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Items: 19

1.

Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.

Whitaker AM, Smith MR, Schaich MA, Freudenthal BD.

Nucleic Acids Res. 2017 Apr 26. doi: 10.1093/nar/gkx293. [Epub ahead of print]

2.

Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ.

Klvaňa M, Bren U, Florián J.

J Phys Chem B. 2016 Dec 29;120(51):13017-13030. doi: 10.1021/acs.jpcb.6b08581. Epub 2016 Dec 19.

PMID:
27992186
3.

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal JP, Andrés Cisneros G.

J Comput Chem. 2016 Apr 30;37(11):1019-29. doi: 10.1002/jcc.24295. Epub 2016 Jan 18.

4.

Arabidopsis DNA polymerase lambda mutant is mildly sensitive to DNA double strand breaks but defective in integration of a transgene.

Furukawa T, Angelis KJ, Britt AB.

Front Plant Sci. 2015 May 27;6:357. doi: 10.3389/fpls.2015.00357. eCollection 2015.

5.

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.

6.

Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase β.

Koag MC, Lee S.

J Am Chem Soc. 2014 Apr 16;136(15):5709-21. doi: 10.1021/ja500172d. Epub 2014 Apr 2.

7.

Computational simulation strategies for analysis of multisubunit RNA polymerases.

Wang B, Feig M, Cukier RI, Burton ZF.

Chem Rev. 2013 Nov 13;113(11):8546-66. doi: 10.1021/cr400046x. Epub 2013 Aug 29. Review. No abstract available.

8.

Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction.

Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH.

J Am Chem Soc. 2013 May 29;135(21):8078-88. doi: 10.1021/ja403842j. Epub 2013 May 16.

9.

Human DNA polymerase β, but not λ, can bypass a 2-deoxyribonolactone lesion together with proliferating cell nuclear antigen.

Crespan E, Pasi E, Imoto S, Hübscher U, Greenberg MM, Maga G.

ACS Chem Biol. 2013 Feb 15;8(2):336-44. doi: 10.1021/cb300542k. Epub 2012 Nov 7.

10.

Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion.

Lior-Hoffmann L, Wang L, Wang S, Geacintov NE, Broyde S, Zhang Y.

Nucleic Acids Res. 2012 Oct;40(18):9193-205. doi: 10.1093/nar/gks653. Epub 2012 Jul 5.

11.

Prechemistry versus preorganization in DNA replication fidelity.

Ram Prasad B, Warshel A.

Proteins. 2011 Oct;79(10):2900-19. doi: 10.1002/prot.23128. Epub 2011 Aug 26.

12.

Effect of transition metal ions on the fluorescence and Taq-catalyzed polymerase chain reaction of tricyclic cytidine analogs.

Stengel G, Purse BW, Kuchta RD.

Anal Biochem. 2011 Sep 1;416(1):53-60. doi: 10.1016/j.ab.2011.04.033. Epub 2011 Apr 27.

13.

Loop 1 modulates the fidelity of DNA polymerase lambda.

Bebenek K, Garcia-Diaz M, Zhou RZ, Povirk LF, Kunkel TA.

Nucleic Acids Res. 2010 Sep;38(16):5419-31. doi: 10.1093/nar/gkq261. Epub 2010 Apr 30.

14.

Interaction between DNA Polymerase lambda and anticancer nucleoside analogs.

Garcia-Diaz M, Murray MS, Kunkel TA, Chou KM.

J Biol Chem. 2010 May 28;285(22):16874-9. doi: 10.1074/jbc.M109.094391. Epub 2010 Mar 26.

15.
16.

Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region.

Romain F, Barbosa I, Gouge J, Rougeon F, Delarue M.

Nucleic Acids Res. 2009 Aug;37(14):4642-56. doi: 10.1093/nar/gkp460. Epub 2009 Jun 5.

17.

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

Rosta E, Woodcock HL, Brooks BR, Hummer G.

J Comput Chem. 2009 Aug;30(11):1634-41. doi: 10.1002/jcc.21312.

18.

Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.

Wang L, Broyde S, Zhang Y.

J Mol Biol. 2009 Jun 19;389(4):787-96. doi: 10.1016/j.jmb.2009.04.029. Epub 2009 Apr 21.

19.

Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues.

Cisneros GA, Perera L, Schaaper RM, Pedersen LC, London RE, Pedersen LG, Darden TA.

J Am Chem Soc. 2009 Feb 4;131(4):1550-6. doi: 10.1021/ja8082818.

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