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. ncbi Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects
    Jose M Sogo
    Institute of Cell Biology, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Science 297:599-602. 2002
  4. 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
  5. ncbi 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications365 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. ncbi Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects
    Jose M Sogo
    Institute of Cell Biology, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Science 297:599-602. 2002
    ..We speculate that, in checkpoint mutants, abnormal replication intermediates begin to form because of uncoordinated replication and are further processed by unscheduled recombination pathways, causing genome instability...
  4. 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...
  5. ncbi 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...
  6. 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...
  7. 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
    ....
  8. 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...
  9. 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...
  10. 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...
  11. 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...
  12. ncbi Saccharomyces cerevisiae Dmc1 protein promotes renaturation of single-strand DNA (ssDNA) and assimilation of ssDNA into homologous super-coiled duplex DNA
    E L Hong
    Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
    J Biol Chem 276:41906-12. 2001
    ..In addition, Dmc1 catalyzes strand assimilation of ssDNA oligonucleotides into homologous supercoiled duplex DNA in a reaction promoted by ATP or the non-hydrolyzable ATP analogue AMP-PNP...
  13. 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...
  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. 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...
  16. pmc Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA
    Elena Bochkareva
    Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
    EMBO J 21:1855-63. 2002
    ..Taken together, our data indicate that switching from 8-10 to 30 nt mode is mediated by DNA binding with the trimerization core...
  17. 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...
  18. 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
    ....
  19. 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...
  20. pmc ATRIP binding to replication protein A-single-stranded DNA promotes ATR-ATRIP localization but is dispensable for Chk1 phosphorylation
    Heather L Ball
    Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
    Mol Biol Cell 16:2372-81. 2005
    ..These data suggest that binding to RPA-ssDNA is not the essential function of ATRIP in ATR-dependent checkpoint signaling and ATR has an important function in properly localizing the ATR-ATRIP complex...
  21. ncbi Stretching single stranded DNA, a model polyelectrolyte
    M N Dessinges
    Laboratoire de Physique Statistique de l ENS, CNRS UMR 8550, Associé aux Universités Paris VI et VII, 24 rue Lhomond, 75231 Paris Cedex 05, France
    Phys Rev Lett 89:248102. 2002
    ..The elastic behavior of such an altered ssDNA deviates strongly from the behavior of an ideal polymer. This deviation is shown to result from the elasticity of the chain and its electrostatic self-avoiding interactions...
  22. ncbi Homologous pairing promoted by the human Rad52 protein
    W Kagawa
    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
    J Biol Chem 276:35201-8. 2001
    ..Our results reveal the striking similarity between HsRad52 and the Escherichia coli RecT protein, which functions in a RecA-independent recombination pathway...
  23. pmc Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution
    S Raghunathan
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 94:6652-7. 1997
    ..The other interface promotes a superhelical structure within the crystal that may reflect tetramer-tetramer interactions involved in the positive cooperative binding of the single-stranded DNA-binding protein to single-stranded DNA...
  24. 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
    ....
  25. 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...
  26. ncbi Recombineering: a powerful new tool for mouse functional genomics
    N G Copeland
    Mouse Cancer Genetic Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    Nat Rev Genet 2:769-79. 2001
    ....
  27. pmc The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA
    Savvas N Savvides
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
    Protein Sci 13:1942-7. 2004
    ..The structure also reveals the conservation of molecular contacts between successive tetramers mediated by the L(45) loops as seen in two other crystal forms of SSBc, suggesting a possible functional relevance of this interaction...
  28. 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
    ....
  29. 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...
  30. 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...
  31. 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...
  32. 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
    ....
  33. 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...
  34. ncbi Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets
    Heiko Kuhn
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, Massachusetts 02215, USA
    J Am Chem Soc 124:1097-103. 2002
    ....
  35. ncbi Human meiotic recombinase Dmc1 promotes ATP-dependent homologous DNA strand exchange
    Michael G Sehorn
    Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
    Nature 429:433-7. 2004
    ..The DNA strand exchange activity of hDmc1 is probably indispensable for repair of DNA double-strand breaks during meiosis and for maintaining the ploidy of meiotic chromosomes...
  36. ncbi A Dimer of Escherichia coli UvrD is the active form of the helicase in vitro
    Nasib K Maluf
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Avenue, Box 8231, St Louis, MO 63110 1093, USA
    J Mol Biol 325:913-35. 2003
    ..Initiation of DNA unwinding in vitro appears to require a dimeric UvrD complex in which one subunit is bound to the ssDNA/dsDNA junction, while the second subunit is bound to the 3' ssDNA tail...
  37. pmc In organello formaldehyde crosslinking of proteins to mtDNA: identification of bifunctional proteins
    B A Kaufman
    Department of Molecular Biology, and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9148, USA
    Proc Natl Acad Sci U S A 97:7772-7. 2000
    ..These data identify bifunctional proteins that participate in the stability of rho(+) mtDNA...
  38. ncbi Differences in the single-stranded DNA binding activities of MCM2-7 and MCM467: MCM2 and MCM5 define a slow ATP-dependent step
    Matthew L Bochman
    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
    J Biol Chem 282:33795-804. 2007
    ..We propose that the DNA binding differences between MCM2-7 and MCM467 correspond to a conformational change at the MCM2/5 active site with putative regulatory significance...
  39. 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
    ....
  40. pmc Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein
    Jin Inoue
    Aisin Cosmos R and D Co Ltd, 2 1 5 Kazusa kamatari, Kisarazu, Chiba 292 0818 Japan
    Nucleic Acids Res 34:e69. 2006
    ..Furthermore, the presence of the TthSSB mutant protein essentially eliminates nonspecific DNA products in RCA reactions...
  41. pmc PriA helicase and SSB interact physically and functionally
    Chris J Cadman
    School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
    Nucleic Acids Res 32:6378-87. 2004
    ..Taken together with previous data, these findings indicate that protein-protein interactions involving SSB may coordinate replication fork reloading from start to finish...
  42. pmc Delineation of the high-affinity single-stranded telomeric DNA-binding domain of Saccharomyces cerevisiae Cdc13
    Emily M Anderson
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, CO 80309 0215, USA
    Nucleic Acids Res 30:4305-13. 2002
    ..The full-length protein exhibited the same rate of dissociation as both domains, however, indicating that the full-length protein contains a region that inhibits association with single-stranded telomeric DNA...
  43. ncbi Synergistic actions of Rad51 and Rad52 in recombination and DNA repair
    F E Benson
    Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, Hertfordshire, UK
    Nature 391:401-4. 1998
    ..Here we show that hRad52 stimulates homologous pairing by hRad51. The DNA-binding properties of hRad52 indicate that Rad52 is involved in an early stage of Rad51-mediated recombination...
  44. pmc Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus
    R I Wadsworth
    Centre for Biomolecular Science, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
    Nucleic Acids Res 29:914-20. 2001
    ..In comparison with Escherichia coli SSB, the tail may play a role in protein-protein interactions during DNA replication and repair...
  45. ncbi CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone
    W Jiang
    Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    J Biol Chem 272:196-202. 1997
    ..Such a function may be crucial for efficient translation of mRNAs at low temperatures and may also have an effect on transcription...
  46. 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...
  47. 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
    ....
  48. 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
    ....
  49. 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...
  50. 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...
  51. 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...
  52. 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...
  53. ncbi Switching human telomerase on and off with hPOT1 protein in vitro
    Ming Lei
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
    J Biol Chem 280:20449-56. 2005
    ..Thus, depending on its location relative to the DNA 3'-end, hPOT1 can either inhibit telomerase action or form a preferred substrate for telomerase. We propose that another factor catalyzes the interconversion of these states in vivo...
  54. 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...
  55. 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...
  56. ncbi The POT1-TPP1 telomere complex is a telomerase processivity factor
    Feng Wang
    Department of Biological Chemistry, University of Michigan Medical School, MSRBIII 5301D, 1150 W Medical Center Drive, Ann Arbor, Michigan 48109, USA
    Nature 445:506-10. 2007
    ..We propose that POT1-TPP1 switches from inhibiting telomerase access to the telomere, as a component of shelterin, to serving as a processivity factor for telomerase during telomere extension...
  57. ncbi Transmission electron microscopy reveals an optimal HIV-1 nucleocapsid aggregation with single-stranded nucleic acids and the mature HIV-1 nucleocapsid protein
    Gilles Mirambeau
    Laboratoire de Microscopie Moléculaire et Cellulaire, CNRS UMR 8126, Institut Gustave Roussy, 94805 Villejuif, France
    J Mol Biol 364:496-511. 2006
    ..Subsequently, disassembly of the nucleocapsid should be favoured once dsDNA is produced by HIV-1 reverse transcriptase...
  58. 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
    ....
  59. 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...
  60. 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...
  61. 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...
  62. 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...
  63. 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...
  64. 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...
  65. 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...
  66. 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...
  67. 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...
  68. 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...
  69. 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...
  70. 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...
  71. 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...
  72. pmc Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage
    Douglas A Bernstein
    Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin Medical School, Madison, WI 53706 1532, USA
    Proc Natl Acad Sci U S A 101:8575-80. 2004
    ..We hypothesize that differences between D. radiodurans SSB and homotetrameric bacterial SSB proteins may confer a selective advantage to D. radiodurans cells that aids viability in environments that challenge genomic stability...
  73. pmc 3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins
    Roman Fedorov
    Institute for Biophysical Chemistry, Hannover Medical Schoo, l Carl Neuberg Strasse 1, D 30625 Hannover, Germany
    Nucleic Acids Res 34:6708-17. 2006
    ..A model for binding this region to the chi subunit of DNA polymerase III is proposed. It explains at a molecular level the reason for the ssb113 phenotype observed in Escherichia coli...
  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. ncbi Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage
    Sarah C Trewick
    Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK
    Nature 419:174-8. 2002
    ..The AlkB enzyme couples oxidative decarboxylation of alpha-ketoglutarate to the hydroxylation of these methylated bases in DNA, resulting in direct reversion to the unmodified base and the release of formaldehyde...
  76. ncbi Identification of residues important for DNA binding in the full-length human Rad52 protein
    Janice A Lloyd
    Department of Biochemistry and Molecular Pharmacology, Aaron Lazare Research Building, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 2324, USA
    J Mol Biol 345:239-49. 2005
    ....
  77. ncbi HIV-1 inactivation by nucleic acid aptamers
    Daniel M Held
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Front Biosci 11:89-112. 2006
    ..Additional nucleic acid-based strategies for inactivation of HIV-1 function (including RNAi, antisense, and ribozymes) have also demonstrated their utility. These approaches are reviewed in other chapters of this volume and elsewhere...
  78. 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...
  79. 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...
  80. 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...
  81. 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...
  82. 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...
  83. 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...
  84. pmc The DnaC helicase loader is a dual ATP/ADP switch protein
    Megan J Davey
    Howard Hughes Medical Institute and Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    EMBO J 21:3148-59. 2002
    ..This dual switching process may underlie the sensitivity of DnaB to even small fluctuations in DnaC levels...
  85. 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
    ....
  86. ncbi Interactions of gene 2.5 protein and DNA polymerase of bacteriophage T7
    Y T Kim
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
    J Biol Chem 267:15032-40. 1992
    ..coli single-stranded DNA-binding protein, T4 gene 32 protein, and E. coli recA protein. All except E. coli recA protein stimulate the activity and processivity of T7 DNA polymerase; E. coli recA protein inhibits these activities...
  87. pmc Biochemical analysis of human Dna2
    Taro Masuda-Sasa
    Braun Laboratories, 147 75, California Institute of Technology, Pasadena, CA 91125, USA
    Nucleic Acids Res 34:1865-75. 2006
    ..These biochemical specificities are very similar to those of the ScDna2 protein, but suggest that the 3'-5' nuclease activity may be more important than previously thought...
  88. ncbi A hypophosphorylated form of RPA34 is a specific component of pre-replication centers
    Patricia Françon
    Institute of Human Genetics, CNRS, Genome Dynamics and Development, 141, rue de la Cardonille, 34396 Montpellier Cedex 5, France
    J Cell Sci 117:4909-20. 2004
    ..In such conditions, replication foci can form, and short RNA-primed nascent DNAs of discrete size are synthesized. These data show that in Xenopus, the hypophosphorylated form of RPA34 is a component of the pre-initiation complex...
  89. pmc Nuclear localization signal peptides induce molecular delivery along microtubules
    Hanna Salman
    Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
    Biophys J 89:2134-45. 2005
    ..In the intact cell, where microtubules project radially from the centrosome, such an interaction would effectively deliver nuclear-targeted cargo to the nuclear envelope in preparation for import...
  90. 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...
  91. 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...
  92. 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...
  93. 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...
  94. 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...
  95. 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...
  96. 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
    ....
  97. 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...
  98. 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...
  99. 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
    ....
  100. ncbi 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
    ....
  101. 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...

Research Grants78

  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. Metnase, PIKK, and RPA Roles in DNA Damage and Replication Stress Responses
    Jac A Nickoloff; Fiscal Year: 2013
    ....
  3. STRUCTURAL STUDIES OF NUCLEOPROTEIN COMPLEXES
    Edward H Egelman; Fiscal Year: 2012
    ..And other complexes are involved in the assembly of viruses, including one that causes leukemia. ..
  4. The in vivo function of A3A and A3G during retrovirus infection
    Spyridon Stavrou; Fiscal Year: 2013
    ..This study will provide insight into the function of the A3 proteins in vivo, and also has the potential to create new models for testing therapeutic strategies for treating retroviral infections in humans. ..
  5. Granzyme a Pathway of CTL-Mediated Cell Death
    Judy Lieberman; Fiscal Year: 2010
    ..These insights may lead to new therapeutic approaches to treat the conditions that granzyme A targets (intracellular infection and cancer) or potentially for autoimmunity and neurological injury. ..
  6. Screens for host DNA replication and repair factors involved in viral infection
    Matthew D Weitzman; Fiscal Year: 2010
    ..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. ..
  7. Self-complementary rAAV9 Systemic Gene Delivery Treatment for MPS Type IIIA
    Douglas M McCarty; Fiscal Year: 2013
    ..Successful completion of the project is expected to have an immediate impact on the MPS IIIA patient population, with a working therapeutic procedure in hand to advance to the clinical testing process. ..
  8. Genetic Analysis of T Cell Leukemogenesis
    Stephen J Brandt; Fiscal Year: 2013
    ..complex that also contains the LIM domain-binding protein Ldb1 and two Ldb1-interacting proteins, single stranded DNA-binding protein-2 (SSBP2) and -3 (SSBP3)...
  9. Role of ABH1's AP endonuclease activity in immunoglobulin gene diversification
    TINA A MUELLER; Fiscal Year: 2010
    ....
  10. Functional Interactions of Telomere Protein with Human Telomerase
    THOMAS ROBERT CECH; Fiscal Year: 2013
    ....
  11. Keratin Gene Targeting for the Treatment of Epidermolysis Bullosa
    Daniel G Miller; Fiscal Year: 2013
    ..Adeno-Associated Virus (AAV) vectors efficiently transduce primary cells in culture, and their single stranded DNA genomes have been shown to recombine with homologous chromosomal sequences...
  12. 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...
  13. Targeting of AID Mutagenic Activity
    David Kazadi; Fiscal Year: 2013
    ..g., c-myc/IgH in Burkitt's lymphoma). Using mouse primary B cells deficient in RNA exosome, we will evaluate genomic instability by molecular cytogenetic techniques and translocation quantitative assays. ..
  14. Mitochondrial DNA Replisome: Mechanism, Structure and Physiology
    LAURIE SIMON KAGUNI; Fiscal Year: 2013
    ..Therefore, a clear understanding of mitochondrial biogenesis and energy production and how these processes are deregulated in common disease states, is essential to treating them effectively (and economically). ..
  15. Molecular Evolution of Multifunctional DNA Nanoparticles
    Bradley T Messmer; Fiscal Year: 2013
    ..RCA) of circular oligonucleotide templates containing randomized nucleotides produces libraries of single stranded DNA nanoparticles that can be screened for cell binding properties...
  16. Mechanisms of Homologous Recombination in Yeast
    Lorraine S Symington; Fiscal Year: 2013
    ..3) The role of each of the identified resection nucleases in telomere length homeostasis, G-tail formation, degradation of uncapped telomeres and survival in the absence of telomerase will be determined. ..
  17. Human Stem Cell Recombineering
    MELVYS VALLEDOR CEBALLOS; Fiscal Year: 2012
    ..With sharper tools, genome engineering will realize its potential to cure genetic diseases, create human disease models, and achieve the promises of the biotechnology revolution. ..
  18. New determinants of the DNA damage response in the fission yeast S. pombe
    MATTHEW J O'CONNELL; Fiscal Year: 2013
    ..Because these processes are ancient in origin, we use simple yeast cells to identify new genes that are relevant to human disease. Our proposal analyses three new genes in the response of cells to DNA damage. ..
  19. Mechansim of activation of innate immunity by ISS-DNA
    Wen Ming Chu; Fiscal Year: 2013
    ....
  20. Parvovirus RNA Processing and Gene Expression Strategies
    David J Pintel; Fiscal Year: 2013
    ..Our systems afford highly tractable, tightly controlled models that are positioned to both advance parvovirology and to deliver significant insight into fundamental aspects of gene expression. ..
  21. MOLECULAR BASIS OF PARVOVIRAL TARGET CELL SPECIFICITY
    PETER J TATTERSALL; Fiscal Year: 2013
    ..The vector expresses the B7-1 co-stimulatory molecule, and will potentially activate cytotoxic killer T-cells specific for melanoma tumor antigens, resulting in tumor eradication. ..
  22. Triplex-based Aptamers to Detect DNA Damage
    Paul S Miller; Fiscal Year: 2010
    ..Simple methods to detect these lesions could provide useful diagnostic or prognostic tools for evaluating disease processes in a clinical setting. ..
  23. Differential Signaling by B cell Receptor in Tolerance Induction
    Haochu Huang; Fiscal Year: 2012
    ..This refined signaling map will be essential to dissect tolerance defects in autoimmune diseases and to develop novel immunomodulatory drugs. ..
  24. Recombination and fork progression in bacteriophage T4
    Stephen W White; Fiscal Year: 2013
    ....
  25. Class Switch Recombination in B Lymphocytes
    Michel C Nussenzweig; Fiscal Year: 2012
    ..is initiated by activation induced cytidine deaminase (AID), an enzyme that converts cytidine to uracyl in single stranded DNA thereby creating U:G mismatches that are recognized and processed by mismatch repair enzymes or Uracyl DNA ..
  26. Rescuing the anti-HIV activity of APOBEC3G with small-molecule chaperons
    Sergey N Savinov; Fiscal Year: 2010
    ..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. ..
  27. STRUCTURE AND FUNCTION OF TELOMERASE
    Kathleen Collins; Fiscal Year: 2013
    ..Also, because human cancers require aberrantly high telomerase activation for continued growth, telomerase inhibitors have widely recognized promise as selective anti-tumor agents. ..
  28. Vector and host cellular biology in AAV vector transduction in vivo
    Hiroyuki Nakai; Fiscal Year: 2012
    ..Results of the study will contribute to designing and developing more efficient and safer rAAV vectors and assessing the safety of the vector. ..
  29. Role of ATR in Cell Cycle Checkpoints
    William G Dunphy; Fiscal Year: 2012
    ..Therefore, a thorough knowledge of checkpoint mechanisms is essential for understanding the root causes of cancer. ..
  30. Acute Myeloid Leukemia: MRD Analysis Using Modular uFluidics and uFlow Cytometry
    Steven Allan Soper; Fiscal Year: 2013
    ..A pilot study will be performed to measure MRD status in AML patients and associate that with the onset of hematologic relapse using the designed fluidic bio-processor with results compared to MFC. ..
  31. Biochemical Insight of Hyperphosphorylation of Replication Protein A
    Yue Zou; Fiscal Year: 2010
    ..This project is highly relevant to cancer biology as DNA damage is the major cause to human cancer. ..
  32. Investigation of DnaB helicase loading for initiating DNA replication
    VALERIE LYNN O'SHEA; Fiscal Year: 2011
    ....
  33. ASSEMBLY AND ACTIVATION OF ENZYME-SSDNA COMPLEXES
    Scott W Morrical; Fiscal Year: 2012
    ..Understanding how recombinase- and helicase- ssDNA complexes are correctly assembled and activated may therefore aid in the prevention, diagnosis, and treatment of cancer. ..
  34. Regulation of RPA Activity in DNA Repair
    James A Borowiec; Fiscal Year: 2012
    ..PUBLIC HEALTH RELEVANCE: We will understand the functional significance of RPA phosphorylation in the cellular response to DNA damage. The results from this work could lead to new threraputics to treat human cancers ..
  35. SSB PROTEIN/DNA INTERACTIONS
    Timothy M Lohman; Fiscal Year: 2013
    ..Single Stranded Binding (SSB) proteins are essential in all organisms due to their interactions with single stranded DNA formed transiently during DNA replication, recombination and repair. Our focus is on E...
  36. SINGLE STRANDED DNA RECOGNITION IN TELOMERES
    Deborah S Wuttke; Fiscal Year: 2013
    ..This hypothesis-driven, highly unified research program will provide novel insights into the fundamental processes that maintain a central mechanism of chromosome stability. ..
  37. Localization of Recombination sites in E. coli
    Steven J Sandler; Fiscal Year: 2010
    ..These new reagents will also provide important molecular tools for others in the research community. PHS 398 (Rev. 09/04) Page 2 Principal Investigator/Program Director (Last, first, middle): SANDLER, STEVEN, J ..
  38. A dual-nanopore platform for sensing and control of polynucleotides
    TREVOR JUSTIN MORIN; Fiscal Year: 2013
    ....
  39. 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. ..
  40. Single Stranded DNA: The Genome's Achilles Heel
    Wenyi Feng; Fiscal Year: 2009
    ..In the long term, I hope that this research will aid in promoting the development of diagnostic and treatment tools for human diseases. ..
  41. Transcribing Activities in N4 Infected E. Coli
    LUCIA B B ROTHMAN-DENES; Fiscal Year: 2013
    ..We will determine its localization on the template in vivo, purify gp1 and analyze its effect on N4 RNAP transcription initiation. ..
  42. Functional Dynamics of Large Molecular Machines. The Primosome.
    W M BUJALOWSKI; Fiscal Year: 2012
    ..abstract_text> ..
  43. Deconvoluting G-quadruplex and i-Motif dynamics: the role of the physiological st
    Randy M Wadkins; Fiscal Year: 2013
    ..Additionally, in support of the AREA program goals, this work provides hands-on learning for students at the University of Mississippi, who will study fundamental questions regarding higher-order DNA dynamics. ..
  44. Use of RecA to Promote Gene Targeting
    Jeffrey J Essner; Fiscal Year: 2010
    ..We propose to use our modified version of RecA to coat single stranded DNA and produce DNA-RecA filaments that are homologous to the gene we wish to target...
  45. In Vivo Selection of Aptamers Targeting Pancreatic Cancer
    KRISTY LYNN RIALON; Fiscal Year: 2011
    ..Current chemotherapies extend survival by only a few weeks. Molecular therapies which target the cancer cells alone can increase the response rate and long-term survival, and decrease systemic toxicities to patients. ..
  46. Enzymatic Mechanisms of DNA Helicases
    Steven W Matson; Fiscal Year: 2010
    ..It is likely that other diseases will be linked with defects in DNA helicases as more disease genes are identified placing added emphasis on the importance of understanding this class of proteins. ..
  47. Roles of CST, a novel telomere associated complex, at the DNA replication fork
    JASON AARON STEWART; Fiscal Year: 2012
    ..CST interactions with replication fork components and fork reinitiation factors will then be explored. Together, these studies will provide an understanding of how CST helps maintain genomic stability through difficult-to-replicate DNA. ..
  48. Structural Studies of RecA-DNA Complexes
    Charles Bell; Fiscal Year: 2009
    ..Thus, understanding the mechanism of action of RecA will contribute greatly to our general knowledge of enzymes involved in virtually all aspects of DNA metabolism. ..
  49. Functional Anergy in B Cells
    Lawrence J Wysocki; Fiscal Year: 2012
    ..The results of this project will almost certainly open new avenues of investigation that could lead to a paradigm shift, and to novel strategies to control autoimmunity and possibly transplant rejection. ..
  50. Single Stranded DNA: The Genome's Achilles Heel
    Wenyi Feng; Fiscal Year: 2013
    ..3. Identify origins of replication and chromosome fragile sites in humans using a combination of ssDNA and chromosome breakage mapping that have been adapted for the mammalian systems. ..
  51. Role of RPA Hyperphosphorylation in DNA Damage Responses
    MOISES ALEJANDRO SERRANO; Fiscal Year: 2012
    ..Do not use suffixes such as 2a, 2b. Kirschstein-NRSA Individual Fellowship Application NAME OF APPLICANT (Last, first, middle initial) Serrano, Moises A (To be completed by applicant - follow PHS 416-1 instructions) 18. ..
  52. Simulating Biomolecular Machines: ATP Powered DNA Translocation in Helicases
    Martin McCullagh; Fiscal Year: 2013
    ..Most helicases translocate along single stranded DNA (ssDNA) and induce melting of DNA base pairs at the dsDNA/ssDNA junction...
  53. PHOSPHATE ACTIVATION MECHANISMS
    Stephen J Benkovic; Fiscal Year: 2013
    ....
  54. SPECIFICITY OF INTERCALATION REACTIONS
    Jonathan B Chaires; Fiscal Year: 2013
    ..The results will be of fundamental use for guiding the design of new drugs targeted toward quadruplexes. ..
  55. Structural basis for RPA and DNA primase functions
    Walter J Chazin; Fiscal Year: 2013
    ..Together, these results will inform the structural basis for the hand-off of ssDNA from RPA to DNA primase and counting of the RNA primer, which are critical steps in the replication of DNA. ..
  56. Novel adeno-associated virus vector production system development
    Weidong Xiao; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): AAV is a single stranded DNA virus which has shown great promise as a gene therapy vector...
  57. INITIATION OF DNA REPLICATION OF YEAST CHROMOSOMES
    Stephen P Bell; Fiscal Year: 2013
    ..In the last aim, we will address how helicase activation and DNA unwinding are coordinated with the initiation of DNA synthesis to prevent the generation of excess single-stranded DNA and activation of DNA-damage checkpoint. ..
  58. Single molecule DNA mapping for DNA and CNV analysis
    Ming Xiao; Fiscal Year: 2012
    ..In this proposal, we aim to develop and optimize a single molecule mapping approach that will make de novo sequence assembly and structural variation analysis possible. ..
  59. Carbon Nanotubes: A New Synthetic Nanopore for Sequencing
    Stuart Lindsay; Fiscal Year: 2010
    ..Making a search of whole genomes for rare variants economically feasible has many implications for medicine. ..
  60. Delineating a New Mechanism of Foreign DNA Restriction in Human Cells
    MICHAEL ALLEN CARPENTER; Fiscal Year: 2012
    ..abstract_text> ..
  61. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2009
    ....
  62. BRCA2 model system
    William K Holloman; Fiscal Year: 2013
    ..Our long-term goal is to provide knowledge of the function of BRCA2 and gain insight into how its dysfunction can lead to initiation of tumorigenic transformation. ..
  63. Mechanisms in Brh2-promoted recombinational repair
    William K Holloman; Fiscal Year: 2013
    ..Our long-term goal is to provide knowledge of the function of BRCA2 and gain insight into how its dysfunction can lead to initiation of tumorigenic transformation. ..
  64. Single stranded DNA Binding Proteins in Trypanosoma cru*
    Noreen Williams; Fiscal Year: 2003
    ..cruzi. ..
  65. 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]..
  66. 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...
  67. SINGLE-STRANDED NUCLEIC ACID BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 1992
    ..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...
  68. ALTERED MECHANICAL LOADS AND SKELETAL MUSCLE PHENOTYPE
    Richard Tsika; Fiscal Year: 2009
    ..abstract_text> ..
  69. 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. ..
  70. 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. ..
  71. 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 ..
  72. 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...
  73. 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. ..
  74. 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]..
  75. 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. ..
  76. 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. ..
  77. REVERSE TRANSCRIPTASES IN THE PROKARYOTES
    Masayori Inouye; Fiscal Year: 2004
    ....
  78. ROLE OF G4-DNA IN THE PAIRING OF CHROMOSOMES
    Walter Gilbert; Fiscal Year: 1991
    ..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...