Thomas A Kunkel

Thomas A Kunkel

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Thomas A Kunkel

Publications by authors named "Thomas A Kunkel"

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Genome-wide mutagenesis resulting from topoisomerase 1-processing of unrepaired ribonucleotides in DNA.

DNA Repair (Amst) 2019 12 3;84:102641. Epub 2019 Jul 3.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2019.102641DOI Listing
December 2019

DNA Polymerase Delta Synthesizes Both Strands during Break-Induced Replication.

Mol Cell 2019 11 5;76(3):371-381.e4. Epub 2019 Sep 5.

Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.07.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862718PMC
November 2019

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.

Nucleic Acids Res 2019 09;47(17):9410-9422

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1093/nar/gkz680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755092PMC
September 2019

Roles for DNA polymerase δ in initiating and terminating leading strand DNA replication.

Nat Commun 2019 09 5;10(1):3992. Epub 2019 Sep 5.

Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC, 27709, USA.

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http://dx.doi.org/10.1038/s41467-019-11995-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728351PMC
September 2019

Opportunities for new studies of nuclear DNA replication enzymology in budding yeast.

Curr Genet 2019 Sep 6. Epub 2019 Sep 6.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIEHS, NIH, DHHS, Research Triangle Park, NC, 27709, USA.

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http://dx.doi.org/10.1007/s00294-019-01023-4DOI Listing
September 2019

The absence of the catalytic domains of Saccharomyces cerevisiae DNA polymerase ϵ strongly reduces DNA replication fidelity.

Nucleic Acids Res 2019 05;47(8):3986-3995

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1093/nar/gkz048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486559PMC
May 2019

A simple but profound mutation in mouse DNA polymerase ε drives tumorigenesis.

Authors:
Thomas A Kunkel

J Clin Invest 2018 08 20;128(9):3754-3756. Epub 2018 Aug 20.

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http://dx.doi.org/10.1172/JCI123021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6118597PMC
August 2018

Studying Topoisomerase 1-Mediated Damage at Genomic Ribonucleotides.

Methods Mol Biol 2018 ;1703:241-257

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, NC, USA.

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http://dx.doi.org/10.1007/978-1-4939-7459-7_17DOI Listing
July 2018

Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis.

Nat Commun 2018 07 6;9(1):2642. Epub 2018 Jul 6.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, 27709, NC, USA.

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http://www.nature.com/articles/s41467-018-05024-8
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http://dx.doi.org/10.1038/s41467-018-05024-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035275PMC
July 2018

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis.

J Vis Exp 2018 07 26(137). Epub 2018 Jul 26.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS.

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http://dx.doi.org/10.3791/58020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126554PMC
July 2018

Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing.

Methods Mol Biol 2018 ;1672:329-345

Genome Integrity and Structural Biology Laboratory, National Institute for Environmental Health Sciences, National Institute of Health (NIH), 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.

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http://dx.doi.org/10.1007/978-1-4939-7306-4_23DOI Listing
June 2018

Muver, a computational framework for accurately calling accumulated mutations.

BMC Genomics 2018 May 9;19(1):345. Epub 2018 May 9.

Integrative Bioinformatics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA.

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http://dx.doi.org/10.1186/s12864-018-4753-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5944071PMC
May 2018

Evidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae.

Nat Commun 2018 02 27;9(1):858. Epub 2018 Feb 27.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA.

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http://dx.doi.org/10.1038/s41467-018-03270-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829166PMC
February 2018

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu.

Nucleic Acids Res 2017 Sep;45(15):9138-9148

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1093/nar/gkx527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587726PMC
September 2017

Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.

Nat Commun 2017 08 15;8(1):253. Epub 2017 Aug 15.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.

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http://dx.doi.org/10.1038/s41467-017-00271-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557891PMC
August 2017

Eukaryotic DNA Replication Fork.

Annu Rev Biochem 2017 06 1;86:417-438. Epub 2017 Mar 1.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709; email:

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http://dx.doi.org/10.1146/annurev-biochem-061516-044709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597965PMC
June 2017

The role of RNase H2 in processing ribonucleotides incorporated during DNA replication.

DNA Repair (Amst) 2017 05 6;53:52-58. Epub 2017 Mar 6.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS Research Triangle Park, NC 27709, USA. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2017.02.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409533PMC
May 2017

Topoisomerase I-mediated cleavage at unrepaired ribonucleotides generates DNA double-strand breaks.

EMBO J 2017 02 8;36(3):361-373. Epub 2016 Dec 8.

Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA

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http://dx.doi.org/10.15252/embj.201592426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5286372PMC
February 2017

Eukaryotic genome instability in light of asymmetric DNA replication.

Crit Rev Biochem Mol Biol 2016 20;51(1):43-52. Epub 2015 Dec 20.

a Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences , Research Triangle Park , NC , USA.

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http://dx.doi.org/10.3109/10409238.2015.1117055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922258PMC
October 2016

Eukaryotic Mismatch Repair in Relation to DNA Replication.

Annu Rev Genet 2015 ;49:291-313

Department of Chemistry and Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599-3290; email:

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http://dx.doi.org/10.1146/annurev-genet-112414-054722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5439269PMC
September 2016

DNA Polymerases Divide the Labor of Genome Replication.

Trends Cell Biol 2016 09 1;26(9):640-654. Epub 2016 Jun 1.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tcb.2016.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4993630PMC
September 2016

Processing ribonucleotides incorporated during eukaryotic DNA replication.

Nat Rev Mol Cell Biol 2016 06 20;17(6):350-63. Epub 2016 Apr 20.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina 27709, USA.

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http://dx.doi.org/10.1038/nrm.2016.37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445644PMC
June 2016

Genome-wide analysis of the specificity and mechanisms of replication infidelity driven by imbalanced dNTP pools.

Nucleic Acids Res 2016 Feb 24;44(4):1669-80. Epub 2015 Nov 24.

Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden

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http://dx.doi.org/10.1093/nar/gkv1298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770217PMC
February 2016

Who Is Leading the Replication Fork, Pol ε or Pol δ?

Mol Cell 2016 Feb;61(4):492-493

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838066PMC
February 2016

Measuring ribonucleotide incorporation into DNA in vitro and in vivo.

Methods Mol Biol 2015 ;1300:123-39

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA.

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http://link.springer.com/content/pdf/10.1007%2F978-1-4939-25
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http://link.springer.com/10.1007/978-1-4939-2596-4_9
Publisher Site
http://dx.doi.org/10.1007/978-1-4939-2596-4_9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321556PMC
January 2016

Celebrating DNA's Repair Crew.

Authors:
Thomas A Kunkel

Cell 2015 Dec;163(6):1301-3

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.11.028DOI Listing
December 2015

Stimulation of Chromosomal Rearrangements by Ribonucleotides.

Genetics 2015 Nov 22;201(3):951-61. Epub 2015 Sep 22.

Department of Environmental and Radiological Health Sciences and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, Colorado 80523 Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709

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http://dx.doi.org/10.1534/genetics.115.181149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649663PMC
November 2015

Creative template-dependent synthesis by human polymerase mu.

Proc Natl Acad Sci U S A 2015 Aug 3;112(33):E4530-6. Epub 2015 Aug 3.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709.

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http://dx.doi.org/10.1073/pnas.1505798112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547271PMC
August 2015

Okazaki fragment maturation involves α-segment error editing by the mammalian FEN1/MutSα functional complex.

EMBO J 2015 Jul 28;34(13):1829-43. Epub 2015 Apr 28.

Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA

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http://dx.doi.org/10.15252/embj.201489865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516434PMC
July 2015

Quantifying the contributions of base selectivity, proofreading and mismatch repair to nuclear DNA replication in Saccharomyces cerevisiae.

DNA Repair (Amst) 2015 Jul 25;31:41-51. Epub 2015 Apr 25.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2015.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465240PMC
July 2015

Alternative solutions and new scenarios for translesion DNA synthesis by human PrimPol.

DNA Repair (Amst) 2015 May 23;29:127-38. Epub 2015 Feb 23.

Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2015.02.013DOI Listing
May 2015

Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading-strand specific.

Nat Struct Mol Biol 2015 Apr 9;22(4):291-7. Epub 2015 Mar 9.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA.

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http://dx.doi.org/10.1038/nsmb.2989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835660PMC
April 2015

Differences in genome-wide repeat sequence instability conferred by proofreading and mismatch repair defects.

Nucleic Acids Res 2015 Apr 30;43(8):4067-74. Epub 2015 Mar 30.

Genome Instability and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA

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http://nar.oxfordjournals.org/content/early/2015/03/30/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv271
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http://dx.doi.org/10.1093/nar/gkv271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417177PMC
April 2015

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation.

Nat Struct Mol Biol 2015 Mar 26;22(3):185-91. Epub 2015 Jan 26.

Genome Integrity &Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health (NIH), Research Triangle Park, North Carolina, USA.

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http://dx.doi.org/10.1038/nsmb.2957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351163PMC
March 2015

Deposition of histone H2A.Z by the SWR-C remodeling enzyme prevents genome instability.

DNA Repair (Amst) 2015 Jan 20;25:9-14. Epub 2014 Nov 20.

Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, United States. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2014.10.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276476PMC
January 2015

Increased and imbalanced dNTP pools symmetrically promote both leading and lagging strand replication infidelity.

PLoS Genet 2014 Dec 4;10(12):e1004846. Epub 2014 Dec 4.

Department of Medical Biochemistry and Biophysics, Umea University, Umea, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umea University, Umea, Sweden.

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http://dx.doi.org/10.1371/journal.pgen.1004846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256292PMC
December 2014

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.

Genome Res 2014 Nov 12;24(11):1751-64. Epub 2014 Sep 12.

Laboratory of Molecular Genetics, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA; Laboratory of Structural Biology, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA;

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http://dx.doi.org/10.1101/gr.178335.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216917PMC
November 2014

Delivering nonidentical twins.

Nat Struct Mol Biol 2014 Aug 6;21(8):649-51. Epub 2014 Jul 6.

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1038/nsmb.2852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5417586PMC
August 2014

Ribonucleotides in DNA: origins, repair and consequences.

DNA Repair (Amst) 2014 Jul 30;19:27-37. Epub 2014 Apr 30.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2014.03.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065383PMC
July 2014

Structures of the Leishmania infantum polymerase beta.

DNA Repair (Amst) 2014 Jun 22;18:1-9. Epub 2014 Mar 22.

Department of Pharmacological Sciences, Stony Brook University, BST 7-169, Stony Brook, NY 11794-8651, USA. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2014.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040948PMC
June 2014

Ribonucleotide incorporation by yeast DNA polymerase ζ.

DNA Repair (Amst) 2014 Jun 24;18:63-7. Epub 2014 Mar 24.

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2014.02.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402711PMC
June 2014

Structure-function studies of DNA polymerase λ.

Biochemistry 2014 May 23;53(17):2781-92. Epub 2014 Apr 23.

Laboratory of Structural Biology and ‡Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health , Research Triangle Park, North Carolina 27709, United States.

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http://dx.doi.org/10.1021/bi4017236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018081PMC
May 2014

Sustained active site rigidity during synthesis by human DNA polymerase μ.

Nat Struct Mol Biol 2014 Mar 2;21(3):253-60. Epub 2014 Feb 2.

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.

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http://dx.doi.org/10.1038/nsmb.2766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164209PMC
March 2014

Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity.

Nature 2014 Feb 22;506(7486):111-5. Epub 2013 Dec 22.

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, North Carolina 27709, USA.

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http://dx.doi.org/10.1038/nature12824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064939PMC
February 2014

DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation.

Nucleic Acids Res 2013 Dec 13;41(22):10323-33. Epub 2013 Sep 13.

Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, 100 Technology Drive, Pittsburgh, PA 15219, USA, Department of Physics, North Carolina State University, 2401 Stinson Drive, Raleigh, NC, 27695, USA, Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA, Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA and Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1093/nar/gkt813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905856PMC
December 2013

Structure-function analysis of ribonucleotide bypass by B family DNA replicases.

Proc Natl Acad Sci U S A 2013 Oct 30;110(42):16802-7. Epub 2013 Sep 30.

Laboratory of Structural Biology and Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institute of Health, Department of Health and Human Services, Research Triangle Park, NC 27709.

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http://dx.doi.org/10.1073/pnas.1309119110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3801065PMC
October 2013

Ribonucleotides are signals for mismatch repair of leading-strand replication errors.

Mol Cell 2013 May 18;50(3):437-43. Epub 2013 Apr 18.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.molcel.2013.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658170PMC
May 2013

Mismatch repair balances leading and lagging strand DNA replication fidelity.

PLoS Genet 2012 11;8(10):e1003016. Epub 2012 Oct 11.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3469411PMC
March 2013

Topoisomerase 1-mediated removal of ribonucleotides from nascent leading-strand DNA.

Mol Cell 2013 Mar 31;49(5):1010-5. Epub 2013 Jan 31.

Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.molcel.2012.12.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595360PMC
March 2013

Exonuclease 1 preferentially repairs mismatches generated by DNA polymerase α.

DNA Repair (Amst) 2013 Feb 11;12(2):92-6. Epub 2012 Dec 11.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH/DHHS, Research Triangle Park, NC 27709, United States.

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http://dx.doi.org/10.1016/j.dnarep.2012.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552065PMC
February 2013

Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ.

DNA Repair (Amst) 2013 Feb 12;12(2):121-7. Epub 2012 Dec 12.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institute of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.dnarep.2012.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552135PMC
February 2013

DNA polymerase λ inactivation by oxidized abasic sites.

Biochemistry 2013 Feb 18;52(5):975-83. Epub 2013 Jan 18.

Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, MD 21218, United States.

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http://pubs.acs.org/doi/10.1021/bi301592x
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http://dx.doi.org/10.1021/bi301592xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566640PMC
February 2013

DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions in Saccharomyces cerevisiae.

Environ Mol Mutagen 2012 Dec 11;53(9):777-86. Epub 2012 Sep 11.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, NC 27709, USA.

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http://dx.doi.org/10.1002/em.21728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678557PMC
December 2012

Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae.

DNA Repair (Amst) 2012 Dec 15;11(12):933-41. Epub 2012 Oct 15.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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December 2012

RNase H2-initiated ribonucleotide excision repair.

Mol Cell 2012 Sep 2;47(6):980-6. Epub 2012 Aug 2.

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.

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September 2012

The catalytic cycle for ribonucleotide incorporation by human DNA Pol λ.

Nucleic Acids Res 2012 Aug 14;40(15):7518-27. Epub 2012 May 14.

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA.

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http://dx.doi.org/10.1093/nar/gks413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424563PMC
August 2012

Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ɛ.

DNA Repair (Amst) 2012 Aug 8;11(8):649-56. Epub 2012 Jun 8.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.dnarep.2012.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407341PMC
August 2012

Altered Ig hypermutation pattern and frequency in complementary mouse models of DNA polymerase ζ activity.

J Immunol 2012 Jun 30;188(11):5528-37. Epub 2012 Apr 30.

Somatic Hypermutation Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.4049/jimmunol.1102629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358437PMC
June 2012

Solution structure of the Dickerson DNA dodecamer containing a single ribonucleotide.

Biochemistry 2012 Mar 14;51(12):2407-16. Epub 2012 Mar 14.

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, United States.

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http://dx.doi.org/10.1021/bi201710qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743102PMC
March 2012

The major roles of DNA polymerases epsilon and delta at the eukaryotic replication fork are evolutionarily conserved.

PLoS Genet 2011 Dec 1;7(12):e1002407. Epub 2011 Dec 1.

Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom.

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December 2011

Kinetic analysis of the unique error signature of human DNA polymerase ν.

Biochemistry 2011 Nov 31;50(46):10126-35. Epub 2011 Oct 31.

Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235957PMC
November 2011

Balancing eukaryotic replication asymmetry with replication fidelity.

Authors:
Thomas A Kunkel

Curr Opin Chem Biol 2011 Oct 19;15(5):620-6. Epub 2011 Aug 19.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.cbpa.2011.07.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189284PMC
October 2011

Lesion bypass by S. cerevisiae Pol ζ alone.

DNA Repair (Amst) 2011 Aug 31;10(8):826-34. Epub 2011 May 31.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.dnarep.2011.04.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146559PMC
August 2011

Replication of ribonucleotide-containing DNA templates by yeast replicative polymerases.

DNA Repair (Amst) 2011 Aug 23;10(8):897-902. Epub 2011 Jun 23.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.dnarep.2011.05.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147116PMC
August 2011

Malaria drug resistance is associated with defective DNA mismatch repair.

Mol Biochem Parasitol 2011 Jun 21;177(2):143-7. Epub 2011 Feb 21.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075314PMC
June 2011

Mutagenic processing of ribonucleotides in DNA by yeast topoisomerase I.

Science 2011 Jun;332(6037):1561-4

Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3380281PMC
June 2011

Modeling of the DNA-binding site of yeast Pms1 by mass spectrometry.

DNA Repair (Amst) 2011 May 26;10(5):454-65. Epub 2011 Feb 26.

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States.

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May 2011

Mismatch repair-independent tandem repeat sequence instability resulting from ribonucleotide incorporation by DNA polymerase ε.

DNA Repair (Amst) 2011 May 16;10(5):476-82. Epub 2011 Mar 16.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States.

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May 2011

The in vitro fidelity of yeast DNA polymerase δ and polymerase ε holoenzymes during dinucleotide microsatellite DNA synthesis.

DNA Repair (Amst) 2011 May 22;10(5):497-505. Epub 2011 Mar 22.

Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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May 2011

Molecular breeding of polymerases for resistance to environmental inhibitors.

Nucleic Acids Res 2011 Apr 4;39(8):e51. Epub 2011 Feb 4.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3082909PMC
April 2011

FEN nucleases: bind, bend, fray, cut.

Cell 2011 Apr;145(2):171-2

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.cell.2011.03.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515068PMC
April 2011

Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools.

Nucleic Acids Res 2011 Mar 20;39(4):1360-71. Epub 2010 Oct 20.

Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.

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March 2011

Replication infidelity via a mismatch with Watson-Crick geometry.

Proc Natl Acad Sci U S A 2011 Feb 13;108(5):1862-7. Epub 2011 Jan 13.

Laboratory of Molecular Genetics, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1073/pnas.1012825108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033279PMC
February 2011

Differential correction of lagging-strand replication errors made by DNA polymerases {alpha} and {delta}.

Proc Natl Acad Sci U S A 2010 Dec 1;107(49):21070-5. Epub 2010 Nov 1.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.

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December 2010

Inhibition of short patch and long patch base excision repair by an oxidized abasic site.

Biochemistry 2010 Nov 20;49(45):9904-10. Epub 2010 Oct 20.

Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States.

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November 2010

The importance of being DNA.

Cell Cycle 2010 Nov 15;9(22):4422-4. Epub 2010 Nov 15.

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http://dx.doi.org/10.4161/cc.9.22.14052DOI Listing
November 2010

Genome instability due to ribonucleotide incorporation into DNA.

Nat Chem Biol 2010 Oct 22;6(10):774-81. Epub 2010 Aug 22.

Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA.

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October 2010

Genome-wide model for the normal eukaryotic DNA replication fork.

Proc Natl Acad Sci U S A 2010 Oct 27;107(41):17674-9. Epub 2010 Sep 27.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

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October 2010

Mutator phenotypes due to DNA replication infidelity.

Semin Cancer Biol 2010 Oct 8;20(5):304-11. Epub 2010 Oct 8.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1016/j.semcancer.2010.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087159PMC
October 2010

Loop 1 modulates the fidelity of DNA polymerase lambda.

Nucleic Acids Res 2010 Sep 30;38(16):5419-31. Epub 2010 Apr 30.

Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC, USA.

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September 2010

Evolutionary conservation of residues in vertebrate DNA polymerase N conferring low fidelity and bypass activity.

Nucleic Acids Res 2010 Jun 9;38(10):3233-44. Epub 2010 Feb 9.

Department of Carcinogenesis, The University of Texas Graduate School of Biomedical Sciences at Houston, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879524PMC
June 2010

Interaction between DNA Polymerase lambda and anticancer nucleoside analogs.

J Biol Chem 2010 May 26;285(22):16874-9. Epub 2010 Mar 26.

Laboratory of Structural Biology and Laboratory of Molecular Genetics, Department of Health and Human Services, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878035PMC
May 2010

SnapShot: DNA mismatch repair.

Cell 2010 May;141(4):730.e1

National Institutes of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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May 2010

Refolding active human DNA polymerase nu from inclusion bodies.

Protein Expr Purif 2010 Apr 21;70(2):163-71. Epub 2009 Oct 21.

Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656056PMC
April 2010

Functional residues on the surface of the N-terminal domain of yeast Pms1.

DNA Repair (Amst) 2010 Apr;9(4):448-57

Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856611PMC
April 2010

An Msh2 conditional knockout mouse for studying intestinal cancer and testing anticancer agents.

Gastroenterology 2010 Mar 18;138(3):993-1002.e1. Epub 2009 Nov 18.

Department of Medicine/Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862591PMC
March 2010

Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases.

Proc Natl Acad Sci U S A 2010 Mar 1;107(11):4949-54. Epub 2010 Mar 1.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1073/pnas.0914857107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841928PMC
March 2010

Template strand scrunching during DNA gap repair synthesis by human polymerase lambda.

Nat Struct Mol Biol 2009 Sep 23;16(9):967-72. Epub 2009 Aug 23.

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, North Carolina, USA.

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http://dx.doi.org/10.1038/nsmb.1654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767187PMC
September 2009

Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase zeta.

Nucleic Acids Res 2009 Jun 20;37(11):3774-87. Epub 2009 Apr 20.

Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences Research, NIH, DHHS, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1093/nar/gkp238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699522PMC
June 2009

The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases delta and eta.

Nucleic Acids Res 2009 May 12;37(9):2830-40. Epub 2009 Mar 12.

Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences Research, NC 27709, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685079PMC
May 2009