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1.

Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements.

Pham, Phuong; Wood, Elizabeth A; Dunbar, Emma L; Cox, Michael M; Goodman, Myron F.

Nucleic Acids Res ; 2024 Apr 27.

Artigo em Inglês | MEDLINE | ID: mdl-38676944

2.

RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli.

Pham, Phuong; Wood, Elizabeth A; Cox, Michael M; Goodman, Myron F.

Nucleic Acids Res ; 51(11): 5527-5546, 2023 06 23.

Artigo em Inglês | MEDLINE | ID: mdl-37070184

3.

Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase ß.

Alnajjar, Khadijeh S; Wang, Katarina; Alvarado-Cruz, Isabel; Chavira, Cristian; Negahbani, Amirsoheil; Nakhjiri, Maryam; Minard, Corinne; Garcia-Barboza, Beatriz; Kashemirov, Boris A; McKenna, Charles E; Goodman, Myron F; Sweasy, Joann B.

Biochemistry ; 63(11): 1412-1422, 2024 Jun 04.

Artigo em Inglês | MEDLINE | ID: mdl-38780930

4.

Genomic landscape of single-stranded DNA gapped intermediates in Escherichia coli.

Pham, Phuong; Shao, Yijun; Cox, Michael M; Goodman, Myron F.

Nucleic Acids Res ; 50(2): 937-951, 2022 01 25.

Artigo em Inglês | MEDLINE | ID: mdl-34951472

5.

Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization.

Jeong, Soo Lim; Zhang, Hongyu; Yamaki, Shanni; Yang, Chenyu; McKemy, David D; Lieber, Michael R; Pham, Phuong; Goodman, Myron F.

Nucleic Acids Res ; 50(20): 11738-11754, 2022 11 11.

Artigo em Inglês | MEDLINE | ID: mdl-36321646

6.

Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase.

Ojha, Debika; Jaszczur, Malgorzata M; Sikand, Adhirath; McDonald, John P; Robinson, Andrew; van Oijen, Antoine M; Mak, Chi H; Pinaud, Fabien; Cox, Michael M; Woodgate, Roger; Goodman, Myron F.

Nucleic Acids Res ; 50(12): 6854-6869, 2022 07 08.

Artigo em Inglês | MEDLINE | ID: mdl-35736210

7.

Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair.

Henrikus, Sarah S; Henry, Camille; McGrath, Amy E; Jergic, Slobodan; McDonald, John P; Hellmich, Yvonne; Bruckbauer, Steven T; Ritger, Matthew L; Cherry, Megan E; Wood, Elizabeth A; Pham, Phuong T; Goodman, Myron F; Woodgate, Roger; Cox, Michael M; van Oijen, Antoine M; Ghodke, Harshad; Robinson, Andrew.

Nucleic Acids Res ; 48(15): 8490-8508, 2020 09 04.

Artigo em Inglês | MEDLINE | ID: mdl-32687193

8.

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

Jaszczur, Malgorzata M; Vo, Dan D; Stanciauskas, Ramunas; Bertram, Jeffrey G; Sikand, Adhirath; Cox, Michael M; Woodgate, Roger; Mak, Chi H; Pinaud, Fabien; Goodman, Myron F.

PLoS Genet ; 15(2): e1007956, 2019 02.

Artigo em Inglês | MEDLINE | ID: mdl-30716079

9.

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

Pham, Phuong; Malik, Sohail; Mak, Chiho; Calabrese, Peter C; Roeder, Robert G; Goodman, Myron F.

Nucleic Acids Res ; 47(20): 10815-10829, 2019 11 18.

Artigo em Inglês | MEDLINE | ID: mdl-31566237

10.

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

Alnajjar, Khadijeh S; Krylov, Ivan S; Negahbani, Amirsoheil; Haratipour, Pouya; Kashemirov, Boris A; Huang, Ji; Mahmoud, Mariam; McKenna, Charles E; Goodman, Myron F; Sweasy, Joann B.

Nucleic Acids Res ; 47(22): 11839-11849, 2019 12 16.

Artigo em Inglês | MEDLINE | ID: mdl-31732732

11.

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

Henrikus, Sarah S; Wood, Elizabeth A; McDonald, John P; Cox, Michael M; Woodgate, Roger; Goodman, Myron F; van Oijen, Antoine M; Robinson, Andrew.

PLoS Genet ; 14(1): e1007161, 2018 01.

Artigo em Inglês | MEDLINE | ID: mdl-29351274

12.

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

Batra, Vinod K; Alnajjar, Khadijeh S; Sweasy, Joann B; McKenna, Charles E; Goodman, Myron F; Wilson, Samuel H.

Biochemistry ; 59(8): 955-963, 2020 03 03.

Artigo em Inglês | MEDLINE | ID: mdl-31999437

13.

A Transition-State Perspective on Y-Family DNA Polymerase Î· Fidelity in Comparison with X-Family DNA Polymerases λ and ß.

Oertell, Keriann; Florián, Jan; Haratipour, Pouya; Crans, Debbie C; Kashemirov, Boris A; Wilson, Samuel H; McKenna, Charles E; Goodman, Myron F.

Biochemistry ; 58(13): 1764-1773, 2019 04 02.

Artigo em Inglês | MEDLINE | ID: mdl-30839203

14.

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

Mak, Chi H; Pham, Phuong; Goodman, Myron F.

J Phys Chem A ; 123(13): 3030-3037, 2019 Apr 04.

Artigo em Inglês | MEDLINE | ID: mdl-30848911

15.

Smoking gun for a rare mutation mechanism.

Goodman, Myron F.

Nature ; 554(7691): 180-181, 2018 Feb.

Artigo em Inglês | MEDLINE | ID: mdl-32094545

16.

Smoking gun for a rare mutation mechanism.

Goodman, Myron F.

Nature ; 554(7691): 180-181, 2018 02 08.

Artigo em Inglês | MEDLINE | ID: mdl-29420502

17.

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

Oertell, Keriann; Harcourt, Emily M; Mohsen, Michael G; Petruska, John; Kool, Eric T; Goodman, Myron F.

Proc Natl Acad Sci U S A ; 113(16): E2277-85, 2016 Apr 19.

Artigo em Inglês | MEDLINE | ID: mdl-27044101

18.

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

Batra, Vinod K; Oertell, Keriann; Beard, William A; Kashemirov, Boris A; McKenna, Charles E; Goodman, Myron F; Wilson, Samuel H.

Biochemistry ; 57(26): 3934-3944, 2018 07 03.

Artigo em Inglês | MEDLINE | ID: mdl-29874056

19.

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

Oertell, Keriann; Kashemirov, Boris A; Negahbani, Amirsoheil; Minard, Corinne; Haratipour, Pouya; Alnajjar, Khadijeh S; Sweasy, Joann B; Batra, Vinod K; Beard, William A; Wilson, Samuel H; McKenna, Charles E; Goodman, Myron F.

Biochemistry ; 57(26): 3925-3933, 2018 07 03.

Artigo em Inglês | MEDLINE | ID: mdl-29889506

20.

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

Eid, Mohammed Mansour Abbas; Shimoda, Mayuko; Singh, Shailendra Kumar; Almofty, Sarah Ameen; Pham, Phuong; Goodman, Myron F; Maeda, Kazuhiko; Sakaguchi, Nobuo.

Int Immunol ; 29(5): 211-220, 2017 05 01.

Artigo em Inglês | MEDLINE | ID: mdl-28541550

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Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements.

RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli.

Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase ß.

Genomic landscape of single-stranded DNA gapped intermediates in Escherichia coli.

Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization.

Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase.

Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair.

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

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

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

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

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

A Transition-State Perspective on Y-Family DNA Polymerase Î· Fidelity in Comparison with X-Family DNA Polymerases λ and ß.

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

Smoking gun for a rare mutation mechanism.

Smoking gun for a rare mutation mechanism.

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

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

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

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