Selected Publications

DNA Replication Fidelity Group

1. Kunkel T.A., Burgers P.M. (2008) Dividing the workload at a eukaryotic replication fork. Trends in cell biology. 18(11), 521-527. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18824354)
2. 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] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18503083)
3. 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] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18503084)
4. 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.
5. 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.
6. 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.
7. Cisneros, G.A., Perera, L., Garcia-Diaz, M., Bebenek, K., Kunkel, T.A., and Pedersen, L.G. (2007) Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio QM/MM studies. DNA Repair, in press.
8. 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.
9. 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.
10. 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.
11. 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.
12. Kadyrov, F.A., Holmes, S.F., Arana, M.E., Lukianova, O.A., O'Donnel, M., Kunkel, T.A., and Modrich, P. Saccharomyces cerevisiae MutL alpha is a mismatch repair endonuclease. The Journal of biological chemistry 2007 282(51):37181-37190. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17951253)
13. Garcia-Diaz, M. and Bebenek, K. Multiple functions of DNA polymerases. Critical reviews in plant sciences 2007 2, 105-122. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=)
14. 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
    
15. 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] (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17803909&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum)
16. 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.
17. 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.
18. 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] (http://www.sciencemag.org/cgi/content/abstract/317/5834/127)
19. 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.
20. Storici, F., Bebenek, K., Kunkel, T.A., Gordenin, D.A., and Resnick, M.A. (2007) RNA-templated DNA repair. Nature 447, 338-341. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17429354&query_hl=6&itool=pubmed_docsum
21. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17475573&query_hl=3&itool=pubmed_docsum
22. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17452367&query_hl=8&itool=pubmed_docsum
23. 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] http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=Multiple%20functions%20for%20the%20N-terminal%20region%20of%20Msh6
24. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17118716&query_hl=37&itool=pubmed_docsum
25. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17159995&query_hl=39&itool=pubmed_docsum
26. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17121822&query_hl=45&itool=pubmed_docsum
27. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17141577&query_hl=51&itool=pubmed_docsum
28. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16545956&query_hl=3&itool=pubmed_docsum
29. Nick McElhinny, S., Pavlov, Y.I., and Kunkel, T.A. (2006) Evidence for extrinsic exonucleolytic proofreading. Cell Cycle 5, 958-962. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16687920&query_hl=64&itool=pubmed_docsum
30. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16936322&query_hl=73&itool=pubmed_docsum
31. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16971464&query_hl=75&itool=pubmed_docsum
32. McCulloch, S.D. and Kunkel, T.A. (2006) Multiple solutions to inefficient lesion bypass by T7 DNA polymerase. DNA Repair 5, 1373-1383. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16876489&query_hl=78&itool=pubmed_docsum
33. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17114294&query_hl=86&itool=pubmed_docsum
34. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16397220
35. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16439207
36. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16431373
37. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16271888
38. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15778218
39. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16061182
40. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15964835
41. Kunkel, T.A. and Erie, D. (2005) DNA mismatch repair. Annu. Rev. Biochem.74, 681-710. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15952900
42. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15608652
43. Clark, A.B. and Kunkel, T.A. (2004) Cadmium inhibits the functions of eukaryotic MutS complexes. J. Biol. Chem.279, 53903-53906. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15513922
44. Bebenek, K. and Kunkel, T.A. (2004) Functions of DNA polymerases. Adv. Protein Chem.69, 137-165. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15588842
45. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15297882
46. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15333698
47. Kunkel, T.A. (2004) DNA Replication Fidelity. J. Biol. Chem.279, 16895-16898. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14988392
48. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14999287
49. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14992725
50. 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] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14744764

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