same side chain enhances the stability of incoming correct dNTPs, such that loss of this interaction on removal of the side chain leads to lower selectivity against mismatches involving incoming pyrimidines...
  83. ncbi Multiple cleavage activities of endonuclease V from Thermotoga maritima: recognition and strand nicking mechanism
    J Huang
    Department of Microbiology and Immunology, Hearst Microbiology Research Center and Strang Cancer Prevention Center, The Joan and Sanford I. Weill Medical College of Cornell University, 1300 York Avenue, Box 62, New York, New York 10021, USA
    Biochemistry 40:8738-48. 2001
    ..A model accounting for the recognition and strand nicking mechanism of endonuclease V is presented...
  84. ncbi T:G mismatch-specific thymine-DNA glycosylase potentiates transcription of estrogen-regulated genes through direct interaction with estrogen receptor alpha
    Dongsheng Chen
    Department of Cancer Medicine, Imperial College London, Du Cane Road, London W12 0NN, United Kingdom
    J Biol Chem 278:38586-92. 2003
    ..Together with recent reports linking TFIIH in regulating NR function, our findings provide new data to further support an important link between DNA repair proteins and nuclear receptor function...
  85. ncbi Roles of MGMT and MLH1 proteins in alkylation-induced apoptosis and mutagenesis
    Yasumitsu Takagi
    Frontier Research Center, Fukuoka Dental College, Fukuoka 814 0193, Japan
    DNA Repair (Amst) 2:1135-46. 2003
    ..The haploinsufficient phenotype of Mlh1-heterozygous cells may be explained by competition in heterodimer formation between MLH1 homologues...
  86. ncbi Differential expression of DOC-1 in microsatellite-unstable human colorectal cancer
    Ziqiang Yuan
    Department of Molecular Genetics, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Ullmann 1219, Bronx, NY 10461, USA
    Oncogene 22:6304-10. 2003
    ....
  87. pmc Stable gene targeting in human cells using single-strand oligonucleotides with modified bases
    Xavier Rios
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 7:e36697. 2012
    ..Further optimization of this method should allow rapid and scalable genome engineering in human cells...
  88. ncbi Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status
    Harith Rajagopalan
    Sidney Kimmel Comprehensive Cancer Centre, Howard Hughes Medical Institution and Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
    Nature 418:934. 2002
    ....
  89. ncbi Structure and mechanism for DNA lesion recognition
    Wei Yang
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Cell Res 18:184-97. 2008
    ..After initial recognition of this shared structural feature of lesions, different DNA repair pathways use unique verification mechanisms to ensure correct lesion identification and removal...
  90. pmc A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing
    Alexander Wait Zaranek
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 6:e1000954. 2010
    ..We show that the NCBI Trace Archive provides a valuable resource for the investigation of the phenomena of DNA and RNA editing, as well as setting the stage for a comprehensive mapping of editing events in large-scale genomic datasets...
  91. pmc Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences
    Takumi Ishizuka
    Research Center for Advanced Science and Technology, The University of Tokyo, 4 6 1 Komaba, Meguro ku, Tokyo, 153 8904 Japan
    Nucleic Acids Res 36:1464-71. 2008
    ..The promotion of double-duplex invasion by the chiral (d) PNA monomer units was ascribed to both destabilization of PNA/PNA duplex and stabilization of PNA/DNA duplexes...
  92. pmc Physical and functional interactions between Werner syndrome helicase and mismatch-repair initiation factors
    Nurten Saydam
    Institute of Molecular Cancer Research of the University of Zurich, Switzerland
    Nucleic Acids Res 35:5706-16. 2007
    ..Our data are consistent with results of genetic experiments in yeast suggesting that MMR factors act in conjunction with a RecQ-type helicase to reject recombination between divergent sequences...
  93. pmc Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ɛ
    Jessica S Williams
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
    DNA Repair (Amst) 11:649-56. 2012
    ..Collectively, the results indicate that although proofreading of an 'incorrect' sugar is less efficient than is proofreading of an incorrect base, Pol ɛ does proofread newly inserted rNMPs to enhance genome stability...
  94. ncbi AID and mismatch repair in antibody diversification
    Alberto Martin
    Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin 403, Bronx, New York 10461, USA
    Nat Rev Immunol 2:605-14. 2002
  95. pmc Catalytic contributions of key residues in the adenine glycosylase MutY revealed by pH-dependent kinetics and cellular repair assays
    Megan K Brinkmeyer
    Department of Chemistry, University of California Davis, Davis, CA 95616, USA
    Chem Biol 19:276-86. 2012
    ..The results show that MutY variations that exhibit reduced mismatch affinity result in more dramatic reductions in cellular OG:A repair than those that only compromise adenine excision catalysis...
  96. pmc Cost-effective interrogation of single nucleotide polymorphisms using the mismatch amplification mutation assay and capillary electrophoresis
    Erin P Price
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    Electrophoresis 31:3881-8. 2010
    ..When real-time PCR technology and instrumentation is unavailable or the reagents are cost-prohibitive, CUMA is a powerful alternative for SNP genotyping...
  97. 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...
  98. pmc Distribution of crossing over on mouse synaptonemal complexes using immunofluorescent localization of MLH1 protein
    L K Anderson
    Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
    Genetics 151:1569-79. 1999
    ..The extended length of pachytene SCs, as compared to more condensed diplotene-metaphase I bivalents, makes mapping crossover events and interference distances using MLH1 foci more accurate than using chiasmata...
  99. ncbi Evidence for a direct association of hMRE11 with the human mismatch repair protein hMLH1
    Chengtao Her
    School of Molecular Biosciences, Center for Reproductive Biology, P O Box 644660, Washington State University, Pullman, WA 99164 4660, USA
    DNA Repair (Amst) 1:719-29. 2002
    ..Together, these data suggest that hMRE11 and hMLH1 might act in a co-operative fashion during DNA damage detection, signaling, and repair...
  100. ncbi Macrocyclic DNA-mismatch-binding ligands: structural determinants of selectivity
    Anton Granzhan
    UMR176 CNRS, Institut Curie, Centre de Recherche, Centre Universitaire, 91405 Orsay, France
    Chemistry 16:878-89. 2010
    ..The study demonstrates that the topology of the ligands plays a crucial role in determining the mismatch-binding affinity and selectivity of the macrocyclic bisintercalators...
  101. pmc Differential subcellular localization of human MutY homolog (hMYH) and the functional activity of adenine:8-oxoguanine DNA glycosylase
    M Takao
    Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, 4 1 Seiryo machi, Aoba ku, Sendai 980 8578, Japan
    Nucleic Acids Res 27:3638-44. 1999
    ..These results represent the first demonstration of the function of the hMYH gene product which is differentially transported into the nucleus or the mitochondria by alternative splicing..

Research Grants63

  1. FLUORESCENT LABELING OF NUCLEIC ACIDS
    LARRY MCLAUGHLIN; Fiscal Year: 2001
    ..The final aspect of this proposal will develop the methodology for affinity labeling, particularly as it is applied to protein-DNA complexes. ..
  2. ULTRAFAST DNA DYNAMICS USING NOVEL PHOTOPHYSICAL PROBES
    Mark Berg; Fiscal Year: 2004
    ....
  3. Cellular Responses to Radiation and Other Types of Damage
    Gray F Crouse; Fiscal Year: 2012
    ..in a TRP5 gene located near a defined origin of replication;each mutation can revert only via a specific base pair mismatch. Another assay uses transformation of yeast with single-stranded oligonucleotides, thereby placing a defined ..
  4. Understanding the role of PCNA in DNA mismatch repair subpathways
    EVA MARIE GOELLNER; Fiscal Year: 2013
    ..This mechanistic data will be used to guide future experiments into how PCNA mutations and MMR sub pathway defects influence human tumor formation and chemotherapy resistance. ..
  5. Structural and functional diversity of the methyl-binding domain protein family
    DAVID COLLIN WILLIAMS; Fiscal Year: 2013
    ..In contrast, MBD4 recognizes a G-T base pair mismatch arising from hydrolytic deamination of methyl-cytosine...
  6. RNA TERTIARY STRUCTURE AND PROTEIN INTERACTIONS
    W David Wilson; Fiscal Year: 1999
    ..The goal of this aim is to correlate the structural information obtained on the model RNAs with specific functional differences that occur as a result of sequence changes in the RNA. ..
  7. DNA Multiplex Hybridization Kinetics and SNP Assays
    ALBERT BENIGHT; Fiscal Year: 2007
    ..of using temperature dependent kinetics to discriminate a perfect match duplex from one containing a single base pair mismatch, i.e. SNP, on a microarray...
  8. Targeting Kupffer Cells With Short-Interfering RNA
    BIDDANDA PONNAPPA; Fiscal Year: 2005
    ..A successful outcome of this study will greatly enhance our ability to use very low concentrations of gene-specific molecules for the treatment of disease such as alcoholic liver disease. ..
  9. NEW HUMAN DNA REPAIR ENDONUCLEASE
    Alfonso Bellacosa; Fiscal Year: 2002
    ..These studies may provide new insights into the mechanisms of eukaryotic mismatch repair and further the link between defective DNA repair and cancer. ..
  10. A Study of Mutation Dynamics in Biological Systems
    Emmanuel Tannenbaum; Fiscal Year: 2005
    ..This study will require the use of genomic and proteomic databases, as well as predictive methods from computational biology, in order to determine the function of the various evolving components of the biological networks under study. ..
  11. BAALC in neurogenesis and hematopoiesis
    Albert de la Chapelle; Fiscal Year: 2007
    ..It is postulated that the high degree of evolutionary conservation of BAALC in mammals will allow observations in mice to be applicable to humans. ..
  12. INCIDENCE AND MOLECULAR SCREENING FOR HEREDITARY CANCER
    Albert de la Chapelle; Fiscal Year: 2004
    ..abstract_text> ..
  13. Error Prone DNA Synthesis and Oncogene Mutagensis
    Bernard Strauss; Fiscal Year: 2004
    ..Blocking the action of the error-prone polymerases should not stop replication. However, mutational cascades, such as those leading to tumor drug resistance, should be inhibited by such a block. ..
  14. Dynamic combinatorial chemistry for nucleic acids
    Steven Benner; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  15. Polymerases for Sequencing by Synthesis
    Steven Benner; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  16. DNA Sequencing using Nanopores
    Steven Benner; Fiscal Year: 2007
    ..These will then be targeted against specific sequences extracted from mammalian genomes. [unreadable] [unreadable]..
  17. FAMILIAL COLORECTAL NEOPLASIA COLLABORATIVE GROUP
    Noralane Lindor; Fiscal Year: 2007
    ..fs20\par \par } ..
  18. DNA replication, DNA repair and microsatellite stability
    Kristin Eckert; Fiscal Year: 2009
    ..Microsatellite allele lengths can directly affect gene expression. As microsatellites are polymorphic in human populations, this effect on gene regulation may be an important factor contributing to individual cancer risk. ..
  19. Dissection and Reconstitution of Human Mismatch Repair
    Guo Min Li; Fiscal Year: 2009
    ..abstract_text> ..
  20. 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. ..
  21. Mechanism of PCNA-dependent 5'->3' Mismatch Excision
    Guo Min Li; Fiscal Year: 2010
    ..g., the EXO1 gene, are associated with cancer development, identifying the components required for the novel 5'excision pathway will provide new diagnostic markers for HNPCC and other MMR deficient cancer syndromes. ..
  22. 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. ..
  23. Identifying Proteins Involved in DNA Damage Response
    Guo Min Li; Fiscal Year: 2005
    ..Because certain cancer chemotherapeutics, e.g., cisplatin and alkylating agents, can signal apoptosis in an MMR-dependent fashion, this study will also impact cancer treatment, particularly cancers caused by MMR defects. ..
  24. Functional Dissection of an F-box Protein in Development
    Michael Weir; Fiscal Year: 2006
    ..abstract_text> ..
  25. Targeted Assisted Combinational Synthesis
    Steven Benner; Fiscal Year: 2004
    ..abstract_text> ..
  26. MUTATIONAL MECHANISMS OF REPETITIVE DNA IN HUMAN CELLS
    Kristin Eckert; Fiscal Year: 2001
    ..Our long-term research objective is to test the hypothesis that mutations in repetitive DNA provide an important source of genotypic variation that drives neoplastic progression. ..
  27. NON-STANDARD BASE PAIRS AS BIOMEDICAL RESEARCH TOOLS
    Steven Benner; Fiscal Year: 2004
    ....
  28. EVOLUTION OF THE RIBONUCLEASE SUPERFAMILY
    Steven Benner; Fiscal Year: 2001
    ....
  29. AUSTRALASIAN C0L0RECTAL CANCER FAMILY STUDY
    Jeremy Jass; Fiscal Year: 2002
    ..These characteristics include manageable yet sufficient size, ethnically diverse, highly localised, stable, and with families that are intact and large. ..
  30. 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. ..
  31. ROLE OF MISMATCH REPAIR IN SPORADIC TUMOR SUPPRESSION
    Guo Min Li; Fiscal Year: 2004
    ..This study will not only provide insight into the etiology of sporadic bladder cancers, but also lead to the identification of novel mismatch repair components. ..
  32. MGMT Gene Transfer To Protect Hematopoietic Stem Cells
    Stanton Gerson; Fiscal Year: 2002
    ..If successful, this approach could also have application in other gene therapy settings such as dual gene transfer using a therapeutic gene and stem cell organ selection. ..
  33. Engineering enzymes for anti-tumor suicide gene therapy
    Barry L Stoddard; Fiscal Year: 2010
    ..Our hypothesis is that decitabine should ultimately couple with engineered enzyme variants to yield improvements in the performance of dCK, due to the lack of this activity in non-cancerous tissues. ..
  34. Mechanisms of Adaptive Amplification
    Philip J Hastings; Fiscal Year: 2010
    ....
  35. NEUROFIBROMIN AS A NEGATIVE REGULATOR FOR ASTROCYTES
    David Gutmann; Fiscal Year: 2002
    ....
  36. A mutable vaccine for biodefense
    Marilia Cascalho; Fiscal Year: 2005
    ..The vaccine will then be tested for ability to promote an immune response against antigenic variants of influenza. ..
  37. Health and QOL among Long-Term Lung Cancer Survivors
    Ping Yang; Fiscal Year: 2010
    ....
  38. ADDRESSING THE ISSUE OF GAP REGIONS IN GENOME SEQUENCING
    John SantaLucia; Fiscal Year: 2001
    ..In addition, the investigator predicts that this information will find wide applications in biotechnology and bioinformatics. ..
  39. Fixing Fixed DNA
    Darryl Shibata; Fiscal Year: 2002
    ..PCR after "repair" by error prone polymerases should yield more and longer products, and may further unlock the utility of this ubiquitous clinical resource. ..
  40. Structure Function Studies of DNA Mismatch Repair
    Dorothy A Erie; Fiscal Year: 2010
    ....
  41. DNA Mismatch and Double-Strand Break Repair
    Martin G Marinus; Fiscal Year: 2010
    ..It also impacts the mechanism by which pathogenic bacteria become resistant to antibiotics and how this resistance is disseminated. ..
  42. SCienceLab
    Bert Ely; Fiscal Year: 2010
    ..To address this problem, SCienceLab provides an opportunity for students to spend a day experiencing research and interacting with students who are working in a biomedical research laboratory. ..
  43. Comparative Genomics of Peroxisomal Lipid Metabolism
    Joseph Hacia; Fiscal Year: 2009
    ..abstract_text> ..
  44. MOLECULAR STAGING OF HUMAN SQUAMOUS CELL SKIN CANCER
    James Gale; Fiscal Year: 2003
    ....
  45. Nanocapillary Electrophoresis for Profiling Cancer
    Arunava Majumdar; Fiscal Year: 2003
    ..This technology would directly address this important public health issue. ..
  46. Kinetic Studies of Transcription Elongation
    DOROTHY ERIE; Fiscal Year: 2005
    ..Accordingly, we will use this information to begin to understand, at the amino acid level, the role of NTP binding and conformational transitions in the regulation of elongation. ..
  47. Oxidative DNA Damage, DNA Repair and Oral Cancer
    Chun Yang Fan; Fiscal Year: 2006
    ..By obtaining a K award, the PI will have the opportunity to develop skills for patient- oriented research under the direction of basic and clinical science mentors. ..
  48. MECHANISTIC STUDIES OF DNA MISMATCH REPAIR
    A Lien Lu Chang; Fiscal Year: 2006
    ..Particularly, alterations in protein-protein interactions under oxidative stress will be investigated. These studies should advance our understanding of the role of DNA repair in genome stability and tumor susceptibility. ..
  49. 9th International Workshop on "Radiation Damage to DNA"
    Susan Wallace; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  50. Elucidation of a DRA signaling pathway in colon cancer
    CLIFFORD SCHWEINFEST; Fiscal Year: 2005
    ..The goals of this proposal are: 1) to demonstrate a role for liprin in DRA growth suppression, and 2) to identify what signal transduction pathways may be involved. ..
  51. Reagents for Preparing Structure-Free DNA and RNA
    Howard Gamper; Fiscal Year: 2007
    ....
  52. Fourteenth Microbial Genomics Conference-2006
    Jeffrey Miller; Fiscal Year: 2006
    ..unreadable] This has a direct bearing on human health. This meeting has become established as a major annual[unreadable] microbial genomics conference during the last fourteen years and has assured status and quality. ..
  53. DNA repair and lg class switching
    Janet Stavnezer; Fiscal Year: 2007
    ..In Aim 4 we will explore how the mutations are introduced into Ig S regions by determining if the translesion DNA polymerase iota is involved in the error-prone repair of S regions and if this involvement is regulated by cytokines. ..
  54. Phase I Clinical Trials of Anti-Cancer Agents
    Francis Giles; Fiscal Year: 2007
    ..abstract_text> ..
  55. DNA MISMATCH REPAIR--LESION REPAIR AND STRAND TARGETING
    James Drummond; Fiscal Year: 2004
    ..We will test this model by asking whether free DNA ends, or defined gaps within circular DNAs, are capable of directing MR to the discontinuous strand. ..
  56. A Genetic Screening Policy Model for Colorectal Cancer
    Scott Ramsey; Fiscal Year: 2006
    ..The model will incorporate QOL information from Aim 2, along with family history, clinical, and screening information from the Seattle CFR. ..
  57. MOUSE MODEL FOR OXIDATIVE DNA DAMAGE REPAIR
    Jeffrey Miller; Fiscal Year: 2004
    ..4. Generate and characterize additional combinations of mMYH knockout mice with other repair gene or tumor suppressor gene knockouts, such as MSH2 and p53. ..
  58. MOLECULAR EPIDEMIOLOGY OF COLORECTAL CANCER
    Stephen Gruber; Fiscal Year: 2008
    ..abstract_text> ..
  59. Molecular Determinants of Neural Stem Cell Function
    David Gutmann; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  60. DNA Damage, Mutation & Cancer Gordon Research Conference
    John Hays; Fiscal Year: 2008
    ..high-fidelity responses blocked replication forts. One will describe successive steps in pathways initiated by specific DNA lesions. [unreadable] [unreadable] [unreadable] [unreadable]..
  61. DNA METHYLOME STUDY IN TYPE 1 DIABETES
    ART PETRONIS; Fiscal Year: 2009
    ..This effort may have a major impact on our understanding of autoimmune mechanisms in T1D and lead to new strategies in diagnostics and treatment of the disease. ..
  62. GENETIC MECHANISMS OF HINDBRAIN SEGMENTATION
    Cecilia Moens; Fiscal Year: 2009
    ..Aim 2 addresses the mechanism of plasticity. Finally, in Aim 3, we consider the mechanism by which long-range signals interact to specify the positions of specific hindbrain boundaries. ..