dna polymerase i

Summary

Summary: A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 2.7.7.7.

Top Publications

  1. pmc The Saccharomyces telomere-binding protein Cdc13p interacts with both the catalytic subunit of DNA polymerase alpha and the telomerase-associated est1 protein
    H Qi
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 1014, USA
    Genes Dev 14:1777-88. 2000
  2. ncbi Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites
    Francene J Lemoine
    Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Cell 120:587-98. 2005
  3. pmc The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism
    Eugene Y Wu
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
    J Biol Chem 286:19758-67. 2011
  4. pmc Mcm10 and And-1/CTF4 recruit DNA polymerase alpha to chromatin for initiation of DNA replication
    Wenge Zhu
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
    Genes Dev 21:2288-99. 2007
  5. pmc Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I
    Svitlana Y Berezhna
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 134:11261-8. 2012
  6. pmc DNA polymerase I activity in Escherichia coli is influenced by spot 42 RNA
    D A Polayes
    Department of Physiological Chemistry, University of Wisconsin, Madison 53706
    J Bacteriol 170:2083-8. 1988
  7. ncbi Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
    D L Ollis
    Nature 313:762-6. 1985
  8. ncbi Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
    J R Kiefer
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
    Nature 391:304-7. 1998
  9. pmc Conformational transitions in DNA polymerase I revealed by single-molecule FRET
    Yusdi Santoso
    Biological Physics Research Group, Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 107:715-20. 2010
  10. ncbi Positive correlation between DNA polymerase alpha-primase pausing and mutagenesis within polypyrimidine/polypurine microsatellite sequences
    Suzanne E Hile
    Department of Pathology, Gittlen Cancer Research Institute, The Pennsylvania State University College of Medicine, Hershey Medical Center, 500 University Drive, Hershey, PA 17033, USA
    J Mol Biol 335:745-59. 2004

Research Grants

  1. Group A Streptococcus responses to oxidative stress
    Ioannis Gryllos; Fiscal Year: 2010
  2. Hoogsteen base pairing in human DNA polymerase iota
    Satya Prakash; Fiscal Year: 2010
  3. A Nanopore-based Instrument for Single Molecule Analysis of DNA-binding Proteins
    WILLIAM BRUCE DUNBAR; Fiscal Year: 2010
  4. Conformational Change in Molecular Biology
    Martin Karplus; Fiscal Year: 2011
  5. DNA Mismatch and Double-Strand Break Repair
    Martin G Marinus; Fiscal Year: 2010
  6. Structure and Function of DNA Polymerase I of E.coli
    NIGEL DAVID GRINDLEY; Fiscal Year: 2010
  7. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2003
  8. Controlling Large DNA Fragments During Nanopore Sequencing
    MARK A AKESON; Fiscal Year: 2010
  9. MECHANISMS OF FIDELITY AND MUTAGENESIS
    Thomas Spratt; Fiscal Year: 2005
  10. CHEMISTRY AND BIOLOGY OF MALONDIALDEHYDE DNA ADDUCTS
    LAWRENCE MARNETT; Fiscal Year: 2004

Detail Information

Publications288 found, 100 shown here

  1. pmc The Saccharomyces telomere-binding protein Cdc13p interacts with both the catalytic subunit of DNA polymerase alpha and the telomerase-associated est1 protein
    H Qi
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 1014, USA
    Genes Dev 14:1777-88. 2000
    ..We propose that Cdc13p's interaction with Est1p promotes TG(1-3) strand lengthening by telomerase and its interaction with Pol1p promotes C(1-3)A strand resynthesis by DNA polymerase alpha...
  2. ncbi Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites
    Francene J Lemoine
    Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Cell 120:587-98. 2005
    ..We demonstrate that this pair of Ty elements constitutes a preferred site for double-strand DNA breaks when DNA replication is compromised, analogous to the fragile sites observed in mammalian chromosomes...
  3. pmc The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism
    Eugene Y Wu
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
    J Biol Chem 286:19758-67. 2011
    ..Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate...
  4. pmc Mcm10 and And-1/CTF4 recruit DNA polymerase alpha to chromatin for initiation of DNA replication
    Wenge Zhu
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
    Genes Dev 21:2288-99. 2007
    ..The discovery also adds to the connection between replication initiation and sister chromatid cohesion...
  5. pmc Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I
    Svitlana Y Berezhna
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 134:11261-8. 2012
    ..Using single-molecule Förster resonance energy transfer, we observed individual Escherichia coli DNA polymerase I (Klenow fragment) molecules performing substrate selection...
  6. pmc DNA polymerase I activity in Escherichia coli is influenced by spot 42 RNA
    D A Polayes
    Department of Physiological Chemistry, University of Wisconsin, Madison 53706
    J Bacteriol 170:2083-8. 1988
    We have shown that the level of DNA polymerase I (Pol I) activity in Escherichia coli is influenced by the level of a 109-nucleotide RNA, spot 42 RNA...
  7. ncbi Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
    D L Ollis
    Nature 313:762-6. 1985
    The 3.3-A resolution crystal structure of the large proteolytic fragment of Escherichia coli DNA polymerase I complexed with deoxythymidine monophosphate consists of two domains, the smaller of which binds zinc-deoxythymidine ..
  8. ncbi Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
    J R Kiefer
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
    Nature 391:304-7. 1998
    ..Here we present high-resolution crystal structures of a thermostable bacterial (Bacillus stearothermophilus) DNA polymerase I large fragments with DNA primer templates bound productively at the polymerase active site...
  9. pmc Conformational transitions in DNA polymerase I revealed by single-molecule FRET
    Yusdi Santoso
    Biological Physics Research Group, Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 107:715-20. 2010
    ..Using DNA polymerase I (Klenow fragment) labeled with both donor and acceptor fluorophores, we have employed single-molecule ..
  10. ncbi Positive correlation between DNA polymerase alpha-primase pausing and mutagenesis within polypyrimidine/polypurine microsatellite sequences
    Suzanne E Hile
    Department of Pathology, Gittlen Cancer Research Institute, The Pennsylvania State University College of Medicine, Hershey Medical Center, 500 University Drive, Hershey, PA 17033, USA
    J Mol Biol 335:745-59. 2004
    ..Thus, a positive correlation exists between polymerase alpha-primase pausing and mutagenesis within microsatellite DNA alleles...
  11. pmc Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication
    Jennifer M Allen
    Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, 1156 High Street Santa Cruz, CA 95060, USA
    Nucleic Acids Res 39:7020-33. 2011
    b>DNA polymerase I (pol I) processes RNA primers during lagging-strand synthesis and fills small gaps during DNA repair reactions...
  12. pmc Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion
    Johannes Hohlbein
    Biological Physics Research Group, Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    Nat Commun 4:2131. 2013
    ..Here, we combine single-molecule FRET with the use of DNA polymerase I and various fidelity mutants to highlight mechanisms by which active-site side chains influence the ..
  13. pmc Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I
    Radoslaw P Markiewicz
    Department of Chemistry, Wayne State University, Detroit, MI, USA
    Nucleic Acids Res 40:7975-84. 2012
    ..Our results show that the binding of Escherichia coli DNA polymerase I (Klenow fragment) to a primer-template is stabilized by the presence of the next correct dNTP, even in the ..
  14. ncbi A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta
    H Pelletier
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093 0506, USA
    Biochemistry 35:12762-77. 1996
    ....
  15. pmc In vivo consequences of putative active site mutations in yeast DNA polymerases alpha, epsilon, delta, and zeta
    Y I Pavlov
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Genetics 159:47-64. 2001
    ..This is supported by the observation that the pol3-Y708A mutation is recessive and its mutator effect is partially suppressed by disruption of the REV3 gene...
  16. pmc Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
    Sean J Johnson
    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 100:3895-900. 2003
    ..that were obtained by extension of a primed template directly in a crystal of the thermostable Bacillus DNA polymerase I. The 6-bp extension involves a 20-A translocation of the DNA duplex, representing the largest molecular ..
  17. pmc New tests for syphilis: rational design of a PCR method for detection of Treponema pallidum in clinical specimens using unique regions of the DNA polymerase I gene
    H Liu
    Centers for Disease Control and Prevention, 1600 Clifton Road, Mail Stop D13, Atlanta, GA 30333, USA
    J Clin Microbiol 39:1941-6. 2001
    ..PCR primers were designed based on two unique features of the DNA polymerase I gene (polA)...
  18. ncbi Ctf4 coordinates the progression of helicase and DNA polymerase alpha
    Hirokazu Tanaka
    Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama City, Kanagawa, Japan
    Genes Cells 14:807-20. 2009
    ..These results lead us to propose that Ctf4 is a key connector between DNA helicase and Pol alpha and is required for the coordinated progression of the replisome...
  19. ncbi The Pol32 subunit of DNA polymerase delta contains separable domains for processive replication and proliferating cell nuclear antigen (PCNA) binding
    Erik Johansson
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
    J Biol Chem 279:1907-15. 2004
    ....
  20. ncbi Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity
    Catherine M Joyce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Biochemistry 47:6103-16. 2008
    ..a FRET-based assay for the fingers-closing conformational transition that occurs when a binary complex of DNA polymerase I (Klenow fragment) with a primer-template binds a complementary dNTP and have used this and other fluorescence ..
  21. pmc Role of Escherichia coli DNA polymerase I in chromosomal DNA replication fidelity
    Karolina Makiela-Dzbenska
    Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, Warsaw, Poland
    Mol Microbiol 74:1114-27. 2009
    ..Instead, our data suggest that the additional errors produced by polAexo are created during the maturation of Okazaki fragments in the lagging strand...
  22. pmc 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases
    Sebastian Klinge
    Department of Biochemistry, University of Cambridge, Cambridge, UK
    EMBO J 28:1978-87. 2009
    ..Our combined findings provide a structural template for the common functional architecture of the three major replicative DNA polymerases...
  23. pmc Molecular architecture of the mouse DNA polymerase alpha-primase complex
    T Mizuno
    The Institute of Physical Research RIKEN, Wako, Saitama 351 0198, Japan
    Mol Cell Biol 19:7886-96. 1999
    ..Taken together, these results allow us to propose the first structural model for the DNA polymerase alpha-primase complex in terms of subunit assembly, domain structure, and stepwise formation at the cellular level...
  24. pmc Distinct roles of the active-site Mg2+ ligands, Asp882 and Asp705, of DNA polymerase I (Klenow fragment) during the prechemistry conformational transitions
    Oya Bermek
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    J Biol Chem 286:3755-66. 2011
    ..we developed previously, we have investigated the role of the carboxylate ligands, Asp(705) and Asp(882), of DNA polymerase I (Klenow fragment) in the early prechemistry steps that prepare the active site for catalysis...
  25. pmc Deoxy- and dideoxynucleotide discrimination and identification of critical 5' nuclease domain residues of the DNA polymerase I from Mycobacterium tuberculosis
    V Mizrahi
    Molecular Biology Unit, South African Institute for Medical Research and Department of Hematology, University of the Witwatersrand Medical School, Johannesburg, South Africa
    Nucleic Acids Res 24:4845-52. 1996
    The DNA polymerase I (PolI) from Mycobacterium tuberculosis (Mtb) was overproduced in Escherichia coli as an enzymatically active, recombinant protein with or without an N-terminal His-tag...
  26. pmc Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase alpha
    Kristi Kincaid
    Department of Chemistry and Biochemistry, University of Colorado Boulder, CO 80309, USA
    Nucleic Acids Res 33:2620-8. 2005
    ..analogues and tested them as substrates for DNA polymerase alpha (pol alpha) and Klenow fragment (exo-) of DNA polymerase I (Escherichia coli)...
  27. ncbi Cloning and sequence analysis of the gene encoding the DNA polymerase I from Mycobacterium tuberculosis
    P Huberts
    Department of Hematology, University of the Witwatersrand Medical School, Johannesburg, South Africa
    Gene 164:133-6. 1995
    The polA gene (encoding DNA polymerase I) from Mycobacterium tuberculosis was cloned using an internal gene segment probe generated by PCR amplification of genomic DNA [Mizrahi et al., Gene 136 (1993) 287-290]...
  28. pmc A conserved motif in the C-terminal tail of DNA polymerase α tethers primase to the eukaryotic replisome
    Mairi L Kilkenny
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
    J Biol Chem 287:23740-7. 2012
    ..These findings indicate that tethering of primase to the replisome by pol α is critical for the normal action of DNA replication forks in eukaryotic cells...
  29. pmc PolA1, a putative DNA polymerase I, is coexpressed with PerR and contributes to peroxide stress defenses of group A Streptococcus
    Chadia Toukoki
    Division of Infectious Diseases, Boston Children s Hospital, and Harvard Medical School, Boston, MA, USA
    J Bacteriol 195:717-25. 2013
    ..We now show that PerR is expressed from an operon encoding a putative DNA polymerase I (PolA1), among other GAS products...
  30. pmc Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus
    Michael Trostler
    Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309, USA
    Biochemistry 48:4633-41. 2009
    We used a series of dATP and dGTP analogues to determine how DNA polymerase I from Bacillus stearothermophilus (BF), a prototypical A family polymerase, uses N-1, N(2), N-3, and N(6) of purine dNTPs to differentiate between right and ..
  31. pmc Discrimination against purine-pyrimidine mispairs in the polymerase active site of DNA polymerase I: a structural explanation
    Dana T Minnick
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 99:1194-9. 2002
    ..Moreover, this same side chain enhances the stability of incoming correct dNTPs, such that loss of this interaction on removal of the side chain leads to lower selectivity against mismatches involving incoming pyrimidines...
  32. pmc Checkpoint activation regulates mutagenic translesion synthesis
    Mihoko Kai
    Department of Pathology, Stanford University School of Medicine, Stanford, California 94305 5324, USA
    Genes Dev 17:64-76. 2003
    ..Moreover, association of DinB with chromatin is dependent on functional Rad17, and DinB physically interacts with the checkpoint-clamp components Hus1 and Rad1. Thus, translesion synthesis is a part of the checkpoint response...
  33. pmc Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection
    Daniel R Garalde
    Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 286:14480-92. 2011
    ..The Klenow fragment of Escherichia coli DNA polymerase I (KF) achieves this through a series of conformational transitions that precede the chemical step of ..
  34. pmc The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis
    Andrei A Golosov
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Structure 18:83-93. 2010
    ..These roles are consistent with the high level of conservation of Y714 and the two glycine residues at these positions. It is likely that a corresponding mechanism is applicable to other polymerases...
  35. pmc Interaction of Saccharomyces Cdc13p with Pol1p, Imp4p, Sir4p and Zds2p is involved in telomere replication, telomere maintenance and cell growth control
    Chia Ling Hsu
    Institute of Biopharmaceutical Science, National Yang Ming University, Shih Pai 112, Taipei, Taiwan, Republic of China
    Nucleic Acids Res 32:511-21. 2004
    ..Together, our results provide evidence for the formation of a Cdc13p-mediated telosome complex through its N-terminal region that is involved in telomere maintenance, telomere length regulation and cell growth control...
  36. pmc Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA
    Kausiki Datta
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
    Biophys J 90:1739-51. 2006
    ..In the case of Klenow, surface area burial can account for only about half of the DeltaCp of binding...
  37. ncbi Structure of the replicating complex of a pol alpha family DNA polymerase
    M C Franklin
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
    Cell 105:657-67. 2001
    ..The duplex product DNA orientation differs by 40 degrees between the polymerizing mode and editing mode structures. The role of the thumb in this DNA motion provides a model for editing in the pol alpha family...
  38. ncbi Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism
    M R Sawaya
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0506, USA
    Biochemistry 36:11205-15. 1997
    ..Such a 90 degrees kink may be a mechanistic feature employed by any polymerase involved in filling gaps to completion...
  39. ncbi Identification of hydrogen bonds between Escherichia coli DNA polymerase I (Klenow fragment) and the minor groove of DNA by amino acid substitution of the polymerase and atomic substitution of the DNA
    T E Spratt
    American Health Foundation, 1 Dana Road, Valhalla, New York 10595, USA
    Biochemistry 40:2647-52. 2001
    ..we have studied these interactions using a combination of site-specific mutagenesis of Escherichia coli DNA polymerase I (Klenow fragment) and atomic substitution of the DNA...
  40. ncbi TopBP1 and DNA polymerase alpha-mediated recruitment of the 9-1-1 complex to stalled replication forks: implications for a replication restart-based mechanism for ATR checkpoint activation
    Shan Yan
    The Biological Laboratories, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
    Cell Cycle 8:2877-84. 2009
    ....
  41. ncbi The role of single-stranded DNA and polymerase alpha in establishing the ATR, Hus1 DNA replication checkpoint
    Zhongsheng You
    Division of Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0349, USA
    J Biol Chem 277:27088-93. 2002
    ..In addition, chromatin association of XATR and Xhus1 are independent of each other. Finally, like XATR, Xhus1 associates with chromatin in unperturbed S phase and dissociates from chromatin following completion of DNA replication...
  42. pmc Nuclear distribution and chromatin association of DNA polymerase alpha-primase is affected by TEV protease cleavage of Cdc23 (Mcm10) in fission yeast
    Xiaowen Yang
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX13PS, UK
    BMC Mol Biol 6:13. 2005
    ..Cdc23/Mcm10 is required for the initiation and elongation steps of DNA replication but its biochemical function is unclear. Here, we probe its function using a novel approach in fission yeast, involving Cdc23 cleavage by the TEV protease...
  43. pmc Reverse transcriptase activity innate to DNA polymerase I and DNA topoisomerase I proteins of Streptomyces telomere complex
    Kai Bao
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 101:14361-6. 2004
    ..Within one of these motifs, and essential to the RT function of Streptomyces TopA, is an Asp-Asp doublet sequence required also for the RT activities of human immunodeficiency virus and eukaryotic cell telomerases...
  44. ncbi Mitochondrial DNA defects in Saccharomyces cerevisiae caused by functional interactions between DNA polymerase gamma mutations associated with disease in human
    Enrico Baruffini
    Department of Genetics, Biology of Microorganisms, Anthropology, Evolution, University of Parma, 43100 Parma, Italy
    Biochim Biophys Acta 1772:1225-35. 2007
    ..Thus, the human E1143G mutation is not a true polymorphism...
  45. pmc Active site substitutions delineate distinct classes of eubacterial flap endonuclease
    Lee M Allen
    The University of Sheffield School of Medicine and Biomedical Sciences, Henry Wellcome Laboratories for Medical Research, Department of Infection and Immunity, Sheffield S102RX, UK
    Biochem J 418:285-92. 2009
    ....
  46. pmc Local conformations and competitive binding affinities of single- and double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases
    Kausiki Datta
    Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon 97403 1229, USA
    J Biol Chem 284:17180-93. 2009
    ..These distributions and the conformational changes in the P/T DNA that occur during template-directed DNA synthesis in solution illuminate some of the mechanisms used by DNA polymerases to assure the fidelity of DNA synthesis...
  47. pmc mip1 containing mutations associated with mitochondrial disease causes mutagenesis and depletion of mtDNA in Saccharomyces cerevisiae
    Jeffrey D Stumpf
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes ofHealth, Research, Triangle Park, NC 27709, USA
    Hum Mol Genet 19:2123-33. 2010
    ....
  48. ncbi Evaluating the contribution of base stacking during translesion DNA replication
    Edmunds Z Reineks
    Department of Pharmacology and the Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Biochemistry 43:393-404. 2004
    ..These kinetic differences are interpreted with regard to the differences in various structural components between the two enzymes and are consistent with the proposed model for DNA polymerization...
  49. ncbi Predicting the contribution of novel POLG mutations to human disease through analysis in yeast model
    Enrico Baruffini
    Department of Genetics, University of Parma, Parma, Italy
    Mitochondrion 11:182-90. 2011
    ..Finally, a significant rescue of extended mutability has been observed for several dominant mutations by treatment with mitochondrial antioxidants...
  50. ncbi Construction and validation of a yeast model system for studying in vivo the susceptibility to nucleoside analogues of DNA polymerase gamma allelic variants
    Enrico Baruffini
    Department of Genetics, Biology of Microorganisms, Anthropology, Evolution, University of Parma, 43124 Parma, Italy
    Mitochondrion 10:183-7. 2010
    ..We showed that mutant Mip1p(R964C) and possibly Mip1p(E1143G) are more sensitive to stavudine, and that stavudine has the potential to cause mitochondrial toxicity in heterozygous subjects harboring recessive mutations...
  51. ncbi In vivo mutagenesis by Escherichia coli DNA polymerase I. Ile(709) in motif A functions in base selection
    A Shinkai
    Department of Pathology, Joseph Gottstein Memorial Cancer Research Laboratory, University of Washington, Seattle, WA 98195-7705, USA
    J Biol Chem 276:46759-64. 2001
    The fidelity of DNA replication by Escherichia coli DNA polymerase I (pol I) was assessed in vivo using a reporter plasmid bearing a ColE1-type origin and an ochre codon in the beta-lactamase gene...
  52. ncbi A conserved Hsp10-like domain in Mcm10 is required to stabilize the catalytic subunit of DNA polymerase-alpha in budding yeast
    Robin M Ricke
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
    J Biol Chem 281:18414-25. 2006
    ..The high degree of evolutionary conservation of this domain implies that stabilizing Cdc17 may be a conserved function of Mcm10...
  53. ncbi Mechanism for N-acetyl-2-aminofluorene-induced frameshift mutagenesis by Escherichia coli DNA polymerase I (Klenow fragment)
    Joshua P Gill
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 44:15387-95. 2005
    ..extension and gel shift binding assays were used to study the mechanism of bypass by the Escherichia coli DNA polymerase I (Klenow fragment) in the presence of these templates...
  54. ncbi DNA polymerase I of Mycobacterium tuberculosis: functional role of a conserved aspartate in the hinge joining the M and N helices
    Cindy Jo Arrigo
    Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry, New Jersey Medical School and Graduate School of Biomedical Sciences, Newark, New Jersey 07103, USA
    J Biol Chem 277:1653-61. 2002
    The highly conserved GXD sequence present in the Mycobacterium tuberculosis DNA polymerase I corresponds to a hinge region in the finger subdomain connecting M and N helices of Escherichia coli pol I...
  55. ncbi Sequence effects on translesion synthesis of an aminofluorene-DNA adduct: conformational, thermodynamic, and primer extension kinetic studies
    V G Vaidyanathan
    Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
    Biochemistry 51:1983-95. 2012
    ..effect on nucleotide insertion efficiencies catalyzed by the Klenow fragment (exonuclease-deficient) of DNA polymerase I. Our (19)F NMR/ICD/DSC results showed that AF in the CG*A duplex sequence adopts a greater population of S-..
  56. ncbi Mcm10 regulates the stability and chromatin association of DNA polymerase-alpha
    Robin M Ricke
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
    Mol Cell 16:173-85. 2004
    ..During elongation, Mcm10 is required for the presence of polalpha at replication forks and may coordinate DNA synthesis with DNA unwinding by the Mcm2-7 complex...
  57. ncbi Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli
    C A Brautigam
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520 8114, USA
    Biochemistry 38:696-704. 1999
    ..in conjunction with various metal ions at the 3'-5' exonucleolytic active site of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli...
  58. pmc Antimutator alleles of yeast DNA polymerase gamma modulate the balance between DNA synthesis and excision
    Francoise Foury
    Institut des Sciences de la Vie, Universite Catholique de Louvain, Louvain la Neuve, Belgium
    PLoS ONE 6:e27847. 2011
    ..These elements modulate in a subtle manner the balance between DNA polymerization and excision...
  59. ncbi Effects of benzo[a]pyrene DNA adducts on Escherichia coli DNA polymerase I (Klenow fragment) primer-template interactions: evidence for inhibition of the catalytically active ternary complex formation
    Y O Alekseyev
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 40:2282-90. 2001
    ..of this process, a gel-retardation assay was used to measure the dissociation constants for the binding of DNA polymerase I (Klenow fragment) (KF) to the primer-templates containing a (+)-trans- or (+)-cis-B[a]P-N(2)-dG adduct...
  60. pmc Unexpected role for Helicobacter pylori DNA polymerase I as a source of genetic variability
    María Victoria García-Ortíz
    CEA, Institut de Radiobiologie Cellulaire et Moleculaire, UMR 217 CNRS CEA, Fontenay aux Roses, France
    PLoS Genet 7:e1002152. 2011
    ..This study provides evidence for an unexpected role of DNA polymerase I in generating genomic plasticity.
  61. pmc A key role for Ctf4 in coupling the MCM2-7 helicase to DNA polymerase alpha within the eukaryotic replisome
    Agnieszka Gambus
    Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK
    EMBO J 28:2992-3004. 2009
    ..These findings indicate that coupling MCM2-7 to replicative polymerases is an important feature of the regulation of chromosome replication in eukaryotes, and highlight a key role for Ctf4 in this process...
  62. pmc Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis
    Joseph P Torella
    Department of Physics and Biological Physics Research Group, University of Oxford, Oxford, United Kingdom
    Biophys J 100:1568-77. 2011
    ..Using BVA, we analyzed the fingers-closing transition in the Klenow fragment of Escherichia coli DNA polymerase I and identified substantial dynamics in polymerase complexes formed prior to nucleotide incorporation; these ..
  63. pmc Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism
    L S Beese
    Department of Molecular Biophysics, Yale University, New Haven, CT 06511
    EMBO J 10:25-33. 1991
    The refined crystal structures of the large proteolytic fragment (Klenow fragment) of Escherichia coli DNA polymerase I and its complexes with a deoxynucleoside monophosphate product and a single-stranded DNA substrate offer a detailed ..
  64. ncbi Detection of single- and double-strand DNA breaks after traumatic brain injury in rats: comparison of in situ labeling techniques using DNA polymerase I, the Klenow fragment of DNA polymerase I, and terminal deoxynucleotidyl transferase
    - Clark RSB
    Department of Anesthesiology, The Safar Center for Resuscitation Research and the Brain Trauma Research Center, University of Pittsburgh School of Medicine, Pennsylvania 15260, USA
    J Neurotrauma 18:675-89. 2001
    ..Available techniques for the in situ identification of DNA damage include DNA polymerase I-mediated biotin-dATP nick-translation (PANT), the Klenow fragment of DNA polymerase I-mediated biotin-dATP ..
  65. pmc Drosophila Ctf4 is essential for efficient DNA replication and normal cell cycle progression
    Justin A Gosnell
    Department of Biology, East Carolina University, Greenville, NC 27858, USA
    BMC Mol Biol 12:13. 2011
    ..As such, understanding the role of Ctf4 within the context of a multicellular organism will be integral to our understanding of its potential role in developmental and disease processes...
  66. ncbi Structure of DNA polymerase I Klenow fragment bound to duplex DNA
    L S Beese
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
    Science 260:352-5. 1993
    Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to ..
  67. ncbi Inhibitory effect of sulfoquinovosyl diacylglycerol on prokaryotic DNA polymerase I activity and cell growth of Escherichia coli
    Tomoyuki Furukawa
    Division of Plant Biotechnology, Tissue Engineering Research Center, Tokyo University of Science, Noda, Chiba, Japan
    J Oleo Sci 56:43-7. 2006
    ..and found that the fraction inhibited the activities of prokaryotic DNA polymerase I from Escherichia coli (E. coli) and cell growth of E. coli...
  68. ncbi NtPolI-like1 and NtPolI-like2, bacterial DNA polymerase I homologs isolated from BY-2 cultured tobacco cells, encode DNA polymerases engaged in DNA replication in both plastids and mitochondria
    Yuriko Ono
    Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
    Plant Cell Physiol 48:1679-92. 2007
    Two cDNAs encoding homologs of bacterial DNA polymerase I were isolated from cultured tobacco (Nicotiana tabacum) BY-2 cells, and the corresponding genes were named NtPolI-like1 and NtPolI-like2...
  69. pmc DNA polymerase I and the bypassing of RecA dependence of constitutive stable DNA replication in Escherichia coli rnhA mutants
    Y Cao
    Cancer Center, University of New Mexico School of Medicine, Albuquerque 87131
    J Bacteriol 175:7247-53. 1993
    ..mutant revealed that the insertion occurs at the 3' end of the coding region of the polA gene, which encodes DNA polymerase I. The mutant allele, designated polA25::miniTn10spc, is expected to abolish the polymerization activity but ..
  70. ncbi Sequential proton NMR resonance assignments, circular dichroism, and structural properties of a 50-residue substrate-binding peptide from DNA polymerase I
    G P Mullen
    Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
    Arch Biochem Biophys 301:174-83. 1993
    Peptide I, a 50-amino acid synthetic peptide based on residues 728 to 777 of DNA polymerase I, binds dNTP substrates and duplex DNA (G. Mullen, P. Shenbagamurthi, and A.S. Mildvan, J. Biol. Chem. 264, 19637-19647, 1988)...
  71. ncbi Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution
    J R Kiefer
    Department of Biochemistry, Duke University Medical Centre, Durham, NC 27710, USA
    Structure 5:95-108. 1997
    ..In order to learn about Pol I function and the basis of thermostability, we undertook structural studies of a new thermostable DNA polymerase...
  72. ncbi Heat-stable DNA polymerase I large fragment resolves hairpin structure in DNA sequencing
    S Y Ye
    Shanghai Institute of Biochemistry, Academia Sinica
    Sci Sin B 30:503-6. 1987
    ..When the sequencing reaction was carried out at this temperature, the hairpin structure was resolved and the sequencing gels obtained were satisfactory...
  73. pmc Requirement for the polymerization and 5'-->3' exonuclease activities of DNA polymerase I in initiation of DNA replication at oriK sites in the absence of RecA in Escherichia coli rnhA mutants
    Y Cao
    Cancer Center, University of New Mexico School of Medicine, Albuquerque 87131
    J Bacteriol 175:7254-9. 1993
    ..in constitutive stable DNA replication (cSDR) can be bypassed by derepression of the LexA regulon and that DNA polymerase I (DNA PolI) is essential for this Rip (RecA-independent process) pathway of cSDR (Y. Cao, R. R. Rowland, and T...
  74. ncbi Effects of DNA mismatches on binding affinity and kinetics of polymerase-DNA complexes as revealed by surface plasmon resonance biosensor
    Pui Yan Tsoi
    Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
    Analyst 128:1169-74. 2003
    ..The results also demonstrated that SPR biosensors may be used as a sensitive technique for studying molecular recognition events such as single-base discrimination involved in protein-DNA interaction...
  75. ncbi Overexpression of the RNR1 gene rescues Saccharomyces cerevisiae mutants in the mitochondrial DNA polymerase-encoding MIP1 gene
    N Lecrenier
    Unite de Biochimie Physiologique, Universite Catholique de Louvain, Louvain la Neuve, Belgium
    Mol Gen Genet 249:1-7. 1995
    ..Our results show that an increased supply of dNTPs in mitochondria can stimulate the mtDNA polymerase activity and indicate that the dNTP concentration may be rate limiting for the replication of mtDNA...
  76. ncbi Significance of nucleobase shape complementarity and hydrogen bonding in the formation and stability of the closed polymerase-DNA complex
    L Dzantiev
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 40:3215-21. 2001
    ..and the geometric shape of the base pair that forms during this process were studied using Escherichia coli DNA polymerase I (Klenow fragment, 3'-exonuclease deficient) and natural dNTPs or non-hydrogen-bonding dNTP analogues...
  77. ncbi Escherichia coli DNA polymerase I (Klenow fragment) uses a hydrogen-bonding fork from Arg668 to the primer terminus and incoming deoxynucleotide triphosphate to catalyze DNA replication
    Aviva S Meyer
    Institute for Cancer Prevention, American Health Foundation Cancer Center, Valhalla, New York 10595, USA
    J Biol Chem 279:33043-6. 2004
    ..In particular, Arg668 of Escherichia coli DNA polymerase I (Klenow fragment) makes a critical contact with the N-3-position of guanine at the primer terminus...
  78. pmc Interaction of human DNA polymerase alpha and DNA polymerase I from Bacillus stearothermophilus with hypoxanthine and 8-oxoguanine nucleotides
    Jennifer N Patro
    Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309, USA
    Biochemistry 48:8271-8. 2009
    ..N(6) and, to a lesser extent, N1 help drive hypoxanthine:adenine base-pair formation by BF. The mechanistic implications of these results showing that different polymerases interact very differently with base lesions are discussed...
  79. ncbi A pre-equilibrium before nucleotide binding limits fingers subdomain closure by Klentaq1
    Paul J Rothwell
    Institute of Structural Molecular Biology, Birkbeck College and University College London, Malet Street, London, WC1E 7HX, United Kingdom
    J Biol Chem 282:28884-92. 2007
    ..As the only difference between the (E x p/t) complexes is the templating base, it would suggest an important role for the templating base in initial ground state selection...
  80. ncbi Preliminary characterization of a thermostable DNA polymerase I from a mesophilic Bacillus sphaericus strain C3-41
    Han Bei
    Wuhan Institute of Virology, Chinese Academy of Science, Wuhan 430071, China
    Arch Microbiol 186:203-9. 2006
    A thermostable DNA polymerase I from a mesophilic Bacillus sphaericus strain C3-41 was characterized in this study. The polI was cloned, sequenced and over-expressed in Escherichia coli...
  81. pmc Tipin/Tim1/And1 protein complex promotes Pol alpha chromatin binding and sister chromatid cohesion
    Alessia Errico
    Genome Stability and Cell Cycle Control Groups, Cancer Research UK, Clare Hall Laboratories, South Mimms, Herts, UK
    EMBO J 28:3681-92. 2009
    ..These data indicate that Tipin/Tim1/And1 form a complex that links stabilization of replication fork and establishment of sister chromatid cohesion...
  82. pmc Alternative mechanisms for coordinating polymerase alpha and MCM helicase
    Chanmi Lee
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Mol Cell Biol 30:423-35. 2010
    ....
  83. pmc Patch length of localized repair events: role of DNA polymerase I in mutY-dependent mismatch repair
    J P Radicella
    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
    J Bacteriol 175:7732-6. 1993
    ..The phenotype of a mutant defective in DNA polymerase I shows that this enzyme plays a significant, though not an essential, role in the in vivo repair of apurinic ..
  84. ncbi A conformational change in E. coli DNA polymerase I (Klenow fragment) is induced in the presence of a dNTP complementary to the template base in the active site
    L Dzantiev
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 39:356-61. 2000
    ..experiments were performed to detect this conformational change in the structure of the exonuclease-deficient DNA polymerase I (Klenow fragment)...
  85. pmc The B-subunit of DNA polymerase alpha-primase associates with the origin recognition complex for initiation of DNA replication
    Masashi Uchiyama
    Department of Pathology, Stanford University School of Medicine, MED CTR R 272, Stanford, CA 94305 5324, USA
    Mol Cell Biol 24:7419-34. 2004
    ..Our results thus suggest a role for the recruited Polalpha-primase in the initiation of both leading and lagging strands at the replication origins...
  86. pmc Dividing the workload at a eukaryotic replication fork
    Thomas A Kunkel
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, 111 T W Alexander Drive, National Institute of Environmental Health Sciences, National Institute of Health, DHHS, Research Triangle Park, NC 27709, USA
    Trends Cell Biol 18:521-7. 2008
    ..We also review earlier studies in light of this model and then consider prospects for future investigations of possible variations on this simple division of labor...
  87. ncbi Deoxynucleoside triphosphate and pyrophosphate binding sites in the catalytically competent ternary complex for the polymerase reaction catalyzed by DNA polymerase I (Klenow fragment)
    M Astatke
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
    J Biol Chem 270:1945-54. 1995
    ..Mutations of Arg682, His734, and Tyr766 affect the binding of DNA, suggesting that these mutations, whose effect on dNTP binding is small, may influence dNTP binding indirectly via the positioning of the DNA template-primer...
  88. pmc Genetic analyses of Schizosaccharomyces pombe dna2(+) reveal that dna2 plays an essential role in Okazaki fragment metabolism
    H Y Kang
    National Creative Research Initiative Center for Cell Cycle Control, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Changan Ku Suwon, Kyunggi Do, 440 746, Korea
    Genetics 155:1055-67. 2000
    ..We propose that dna2(+) acts as a central protein to form a complex with other proteins required to coordinate the multienzyme process for Okazaki fragment elongation and maturation...
  89. ncbi Mechanistic insights into replication across from bulky DNA adducts: a mutant polymerase I allows an N-acetyl-2-aminofluorene adduct to be accommodated during DNA synthesis
    Samer Lone
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 42:3826-34. 2003
    ..A model is proposed in which the looser active site of the mutant is able to better accommodate the AAF adduct...
  90. pmc DNA polymerase I is not required for replication of linear chromosomes in streptomyces
    Tzu Wen Huang
    Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Shih Pai, Taipei 112, Taiwan
    J Bacteriol 190:755-8. 2008
    Both polA (encoding DNA polymerase I; Pol I) and a paralog were deleted from Streptomyces strains. Despite the UV sensitivity and slow growth caused by the DeltapolA mutation, the double mutant was viable...
  91. ncbi Control of complex formation of DNA polymerase alpha-primase and cell-free DNA replication by the C-terminal amino acids of the largest subunit p180
    R W P Smith
    Abteilung Biochemie, Institut fur Molekulare Biotechnologie, Abteilung Biochemie, Beutenbergstr 11, D 07745, Jena, Germany
    FEBS Lett 527:143-6. 2002
    ..Furthermore, we demonstrate that exchanging these residues to those of mouse origin can only partially rescue the SV40 DNA replication activity of DNA polymerase alpha-primase...
  92. ncbi The conserved active site motif A of Escherichia coli DNA polymerase I is highly mutable
    A Shinkai
    Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology, University of Washington, Seattle, Washington 98195-7705, USA
    J Biol Chem 276:18836-42. 2001
    Escherichia coli DNA polymerase I participates in DNA replication, DNA repair, and genetic recombination; it is the most extensively studied of all DNA polymerases...
  93. ncbi DNA polymerase I-mediated translesion synthesis in RecA-independent DNA interstrand cross-link repair in E. coli
    Laura Zietlow
    The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, Nebraska 68198 6805, USA
    Biochemistry 47:5460-4. 2008
    ..We demonstrated that the Klenow fragment (DNA polymerase I) performs translesion synthesis on this model substrate...
  94. ncbi The DNA polymerase alpha-primase complex: multiple functions and interactions
    Marco Muzi-Falconi
    Dipartimento di Genetica e di Biologia dei Microrganismi, Universita degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
    ScientificWorldJournal 3:21-33. 2003
    ..However, pol-prim seems to play additional roles in other complex cellular processes, such as the response to DNA damage, telomere maintenance, and the epigenetic control of higher order chromatin assembly...
  95. ncbi Genetic characterization of early amber mutations in the Escherichia coli polA gene and purification of the amber peptides
    W S Kelley
    J Mol Biol 164:529-60. 1983
    ..The peptides are immunologically related and react weakly but specifically with antibody to whole DNA polymerase I. In their purified form the peptides are less heat-labile than the whole enzyme or the Klenow fragment ..
  96. pmc The roles of Klenow processing and flap processing activities of DNA polymerase I in chromosome instability in Escherichia coli K12 strains
    Yuki Nagata
    Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980 8578, Japan
    Genetics 160:13-23. 2002
    ..The DeltapolA strain, which is deficient in both Klenow domain and 5' --> 3' exonuclease domain of DNA polymerase I, shows a marked increase in categories 1-4...
  97. pmc Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns
    J Horlacher
    Bio Organische Chemie, Eidgenössiche Technische Hochschule Zurich, Switzerland
    Proc Natl Acad Sci U S A 92:6329-33. 1995
    ..These results are discussed in light of the crystal structure for pol beta and general considerations of how polymerases must interact with an incoming base pair to faithfully copy genetic information...
  98. ncbi Chlamydial DNA polymerase I can bypass lesions in vitro
    Xipeng Liu
    College of Life Sciences and Technology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
    Biochem Biophys Res Commun 345:1083-91. 2006
    We found that DNA polymerase I from Chlamydiophila pneumoniae AR39 (CpDNApolI) presents DNA-dependent DNA polymerase activity, but has no detectable 3' exonuclease activity...
  99. ncbi Ctf4p facilitates Mcm10p to promote DNA replication in budding yeast
    Jiafeng Wang
    School of Life Sciences, Sun Yat Sen University, Guangzhou 510275, China
    Biochem Biophys Res Commun 395:336-41. 2010
    ..Finally, deletion of CTF4 destabilizes Mcm10p and Pol alpha in both mcm10-1 and MCM10 cells. These data indicate that Ctf4p facilitates Mcm10p to promote the DNA replication...
  100. ncbi Escherichia coli DNA polymerase I. Sequence characterization and secondary structure prediction
    W E Brown
    J Biol Chem 257:1965-72. 1982
    The primary sequence of DNA polymerase I from Escherichia coli K12 as derived from the DNA sequence (Joyce, C. M., Kelley, W. S., and Grindley, N. D. F. (1982) J. Biol. Chem. 257, 1958-1964) has been verified...
  101. pmc A novel DNA polymerase homologous to Escherichia coli DNA polymerase I from a higher plant, rice (Oryza sativa L.)
    Seisuke Kimura
    Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278 8510, Japan
    Nucleic Acids Res 30:1585-92. 2002
    ..These properties indicated that OsPolI-like is a novel plant DNA polymerase. The function of OsPolI-like is discussed in relation to plastid maturation...

Research Grants48

  1. Group A Streptococcus responses to oxidative stress
    Ioannis Gryllos; Fiscal Year: 2010
    ..Of these, polA.1 encodes DNA polymerase I, which has been implicated in DNA damage repair in several bacterial species, as well as in virulence of ..
  2. Hoogsteen base pairing in human DNA polymerase iota
    Satya Prakash; Fiscal Year: 2010
    The long term objectives are to delineate the action mechanisms of human DNA polymerase i (Poll) on undamaged and damaged DNAs...
  3. A Nanopore-based Instrument for Single Molecule Analysis of DNA-binding Proteins
    WILLIAM BRUCE DUNBAR; Fiscal Year: 2010
    ..molecule analysis of polynucleotide-binding proteins, using the Klenow fragment (KF) of Escherichia coli DNA polymerase I as the model enzyme...
  4. Conformational Change in Molecular Biology
    Martin Karplus; Fiscal Year: 2011
    ..The two molecular motors Fi-ATPase and DNA polymerase I (pol I) will be investigated...
  5. DNA Mismatch and Double-Strand Break Repair
    Martin G Marinus; Fiscal Year: 2010
    ..We recently showed that cisplatin-induced recombination and double-strand break repair require DNA polymerase I and in the fourth aim, we will determine its role in these processes by inactivating either its exonuclease ..
  6. Structure and Function of DNA Polymerase I of E.coli
    NIGEL DAVID GRINDLEY; Fiscal Year: 2010
    ..DNA polymerases are also a crucial part of many of the diagnostic tools used in modern medicine and will be pivotal in the development of new DNA sequencing technologies for diagnostic purposes. ..
  7. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2003
    ..During the last grant period, four protein systems involved in these processes were studied: the DNA polymerase I from Thermus aquaticus, Escherichia coli single strand DNA-binding protein SSB, and the E...
  8. Controlling Large DNA Fragments During Nanopore Sequencing
    MARK A AKESON; Fiscal Year: 2010
    ..Our work will focus on T7 DNA polymerase (T7 DNApol) and the Klenow fragment of DNA polymerase I (KF), coupled to the alpha hemolysin biopore (1-HL). There are three aims: Aim 1...
  9. MECHANISMS OF FIDELITY AND MUTAGENESIS
    Thomas Spratt; Fiscal Year: 2005
    ..Two polymerases will be studied, DNA polymerase I of E. coli and mammalian DNA polymerase beta...
  10. CHEMISTRY AND BIOLOGY OF MALONDIALDEHYDE DNA ADDUCTS
    LAWRENCE MARNETT; Fiscal Year: 2004
    ..of bypass of M1G, N2- oxopropenyl-G, M1A, and an N2-G-N2-G trimethylene cross-link by the Klenow fragment of DNA polymerase I and by DNA polymerase V; and 4) determine the effects of M1G, N2-oxopropenyl-G, M1A, and an N2-G-N2-G ..
  11. CELLULAR DNA REPAIR MECHANISMS AND MUTAGENESIS
    Robb Moses; Fiscal Year: 1992
    ..of these cells by development of an in vitro system for repair synthesis in which the holoenzyme containing DNA polymerase I is functional...
  12. High Throughput Screen for Novel DNA Polymerases
    PHILLIP BRUMM; Fiscal Year: 2005
    ..coli, and are stably expressed in E. coli. In E. coli, either DNA polymerase I, the product of the polA gene, or recombinase A, the product of the recA gene, is required for growth of E...
  13. PROTEIN-DNA INTERACTIONS--AFFINITY LABELING APPROACH
    MICHAEL DOUGHTY; Fiscal Year: 1992
    ..b>DNA polymerase I is employed as a test system to demonstrate the effectiveness of our approach in complimenting kinetic, ..
  14. TARGETING DRUG EVASION BY HIV REVERSE TRANSCRIPTASE
    LAWRENCE LOEB; Fiscal Year: 1999
    ..We have recently established that HIV RT can substitute for DNA polymerase I in promoting growth of E. coli. Furthermore, HIV RT-dependent growth of E...
  15. Effects of Formamidopyrimidine Lesions on DNA
    Marc Greenberg; Fiscal Year: 2006
    ..abstract_text> ..
  16. Genetic Recombination and Chromosome Rearrangements
    LORRAINE SYMINGTON; Fiscal Year: 2007
    ..Much of the conference will be devoted to topics of concern both to the National Cancer Institute and to the Institute of Environmental and Health Sciences. [unreadable] [unreadable] [unreadable] [unreadable]..
  17. Mechanisms of Double-strand Break Repair in Yeast
    LORRAINE SYMINGTON; Fiscal Year: 2009
    ..The last aim includes in vitro studies to identify preferred DNA substrates for Rad55:Rad57 binding and stabilization of the Rad51 nucleoprotein by Rad55:Rad57 in the presence or absence of Srs2. ..
  18. DNA replication, DNA repair and microsatellite stability
    Kristin Eckert; Fiscal Year: 2009
    ..Microsatellite allele lengths can directly affect gene expression. As microsatellites are polymorphic in human populations, this effect on gene regulation may be an important factor contributing to individual cancer risk. ..
  19. DNA Damage and Neurodegeneration in Cockayne Syndrome
    James Cleaver; Fiscal Year: 2009
    ..Successful conclusion of these studies will expand our knowledge of mechanisms of neurodegeneration and lay groundwork for development of therapeutic approaches for CS patients. ..
  20. DNA REPAIR ACTIVITIES OF HUMAN ABASIC ENDONUCLEASE
    Daniel Barsky; Fiscal Year: 2001
    ..The studies described within will go a long way towards defining the repair activities of Ape and will help understand the intracacies of two critical DNA repair pathways. ..
  21. Non-natural Nucleoside Inhibitors of DNA Polymerases
    Anthony Berdis; Fiscal Year: 2009
    ..This knowledge will facilitate the development of new drugs as the repertoire of targets becomes more differentiated. ..
  22. Regulation of DNA Replication and Repair
    Mark Sutton; Fiscal Year: 2008
    ..abstract_text> ..
  23. Defining Molecular Markers for Tumor Hypoxia
    QUYNH THU XUAN LE; Fiscal Year: 2010
    ..abstract_text> ..
  24. Mechanisms of Adaptive Amplification
    Philip J Hastings; Fiscal Year: 2010
    ....
  25. MOUSE MODELS OF DNA REPAIR - DEFECTIVE HUMAN DISEASES
    Errol Friedberg; Fiscal Year: 2011
    ..abstract_text> ..
  26. Post-translational Modifications of High-mobility Group Proteins
    Yinsheng Wang; Fiscal Year: 2009
    ..In addition, the outcome of proposed studies may provide important molecular biomarkers for cancer diagnosis and prognosis. ..
  27. Combined Substrate Polymerase Inhibitors
    MICHAEL DOUGHTY; Fiscal Year: 2007
    ..These targets include DNA polymerase, reverse transcriptases, viral RNA dependent DNA polymerases, and inosine monophosphate dehydrogenase, a control enzyme in the cell synthesis of GMP. [unreadable] [unreadable] [unreadable]..
  28. High-throughput Sequencing by Pyrosequencing
    Mostafa Ronaghi; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  29. ROS-induced Nucleic Acid Damage
    Yinsheng Wang; Fiscal Year: 2006
    ..The outcome of the research proposed here will provide better understanding of the biological consequences of oxidative damage on nucleic acids by ROS and their implications in human health. ..
  30. DNA REPAIR AND ITS RELATIONSHIP TO CARCINOGENESIS
    Errol Friedberg; Fiscal Year: 2001
    ..There is reason to believe that the proteins encoded by these genes operate in a different chromatin-modulating complex, and it is proposed to isolate and characterize this putative complex as well. ..
  31. HYPOTRICH GENOME IN DEVELOPMENT AND EVOLUTION
    David Prescott; Fiscal Year: 2001
    ..The experiments deal with the general problem of how an organism can manipulate its own DNA. ..
  32. DNA REPAIR AND CANCER PRONE HEREDITARY HUMAN DISEASE
    Errol Friedberg; Fiscal Year: 2002
    ....
  33. MECHANISM OF DNA-PROTEIN INTERACTION IN DNA REPLICATION
    Subhasis Biswas; Fiscal Year: 2002
    ..Biochemical studies of purified helicase A will characterize the nucleotidase and helicase activities of this protein. ..
  34. Conference--CSHL on Quantitative Biology
    Bruce Stillman; Fiscal Year: 2003
    ..The annual Symposia will continue to be planned to further the progress of advancements in biomedical science. This proposal requests support for 2003 to cover the 68th Cold Spring Harbor Symposium. ..
  35. Is Basonuclin essential for Oogenesis
    Hung Tseng; Fiscal Year: 2004
    ..Sub aim 1 will use an RNAi approach to reduce the amount of basonuclin in oocytes; Sub aim 2 will use the Cre recombinase to knockout [the] basonuclin gene in oocytes. ..
  36. Repression of Oral Virus by Interferon & Nuclear Bodies
    Jerry Taylor; Fiscal Year: 2004
    ..This understanding should allow the development of strategies for treatment of secondary viral infections in the oral cavity of HIV-infected individuals that enhance or mimic these repressive activities. ..
  37. Genetic Recombination/Genomic Rearrangements Conference
    LORRAINE SYMINGTON; Fiscal Year: 2005
    ..abstract_text> ..
  38. Innate Corneal Cell Immunity to Virus Infection
    Jerry Taylor; Fiscal Year: 2004
    ..This knowledge may be utilized to enhance this innate antiviral response and thereby limit initial and recurrent viral infections in the eye. ..
  39. EUKARYOTIC DNA REPLICATION CONFERENCE
    Bruce Stillman; Fiscal Year: 2005
    ..The subsequent meetings (2003 and 2005) will follow a similar format which will include topics that are highly relevant to the current research at the time of the meeting. ..
  40. CSHL Symposium on Quantitative Biology
    Bruce Stillman; Fiscal Year: 2004
    ..The meeting will address the molecular basis of epigenetic phenomena and their relationship to chromatin and chromosome structure and function. ..
  41. COLD SPRING HARBOR SYMPOSIUM ON QUANTITATIVE BIOLOGY
    Bruce Stillman; Fiscal Year: 2005
    ..The annual Symposia will continue to be planned to further the progress of advancements in biomedical science. ..
  42. The XP Variant: A Human Mutator Gene for UV Damage
    James Cleaver; Fiscal Year: 2005
    ..We will express hRad3O on the keratin 14 promoter for over-expression in the skin, and make targeted knockout of mRad3O in vivo to identify roles for hRad3O in promoting and preventing carcinogenesis. ..
  43. Structure Determination of the Polymerase alpha-primase
    DEWIGHT WILLIAMS; Fiscal Year: 2006
    ..abstract_text> ..
  44. CSHL Symposium on Quantitative Biology
    Bruce Stillman; Fiscal Year: 2006
    ..The meeting will address the phenomenon of small ribonucleic acids and their function in a variety of regulatory phenomena in the cell. [unreadable] [unreadable] [unreadable]..
  45. MUTATIONAL MECHANISMS OF REPETITIVE DNA IN HUMAN CELLS
    Kristin Eckert; Fiscal Year: 2001
    ..Our long-term research objective is to test the hypothesis that mutations in repetitive DNA provide an important source of genotypic variation that drives neoplastic progression. ..