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

Donnianni RA, Zhou ZX, Lujan SA, Al-Zain A, Garcia V, Glancy E, Burkholder AB, Kunkel TA, Symington LS.

Mol Cell. 2019 Nov 7;76(3):371-381.e4. doi: 10.1016/j.molcel.2019.07.033. Epub 2019 Sep 5.


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

Garbacz MA, Lujan SA, Kunkel TA.

Curr Genet. 2019 Sep 6. doi: 10.1007/s00294-019-01023-4. [Epub ahead of print] Review.


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

Zhou ZX, Lujan SA, Burkholder AB, Garbacz MA, Kunkel TA.

Nat Commun. 2019 Sep 5;10(1):3992. doi: 10.1038/s41467-019-11995-z.


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

Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC.

Nucleic Acids Res. 2019 Sep 26;47(17):9410-9422. doi: 10.1093/nar/gkz680.


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

Williams JS, Lujan SA, Zhou ZX, Burkholder AB, Clark AB, Fargo DC, Kunkel TA.

DNA Repair (Amst). 2019 Dec;84:102641. doi: 10.1016/j.dnarep.2019.102641. Epub 2019 Jul 3.


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

Garbacz MA, Cox PB, Sharma S, Lujan SA, Chabes A, Kunkel TA.

Nucleic Acids Res. 2019 May 7;47(8):3986-3995. doi: 10.1093/nar/gkz048.


Ribonucleotide Excision Repair Is Essential to Prevent Squamous Cell Carcinoma of the Skin.

Hiller B, Hoppe A, Haase C, Hiller C, Schubert N, Müller W, Reijns MAM, Jackson AP, Kunkel TA, Wenzel J, Behrendt R, Roers A.

Cancer Res. 2018 Oct 15;78(20):5917-5926. doi: 10.1158/0008-5472.CAN-18-1099. Epub 2018 Aug 28.


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

Kunkel TA.

J Clin Invest. 2018 Aug 31;128(9):3754-3756. doi: 10.1172/JCI123021. Epub 2018 Aug 20.


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

Kaminski AM, Tumbale PP, Schellenberg MJ, Williams RS, Williams JG, Kunkel TA, Pedersen LC, Bebenek K.

Nat Commun. 2018 Jul 6;9(1):2642. doi: 10.1038/s41467-018-05024-8.


Muver, a computational framework for accurately calling accumulated mutations.

Burkholder AB, Lujan SA, Lavender CA, Grimm SA, Kunkel TA, Fargo DC.

BMC Genomics. 2018 May 9;19(1):345. doi: 10.1186/s12864-018-4753-3.


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

Garbacz MA, Lujan SA, Burkholder AB, Cox PB, Wu Q, Zhou ZX, Haber JE, Kunkel TA.

Nat Commun. 2018 Feb 27;9(1):858. doi: 10.1038/s41467-018-03270-4.


Studying Topoisomerase 1-Mediated Damage at Genomic Ribonucleotides.

Williams JS, Kunkel TA.

Methods Mol Biol. 2018;1703:241-257. doi: 10.1007/978-1-4939-7459-7_17.


Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing.

Orebaugh CD, Lujan SA, Burkholder AB, Clausen AR, Kunkel TA.

Methods Mol Biol. 2018;1672:329-345. doi: 10.1007/978-1-4939-7306-4_23.


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

Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC.

Nucleic Acids Res. 2017 Sep 6;45(15):9138-9148. doi: 10.1093/nar/gkx527.


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

Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH.

Nat Commun. 2017 Aug 15;8(1):253. doi: 10.1038/s41467-017-00271-7.


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

Williams JS, Gehle DB, Kunkel TA.

DNA Repair (Amst). 2017 May;53:52-58. doi: 10.1016/j.dnarep.2017.02.016. Epub 2017 Mar 6.


Eukaryotic DNA Replication Fork.

Burgers PMJ, Kunkel TA.

Annu Rev Biochem. 2017 Jun 20;86:417-438. doi: 10.1146/annurev-biochem-061516-044709. Epub 2017 Mar 1. Review.


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

Huang SN, Williams JS, Arana ME, Kunkel TA, Pommier Y.

EMBO J. 2017 Feb 1;36(3):361-373. doi: 10.15252/embj.201592426. Epub 2016 Dec 8.


DNA Polymerases Divide the Labor of Genome Replication.

Lujan SA, Williams JS, Kunkel TA.

Trends Cell Biol. 2016 Sep;26(9):640-654. doi: 10.1016/j.tcb.2016.04.012. Epub 2016 Jun 1. Review.


Processing ribonucleotides incorporated during eukaryotic DNA replication.

Williams JS, Lujan SA, Kunkel TA.

Nat Rev Mol Cell Biol. 2016 Jun;17(6):350-63. doi: 10.1038/nrm.2016.37. Epub 2016 Apr 20. Review.


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

Burgers PMJ, Gordenin D, Kunkel TA.

Mol Cell. 2016 Feb 18;61(4):492-493. doi: 10.1016/j.molcel.2016.01.017. No abstract available.


Eukaryotic genome instability in light of asymmetric DNA replication.

Lujan SA, Williams JS, Kunkel TA.

Crit Rev Biochem Mol Biol. 2016;51(1):43-52. doi: 10.3109/10409238.2015.1117055. Epub 2015 Dec 20. Review.


Celebrating DNA's Repair Crew.

Kunkel TA.

Cell. 2015 Dec 3;163(6):1301-3. doi: 10.1016/j.cell.2015.11.028.


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

Watt DL, Buckland RJ, Lujan SA, Kunkel TA, Chabes A.

Nucleic Acids Res. 2016 Feb 29;44(4):1669-80. doi: 10.1093/nar/gkv1298. Epub 2015 Nov 24.


Polymerase δ replicates both strands after homologous recombination-dependent fork restart.

Miyabe I, Mizuno K, Keszthelyi A, Daigaku Y, Skouteri M, Mohebi S, Kunkel TA, Murray JM, Carr AM.

Nat Struct Mol Biol. 2015 Nov;22(11):932-8. doi: 10.1038/nsmb.3100. Epub 2015 Oct 5.


Eukaryotic Mismatch Repair in Relation to DNA Replication.

Kunkel TA, Erie DA.

Annu Rev Genet. 2015;49:291-313. doi: 10.1146/annurev-genet-112414-054722. Review.


Stimulation of Chromosomal Rearrangements by Ribonucleotides.

Conover HN, Lujan SA, Chapman MJ, Cornelio DA, Sharif R, Williams JS, Clark AB, Camilo F, Kunkel TA, Argueso JL.

Genetics. 2015 Nov;201(3):951-61. doi: 10.1534/genetics.115.181149. Epub 2015 Sep 22.


Creative template-dependent synthesis by human polymerase mu.

Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek K.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):E4530-6. doi: 10.1073/pnas.1505798112. Epub 2015 Aug 3.


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

St Charles JA, Liberti SE, Williams JS, Lujan SA, Kunkel TA.

DNA Repair (Amst). 2015 Jul;31:41-51. doi: 10.1016/j.dnarep.2015.04.006. Epub 2015 Apr 25.


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

Liu S, Lu G, Ali S, Liu W, Zheng L, Dai H, Li H, Xu H, Hua Y, Zhou Y, Ortega J, Li GM, Kunkel TA, Shen B.

EMBO J. 2015 Jul 2;34(13):1829-43. doi: 10.15252/embj.201489865. Epub 2015 Apr 28.


Measuring ribonucleotide incorporation into DNA in vitro and in vivo.

Clausen AR, Williams JS, Kunkel TA.

Methods Mol Biol. 2015;1300:123-39. doi: 10.1007/978-1-4939-2596-4_9.


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

Lujan SA, Clark AB, Kunkel TA.

Nucleic Acids Res. 2015 Apr 30;43(8):4067-74. doi: 10.1093/nar/gkv271. Epub 2015 Mar 30.


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

Williams JS, Clausen AR, Lujan SA, Marjavaara L, Clark AB, Burgers PM, Chabes A, Kunkel TA.

Nat Struct Mol Biol. 2015 Apr;22(4):291-7. doi: 10.1038/nsmb.2989. Epub 2015 Mar 9.


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

Martínez-Jiménez MI, García-Gómez S, Bebenek K, Sastre-Moreno G, Calvo PA, Díaz-Talavera A, Kunkel TA, Blanco L.

DNA Repair (Amst). 2015 May;29:127-38. doi: 10.1016/j.dnarep.2015.02.013. Epub 2015 Feb 23.


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

Clausen AR, Lujan SA, Burkholder AB, Orebaugh CD, Williams JS, Clausen MF, Malc EP, Mieczkowski PA, Fargo DC, Smith DJ, Kunkel TA.

Nat Struct Mol Biol. 2015 Mar;22(3):185-91. doi: 10.1038/nsmb.2957. Epub 2015 Jan 26.


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

Buckland RJ, Watt DL, Chittoor B, Nilsson AK, Kunkel TA, Chabes A.

PLoS Genet. 2014 Dec 4;10(12):e1004846. doi: 10.1371/journal.pgen.1004846. eCollection 2014 Dec.


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

Van C, Williams JS, Kunkel TA, Peterson CL.

DNA Repair (Amst). 2015 Jan;25:9-14. doi: 10.1016/j.dnarep.2014.10.010. Epub 2014 Nov 20.


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

Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, Kunkel TA.

Genome Res. 2014 Nov;24(11):1751-64. doi: 10.1101/gr.178335.114. Epub 2014 Sep 12.


Delivering nonidentical twins.

Kunkel TA, Burgers PM.

Nat Struct Mol Biol. 2014 Aug;21(8):649-51. doi: 10.1038/nsmb.2852. Epub 2014 Jul 6. No abstract available.


Ribonucleotides in DNA: origins, repair and consequences.

Williams JS, Kunkel TA.

DNA Repair (Amst). 2014 Jul;19:27-37. doi: 10.1016/j.dnarep.2014.03.029. Epub 2014 Apr 30. Review.


Structure-function studies of DNA polymerase λ.

Bebenek K, Pedersen LC, Kunkel TA.

Biochemistry. 2014 May 6;53(17):2781-92. doi: 10.1021/bi4017236. Epub 2014 Apr 23. Review.


Ribonucleotide incorporation by yeast DNA polymerase ζ.

Makarova AV, Nick McElhinny SA, Watts BE, Kunkel TA, Burgers PM.

DNA Repair (Amst). 2014 Jun;18:63-7. doi: 10.1016/j.dnarep.2014.02.017. Epub 2014 Mar 24.


Structures of the Leishmania infantum polymerase beta.

Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA, Bebenek K, Garcia-Diaz M.

DNA Repair (Amst). 2014 Jun;18:1-9. doi: 10.1016/j.dnarep.2014.03.001. Epub 2014 Mar 22.


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

Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC.

Nat Struct Mol Biol. 2014 Mar;21(3):253-60. doi: 10.1038/nsmb.2766. Epub 2014 Feb 2.


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

Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS.

Nature. 2014 Feb 6;506(7486):111-5. doi: 10.1038/nature12824. Epub 2013 Dec 22.


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

Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16802-7. doi: 10.1073/pnas.1309119110. Epub 2013 Sep 30.


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

Lormand JD, Buncher N, Murphy CT, Kaur P, Lee MY, Burgers P, Wang H, Kunkel TA, Opresko PL.

Nucleic Acids Res. 2013 Dec;41(22):10323-33. doi: 10.1093/nar/gkt813. Epub 2013 Sep 13.


Mammalian Exo1 encodes both structural and catalytic functions that play distinct roles in essential biological processes.

Schaetzlein S, Chahwan R, Avdievich E, Roa S, Wei K, Eoff RL, Sellers RS, Clark AB, Kunkel TA, Scharff MD, Edelmann W.

Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):E2470-9. doi: 10.1073/pnas.1308512110. Epub 2013 Jun 10.

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