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Selected Publications

DNA Replication Fidelity Group

  1. Williams, J.A., Gehle, D. and Kunkel, T.A. (2017) The role of RNase H2 in processing ribonucleotides incorporated during DNA replication. DNA Repair, in press. 53, 52-58 [Abstract]
  2. Kunkel, T.A. and Burgers, P.M.J. (2017) Arranging eukaryotic nuclear DNA polymerases for replication. BioEssays, in press.
  3. Huang SN, Williams JS, Arana ME, Kunkel TA, Pommier Y. Topoisomerase I-mediated cleavage at unrepaired ribonucleotides generates DNA double-strand breaks. The EMBO journal 2017 36(3):361-373.  [Abstract]
  4. Lujan SA, Williams JS, Kunkel TA. DNA Polymerases Divide the Labor of Genome Replication. Trends in cell biology 2016 26(9):640-654. [Abstract]
  5. Watt, D.L., Buckland, R.J., Lujan, S.A., Kunkel, T.A. and Chabes, A. (2016) Genome-wide analysis of the specificity and mechanisms of replication infidelity driven by imbalanced dNTP pools. Nucleic Acids Research 44, 1669-1680. PMCID: PMC4770217
  6. Burgers, P.M.J., Gordenin, D. and Kunkel, T.A. (2016) Who is leading the replication fork, Pol ε or Pol δ? Molecular Cell 61. 492-493. PMCID: PMC4838066
  7. Orebaugh, C.D., Lujan, S.A., Burkholder, A.B., Clausen, A. R. and Kunkel, T.A. (2016) Mapping ribonucleotides incorporated into the yeast genome during nuclear DNA replication by Hydrolytic End-Sequencing (HydEn-seq). Methods in Molecular Biology, Genome Instability: Methods and Protocols, in press.
  8. Williams, J.A and Kunkel, T.A. (2016) Studying topoisomerase 1-mediated damage at genomic ribonucleotides. Methods in Molecular Biology, Methods and Protocols, Springer Verlag, in press.
  9. Lujan SA, Williams JS, Kunkel TA. Eukaryotic genome instability in light of asymmetric DNA replication. Critical reviews in biochemistry and molecular biology 2016 51(1):43-52. [Abstract]
  10. Williams JS, Lujan SA, Kunkel TA. Processing ribonucleotides incorporated during eukaryotic DNA replication. Nature reviews. Molecular cell biology 2016 17(6):350-363. [Abstract]
  11. Clausen, A.R., Williams, J.S. and Kunkel, T.A. (2015) Measuring ribonbucleotide incorporation into DNA in vitro and in vivo. Methods in Molecular Biology, Vol. 1300, 123-139, Chapter 9. Vengrova, Sonya, Dalgaard, Jacob (Eds.), Humana Press.
  12. Martínez-Jiménez, M.I., García-Gómez, S., Bebenek, K., Sastre-Moreno, G., Calvo, P., Diaz-Talavera, A., Kunkel, T.A. and Blanco, L. (2015) Alternative solutions and new scenarios for translesion DNA synthesis by human PrimPol. DNA Repair, 129-137.
  13. Williams, J.S., Clausen, A.R., Marjavaara, L., Clark, A.B., Burgers, P.M., Chabes, A. and Kunkel, T.A. (2015) Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading strand-specific. Nature Structural Molecular Biology 22, 291-297. PMCID: PMC4835660
  14. Liu, S., Lu, G., Ali, S., Liu, W., Zheng, L. Dai, H., Li, H., Hu, H., Hua, Y., Zhou, Y., Ortega, J., Li, G.-M., Kunkel, T.A. and Shen, B. (2015) Okazaki fragment maturation involves alpha-segment error editing by the mammalian FEN1/MutSalpha functional complex. EMBO Journal 34, 1829-1843. PMCID: PMC4516434.
  15. Moon, A.F., Gosavi, R., Kunkel, T.A., Pedersen, L.C. and Bebenek, K. (2015) Creative template-dependent synthesis by DNA polymerase mu. Proc. Natl. Acad. Sci. U.S.A. 112, E4530-6. PMCID: PMC 4547271
  16. Kunkel, T.A. and Erie, D.E. (2015) Eukaryotic mismatch repair in relation to replication. Annual Reviews Genetics 49, 291–313.
  17. Kunkel, T.A. (2015) Celebrating DNA's Repair Crew. Cell 163, 1301-1303.
  18. Conover, H.N., Lujan, S.A., Chapman, M.J., Cornelio, D.A., Sharif, R., Williams, J.S., Clark, A.B., Camilo, F., Thomas A. Kunkel, T.A. and Argueso, J.L. (2015) Stimulation of chromosomal rearrangements by ribonucleotides. Genetics 201, 951-961. PMCID: PMC4649663
  19. Miyabe, I., Mizuno, K., Keszthelyi, A., Daigaku, Y. Skouteri, M., Mohebi, S., Kunkel, T.A., Murray, J.M. and Carr, A.M. (2015) Polymerase δ replicates both strands after homologous recombination-dependent fork restart. Nature Structural Molecular Biology 22, 932-939. PMCID: PMC4655445
  20. Huang, S.N., Williams, J.S., Ghosh, S., Arana, M.E., Kunkel, T.A. and Pommier, Y. (2015) Double-strand beaks are formed by topoisomerase 1 cleavage at unrepaired ribonucleotides in DNA. EMBO Journal, in press.
  21. St Charles JA, Liberti SE, Williams JS, Lujan SA, Kunkel TA. Quantifying the contributions of base selectivity, proofreading and mismatch repair to nuclear DNA replication in Saccharomyces cerevisiae. DNA repair 2015 31():41-51. [Abstract]
  22. Lujan SA, Clark AB, Kunkel TA. Differences in genome-wide repeat sequence instability conferred by proofreading and mismatch repair defects. Nucleic acids research 2015 43(8):4067-4074. [Abstract]
  23. Williams JS, Clausen AR, Lujan SA, Marjavaara L, Clark AB, Burgers PM, Chabes A, Kunkel TA. Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading-strand specific. Nature structural & molecular biology 2015 22(4):291-297. [Abstract]
  24. Clausen, A.R., Lujan, S.A., Burkholder, A.B., Orebaugh, C.D., Williams, J.S., Clausen, M.F., Malc, E.P., Mieczkowski, P.A., Fargo, D.C., Smith, D.J. and Kunkel, T.A. (2015) Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation. Nature Structural Molecular Biology 22, 185-191. PMCID: PMC4351163
  25. Van C, Williams JS, Kunkel TA, Peterson CL. Deposition of histone H2A.Z by the SWR-C remodeling enzyme prevents genome instability. DNA repair 2015 25(January):9-14. [Abstract]
  26. Kunkel, T.A. and Burgers, P.M. (2014) Delivering non-identical twins. Nature Struct. Molec. Biol. 21, 649-651
  27. Mejia, E., Burak, M., Alonso, A., Larraga, V., Kunkel, T.A., Bebenek, K. and Garcia-Diaz, M. (2014) Structures of the Leishmania infantum polymerase beta. DNA Repair 18, 1-9 [Abstract]
  28. Bebenek, K., Pedersen, L.C. and Kunkel, T.A. (2014) Structure-functions studies of DNA polymerase lambda. Biochemistry 53, 2781-2792 [Abstract]
  29. Makarova, A.V., Nick McElhinny, S.A., Watts, B.E., Kunkel, T.A. and Burgers,P.M. (2014) Ribonucleotide incorporation by yeast DNA polymerase ζ. DNA Repair 18, 63-67 [Abstract]
  30. Buckland RJ, Watt DL, Chittoor B, Nilsson AK, Kunkel TA, Chabes A1. Increased and Imbalanced dNTP Pools Symmetrically Promote Both Leading and Lagging Strand Replication Infidelity. PLoS genetics 2014 10(12):e1004846-. [Abstract]
  31. Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, Kunkel TA. Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. Genome research 2014 24(11):1751-1764. [Abstract]
  32. Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC. Sustained active site rigidity during synthesis by human DNA polymerase μ. Nature structural & molecular biology 2014 21(3):253-260. [Abstract]
  33. Williams JS, Kunkel TA. (2014) Ribonucleotides in DNA: Origins, repair and consequences. DNA repair 19:27-37. [Abstract]
  34. Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS. Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity. Nature 506(7486):111-115 (2014). [Abstract]
  35. Schaetzlein, S., Chahwan, R., Avdievich, E., Roa, S., Wei, K., Eoff, R.L., Sellers, R.S., Clark, A.B., Kunkel, T.A., Scharff, M.D. and Edelmann, W. (2013) Mammalian Exo1 encodes both structural and catalytic functions that play distinct roles in essential biological processes. Proc. Natl. Acad. Sci. U.S.A., doi/10.1073/pnas.1308512110 [Abstract]
  36. Clausen, A.R., Murray, M.S., Passer, A.R., Pedersen, L.C. and Kunkel, T.A. (2013) Structure-function analysis of ribonucleotide bypass by B family DNA replicases. Proc. Natl. Acad. Sci. U.S.A. 110, 16802-16807 [Abstract]
  37. Lormand, J., Buncher, N., Murphy, C.T., Kaur, P., Lee, M.Y., Burgers, P., Wang, H., Kunkel, T.A. and Opresko, P.L. (2013) DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation. Nucleic Acids Research 41, 10323-10333 [Abstract]
  38. Stevens, A.J., Guan, L. Bebenek, K., Kunkel T.A. and Greenberg, M.M. (2013) DNA polymerase lambda inactivation by oxidized abasic sites. Biochemistry 52:975-983. [Abstract]
  39. Liberti, S.E., Larrea, A.A. and Kunkel, T.A. (2013) Exonuclease 1 preferentially repairs mismatches generated by DNA polymerase α. DNA Repair 12, 92-96. [Abstract]
  40. Lujan SA, Williams JS, Clausen AR, Clark AB, Kunkel TA. (2013) Ribonucleotides are signals for mismatch repair of leading-strand replication errors.. Molecular cell 50(3):437-443. [Abstract]
  41. Williams JS, Smith DJ, Marjavaara L, Lujan SA, Chabes A, Kunkel TA. (2013) Topoisomerase 1-mediated removal of ribonucleotides from nascent leading-strand DNA. Molecular cell 49(5):1010-1015.  [Abstract]
  42. Clausen AR, Zhang S, Burgers PM, Lee MY, Kunkel TA. (2013) Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ. DNA repair 12(2):121-7. [Abstract]
  43. Sparks, J.L., Chon, H., Cerritelli, S.M., Kunkel, T.A., Johansson, E., Crouch, R.J. and Burgers, P.M. (2012) RNase H2-Initiated Ribonucleotide Excision Repair. Molecular Cell 47, 980-986. [Abstract]
  44. Stone JE, Lujan SA, Kunkel TA. (2012) DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions in Saccharomyces cerevisiae. Environmental and molecular mutagenesis 53(9):777-786. [Abstract]
  45. Arana ME, Kerns RT, Wharey L, Gerrish KE, Bushel PR, Kunkel TA. Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae. DNA repair. 2012 11(12):933-41. [Abstract]
  46. Williams JS, Clausen AR, Nick McElhinny SA, Watts BE, Johansson E, Kunkel TA. Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ɛ. DNA repair 2012 11(8):649-56. [Abstract]
  47. Lujan SA, Williams JS, Pursell ZF, Abdulovic-Cui AA, Clark AB, Nick McElhinny SA, Kunkel TA. (2012) Mismatch repair balances leading and lagging strand DNA replication fidelity. PLoS genetics 8(10):e1003016-. [Abstract]
  48. Daly J, Bebenek K, Watt DL, Richter K, Jiang C, Zhao ML, Ray M, McGregor WG, Kunkel TA, Diaz M. (2012) Altered Ig hypermutation pattern and frequency in complementary mouse models of DNA polymerase ζ activity. Journal of Immunology  188(11):5528-37. [Abstract]
  49. Lazzaro, F., Novarina, D., Amara, F., Watt, D.L., Stone, J.E., Costanzo, V., Burgers, P.M., Kunkel, T.A., Plevani, P. and Muzi-Falconi, M. (2012) RNase H and post-replication repair protect cells from ribonucleotides incorporated in DNA. Molecular Cell 45, 99-110. [Abstract]
  50. Daly, J., Bebenek, K., Watt, D.L., Richter, K., Jiang, C., Zhao, M.-L., Ray, M., McGregor, W.G., Kunkel, T.A. and Diaz, M. (2012) DNA polymerase ζ plays a direct role in somatic hypermutation of immunoglobulin genes. J. Immunology 188: 5528-5537.
  51. DeRose, E., Perera, L., Murray, M.S., Kunkel, T.A. and London, R.E. (2012) Solution structure of the Dickerson DNA dodecamer containing a single ribonucleotide. Biochemistry 51:2407-2416. [Abstract]
  52. Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek K. (2012) Catalytic cycle for ribonucleotide incorporation by human DNA Pol λ. Nucleic Acids Research. 40(15):7518-27. [Abstract]
  53. Arana, M. E., Potapova, O., Kunkel, T.A. and Joyce, C. M. (2011) Kinetic analysis of the unique error signature of human DNA polymerase ν. Biochemistry 50, 10126-10135. [Abstract]
  54. Miyabe, I., Kunkel, T.A. and Carr, A.M. (2011) The major roles of DNA polymerases epsilon and delta at the eukaryotic replication fork are evolutionarily conserved. PLoS Genetics, 7, e1002407. [Abstract]
  55. García-Ortiz, M.V., Marsin, S., Arana, M.E., Gasparutto, D., Guérois, R., Kunkel, T.A. and Radicella, J.P. (2011) Unexpected role for Helicobacter pylori DNA polymerase I as a source of genetic variability. PLoS Genetics 7, e1002152. [Abstract]
  56. Kim, N., Huang, S., Williams, J.S., Li, Y.C., Clark, A.B., Cho, J.-E., Kunkel, T.A., Pommier, Y. and Jinks-Robertson, S. (2011) Mutagenic processing of ribonucleotides in DNA by yeast topoisomerase 1. Science 332, 1561-1564. [Abstract]
  57. Stone, J.E., Kumar, D., Binz, S.K., Inase, A., Iwai, S., Chabes, A., Burgers, P.M., and Kunkel, T.A. (2011) Lesion bypass by Saccharomyces cerevisiae Pol ζ alone. DNA Repair 10, 826-834. [Abstract]
  58. Kunkel, T.A. (2011) Balancing eukaryotic replication asymmetry with replication fidelity. Curr. Opin. Chem. Biol. 15, 620-626. [Abstract]  
  59. Watt, D.L, Johansson, E., Burgers, P.M. and Kunkel, T.A. (2011) Replication of ribonucleotide-containing DNA templates by yeast replicative polymerases. DNA Repair 10, 897-902. [Abstract]  
  60. Clark, A.B., Lujan, S.A., Kissling, G.E. and Kunkel, T.A. (2011) Mismatch repair-independent tandem repeat sequence instability resulting from ribonucleotide incorporation by DNA polymerase {varepsilon}. DNA Repair 10(5), 476-482. [Abstract]
  61. Schorzman, A.N., Perera, L, Cutalo, J.M., Pedersen, L.C., Pedersen, L.G., Kunkel, T.A. and Tomer, K.B. (2011) Modeling of the DNA-binding site of yeast PMS1 by mass spectrometry. DNA Repair 10 (5), 454-465. [Abstract]
  62. Castellini, M.A., Buguliskis, J.S., Casta, L.J., Butz, C.E., Clark, A.B., Kunkel, T.A., and Taraschi, T. F. (2011) Malaria drug resistance is associated with defective DNA mismatch repair. Molec. Biochem. Parasit. 177(2), 143-147. [Abstract]
  63. Williams, R.S. and Kunkel, T.A. (2011) FEN Nucleases: Bind, Bend, Fray, Cut. Cell 145 (2), 171-172. [Abstract]
  64. Jirawatnotai, S., Hu, Y., Michowski, W., Elias, J.E., Becks, L. Bienvenu, F., Zagozdzon, A., Goswami, T. Wang, Y.E., Clark, A.B., Kunkel, T.A., van Harn, T., Xia, B., Correll, M., Quackenbush, J., Livingston, D.M., Gygi, S.P. and Sicinski, P. (2011) A function for cyclin D1 in DNA repair uncovered by interactome analyses in human cancers. Nature 474 (7350), 230-234. [Abstract]
  65. Baar, C., d'Abbadie, M., Vaisman, A., Arana, M.E., Hofreiter, M., Woodgate, R., Kunkel, T.A., and Holliger, P. (2011) Molecular breeding of polymerases for resistance to environmental inhibitors. Nucleic Acids Research. 39(8), e51. [Abstract]
  66. Abdulovic, Amy L., Hile, Suzanne E., Kunkel, Thomas A., Eckert, Kristin E. (2011) The in vitro fidelity of yeast DNA polymerase delta and polymerase varepsilon holoenzymes during dinucleotide microsatellite DNA synthesis. DNA repair 10(5):497-505. [Abstract]
  67. Bebenek, K., Pedersen, L.C. and Kunkel, T.A. (2011) Replication infidelity via a mismatch with Watson-Crick geometry. Proceedings of the National Academy Sciences U.S.A., 108(5): 1862-1867. [Abstract]
  68. Kumar, D., Abdulovic, A.L., Viberg, J., Nilsson, A.K., Kunkel, T.A. and Chabes, A. (2011) Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools. Nucleic Acids Research, 39(4): 1360-1371 [Abstract]
  69. Nick McElhinny, S.A., Kissling, G.E. and Kunkel, T.A. (2010) Differential correction of lagging strand DNA replication errors made by DNA polymerases {alpha} and {delta}. Proc. Natl. Acad. Sci. U.S.A. 107(49), 21070-21075. [Abstract]
  70. Guan, L., Bebenek, K., Kunkel, T.A. and Greenberg, M.M. (2010) Inhibition of short patch and long patch base excision repair by an oxidized abasic site. Biochemistry 49, 9904-9910. [Abstract]
  71. Clark, A.B. and Kunkel, T.A. (2010) The importance of being DNA. Cell Cycle 9, 4422-4424.
  72. Arana, M.E. and Kunkel, T.A. (2010) Mutator phenotypes due to replication infidelity. Seminars in Cancer Biology 20, 304-311. [Abstract]
  73. Aksenova, A., Volkov, K., Maceluch, J., Pursell, Z.F., Rogozin, I.B., Kunkel, T.A., Pavlov, Y.I. and Johansson, E. (2010) Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε. PLoS Genetics 6, 1-11, e1001209 [Abstract]
  74. Larrea, A.A., Lujan, S.A., Nick McElhinny, S.A., Mieczkowski, P.A., Resnick, M.A., Gordenin, D.A. and Kunkel, T.A. (2010) A genome-wide model for the normal eukaryotic DNA replication fork. Proceedings of the National Academy of Sciences U.S.A. 107, 17674-17679. [Abstract]
  75. Nick McElhinny, S.A., Kumar, D., Clark, A.B., Watt, D.L., Watts, B.E., Lundström, E-B., Johansson, E., Chabes, A. and Kunkel, T.A. (2010) Genome instability due to ribonucleotide incorporation into DNA. Nature Chemical Biology 6, 774-781. [Abstract]
  76. Smogorzewska, A., Desetty, R., Saito, T., Schlabach, M., Lach, F.P., Sowa, M.E., Clark, A.B., Kunkel, T.A., Harper, J.W., Colaiácovo, M.P. and Elledge, S.J. (2010) A genetic screen identifies FAN1, a Fanconi anemia-associated nuclease necessary for DNA interstrand crosslink repair. Molecular Cell 39, 36-47.   [Abstract]
  77. Bebenek, K., Garcia-Diaz, M., Zhou, R-Z., Povirk, L.F. and Kunkel, T.A. (2010) Loop 1 modulates the fidelity of DNA polymerase lambda. Nucleic Acids Research 38(16):5419-5431. [Abstract]
  78. Takata, K., Arana, M.E., Seki, M., Kunkel, T.A. and Richard D. Wood, R.D. (2010) Evolutionary conservation in vertebrate POLN of a residue controlling low fidelity and bypass activity. Nucl. Acids Res., 38:3233-3244. [Abstract]
  79. Bebenek, K., Garcia-Diaz, M.D., Zhou, R-Z., Povirk, L.F. and Kunkel, T.A. (2010) Loop 1 modulates the fidelity of DNA polymerase λ. Nucl. Acids Res. [Abstract]
  80. Kunkel, T.A. (2010) Evolving views of DNA replication (in)fidelity. Cold Spring Harbor Symposia on Quantitative Biology: Evolution: The Molecular Landscape 74:91-101. [Abstract]
  81. Larrea, A.A., Lujan, S.A. and Kunkel, T.A. (2010) SnapShot: DNA Mismatch Repair. Cell 141, 730-730.e1. [Abstract]
  82. Garcia-Diaz, M., Murray, M.S., Kunkel, T.A. and Chou, K-M. (2010) The interaction between DNA polymerase lambda and anticancer nucleoside analogs. J. Biol. Chem. 285, 16874-16879. [Abstract]
  83. Nick McElhinny, S.A., Watts, B.E., Kumar, D., Watt, D. L., Lundström, E-B., Burgers, P.M.J., Johansson, E., Chabes, A. and Kunkel, T.A.(2010) Abundant ribonucleotide incorporation into DNA by yeast replicative DNA polymerases. Proc. Natl. Acad. Sci. U.S.A., 107, 4949-4954. [Abstract]
  84. Nick McElhinny, S.A., Pursell, Z.F. and Kunkel, T.A. (2010) Mechanisms for High Fidelity DNA Replication. In: Molecular Themes in DNA Replication, pp. 86-104, Editor by Lynne S. Cox, Published by the Royal Society of Chemistry, Cambridge.
  85. Arana, M.E., Powell, G.K., Edwards, L.L., Kunkel, T.A. and Petrovich, R.M. (2010) Refolding active human DNA polymerase nu from inclusion bodies. Protein Expression and Purification 70, 163-171. [Abstract]
  86. Kucherlapati, M.H., Lee, K., Nguyen, A., Clark, A.B., Hou Jr., H., Rosulek, A., Li, H., Yang, K., Fan, K., Lipkin, M., Bronson, R.T., Jelicks, L., Kunkel, T.A., Kucherlapati, R. and Edelmann, W. (2010) An Msh2 conditional knockout mouse for studying intestinal cancer and testing anti-cancer agents. Gasteroenterology 138, 993-1002. [Abstract]
  87. Arana, M.E., Holmes, S.F., Fortune, J.M., Moon, A.F., Pedersen, L.C. and Kunkel, T.A. (2010) Functional residues on the surface of the N-terminal domain of yeast Pms1. DNA Repair 9, 448-457. [Abstract]
  88. Terrados, G., Capp, J.-P., Canitrot, Y., Garcia-Diaz, M., Bebenek, K., Kirchoff, T., Villanueva, A., Boudsocq, F., Bergoglio, V., Cazaux, C., Kunkel, T.A., Hoffman, J.-S. and Blanco, L. (2009) Characterization of a natural mutator variant of human DNA polymerase lambda which promotes chromosomal instability by compromising NHEJ. PLoS ONE 4, e7290. [Abstract]
  89. Garcia-Diaz, M., Bebenek, K., Larrea, A., Havener, J.M., Perera, L., Krahn, J., Pedersen, L.C., Ramsden, D.A. and Kunkel, T.A. (2009) Template strand scrunching during DNA gap repair synthesis by human DNA polymerase λ. Nature Struct. Molec. Biol. 16, 967-972. [Abstract]
  90. Stone, J.E., Kissling, G.E., Lujan, S.A., Rogozin, I.B., Stith, C.M., Burgers, P.M.J. and Kunkel, T.A. (2009) Low fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerases. Nucl. Acids Res. 37, 2830-2840. [Abstract]
  91. McCulloch, S.D., Kokoska, R.J., Garg, P., Burgers, P.M. and Kunkel, T.A. (2009) The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases delta and eta. Nucl. Acids Res. 37, 2830-2840. [Abstract]
  92. Pursell, Z.F. and Kunkel, T.A. (2008) DNA polymerase epsilon: a polymerase of unusual size (and complexity). Prog. Nucl. Acid Res. Molec. Biol. 82, 101-145. [Abstract]
  93. Kunkel T.A., Burgers P.M. (2008) Dividing the workload at a eukaryotic replication fork. Trends in cell biology. 18(11), 521-527. [Abstract]
  94. Zhong, X., Pedersen, L.C., and Kunkel, T.A. (2008) Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity. Nucleic Acids Research. 36(12), 3892-3904 [Abstract]
  95. Arana, M.E., Seki, M., Wood, R.D., Rogozin, I.B., and Kunkel, T.A. ( 2008) Low fidelity DNA synthesis by human DNA polymerase theta. Nucleic acids research 36(11), 3847-3856. [Abstract]
  96. Zhou, R.-Z., Blanco, L., Garcia-Diaz, M., Bebenek, K., Kunkel, T.A., and Povirk, L.F. (2008) Tolerance for 8-oxoguanine but not thymine glycol in alignment-based gap-filling of partially complementary double-strand break ends by DNA polymerases lambda in human nuclear extracts. Nucl. Acids Res. 36, 2895-2905.
  97. Zhong, X., Pedersen, L.C., and Kunkel, T.A. (2008) Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity. Nucl. Acids Res. 36, 3892-3904.
  98. Arana, M.E., Seki, M., Rogozin, I.B., Wood, R.D., and Kunkel, T.A. (2008) Low fidelity DNA synthesis by human DNA polymerase theta, Nucleic Acids Res. 36, 3847-3856.
  99. Cisneros, G.A., Perera, L., Garcia-Diaz, M., Bebenek, K., Kunkel, T.A. and Pedersen, L.G. (2008) Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio QM/MM studies. DNA Repair 7, 1824-1834. [Abstract]
  100. McCulloch, S.D. and Kunkel, T.A. (2008) The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. Cell Research 18, 148-161.
  101. Bebenek, K., Garcia-Diaz, M., Foley, M.C., Schlick, T., and Kunkel, T.A. (2008) Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. EMBO reports 9, 459-464.
  102. Pursell, Z.F., MacDonald, J.T., Mathews, C.K., and Kunkel, T.A. (2008) Trace amounts of 8-oxo-dGTP in mitochondrial dNTPs reduce DNA polymerase ³ replication fidelity. Nucl. Acids Res., 36, 2174-2181.
  103. Nick McElhinny, S.A., Gordenin, D.A., Stith, C.M., Burgers, P.M.J., and Kunkel, T.A. (2008) Division of labor at the eukaryotic replication fork. Molec. Cell, 30, 137-144.
  104. Kadyrov, F.A., Holmes, S.F., Arana, M.E., Lukianova, O.A., O'Donnel, M., Kunkel, T.A., and Modrich, P. (2007) Saccharomyces cerevisiae MutL alpha is a mismatch repair endonuclease. The Journal of biological chemistry 282(51):37181-37190. [Abstract]
  105. Garcia-Diaz, M. and Bebenek, K. (2007) Multiple functions of DNA polymerases. Critical reviews in plant sciences 2, 105-122. [Abstract]
  106. Sacho, E.J., Karyrov, F.A., Modrich, P., Kunkel, T.A., and Erie, D.A. (2008) Direct visualization of asymmetric adenine nucleotide induced conformational changes in MutLalpha. Molec. Cell 29, 112-121
  107. Schaetzlein, S., Kodandaramireddy, N.R., Ju, Z., Lechel, A., Stepzynska, A., Lilli, D.R., Clark, A.B., Rudolph, C., Kuhnel, F., Wei, K., Schlegelberger, B., Schirmacher, P., Kunkel, T.A., Greenberg, R.A., Edelmann, W., and Rudolph, K.L. (2007) Exouclease-1 deletion impairs DNA damage signal induction and prolongs lifespan of telomere-dysfunctional mice. Cell 130, 863-877. [Abstract]
  108. Sakamoto, A., Stone, J.E., Kissling, G.E., McCulloch, S.D., Pavlov, Y.I., and Kunkel, T.A. (2007) Mutator alleles of yeast DNA polymerase. DNA Repair, 6, 1829-1838.
  109. Moon, A.F., Garcia-Diaz, M., Batra, V.K., Beard, W.A., Bebenek, K., Kunkel, T.A., Wilson, S.H., and Pedersen, L.C. (2007) The X family portrait: Structural insights into biological functions of X family DNA polymerases. DNA Repair, 6, 1709-1725.
  110. Pursell, Z.F., Isoz, I., Lundström, E.B., Johansson, E., and Kunkel, T.A. (2007) Yeast DNA polymerase ε participates in leading strand DNA replication. Science 317, 127-130. [Abstract]
  111. McCulloch, S.D., Garg, P., Burgers, P.J.M., and Kunkel, T.A. (2006) Effects of accessory proteins on bypass of a cis-syn thymine-thymine dimer by Saccharomyces cerivisiae DNA polymerase ·. Biochemistry 46, 8888-8896.
  112. Storici, F., Bebenek, K., Kunkel, T.A., Gordenin, D.A., and Resnick, M.A. (2007) RNA-templated DNA repair. Nature 447, 338-341. [Abstract]
  113. Garcia-Diaz, M., Bebenek, K., Pedersen, L.C., and Kunkel, T.A. (2007) Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair 6, 1333-1340. [Abstract]
  114. Pursell, Z.P., Isoz, I., Lundström, E.-B., Johansson, E., and Kunkel, T.A. (2007) Regulation of B family DNA polymerase fidelity by a conserved active site residue: Characterization of M644W, M644L and M644F mutants of yeast DNA polymerase µ. Nucl. Acids Res. 35, 3076-3086. [Abstract]
  115. Clark, A.B., Deterding, L., Tomer, K.B., and Kunkel, T.A. (2007) Multiple functions for the N-terminal region of Msh6. Nucl. Acids Res. 35, 4114-4123. [Abstract]
  116. Arana, M.E., Takata, K., Garcia-Diaz, M., Wood, R.D., and Kunkel, T.S. (2007) A unique error signature for human DNA polymerase ν. DNA Repair 6, 213-223. [Abstract]
  117. Moon, A.F., Garcia-Diaz, M., Bebenek, K., Davis, B.J., Zhong, X., Ramsden, D.A., Kunkel, T.A., and Pedersen, L.C. (2007) Structural insight into the substrate specificity of DNA polymerase μ. Nature Struct. Molec. Biol. 14, 45-53. [Abstract]
  118. Nick McElhinny, S.A., Stith, C.M., Burgers, P.M.J., and Kunkel, T.A. (2007) Inefficient proofreading and biased error rates during inaccurate DNA synthesis by a mutant derivative of Saccharomyces cerevisiae DNA polymerase δ. J. Biol. Chem. 282, 2324-2332. [Abstract]
  119. Holmes, S.F., Drotschmann Scarpinato, K., McCulloch, S.D., Schaaper, R.M., and Kunkel, T.A. (2007) Specialized mismatch repair function of Glu339 in the Phe-X-Glu motif of yeast Msh6. DNA Repair 6, 293-303. [Abstract]
  120. Nick McElhinny S.A., Pavlov Y.I., Kunkel T.A. (2006) Evidence for extrinsic exonucleolytic proofreading. Cell cycle (Georgetown, Tex.) 5(9):958-962. [Abstract]
  121. Garcia-Diaz, M. and Kunkel, T.A. (2006) Mechanism of a genetic glissando: structural biology of indel mutations. Trends Biochem. Sci. 31, 206-214. [Abstract]
  122. Nick McElhinny, S., Pavlov, Y.I., and Kunkel, T.A. (2006) Evidence for extrinsic exonucleolytic proofreading. Cell Cycle 5, 958-962. [Abstract]
  123. Fortune, J., Stith, C.M., Kissling, G.E., Burgers, P.M.J., and Kunkel, T.A. (2006) RPA and PCNA suppress formation of large deletion errors by yeast DNA polymerase δ. Nucl. Acids Res. 34, 4335-4341. [Abstract]
  124. Zhong, X., Garg, P., Stith, C.M., Nick McElhinny, S.A., Burgers, P.M.J., and Kunkel, T.A. (2006) The fidelity of DNA synthesis by yeast DNA polymerase ζ with and without accessory proteins. Nucl. Acids Res. 34, 4731-4742. [Abstract]
  125. McCulloch, S.D. and Kunkel, T.A. (2006) Multiple solutions to inefficient lesion bypass by T7 DNA polymerase. DNA Repair 5, 1373-1383. [Abstract]
  126. Dumsdorf, C., Clark, A.C., Lin, Q., Kissling, G.E., Yaun, T., Kucherlapati, R., McGregor, W.G., and Kunkel, T.A. (2006) Participation of mouse DNA polymerase iota in strand biased mutagenic bypass of UV photoproducts and suppression of skin cancer. Proc. Natl. Acad. Sci. U.S.A. 103, 18083-18088. [Abstract]
  127. Lin, Q., Clark, A.B., McCulloch, S.D., Yuan, T., Bronson, R.T., Kunkel, T.A., and Kucherlapati, R. (2006) Increased susceptibility to UV-induced skin carcinogenesis in polymerase eta-deficient mice. Cancer Research 66, 87-94. [Abstract]
  128. Gacia-Diaz, M., Bebenek, K., Krahn, J.M, Pedersen, L.C., and Kunkel, T.A. (2006) Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase. Cell 124, 331-342. [Abstract]
  129. Pavlov, Y.I, Frahm, C., Nick-McElhinny, S., Niimi, A., Suzuki, M., and Kunkel, T.A. (2006) Evidence that errors made by DNA polymerase alpha are corrected by DNA polymerase delta. Current Biology 16, 202-207. [Abstract]
  130. Brieba, L.G., Kokoska, R.J., Bebenek, K., Kunkel, T.A., and Ellenberger, T. (2005) A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine. Structure 13, 1653-1659. [Abstract]
  131. Bebenek, K., Garcia-Diaz, M., Patishall, S.R., and Kunkel, T.A. (2005) Biochemical properties of Saccharomyces cerevisiae DNA polymerase IV. J. Biol. Chem. 280, 20051-20058. [Abstract]
  132. Nick-McElhinny, S.A., Havener, J.M., Garcia-Diaz, M., Juárez, R., Bebenek, K., Kee, B.L., Blanco, L., Kunkel, T.A., and Ramsden, D.A. (2005) A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end-joining. Molec. Cell 19, 357-366. [Abstract]
  133. Fortune, J., Pavlov, Y.I, Welch, C.M., Burgers, P.M.J., and Kunkel, T.A. (2005) Saccharomyces cerevisiae DNA polymerase delta: High fidelity for base substitutions but low fidelity for single- and multi-base deletions. J. Biol. Chem. 280, 29980-29987. [Abstract]
  134. Kunkel, T.A. and Erie, D. (2005) DNA mismatch repair. Annu. Rev. Biochem.74, 681-710. [Abstract]
  135. Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., and Pedersen, L.C. (2005) A closed conformation for the pol lambda catalytic cycle. Nat. Struct. Mol. Biol.12, 97-98. [Abstract]
  136. Clark, A.B. and Kunkel, T.A. (2004) Cadmium inhibits the functions of eukaryotic MutS complexes. J. Biol. Chem.279, 53903-53906. [Abstract]
  137. Bebenek, K. and Kunkel, T.A. (2004) Functions of DNA polymerases. Adv. Protein Chem.69, 137-165. [Abstract]
  138. Brieba, L.G., Eichman, B.F., Kokoska, R.J., Doublié, S, Kunkel, T.A., and Ellenberger, T. (2004) Structural basis for the dual coding potential of 8-oxoguanosine by a high fidelity DNA polymerase. EMBO J.23, 3452-3461. [Abstract]
  139. McCulloch, S.D., Kokoska, R.J., Chilkova, O., Welch, C.M., Johansson, E., Burgers, P.M.J., and Kunkel, T.A. (2004) Enzymatic switching for efficient and accurate translesion DNA replication. Nucl. Acids Res.32, 4665-4675. [Abstract]
  140. Kunkel, T.A. (2004) DNA Replication Fidelity. J. Biol. Chem.279, 16895-16898. [Abstract]
  141. McCulloch, S.D., Kokoska, R.J., Masutani, C., Iwai, S., Hanaoka, F., and Kunkel, T.A. (2004) Preferential cis-syn thymine dimer bypass by DNA polymerase eta occurs with biased fidelity. Nature 428, 97-100. [Abstract]
  142. Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Blanco, L., Kunkel, T.A., and Pedersen, L. C. (2004) A structural solution for the DNA polymerase lamda-dependent repair of DNA gaps with minimal homology. Mol. Cell13, 561-572. [Abstract]
  143. Lin, D.P., Wang, Y., Scherer, S.J., Clark, A.B., Yang, K., Avdievich, E., Jin, B., Werling, U., Parris, T., Kurihara, N., Umar, A., Kucherlapati, R., Lipkin, M., Kunkel, T.A., and Edelmann, W. (2004) An Msh2 point mutation uncouples DNA mismatch repair and apoptosis. Cancer Res.64, 517-522. [Abstract]
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