Selected Publications

DNA Replication Fidelity Group

1. 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.
2. 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, in press.
3. 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., in press.
4. 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, in press.
5. Kadyrov FA, Holmes SF, Arana ME, Lukianova OA, O'Donnel M, Kunkel TA, 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)
6. Garcia-Diaz M, 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=)
7. 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
   
8. 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)
9. 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.
10. 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.
11. 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)
12. 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.
13. 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
14. 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
15. 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
16. 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
17. Cutalo, J. M., Darden, T.A., Kunkel, T.A. and Tomer, K.B. (2006) Mapping the dimer interface in the C-terminal domains of the yeast Mlh1-Pms1 heterodimer. Biochemistry, 45, 15458-15467. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17176067&query_hl=34&itool=pubmed_docsum
18. 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
19. 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
20. 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
21. Luciani, M.G., Campregher, C., Fortune, J.M., Kunkel, T.A. and Gasche, C. (2007) 5-ASA affects cell cycle progression in colorectal cells by reversibly activating a replication checkpoint. Gastroenterology 132, 221-235. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17241873&query_hl=48&itool=pubmed_docsum
22. 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
23. Barone, F., McCulloch, S.D., MacPherson, P., Maga, G., Yamada, M., Nohmi, T., Minoprio, A., Mazzei, F., Kunkel, T.A., Karran, P. and Bignami, M. (2007) Replication of 2-hydroxyadenine-containing DNA substrates and recognition by human MutSα. DNA Repair 6, 355-366. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17188944&query_hl=15&itool=pubmed_docsum
24. 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
25. 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
26. Shcherbakova, P.V. and Kunkel, T.A. (2006) DNA polymerases and the fidelity of DNA replication. In DNA replication and human disease (ed. M.L. DePamphilis), pp. 391-410. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
27. Kunkel, T.A. and Van Houten, B. (2006) Survival choices. Nature Cell Biol. 8, 547-549. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16738701&query_hl=56&itool=pubmed_docsum
28. Picher, A.J., García-Díaz, M., Bebenek, K., Pedersen, L.C., Kunkel, T.A. and Blanco, L. (2006) Promiscuous mismatch extension by human DNA polymerase lambda. Nucl. Acids Res. 34, 3259-3266. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16807316&query_hl=70&itool=pubmed_docsum
29. 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
30. 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
31. 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
32. 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
33. McCulloch, S.D and Kunkel, T.A. (2006) Measuring the fidelity of translesion DNA synthesis. Meth. Enzymol., 408, 341-55. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16793379
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. Garcia-Diaz, M., Bebenek, K., Gao, G., Pedersen, L.C., London, R.E. and Kunkel, T.A. (2005) Structure-function studies of DNA polymerase lambda. DNA Repair 4, 1358-1367. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16213194
38. 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
39. 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
40. 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
41. 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
42. Song, S., Pursell, Z., Copeland, W.C., Longley, M.J., Kunkel, T.A. and Mathews, C.K. (2005) DNA precursor asymmetries in mammalian tissue mitochondria and possible contribution to mitochondrial mutagenesis through reduced replication fidelity. Proc. Natl. Acad. Sci. U.S.A., 102, 4990-4995. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15784738
43. 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
44. 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
45. Jin, Y.H., Garg, P., Stith, C.M.W., Al-Refai, H., Sterling, J.F., Murray, L.J.W., Kunkel, T.A., Resnick, M.A., Burgers, P.M. and Gordenin, D.A. (2005) The multiple biological roles of the 3'-->5' exonuclease of Saccharomyces cerevisiae DNA polymerase delta require switching between the polymerase and exonuclease domains.Mol. Cell. Biol.25, 461-471. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15601866
46. 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
47. 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
48. 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
49. 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
50. 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
51. 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
52. 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
53. Wang, M., Devereux, T.R., Vikis, H.G., McCulloch, S.D., Holliday, W., Anna, C., Wang, Y., Bebenek, K., Kunkel, T.A., Guan, K. and You, M. (2004) Pol iota is a candidate for the mouse pulmonary adenoma resistance 2 locus, a major modifier of chemically induced lung neoplasia. Cancer Res.64, 1924-1931. [Abstract] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15026325
54. 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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