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Revealing an Internal Stabilization Deficiency in the DNA Polymerase β K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.

Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH.

Biochemistry. 2020 Mar 3;59(8):955-963. doi: 10.1021/acs.biochem.9b01072. Epub 2020 Feb 12.


A pre-catalytic non-covalent step governs DNA polymerase β fidelity.

Alnajjar KS, Krylov IS, Negahbani A, Haratipour P, Kashemirov BA, Huang J, Mahmoud M, McKenna CE, Goodman MF, Sweasy JB.

Nucleic Acids Res. 2019 Dec 16;47(22):11839-11849. doi: 10.1093/nar/gkz1076.


AID-RNA polymerase II transcription-dependent deamination of IgV DNA.

Pham P, Malik S, Mak C, Calabrese PC, Roeder RG, Goodman MF.

Nucleic Acids Res. 2019 Nov 18;47(20):10815-10829. doi: 10.1093/nar/gkz821.


Role of RNase H enzymes in maintaining genome stability in Escherichia coli expressing a steric-gate mutant of pol VICE391.

Walsh E, Henrikus SS, Vaisman A, Makiela-Dzbenska K, Armstrong TJ, Łazowski K, McDonald JP, Goodman MF, van Oijen AM, Jonczyk P, Fijalkowska IJ, Robinson A, Woodgate R.

DNA Repair (Amst). 2019 Dec;84:102685. doi: 10.1016/j.dnarep.2019.102685. Epub 2019 Aug 10.


Random Walk Enzymes: Information Theory, Quantum Isomorphism, and Entropy Dispersion.

Mak CH, Pham P, Goodman MF.

J Phys Chem A. 2019 Apr 4;123(13):3030-3037. doi: 10.1021/acs.jpca.9b00910. Epub 2019 Mar 21.


A Transition-State Perspective on Y-Family DNA Polymerase η Fidelity in Comparison with X-Family DNA Polymerases λ and β.

Oertell K, Florián J, Haratipour P, Crans DC, Kashemirov BA, Wilson SH, McKenna CE, Goodman MF.

Biochemistry. 2019 Apr 2;58(13):1764-1773. doi: 10.1021/acs.biochem.9b00087. Epub 2019 Mar 14.


Conformational regulation of Escherichia coli DNA polymerase V by RecA and ATP.

Jaszczur MM, Vo DD, Stanciauskas R, Bertram JG, Sikand A, Cox MM, Woodgate R, Mak CH, Pinaud F, Goodman MF.

PLoS Genet. 2019 Feb 4;15(2):e1007956. doi: 10.1371/journal.pgen.1007956. eCollection 2019 Feb.


Relating DNA base-pairing in aqueous media to DNA polymerase fidelity.

Petruska J, Goodman MF.

Nat Rev Chem. 2017 Sep;1(9). pii: 0074. doi: 10.1038/s41570-017-0074. Epub 2017 Sep 6.


Probing DNA Base-Dependent Leaving Group Kinetic Effects on the DNA Polymerase Transition State.

Oertell K, Kashemirov BA, Negahbani A, Minard C, Haratipour P, Alnajjar KS, Sweasy JB, Batra VK, Beard WA, Wilson SH, McKenna CE, Goodman MF.

Biochemistry. 2018 Jul 3;57(26):3925-3933. doi: 10.1021/acs.biochem.8b00417. Epub 2018 Jun 19.


Mapping Functional Substrate-Enzyme Interactions in the pol β Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.

Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH.

Biochemistry. 2018 Jul 3;57(26):3934-3944. doi: 10.1021/acs.biochem.8b00418. Epub 2018 Jun 21.


Smoking gun for a rare mutation mechanism.

Goodman MF.

Nature. 2018 Feb 8;554(7691):180-181. doi: 10.1038/d41586-018-00418-6. No abstract available.


Smoking gun for a rare mutation mechanism.

Goodman MF.

Nature. 2018 Feb;554(7691):180-181. doi: 10.1038/d41586-018-00418-6. No abstract available.


DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli.

Henrikus SS, Wood EA, McDonald JP, Cox MM, Woodgate R, Goodman MF, van Oijen AM, Robinson A.

PLoS Genet. 2018 Jan 19;14(1):e1007161. doi: 10.1371/journal.pgen.1007161. eCollection 2018 Jan.


DNA Polymerase β Cancer-Associated Variant I260M Exhibits Nonspecific Selectivity toward the β-γ Bridging Group of the Incoming dNTP.

Alnajjar KS, Negahbani A, Nakhjiri M, Krylov IS, Kashemirov BA, McKenna CE, Goodman MF, Sweasy JB.

Biochemistry. 2017 Oct 10;56(40):5449-5456. doi: 10.1021/acs.biochem.7b00713. Epub 2017 Sep 20.


Integrity of immunoglobulin variable regions is supported by GANP during AID-induced somatic hypermutation in germinal center B cells.

Eid MMA, Shimoda M, Singh SK, Almofty SA, Pham P, Goodman MF, Maeda K, Sakaguchi N.

Int Immunol. 2017 May 1;29(5):211-220. doi: 10.1093/intimm/dxx032.


Activation-induced deoxycytidine deaminase: Structural basis for favoring WRC hot motif specificities unique among APOBEC family members.

Pham P, Afif SA, Shimoda M, Maeda K, Sakaguchi N, Pedersen LC, Goodman MF.

DNA Repair (Amst). 2017 Jun;54:8-12. doi: 10.1016/j.dnarep.2017.03.007. Epub 2017 Mar 28. No abstract available.


A Change in the Rate-Determining Step of Polymerization by the K289M DNA Polymerase β Cancer-Associated Variant.

Alnajjar KS, Garcia-Barboza B, Negahbani A, Nakhjiri M, Kashemirov B, McKenna C, Goodman MF, Sweasy JB.

Biochemistry. 2017 Apr 18;56(15):2096-2105. doi: 10.1021/acs.biochem.6b01230. Epub 2017 Apr 6.


Better living with hyper-mutation.

Goodman MF.

Environ Mol Mutagen. 2016 Jul;57(6):421-34. doi: 10.1002/em.22023. Epub 2016 Jun 7. Review.


Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification.

Pham P, Afif SA, Shimoda M, Maeda K, Sakaguchi N, Pedersen LC, Goodman MF.

DNA Repair (Amst). 2016 Jul;43:48-56. doi: 10.1016/j.dnarep.2016.05.029. Epub 2016 May 13.


Insights into the complex levels of regulation imposed on Escherichia coli DNA polymerase V.

Goodman MF, McDonald JP, Jaszczur MM, Woodgate R.

DNA Repair (Amst). 2016 Aug;44:42-50. doi: 10.1016/j.dnarep.2016.05.005. Epub 2016 May 13. Review.


Kinetic selection vs. free energy of DNA base pairing in control of polymerase fidelity.

Oertell K, Harcourt EM, Mohsen MG, Petruska J, Kool ET, Goodman MF.

Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2277-85. doi: 10.1073/pnas.1600279113. Epub 2016 Apr 4.


Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword.

Jaszczur M, Bertram JG, Robinson A, van Oijen AM, Woodgate R, Cox MM, Goodman MF.

Biochemistry. 2016 Apr 26;55(16):2309-18. doi: 10.1021/acs.biochem.6b00117. Epub 2016 Apr 12. Review.


Tomas Lindahl: 2015 Nobel Laureate.

Miller JH, Goodman MF.

DNA Repair (Amst). 2016 Jan;37:A29-34. doi: 10.1016/j.dnarep.2015.12.006. No abstract available.


Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution.

Senavirathne G, Bertram JG, Jaszczur M, Chaurasiya KR, Pham P, Mak CH, Goodman MF, Rueda D.

Nat Commun. 2015 Dec 18;6:10209. doi: 10.1038/ncomms10209.


Random-walk enzymes.

Mak CH, Pham P, Afif SA, Goodman MF.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Sep;92(3):032717. doi: 10.1103/PhysRevE.92.032717. Epub 2015 Sep 17.


Regulation of Mutagenic DNA Polymerase V Activation in Space and Time.

Robinson A, McDonald JP, Caldas VE, Patel M, Wood EA, Punter CM, Ghodke H, Cox MM, Woodgate R, Goodman MF, van Oijen AM.

PLoS Genet. 2015 Aug 28;11(8):e1005482. doi: 10.1371/journal.pgen.1005482. eCollection 2015 Aug.


Preparation of fluorinated RNA nucleotide analogs potentially stable to enzymatic hydrolysis in RNA and DNA polymerase assays.

Shakhmin A, Jones JP, Bychinskaya I, Zibinsky M, Oertell K, Goodman MF, Prakash GK.

J Fluor Chem. 2014 Oct;167:226-230.


Two Scaffolds from Two Flips: (α,β)/(β,γ) CH2/NH "Met-Im" Analogues of dTTP.

Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson SH, Goodman MF, McKenna CE.

Org Lett. 2015 Jun 5;17(11):2586-9. doi: 10.1021/acs.orglett.5b00799. Epub 2015 May 13.


A RecA protein surface required for activation of DNA polymerase V.

Gruber AJ, Erdem AL, Sabat G, Karata K, Jaszczur MM, Vo DD, Olsen TM, Woodgate R, Goodman MF, Cox MM.

PLoS Genet. 2015 Mar 26;11(3):e1005066. doi: 10.1371/journal.pgen.1005066. eCollection 2015 Mar.


Overlapping hotspots in CDRs are critical sites for V region diversification.

Wei L, Chahwan R, Wang S, Wang X, Pham PT, Goodman MF, Bergman A, Scharff MD, MacCarthy T.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):E728-37. doi: 10.1073/pnas.1500788112. Epub 2015 Feb 2.


The discovery of error-prone DNA polymerase V and its unique regulation by RecA and ATP.

Goodman MF.

J Biol Chem. 2014 Sep 26;289(39):26772-82. doi: 10.1074/jbc.X114.607374. Epub 2014 Aug 26.


Engineering processive DNA polymerases with maximum benefit at minimum cost.

Reha-Krantz LJ, Woodgate S, Goodman MF.

Front Microbiol. 2014 Aug 4;5:380. doi: 10.3389/fmicb.2014.00380. eCollection 2014.


DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent ATPase.

Erdem AL, Jaszczur M, Bertram JG, Woodgate R, Cox MM, Goodman MF.

Elife. 2014 Apr 24;3:e02384. doi: 10.7554/eLife.02384.


Transition state in DNA polymerase β catalysis: rate-limiting chemistry altered by base-pair configuration.

Oertell K, Chamberlain BT, Wu Y, Ferri E, Kashemirov BA, Beard WA, Wilson SH, McKenna CE, Goodman MF.

Biochemistry. 2014 Mar 25;53(11):1842-8. doi: 10.1021/bi500101z. Epub 2014 Mar 12.


The steric gate of DNA polymerase ι regulates ribonucleotide incorporation and deoxyribonucleotide fidelity.

Donigan KA, McLenigan MP, Yang W, Goodman MF, Woodgate R.

J Biol Chem. 2014 Mar 28;289(13):9136-45. doi: 10.1074/jbc.M113.545442. Epub 2014 Feb 14.


Investigating the mechanisms of ribonucleotide excision repair in Escherichia coli.

Vaisman A, McDonald JP, Noll S, Huston D, Loeb G, Goodman MF, Woodgate R.

Mutat Res. 2014 Mar;761:21-33. doi: 10.1016/j.mrfmmm.2014.01.005. Epub 2014 Feb 1.


GANP interacts with APOBEC3G and facilitates its encapsidation into the virions to reduce HIV-1 infectivity.

Maeda K, Almofty SA, Singh SK, Eid MMA, Shimoda M, Ikeda T, Koito A, Pham P, Goodman MF, Sakaguchi N.

J Immunol. 2013 Dec 15;191(12):6030-6039. doi: 10.4049/jimmunol.1302057. Epub 2013 Nov 6.


A mathematical model for scanning and catalysis on single-stranded DNA, illustrated with activation-induced deoxycytidine deaminase.

Mak CH, Pham P, Afif SA, Goodman MF.

J Biol Chem. 2013 Oct 11;288(41):29786-95. doi: 10.1074/jbc.M113.506550. Epub 2013 Aug 26.


A biochemical analysis linking APOBEC3A to disparate HIV-1 restriction and skin cancer.

Pham P, Landolph A, Mendez C, Li N, Goodman MF.

J Biol Chem. 2013 Oct 11;288(41):29294-304. doi: 10.1074/jbc.M113.504175. Epub 2013 Aug 26.


DNA polymerases are error-prone at RecA-mediated recombination intermediates.

Pomerantz RT, Goodman MF, O'Donnell ME.

Cell Cycle. 2013 Aug 15;12(16):2558-63. doi: 10.4161/cc.25691. Epub 2013 Jul 29.


Translesion DNA polymerases.

Goodman MF, Woodgate R.

Cold Spring Harb Perspect Biol. 2013 Oct 1;5(10):a010363. doi: 10.1101/cshperspect.a010363. Review.


Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination.

Pomerantz RT, Kurth I, Goodman MF, O'Donnell ME.

Nat Struct Mol Biol. 2013 Jun;20(6):748-55. doi: 10.1038/nsmb.2573. Epub 2013 May 19.


GANP regulates recruitment of AID to immunoglobulin variable regions by modulating transcription and nucleosome occupancy.

Singh SK, Maeda K, Eid MM, Almofty SA, Ono M, Pham P, Goodman MF, Sakaguchi N.

Nat Commun. 2013;4:1830. doi: 10.1038/ncomms2823.


Competitive fitness during feast and famine: how SOS DNA polymerases influence physiology and evolution in Escherichia coli.

Corzett CH, Goodman MF, Finkel SE.

Genetics. 2013 Jun;194(2):409-20. doi: 10.1534/genetics.113.151837. Epub 2013 Apr 15.


RecA acts as a switch to regulate polymerase occupancy in a moving replication fork.

Indiani C, Patel M, Goodman MF, O'Donnell ME.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5410-5. doi: 10.1073/pnas.1303301110. Epub 2013 Mar 18.


AID and Apobec3G haphazard deamination and mutational diversity.

Jaszczur M, Bertram JG, Pham P, Scharff MD, Goodman MF.

Cell Mol Life Sci. 2013 Sep;70(17):3089-108. doi: 10.1007/s00018-012-1212-1. Epub 2012 Nov 22. Review.


Mechanisms employed by Escherichia coli to prevent ribonucleotide incorporation into genomic DNA by Pol V.

McDonald JP, Vaisman A, Kuban W, Goodman MF, Woodgate R.

PLoS Genet. 2012;8(11):e1003030. doi: 10.1371/journal.pgen.1003030. Epub 2012 Nov 8.


Effect of β,γ-CHF- and β,γ-CHCl-dGTP halogen atom stereochemistry on the transition state of DNA polymerase β.

Oertell K, Wu Y, Zakharova VM, Kashemirov BA, Shock DD, Beard WA, Wilson SH, McKenna CE, Goodman MF.

Biochemistry. 2012 Oct 30;51(43):8491-501. doi: 10.1021/bi3010335. Epub 2012 Oct 19.


Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment.

Klvaňa M, Murphy DL, Jeřábek P, Goodman MF, Warshel A, Sweasy JB, Florián J.

Biochemistry. 2012 Nov 6;51(44):8829-43. doi: 10.1021/bi300783t. Epub 2012 Oct 29.


An accidental biochemist.

Goodman MF.

DNA Repair (Amst). 2012 Jun 1;11(6):527-36. No abstract available.


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