single stranded dna

Summary

Summary: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.

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. ncbi Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes
    Lee Zou
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Science 300:1542-8. 2003
  3. pmc Human CtIP promotes DNA end resection
    Alessandro A Sartori
    The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
    Nature 450:509-14. 2007
  4. pmc Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint
    Tony S Byun
    Department of Molecular Pharmacology, Stanford University, Stanford, CA 94305, USA
    Genes Dev 19:1040-52. 2005
  5. pmc High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides
    H M Ellis
    Gene Regulation and Chromosome Biology Laboratory, Division of Basic Sciences, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 98:6742-6. 2001
  6. pmc Genetic steps of mammalian homologous repair with distinct mutagenic consequences
    Jeremy M Stark
    Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10021, USA
    Mol Cell Biol 24:9305-16. 2004
  7. ncbi The Mcm2-7 complex has in vitro helicase activity
    Matthew L Bochman
    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
    Mol Cell 31:287-93. 2008
  8. ncbi Trex1 exonuclease degrades ssDNA to prevent chronic checkpoint activation and autoimmune disease
    Yun gui Yang
    Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK
    Cell 131:873-86. 2007
  9. ncbi APOBEC3G DNA deaminase acts processively 3' --> 5' on single-stranded DNA
    Linda Chelico
    Department of Biological Sciences Molecular and Computational Section, University of Southern California, Los Angeles, California 90089 2910, USA
    Nat Struct Mol Biol 13:392-9. 2006
  10. ncbi DNA double-strand break repair: all's well that ends well
    Claire Wyman
    Department of Cell Biology and Genetics and Department of Radiation Oncology, Erasmus MC, 3000 DR Rotterdam, The Netherlands
    Annu Rev Genet 40:363-83. 2006

Detail Information

Publications334 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. ncbi Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes
    Lee Zou
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Science 300:1542-8. 2003
    ..Our data suggest that RPA-coated ssDNA is the critical structure at sites of DNA damage that recruits the ATR-ATRIP complex and facilitates its recognition of substrates for phosphorylation and the initiation of checkpoint signaling...
  3. pmc Human CtIP promotes DNA end resection
    Alessandro A Sartori
    The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
    Nature 450:509-14. 2007
    ..These findings establish evolutionarily conserved roles for CtIP-like proteins in controlling DSB resection, checkpoint signalling and homologous recombination...
  4. pmc Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint
    Tony S Byun
    Department of Molecular Pharmacology, Stanford University, Stanford, CA 94305, USA
    Genes Dev 19:1040-52. 2005
    ....
  5. pmc High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides
    H M Ellis
    Gene Regulation and Chromosome Biology Laboratory, Division of Basic Sciences, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 98:6742-6. 2001
    ..Beta protein and ssDNA may prove generally applicable for repairing DNA in many organisms...
  6. pmc Genetic steps of mammalian homologous repair with distinct mutagenic consequences
    Jeremy M Stark
    Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10021, USA
    Mol Cell Biol 24:9305-16. 2004
    ..These results imply that the proper genetic interplay of repair factors is essential to limit the mutagenic potential of DSB repair...
  7. ncbi The Mcm2-7 complex has in vitro helicase activity
    Matthew L Bochman
    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
    Mol Cell 31:287-93. 2008
    ..Our results show that purified Mcm2-7 acts as a helicase, provides functional evidence of a Mcm2/5 gate, and lays the foundation for future mechanistic studies of this critical factor...
  8. ncbi Trex1 exonuclease degrades ssDNA to prevent chronic checkpoint activation and autoimmune disease
    Yun gui Yang
    Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK
    Cell 131:873-86. 2007
    ..Our data indicate that Trex1 acts on a single-stranded DNA polynucleotide species generated from processing of aberrant replication intermediates to attenuate DNA damage checkpoint signaling and prevent pathological immune activation...
  9. ncbi APOBEC3G DNA deaminase acts processively 3' --> 5' on single-stranded DNA
    Linda Chelico
    Department of Biological Sciences Molecular and Computational Section, University of Southern California, Los Angeles, California 90089 2910, USA
    Nat Struct Mol Biol 13:392-9. 2006
    ..Our data suggest that the G --> A mutational gradient generated in viral genomic DNA in vivo could result from an intrinsic processive directional attack by APOBEC3G on single-stranded cDNA...
  10. ncbi DNA double-strand break repair: all's well that ends well
    Claire Wyman
    Department of Cell Biology and Genetics and Department of Radiation Oncology, Erasmus MC, 3000 DR Rotterdam, The Netherlands
    Annu Rev Genet 40:363-83. 2006
    ....
  11. ncbi Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA
    Alicia K Byrd
    Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
    Nat Struct Mol Biol 11:531-8. 2004
    ..Such a bias leads to protein-protein interactions when the lead monomer stalls owing to the presence of the streptavidin block...
  12. ncbi DNA helicase Srs2 disrupts the Rad51 presynaptic filament
    Lumir Krejci
    Institute of Biotechnology and Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 15355 Lambda Drive, San Antonio, Texas 78245, USA
    Nature 423:305-9. 2003
    ....
  13. ncbi Repetitive shuttling of a motor protein on DNA
    Sua Myong
    Physics Department, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Nature 437:1321-5. 2005
    ..Thus, the binding of a single Rep monomer to a stalled replication fork can lead to repetitive shuttling along the single-stranded region, possibly keeping the DNA clear of toxic recombination intermediates...
  14. ncbi Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions
    Massimo Lopes
    Department of Biology, Institute of Cell Biology, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Mol Cell 21:15-27. 2006
    ....
  15. pmc Detecting single stranded DNA with a solid state nanopore
    Daniel Fologea
    Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
    Nano Lett 5:1905-9. 2005
    Voltage biased solid-state nanopores are used to detect and characterize individual single stranded DNA molecules of fixed micrometer length by operating a nanopore detector at pH values greater than approximately 11.6...
  16. pmc Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1
    Oleg V Tsodikov
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 102:11236-41. 2005
    ....
  17. pmc Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis
    Charikleia Ioannou
    Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Nucleic Acids Res 34:5247-58. 2006
    ..DnaI is sufficient to load the replicative helicase from a complex with six DnaI molecules, so there is no requirement for a dual helicase loader system...
  18. pmc Sae2 is an endonuclease that processes hairpin DNA cooperatively with the Mre11/Rad50/Xrs2 complex
    Bettina M Lengsfeld
    Department of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
    Mol Cell 28:638-51. 2007
    ....
  19. ncbi Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication
    Ming Yao Yang
    MRC Dunn Human Nutrition Unit, Hills Road, CB2 2XY, Cambridge, United Kingdom
    Cell 111:495-505. 2002
    ..Mammalian mitochondrial DNA replication thus proceeds mainly, or exclusively, by a strand-coupled mechanism...
  20. ncbi The Rad51-dependent pairing of long DNA substrates is stabilized by replication protein A
    Aimee L Eggler
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Biol Chem 277:39280-8. 2002
    ....
  21. doi Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures
    Zhucheng Chen
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 453:489-4. 2008
    ..The underwound, stretched filament conformation probably evolved to destabilize the donor duplex, freeing the complementary strand for homology sampling...
  22. pmc Mechanism of IS200/IS605 family DNA transposases: activation and transposon-directed target site selection
    Orsolya Barabas
    Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 132:208-20. 2008
    ..Our structural results explain why the transposon ends are asymmetric and how the transposon selects a target site for integration, and they allow us to propose a molecular model for the entire transposition reaction...
  23. ncbi Enzyme-free nucleic acid logic circuits
    Georg Seelig
    Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Science 314:1585-8. 2006
    ..Biological nucleic acids such as microRNAs can serve as inputs, suggesting applications in biotechnology and bioengineering...
  24. ncbi Identification of a domain of Escherichia coli primase required for functional interaction with the DnaB helicase at the replication fork
    K Tougu
    Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021
    J Biol Chem 269:4675-82. 1994
    ....
  25. ncbi Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination
    Yunmei Ma
    Norris Comprehensive Cancer Center, Rm 5428, Departments of Biochemistry and Molecular Biology, Pathology, Biological Sciences, and Molecular Microbiology and Immunology, 1441 Eastlake Avenue, Los Angeles, CA 90033, USA
    Cell 108:781-94. 2002
    ....
  26. ncbi The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments
    Xavier Veaute
    CEA, DSV, Departement de Radiobiologie et Radiopathologie, UMR217 CNRS CEA, BP6, 92265 Fontenay aux Roses Cedex, France
    Nature 423:309-12. 2003
    ..These data provide an explanation for the anti-recombinogenic role of Srs2 in vivo and highlight a previously unknown mechanism for recombination control...
  27. pmc Human Fbh1 helicase contributes to genome maintenance via pro- and anti-recombinase activities
    Kasper Fugger
    Institute of Cancer Biology and Center for Genotoxic Stress Research, Danish Cancer Society, DK 2100 Copenhagen, Denmark
    J Cell Biol 186:655-63. 2009
    ..Thus, by possessing both pro- and anti-recombinogenic potential, hFbh1 may cooperate with other DNA helicases in tightly controlling cellular HR activity...
  28. ncbi The single-end invasion: an asymmetric intermediate at the double-strand break to double-holliday junction transition of meiotic recombination
    N Hunter
    Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
    Cell 106:59-70. 2001
    ..This feature can explain crossover suppression between homeologous and structurally heterozygous chromosomes...
  29. pmc Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators
    Melissa L Mott
    Molecular and Cell Biology Department, Quantitative Biosciences Institute, University of California, Berkeley, CA 94720, USA
    Cell 135:623-34. 2008
    ..These findings implicate DnaC as a molecular adaptor that uses ATP-activated DnaA as a docking site for regulating the recruitment and correct spatial deposition of the DnaB helicase onto origins...
  30. ncbi Multiple full-length NS3 molecules are required for optimal unwinding of oligonucleotide DNA in vitro
    Alan J Tackett
    Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, Arkansas 72205, USA
    J Biol Chem 280:10797-806. 2005
    ..The unwinding data are discussed in terms of a model whereby multiple molecules of NS3 bound to the single-stranded DNA portion of the substrate are required for optimal unwinding...
  31. 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...
  32. pmc Ubiquitin/SUMO modification of PCNA promotes replication fork progression in Xenopus laevis egg extracts
    Craig A Leach
    The Biological Laboratories, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    J Cell Biol 171:947-54. 2005
    ..Furthermore, they suggest that PCNA monoubiquitylation serves as a molecular gas pedal that controls the speed of replisome movement during S phase...
  33. ncbi Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism
    S S Velankar
    Sir William Dunn School of Pathology, University of Oxford, United Kingdom
    Cell 97:75-84. 1999
    ..Taken together, these structures provide evidence against an "active rolling" model for helicase action but are instead consistent with an "inchworm" mechanism...
  34. pmc Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the recJ gene of Escherichia coli
    S T Lovett
    Department of Cell and Molecular Biology, Dana Farber Cancer Institute, Boston, MA 02115
    Proc Natl Acad Sci U S A 86:2627-31. 1989
    ..The RecJ exonuclease had greater activity on duplex DNA molecules with 5'-rather than 3'-single-stranded tails...
  35. pmc Human replication protein A-Rad52-single-stranded DNA complex: stoichiometry and evidence for strand transfer regulation by phosphorylation
    Xiaoyi Deng
    The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 987696 Nebraska Medical Center, Omaha, Nebraska 68198 7696, USA
    Biochemistry 48:6633-43. 2009
    ..This suggests that RPA phosphorylation may regulate the first steps of DSB repair and is necessary for the mediator function of Rad52...
  36. ncbi PML-nuclear bodies accumulate DNA in response to polyomavirus BK and simian virus 40 replication
    Asne Jul-Larsen
    Section of Anatomy and Cell Biology, Department of Biomedicine, University of Bergen, 5009, Norway
    Exp Cell Res 298:58-73. 2004
    ..These results indicate a role of PML and PML-NBs in post-replication DNA processing, and suggest that PML-NBs become linked to sites of viral DNA synthesis due to a role of these structures in DNA metabolism...
  37. ncbi Recent expansion of the telomeric complex in rodents: Two distinct POT1 proteins protect mouse telomeres
    Dirk Hockemeyer
    Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Cell 126:63-77. 2006
    ..We conclude that mouse telomeres require two distinct POT1 proteins whereas human telomeres have one. Such divergence is unprecedented in mammalian chromosome biology and has implications for modeling human telomere biology in mice...
  38. ncbi AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli
    Pål Ø Falnes
    Centre for Molecular Biology and Neuroscience, and Institute of Medical Microbiology, University of Oslo, National Hospital, 0027 Oslo, Norway
    Nature 419:178-82. 2002
    ..This mechanism represents a new pathway for DNA repair and the third type of DNA damage reversal mechanism so far discovered...
  39. pmc The Bloom's syndrome helicase promotes the annealing of complementary single-stranded DNA
    Chit Fang Cheok
    Cancer Research UK Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS, UK
    Nucleic Acids Res 33:3932-41. 2005
    ..We present a model in which the ssDNA annealing activity of BLM facilitates its role in the processing of DNA intermediates that arise during repair of damaged replication forks...
  40. pmc Novel pro- and anti-recombination activities of the Bloom's syndrome helicase
    Dmitry V Bugreev
    Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
    Genes Dev 21:3085-94. 2007
    ..Using in vitro reconstitution reactions, we analyzed how different biochemical activities of BLM contribute to its functions in homologous recombination...
  41. ncbi Independent and coordinated functions of replication protein A tandem high affinity single-stranded DNA binding domains
    Alphonse I Arunkumar
    Departments of Biochemistry and Physics and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232 8725, USA
    J Biol Chem 278:41077-82. 2003
    ..Taken together, our data are consistent with a sequential model of DNA binding by RPA according to which RPA70A binds the majority of DNA first and subsequent loading of RPA70B domain is facilitated by the linkage effect...
  42. ncbi DNA strand exchange promoted by RecA K72R. Two reaction phases with different Mg2+ requirements
    Q Shan
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    J Biol Chem 271:5712-24. 1996
    ..The mutant protein also facilitates the autocatalytic cleavage of the LexA repressor, but at a reduced rate...
  43. pmc Devoted to the lagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly
    Z Kelman
    Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    EMBO J 17:2436-49. 1998
    ..These results establish a role for the psi subunit in contacting SSB, thus enhancing the clamp loading and processivity of synthesis of the holoenzyme, presumably by helping to localize the holoenzyme to sites of SSB-coated ssDNA...
  44. ncbi Biochemical analysis of the DNA unwinding and strand annealing activities catalyzed by human RECQ1
    Sudha Sharma
    Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224, USA
    J Biol Chem 280:28072-84. 2005
    ..The enzymatic properties of the RECQ1 helicase and strand annealing activities are discussed in the context of proposed cellular DNA metabolic pathways that are important in the maintenance of genomic stability...
  45. ncbi DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase
    P Soultanas
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
    J Mol Biol 290:137-48. 1999
    ..A part of the associated conformational change in the protein forces the side-chain of K37 to vacate the Mg2+binding site, allowing the cation to bind and interact with ATP...
  46. ncbi A distinctive single-strand DNA-binding protein from the Archaeon Sulfolobus solfataricus
    Cynthia A Haseltine
    Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, Center for Genetics and Development, University of California Davis, 95616 8665, USA
    Mol Microbiol 43:1505-15. 2002
    ..coli respectively. We discuss possible evolutionary relationships amongst the various members of the SSB/RPA family...
  47. pmc DNA display I. Sequence-encoded routing of DNA populations
    David R Halpin
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E173. 2004
    ..Partitioning steps can be iterated indefinitely, with worst-case yields of 85% per step. These techniques facilitate DNA-programmed chemical synthesis, and thus enable a materials biology that could revolutionize drug discovery...
  48. ncbi AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation
    Michelle L Duquette
    Department of Biochemistry, University of Washington Medical School, Seattle, 98195 7650, USA
    Oncogene 24:5791-8. 2005
    ..Aberrant targeting of AID to DNA structures formed upon c-MYC transcription may therefore contribute to the genetic instability of c-MYC in B-cell malignancies...
  49. pmc Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein
    Iain D Kerr
    Centre for Biomolecular Science, St Andrews University, Fife, KY16 9ST, UK
    EMBO J 22:2561-70. 2003
    ..The high resolution of the structure, together with thermodynamic and mutational studies of DNA binding, allow us to propose a molecular basis for DNA binding and define the features required for eukaryotic and archaeal OB folds...
  50. ncbi The Rad52-Rad59 complex interacts with Rad51 and replication protein A
    Allison P Davis
    Department of Microbiology and Institute of Cancer Research, Columbia University College of Physicians and Surgeons, 701 W 168th St, New York, NY 10032, USA
    DNA Repair (Amst) 2:1127-34. 2003
    ....
  51. pmc Single-stranded DNA orchestrates an ATM-to-ATR switch at DNA breaks
    Bunsyo Shiotani
    Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
    Mol Cell 33:547-58. 2009
    ..Thus, single-stranded DNA orchestrates ATM and ATR to function in an orderly and reciprocal manner in two distinct phases of DSB response...
  52. pmc Anti-DNA antibodies from autoimmune mice arise by clonal expansion and somatic mutation
    M Shlomchik
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
    J Exp Med 171:265-92. 1990
    ....
  53. pmc Schizosaccharomyces pombe Swi1, Swi3, and Hsk1 are components of a novel S-phase response pathway to alkylation damage
    Elena Sommariva
    Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, United Kingdom
    Mol Cell Biol 25:2770-84. 2005
    ..In conclusion, Swi1, Swi3, and Hsk1 act in a novel S-phase checkpoint pathway that contributes to replication fork maintenance and to survival of alkylation damage...
  54. pmc Lrp, a major regulatory protein in Escherichia coli, bends DNA and can organize the assembly of a higher-order nucleoprotein structure
    Q Wang
    Section of Genetics and Development, Cornell University, Ithaca, NY 14853
    EMBO J 12:2495-501. 1993
    ..Lrp-induced DNA bending, and a natural sequence-directed bend that exists within ilvIH DNA, may be architectural elements that facilitate the assembly of a nucleoprotein complex...
  55. pmc Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein
    Rahul Roy
    Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, IL 61801, USA
    J Mol Biol 369:1244-57. 2007
    ....
  56. pmc Bipartite stimulatory action of the Hop2-Mnd1 complex on the Rad51 recombinase
    Peter Chi
    Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Genes Dev 21:1747-57. 2007
    ..Thus, our results unveil a bipartite mechanism of Hop2-Mnd1 in homologous DNA pairing: stabilization of the Rad51 presynaptic filament and duplex DNA capture to enhance synaptic complex formation...
  57. pmc Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants
    Nina Costantino
    Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Building 539, PO Box B, Frederick, MD 21702 1201, USA
    Proc Natl Acad Sci U S A 100:15748-53. 2003
    ..Our results show that Beta is the only bacteriophage function required for this level of recombination and suggest that Beta directs the ssDNA to the replication fork as it passes the target sequence...
  58. ncbi A postsynaptic role for single-stranded DNA-binding protein in recA protein-promoted DNA strand exchange
    P E Lavery
    Department of Cell, Molecular, and Structural Biology, Northwestern University Medical School, Chicago, Illinois 60611
    J Biol Chem 267:9315-20. 1992
    ....
  59. ncbi Non-hexameric DNA helicases and translocases: mechanisms and regulation
    Timothy M Lohman
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Avenue, St Louis, Missouri 63110, USA
    Nat Rev Mol Cell Biol 9:391-401. 2008
    ..For some of these enzymes, self assembly and/or interactions with accessory proteins seem to regulate their translocase and helicase activities...
  60. ncbi Characterization of the Escherichia coli SSB-113 mutant single-stranded DNA-binding protein. Cloning of the gene, DNA and protein sequence analysis, high pressure liquid chromatography peptide mapping, and DNA-binding studies
    J W Chase
    J Biol Chem 259:805-14. 1984
    ..Williams, K. R., Chase, J. W., and Rupp, W. D. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 4274-4278). The second correction to the DNA sequence is in the serine 39 codon, previously reported to be TCA and now correctly shown to be TCC...
  61. doi Mechanistic basis of 5'-3' translocation in SF1B helicases
    Kayarat Saikrishnan
    Cancer Research UK Clare Hall Laboratories, The London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN63LD, UK
    Cell 137:849-59. 2009
    ....
  62. pmc The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase
    Thomas Gerken
    Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, Oxon OX1 3TA, UK
    Science 318:1469-72. 2007
    ..Studies can now be directed toward determining the physiologically relevant FTO substrate and how nucleic acid methylation status is linked to increased fat mass...
  63. ncbi Differential single-stranded DNA binding properties of the paralogous SsbA and SsbB proteins from Streptococcus pneumoniae
    Diane E Grove
    Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Biol Chem 280:11067-73. 2005
    ..These results represent the first analysis of paralogous SSB proteins from any bacterial species and provide a foundation for further investigations into the biological roles of these proteins...
  64. ncbi Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site
    Seijiro Shioi
    Department of Immunology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3 1 1 Maidashi, Higashi ku, Fukuoka 812 8582, Japan
    Biochem Biophys Res Commun 326:766-76. 2005
    ..The significance of these results with respect to the functional role of PriB in the assembly of primosome is discussed...
  65. ncbi Analysis of the DNA substrate specificity of the human BACH1 helicase associated with breast cancer
    Rigu Gupta
    Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224, USA
    J Biol Chem 280:25450-60. 2005
    ....
  66. ncbi Conserved structure for single-stranded telomeric DNA recognition
    Rachel M Mitton-Fry
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 296:145-7. 2002
    ..The common usage of an OB fold for telomeric DNA interaction demonstrates conservation of end-protection mechanisms among eukaryotes...
  67. pmc Preferential binding to branched DNA strands and strand-annealing activity of the human Rad51B, Rad51C, Rad51D and Xrcc2 protein complex
    Hiroshi Yokoyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 32:2556-65. 2004
    ..2 kb in length) and its complementary circular ssDNA. These properties of the BCDX2 complex may be important for its roles in the maintenance of chromosomal integrity...
  68. pmc Accumulation of single-stranded DNA and destabilization of telomeric repeats in yeast mutant strains carrying a deletion of RAD27
    J Parenteau
    Departement De Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
    Mol Cell Biol 19:4143-52. 1999
    ..Our data thus provide in vivo evidence for the types of DNA lesions predicted to occur when lagging-strand synthesis is deficient and suggest that Dna2p and Rad27p collaborate in the processing of Okazaki fragments...
  69. pmc Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase
    Daniel S Johnson
    Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
    Cell 129:1299-309. 2007
    ..However, an active unwinding model fully supports the data even though the helicase on its own does not unwind at its optimal rate. This work offers insights into possible ways helicase activity is enhanced by associated proteins...
  70. doi In vitro reconstitution of a single-stranded transposition mechanism of IS608
    Catherine Guynet
    Laboratoire de Microbiologie et Genetique Moleculaires, CNRS UMR5100, 118 Rte de Narbonne, F31062 Toulouse Cedex, France
    Mol Cell 29:302-12. 2008
    ..This single-strand transposition mode has important implications not only for dispersion of IS608 but also for the other members of this very large IS family...
  71. pmc AID associates with single-stranded DNA with high affinity and a long complex half-life in a sequence-independent manner
    Mani Larijani
    Department of Immunology, University of Toronto, Medical Sciences Bldg 5265, Toronto, Ontario, Canada M5S 1A8
    Mol Cell Biol 27:20-30. 2007
    ..These findings suggest that AID may persist on immunoglobulin and other target sequences after deamination, possibly acting as a scaffolding protein to recruit other factors...
  72. pmc SSB protein diffusion on single-stranded DNA stimulates RecA filament formation
    Rahul Roy
    Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, Illinois 61801, USA
    Nature 461:1092-7. 2009
    ..This observation of diffusional movement of a protein on ssDNA introduces a new model for how an SSB protein can be redistributed, while remaining tightly bound to ssDNA during recombination and repair processes...
  73. pmc Isolation of human Dna2 endonuclease and characterization of its enzymatic properties
    Jeong Hoon Kim
    National Creative Research Initiative Center for Cell Cycle Control, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305 701, Korea
    Nucleic Acids Res 34:1854-64. 2006
    ..Based on this and other properties of hDna2, it is likely that this enzyme facilitates the removal of 5' and 3' regions in equilibrating flaps that are likely to arise during the processing of Okazaki fragments in human cells...
  74. pmc A dynamic model for replication protein A (RPA) function in DNA processing pathways
    Ellen Fanning
    Department of Biological Sciences, Vanderbilt University, VU Station B 351634, Nashville, TN 37235 1634, USA
    Nucleic Acids Res 34:4126-37. 2006
    ..This article reviews the structure and function of RPA, summarizes recent studies of RPA in DNA replication and other DNA processing pathways, and proposes a general model for the role of RPA in protein-mediated hand-off...
  75. pmc Single-stranded DNA-binding protein of Deinococcus radiodurans: a biophysical characterization
    Gregor Witte
    Department of Biophysical Chemistry, Medical School Hannover Hannover, Germany
    Nucleic Acids Res 33:1662-70. 2005
    ..coli, DraSSB took over the in vivo function of EcoSSB. With DraSSB behaving almost identical to EcoSSB the question remains open as to why dimeric SSB proteins have evolved in the Thermus group of bacteria...
  76. ncbi Structural insights into single-stranded DNA binding and cleavage by F factor TraI
    Saumen Datta
    Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
    Structure 11:1369-79. 2003
    ..The full positive charge on the Mg(2+) and the architecture of the active site suggest multiple roles for Mg(2+) in DNA cleavage...
  77. ncbi Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding
    J L Kim
    Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139 4242, USA
    Structure 6:89-100. 1998
    ..The structures of several helicases have been published but the structural details as to how ATP binding and hydrolysis are coupled to RNA unwinding are unknown...
  78. ncbi The beta protein of phage lambda promotes strand exchange
    Z Li
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
    J Mol Biol 276:733-44. 1998
    ..These observations reveal a mechanism by which a protein can drive strand exchange in one direction without using ATP or any other exogenous source of energy...
  79. ncbi Bacillus subtilis bacteriophage SPP1-encoded gene 34.1 product is a recombination-dependent DNA replication protein
    Maria I Martinez-Jimenez
    Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, Darwin 3, Campus de la Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid, Spain
    J Mol Biol 351:1007-19. 2005
    ..1P and G36P in concert might lead to the re-establishment of a unidirectional recombination-dependent replication that accounts for the direction of DNA packaging...
  80. ncbi Cdc13p: a single-strand telomeric DNA-binding protein with a dual role in yeast telomere maintenance
    C I Nugent
    Department of Molecular and Human Genetics and Cell and Molecular Biology Program, Baylor College of Medicine, Houston, TX 77030, USA
    Science 274:249-52. 1996
    ..In vitro, purified Cdc13p binds to single-strand yeast telomeric DNA. Therefore, Cdc13p is a telomere-binding protein required to protect the telomere and mediate access of telomerase to the chromosomal terminus...
  81. pmc Fine-structure analysis of activation-induced deaminase accessibility to class switch region R-loops
    Kefei Yu
    Department of Biochemistry and Molecular Biology, USC Norris Cancer Ctr, Rm 5428, 1441 Eastlake Ave, MC9176, Los Angeles, CA 90033, USA
    Mol Cell Biol 25:1730-6. 2005
    ..This phenomenon may explain the lack of WRC site preference at the mutations surrounding class switch recombination junctions...
  82. pmc Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes
    Eli Rothenberg
    Howard Hughes Medical Institute and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 105:20274-9. 2008
    ..In light of these observations we propose a model for hRad52-mediated DNA annealing where ssDNA release and dsDNA zippering are coordinated through successive rearrangement of overlapping nucleoprotein complexes...
  83. ncbi BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure
    Haijuan Yang
    Department of Pharmacology, Sloan Kettering Division, Joan and Sanford I Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA
    Science 297:1837-48. 2002
    ..These findings establish that BRCA2 functions directly in homologous recombination and provide a structural and biochemical basis for understanding the loss of recombination-mediated DSB repair in BRCA2-associated cancers...
  84. ncbi Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution
    C Yang
    Department of Biochemistry and Biophysics, Washington State University, Pullman 99164 4660, USA
    Nat Struct Biol 4:153-7. 1997
    ..We propose that ssDNA wraps around the tetrameric HsmtSSB protein through electropositive channels guided by flexible loops...
  85. ncbi PriB stimulates PriA helicase via an interaction with single-stranded DNA
    Chris J Cadman
    School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
    J Biol Chem 280:39693-700. 2005
    ..However, stimulation of PriA by PriB is not DNA structure-specific, demonstrating that targeting of stalled forks and recombination intermediates during replication restart likely resides with PriA alone...
  86. ncbi Physical interaction between replication protein A and Rad51 promotes exchange on single-stranded DNA
    Melissa E Stauffer
    Departments of Biochemistry and Physics and the Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232 8725, USA
    J Biol Chem 279:25638-45. 2004
    ..Rates of RPA displacement for the mutant were significantly below those of wild-type Rad51, suggesting that a direct RPA-Rad51 interaction is involved in displacing RPA in the initiation stage of genetic recombination...
  87. ncbi Saccharomyces Ku70, mre11/rad50 and RPA proteins regulate adaptation to G2/M arrest after DNA damage
    S E Lee
    Rosenstiel Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02454 9110, USA
    Cell 94:399-409. 1998
    ..We suggest that escape from the DNA damage-induced G2/M checkpoint depends on the extent of ssDNA created at broken chromosome ends. RPA appears to play a key intermediate step in this adaptation...
  88. pmc Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism
    Meigang Gu
    Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 107:521-8. 2010
    ..These findings suggest feasible strategies for developing specific inhibitors to block the action of this attractive, yet largely unexplored drug target...
  89. ncbi The ordered assembly of the phiX174-type primosome. I. Isolation and identification of intermediate protein-DNA complexes
    J Y Ng
    Graduate Program in Molecular Biology, Cornell University Graduate School of Medical Sciences, New York, New York 10021, USA
    J Biol Chem 271:15642-8. 1996
    ..As described in an accompanying article (Ng, J. Y., and Marians, K. J. (1996) J. Biol. Chem. 271, 15649-15655), when assembled on intact phiX174 phage DNA, the primosome also contains PriC...
  90. pmc Mechanism of interaction between single-stranded DNA binding protein and DNA
    Simone Kunzelmann
    MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
    Biochemistry 49:843-52. 2010
    ..1 microM at a high ionic strength (200 mM NaCl). Shorter lengths of ssDNA were tested for binding: only when the length is reduced to 20 bases is the affinity significantly reduced...
  91. pmc Dynamics of RecA filaments on single-stranded DNA
    Marijn T J van Loenhout
    Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
    Nucleic Acids Res 37:4089-99. 2009
    ..Taken together, our results demonstrate that ATP hydrolysis has a major influence on the structure and state of RecA filaments on ssDNA...
  92. pmc DNA length dependence of the single-strand annealing pathway and the role of Saccharomyces cerevisiae RAD59 in double-strand break repair
    N Sugawara
    Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02454 9110, USA
    Mol Cell Biol 20:5300-9. 2000
    ..A msh3 rad59 double mutant was more severely defective in SSA than either single mutant...
  93. ncbi Solution of a 20-variable 3-SAT problem on a DNA computer
    Ravinderjit S Braich
    University of Southern California, Laboratory for Molecular Science, Los Angeles, CA 90089 1340, USA
    Science 296:499-502. 2002
    ..This computational problem may be the largest yet solved by nonelectronic means. Problems of this size appear to be beyond the normal range of unaided human computation...
  94. ncbi DNA repair synthesis facilitates RAD52-mediated second-end capture during DSB repair
    Michael J McIlwraith
    Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
    Mol Cell 29:510-6. 2008
    ..coli SSB. Following repair synthesis and second-end capture, de novo DNA synthesis was observed from the captured second DNA end...
  95. pmc The structural determinants of checkpoint activation
    Christina A MacDougall
    Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
    Genes Dev 21:898-903. 2007
    ..These observations define the minimal DNA requirements for checkpoint activation and suggest that primed ssDNA represents a common checkpoint activating-structure formed following many types of damage...
  96. ncbi The ordered assembly of the phiX174-type primosome. III. PriB facilitates complex formation between PriA and DnaT
    J Liu
    Graduate Program in Molecular Biology, Cornell University Graduate School of Medical Sciences, New York, New York 10021, USA
    J Biol Chem 271:15656-61. 1996
    ..Thus, during primosome assembly, PriB facilitates complex formation between PriA and DnaT...
  97. ncbi Thermophoresis of single stranded DNA
    Philipp Reineck
    Department of Physics, Systems Biophysics, Center for Nanoscience, Ludwig Maximilians Universitat Munchen, Munchen, Germany
    Electrophoresis 31:279-86. 2010
    ..Here we measured the thermophoresis of highly diluted single stranded DNA using an all-optical capillary approach. Temperature gradients were created locally by an infrared laser...
  98. pmc Human AlkB homolog 1 is a mitochondrial protein that demethylates 3-methylcytosine in DNA and RNA
    Marianne Pedersen Westbye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N 7489 Trondheim, Norway
    J Biol Chem 283:25046-56. 2008
    ..In conclusion, hABH1 is a functional mitochondrial AlkB homolog that repairs 3-methylcytosine in single-stranded DNA and RNA...
  99. ncbi A dimeric mutant of the homotetrameric single-stranded DNA binding protein from Escherichia coli
    Marco Landwehr
    Biophysical Chemistry, Medical School Hannover, Germany
    Biol Chem 383:1325-33. 2002
    A single amino acid substitution (Y78R) at the dimer-dimer interface of homotetrameric single stranded DNA binding protein from E. coli (EcoSSB) renders the protein a stable dimer...
  100. pmc NMR study on the interaction between RPA and DNA decamer containing cis-syn cyclobutane pyrimidine dimer in the presence of XPA: implication for damage verification and strand-specific dual incision in nucleotide excision repair
    Joon Hwa Lee
    Department of Chemistry and National Creative Research Initiative Center, Korea Advanced Institute of Science and Technology, 373 1, Guseong Dong, Yuseong Gu, Daejon 305 701, Korea
    Nucleic Acids Res 31:4747-54. 2003
    ..The strand-specific binding of RPA and XPA to the damaged duplex DNA shows that RPA and XPA play crucial roles in damage verification and guiding cleavage of damaged DNA during NER...
  101. ncbi Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association
    K Saikrishnan
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Acta Crystallogr D Biol Crystallogr 61:1140-8. 2005
    ..coli SSB partly on account of the difference in the shape of the tetramers. Another difference between the two modes is that the former contains additional ionic interactions and is more susceptible to salt concentration...

Research Grants82

  1. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ..This technology promises to broadly impact the landscape of the biomedical sciences, both meeting the clinical diagnostic challenges of today and pioneering the paradigm-shifting discoveries of tomorrow. ..
  2. AAV Gene Therapy for AAT deficiency
    RICHARD SAMULSKI; Fiscal Year: 2009
    ..These new variants will be generated using an approach with in vitro "DNA shuffling" and in vivo selection in liver. This study would be very important to design AAV/AAT vector for future human clinical trials. ..
  3. AAV Gene Therapy for AAT deficiency
    RICHARD J contact SAMULSKI; Fiscal Year: 2010
    ..These new variants will be generated using an approach with in vitro "DNA shuffling" and in vivo selection in liver. This study would be very important to design AAV/AAT vector for future human clinical trials. ..
  4. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2009
    ....
  5. Functional Anergy in B Cells
    LAWRENCE WYSOCKI; Fiscal Year: 2009
    ..Moreover, because lymphocytes also reject transplanted tissue, our discoveries may open a clinical avenue to prevent immune rejection of transplanted tissues and organs. ..
  6. ROLE OF TOPOISOMERASES IN DNA REPLICATION
    KENNETH MARIANS; Fiscal Year: 1990
    ....
  7. Targeting of AID Mutagenic Activity
    David Kazadi; Fiscal Year: 2012
    ..Full understanding of the roles played by these two factors would constitute crucial progress in the quest for novel therapies against diseases of the immune system. ..
  8. Base-selective heavy atom labels for electron microscopy-based DNA sequencing
    F D Toste; Fiscal Year: 2012
    ..electron scattering to a detector is highly dependent on atomic number (Z), it is possible to label single stranded DNA (ssDNA) with heavy atoms...
  9. Base-selective heavy atom labels for electron microscopy-based DNA sequencing
    F D Toste; Fiscal Year: 2010
    ..electron scattering to a detector is highly dependent on atomic number (Z), it is possible to label single stranded DNA (ssDNA) with heavy atoms...
  10. Human Parvovirus B19 Vectors: Mechanism of Transduction
    Arun Srivastava; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  11. Human Parvovirus B19 Vectors: Mechanism of Transduction
    Arun Srivastava; Fiscal Year: 2004
    ..The knowledge gained from these studies will shed light on parvovirus Bl9-host cell interactions, and will lead to further improvements in recombinant parvovirus B19 vectors for their potential use in human gene therapy. ..
  12. Human Parvovirus B19 Vectors: Mechanism of Transduction
    Arun Srivastava; Fiscal Year: 2005
    ..The knowledge gained from these studies will shed light on parvovirus Bl9-host cell interactions, and will lead to further improvements in recombinant parvovirus B19 vectors for their potential use in human gene therapy. ..
  13. Human Parvovirus B19 Vectors: Mechanism of Transduction
    Arun Srivastava; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  14. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2007
    ..The results we would obtain during this Phase I study will help determine if pWGA has less bias when small quantities of template DNA is used. [unreadable] [unreadable] [unreadable]..
  15. GENETIC STUDIES OF ADENO-ASSOCIATED VIRUS
    Nicholas Muzyczka; Fiscal Year: 1991
    ....
  16. MINORITY SCHOOL FACULTY DEVELOPMENT AWARD
    SEIGO OHI; Fiscal Year: 1990
    ....
  17. Single stranded DNA Binding Proteins in Trypanosoma cru*
    Noreen Williams; Fiscal Year: 2001
    ..cruzi. ..
  18. Single stranded DNA Binding Proteins in Trypanosoma cru*
    Noreen Williams; Fiscal Year: 2003
    ..cruzi. ..
  19. Single stranded DNA Binding Proteins in Trypanosoma cru*
    Noreen Williams; Fiscal Year: 2002
    ..cruzi. ..
  20. AFM AND STM IN NOVEL APPROACHES TO SEQUENCING
    Stuart Lindsay; Fiscal Year: 1993
    ..3) They will continue to develop atomic force microscopy (AFM) for DNA imaging, both to check their STM methods and to develop better methods for imaging DNA- protein complexes...
  21. IMMUNOGLOBULINS IN MULTIPLE MYELOMA & AMYLOIDOSIS
    Allen Edmundson; Fiscal Year: 1993
    ..of antifluorescyl antibodies expressing cross-reactive idiotypes to the high-affinity molecules, and anti-single stranded DNA antibodies from mice with a syndrome similar to lupus erythematosus...
  22. IMMUNOGLOBULINS IN MULTIPLE MYELOMA AND AMYLOIDOSIS
    Allen Edmundson; Fiscal Year: 1991
    ..of antifluorescyl antibodies expressing cross-reactive idiotypes to the high-affinity molecules, and anti-single stranded DNA antibodies from mice with a syndrome similar to lupus erythematosus...
  23. SINGLE-STRANDED NUCLEIC ACID BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 1990
    ..These proposed studies are basic to our understanding of those physiological processes such as DNA replication, transcription and translation that require a single-stranded nucleic acid template...
  24. MOLECULAR BASIS OF PARVOVIRUS TARGET CELL SPECIFICITY
    Peter Tattersall; Fiscal Year: 2000
    ....
  25. ALTERED MECHANICAL LOADS AND SKELETAL MUSCLE PHENOTYPE
    Richard Tsika; Fiscal Year: 2006
    ..abstract_text> ..
  26. Recombination and fork progression in bacteriophage T4
    STEPHEN W contact WHITE; Fiscal Year: 2010
    ..The project encompasses structural, genetics and biochemical techniques working in tandem to study these important biological questions. ..
  27. Investigation of DnaB helicase loading for initiating DNA replication
    VALERIE LYNN O apos SHEA; Fiscal Year: 2010
    ....
  28. ALTERED MECHANICAL LOADS AND SKELETAL MUSCLE PHENOTYPE
    Richard Tsika; Fiscal Year: 2007
    ..abstract_text> ..
  29. ALTERED MECHANICAL LOADS AND SKELETAL MUSCLE PHENOTYPE
    Richard Tsika; Fiscal Year: 2005
    ..abstract_text> ..
  30. MOLECULAR BASIS OF PARVOVIRUS TARGET CELL SPECIFICITY
    Peter Tattersall; Fiscal Year: 1999
    ....
  31. ALTERED MECHANICAL LOADS AND SKELETAL MUSCLE PHENOTYPE
    Richard Tsika; Fiscal Year: 2009
    ..abstract_text> ..
  32. ACTIVATION OF RNA POLYMERASE BY SSDNA BINDING PROTEIN
    LUCIA ROTHMAN DENES; Fiscal Year: 1999
    ..6) Initiate structural studies of N4SSB. We expect that the proposed studies will provide new insights into the mechanism of transcription activation in prokaryotes as well as eukaryotes. ..
  33. GENETIC STUDIES OF ADENO-ASSOCIATED VIRUS
    Nicholas Muzyczka; Fiscal Year: 1999
    ..2) To purify and identify the cellular DNA replication enzymes that are required for AAV DNA replication. 3) To identify the cellular enzymes that interact with the AAV Rep protein. ..
  34. SSDP2 Gene Pathway in Myeloid Neoplasms
    Lalitha Nagarajan; Fiscal Year: 2006
    ..3 locus. Recently the Pl's laboratory has identified a novel gene SSBP2 (sequence specific single stranded DNA binding protein 2), homologous to a chicken gene encoding a protein that binds pyrimidine rich single ..
  35. SSDP2 Gene Pathway in Myeloid Neoplasms
    Lalitha Nagarajan; Fiscal Year: 2006
    ..3 locus. Recently the Pl's laboratory has identified a novel gene SSBP2 (sequence specific single stranded DNA binding protein 2), homologous to a chicken gene encoding a protein that binds pyrimidine rich single ..
  36. SSDP2 Gene Pathway in Myeloid Neoplasms
    Lalitha Nagarajan; Fiscal Year: 2005
    ..3 locus. Recently the Pl's laboratory has identified a novel gene SSBP2 (sequence specific single stranded DNA binding protein 2), homologous to a chicken gene encoding a protein that binds pyrimidine rich single ..
  37. SSDP2 Gene Pathway in Myeloid Neoplasms
    Lalitha Nagarajan; Fiscal Year: 2004
    ..3 locus. Recently the Pl's laboratory has identified a novel gene SSBP2 (sequence specific single stranded DNA binding protein 2), homologous to a chicken gene encoding a protein that binds pyrimidine rich single ..
  38. SSDP2 Gene Pathway in Myeloid Neoplasms
    Lalitha Nagarajan; Fiscal Year: 2003
    ..3 locus. Recently the Pl's laboratory has identified a novel gene SSBP2 (sequence specific single stranded DNA binding protein 2), homologous to a chicken gene encoding a protein that binds pyrimidine rich single ..
  39. DAMAGED DNA AND REPAIR
    Chulhee Kang; Fiscal Year: 1999
    ..We also propose to solve the crystal structure of human mitochondria single stranded DNA binding protein, which performs a vital role in repair of DNA...
  40. Screens for host DNA replication and repair factors involved in viral infection
    Matthew Weitzman; Fiscal Year: 2009
    ..These screens will identify cellular factors that regulate viral infection, will provide insights into virus-host interactions and fundamental cellular processes, and may suggest targets for anti-viral therapies. ..
  41. REGULATION OF DNA REPLICATION
    CHARLES MCHENRY; Fiscal Year: 2000
    ....
  42. Ultrasensitive, Label-free Silicon Nanowire Biosensing Arrays
    SEASON WONG; Fiscal Year: 2009
    ..It will help guard against the spread of infectious diseases (e.g., pandemic flu), can be deployed to perform food and water safety testing, and can help arrest the propagation of antibiotic-resistant microorganisms. ..
  43. REGULATION OF DNA REPLICATION
    CHARLES MCHENRY; Fiscal Year: 1999
    ....
  44. Mechanism of Hepatocyte Transduction by AAV Vectors
    Arun Srivastava; Fiscal Year: 2007
    ..abstract_text> ..
  45. Mechanism of Hepatocyte Transduction by AAV Vectors
    Arun Srivastava; Fiscal Year: 2005
    ..abstract_text> ..
  46. Development of a HTS Assay Targeting End Protection of Telomeres
    DEBORAH WUTTKE; Fiscal Year: 2007
    ..Small molecules that specifically target telomeres will provide valuable tools for dissecting the mechanism of telomere function and lay the groundwork for the discovery of cancer therapeutics. [unreadable]..
  47. MITOCHONDRIAL DNA POLYMERASE--MECHANISM AND STRUCTURE
    LAURIE KAGUNI; Fiscal Year: 1999
    ..To initiate the development of a transgenic fly model to examine the relationship between Pol gamma function, mitochondrial DNA replication fidelity, aging and disease. ..
  48. MITOCHONDRIAL DNA POLYMERASE--MECHANISM AND STRUCTURE
    LAURIE KAGUNI; Fiscal Year: 2000
    ..To initiate the development of a transgenic fly model to examine the relationship between Pol gamma function, mitochondrial DNA replication fidelity, aging and disease. ..
  49. FUNCTIONS OF AN EIA-ASSOCIATED CELLULAR PROTEIN
    Bayar Thimmapaya; Fiscal Year: 1999
    ..Ad) early promoter (E2-early) which transcribes a region of the viral genome that encodes a 72 kD single stranded DNA binding protein, an 80 kD precursor terminal protein and the 140 kD DNA polymerase all of which are vital ..
  50. FUNCTIONS OF AN EIA-ASSOCIATED CELLULAR PROTEIN
    Bayar Thimmapaya; Fiscal Year: 2002
    ..Ad) early promoter (E2-early) which transcribes a region of the viral genome that encodes a 72 kD single stranded DNA binding protein, an 80 kD precursor terminal protein and the 140 kD DNA polymerase all of which are vital ..
  51. FUNCTIONS OF AN EIA-ASSOCIATED CELLULAR PROTEIN
    Bayar Thimmapaya; Fiscal Year: 2001
    ..Ad) early promoter (E2-early) which transcribes a region of the viral genome that encodes a 72 kD single stranded DNA binding protein, an 80 kD precursor terminal protein and the 140 kD DNA polymerase all of which are vital ..
  52. FUNCTIONS OF AN EIA-ASSOCIATED CELLULAR PROTEIN
    Bayar Thimmapaya; Fiscal Year: 2000
    ..Ad) early promoter (E2-early) which transcribes a region of the viral genome that encodes a 72 kD single stranded DNA binding protein, an 80 kD precursor terminal protein and the 140 kD DNA polymerase all of which are vital ..
  53. FUNCTIONS OF AN EIA-ASSOCIATED CELLULAR PROTEIN
    Bayar Thimmapaya; Fiscal Year: 2001
    ..Ad) early promoter (E2-early) which transcribes a region of the viral genome that encodes a 72 kD single stranded DNA binding protein, an 80 kD precursor terminal protein and the 140 kD DNA polymerase all of which are vital ..
  54. ORGANIZATION AND EXPRESSION OF DNA TUMOR VIRUS GENOMES
    Bayar Thimmapaya; Fiscal Year: 1993
    ..Ad) early promoter (E2-early) which transcribes a region of the viral genome that encodes a 72 kD single stranded DNA binding protein, an 80 kD precursor terminal protein and the 140 kD DNA polymerase all of which are vital ..
  55. Molecular Analysis of Tral IE. Coli Helicase 1) Function
    JOEL SCHILDBACH; Fiscal Year: 2007
    ..The proposed experiments will provide a better understanding of the mechanism of conjugation, eventually allowing manipulations designed to improve human health. ..
  56. Molecular Analysis of Tral IE. Coli Helicase 1) Function
    Joel F Schildbach; Fiscal Year: 2010
    ..The proposed experiments will provide a better understanding of the mechanism of conjugation, eventually allowing manipulations designed to improve human health. ..
  57. Molecular Analysis of Tral IE. Coli Helicase 1) Function
    JOEL SCHILDBACH; Fiscal Year: 2009
    ..The proposed experiments will provide a better understanding of the mechanism of conjugation, eventually allowing manipulations designed to improve human health. ..
  58. Molecular Analysis of Tral IE. Coli Helicase 1) Function
    JOEL SCHILDBACH; Fiscal Year: 2009
    ..The proposed experiments will provide a better understanding of the mechanism of conjugation, eventually allowing manipulations designed to improve human health. ..
  59. Rescuing the anti-HIV activity of APOBEC3G with small-molecule chaperons
    SERGEY SAVINOV; Fiscal Year: 2009
    ..We propose to develop a novel anti-HIV therapeutic strategy that will rescue the natural antiviral mechanism without the danger of producing drug-resistant viruses. ..
  60. ASSEMBLY AND ACTIVATION OF ENZYME-SSDNA COMPLEXES
    Scott W Morrical; Fiscal Year: 2010
    ..Our studies of enzyme-ssDNA assembly mechanisms may therefore shed light on how tumors develop and how infectious diseases progress, and may also suggest new treatment strategies. ..
  61. Vector and host cellular biology in AAV vector transduction in vivo
    Hiroyuki Nakai; Fiscal Year: 2010
    ..Results of the study will contribute to designing and developing more efficient and safer rAAV vectors and assessing the safety of the vector. ..
  62. Vector and host cellular biology in AAV vector transduction in vivo
    Hiroyuki Nakai; Fiscal Year: 2009
    ..Results of the study will contribute to designing and developing more efficient and safer rAAV vectors and assessing the safety of the vector. ..
  63. ASSEMBLY AND ACTIVATION OF ENZYME-SSDNA COMPLEXES
    SCOTT MORRICAL; Fiscal Year: 2009
    ..Our studies of enzyme-ssDNA assembly mechanisms may therefore shed light on how tumors develop and how infectious diseases progress, and may also suggest new treatment strategies. ..
  64. Thermodynamics and kinetics of DNA binding protein probed by DNA overstretching
    Andreas Hanke; Fiscal Year: 2010
    ..This project is the continuation of a S06 SCORE pilot project with the same general scope. It is a starting point for future long-term collaborative research and will therefore be an important tool for the PI's faculty development. ..
  65. Thermodynamics and kinetics of DNA binding protein probed by DNA overstretching
    Andreas Hanke; Fiscal Year: 2009
    ..This project is the continuation of a S06 SCORE pilot project with the same general scope. It is a starting point for future long-term collaborative research and will therefore be an important tool for the PI's faculty development. ..
  66. SSB PROTEINS AS ORGANIZERS OF DNA PRECURSOR BIOSYNTHESIS
    Christopher Mathews; Fiscal Year: 2000
    ..Characterization of the phosphorylation of SSB will explore the role of this modification on protein-protein and protein-DNA associations. ..
  67. Human cytomegalovirus alkaline nuclease (pUL98): potential antiviral target?
    Michael McVoy; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  68. SSB PROTEINS AS ORGANIZERS OF DNA PRECURSOR BIOSYNTHESIS
    Christopher Mathews; Fiscal Year: 1999
    ..Characterization of the phosphorylation of SSB will explore the role of this modification on protein-protein and protein-DNA associations. ..
  69. SSB PROTEINS AS ORGANIZERS OF DNA PRECURSOR BIOSYNTHESIS
    Christopher Mathews; Fiscal Year: 2001
    ..Characterization of the phosphorylation of SSB will explore the role of this modification on protein-protein and protein-DNA associations. ..
  70. Vector and host cellular biology in AAV vector transduction in vivo
    Hiroyuki Nakai; Fiscal Year: 2007
    ..The proposed project should substantially contribute to building an intellectual foundation for successful human gene therapy. ..
  71. REVERSE TRANSCRIPTASES IN THE PROKARYOTES
    Masayori Inouye; Fiscal Year: 2004
    ....
  72. REVERSE TRANSCRIPTASES IN THE PROKARYOTES
    Masayori Inouye; Fiscal Year: 2003
    ....
  73. REVERSE TRANSCRIPTASES IN THE PROKARYOTES
    Masayori Inouye; Fiscal Year: 2001
    ....
  74. ROLE OF G4-DNA IN THE PAIRING OF CHROMOSOMES
    Walter Gilbert; Fiscal Year: 1990
    ..The significance of the G4-DNA hypothesis is that it provides an understanding of how chromosome pairing is accomplished throughout eukaryotic organisms and explains why four chromatids are involved in recombination...