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Goodman MF

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Publications:

Title Authors Year Journal
DNA polymerases are error-prone at RecA-mediated recombination intermediates. Goodman MF 2013 Cell cycle (Georgetown, Tex.)
Competitive Fitness during Feast and Famine: How SOS DNA Polymerases Influence Physiology and Evolution in Escherichia coli. Goodman MF 2013 Genetics
Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination. Goodman MF 2013 Nature structural & molecular biology
RecA acts as a switch to regulate polymerase occupancy in a moving replication fork. Goodman MF 2013 Proceedings of the National Academy of Sciences of the United States of America
Simple and efficient purification of Escherichia coli DNA polymerase V: Cofactor requirements for optimal activity and processivity in vitro. Goodman MF 2012 DNA repair
Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity. Goodman MF 2012 Nucleic acids research
β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures and absolute configurations of new stereochemical probes for DNA polymerases. Goodman MF 2012 Journal of the American Chemical Society
Escherichia coli UmuC active site mutants: Effects on translesion DNA synthesis, mutagenesis and cell survival. Goodman MF 2012 DNA repair
Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment. Goodman MF 2012 Biochemistry
Effect of β,γ-CHF- and β,γ-CHCl-dGTP Halogen Atom Stereochemistry on the Transition State of DNA Polymerase β Goodman MF 2012 Biochemistry
Mechanisms Employed by Escherichia coli to Prevent Ribonucleotide Incorporation into Genomic DNA by Pol V. Goodman MF 2012 PLoS genetics
Role of high-fidelity Escherichia coli DNA polymerase I in replication bypass of a deoxyadenosine DNA-peptide cross-link. Goodman MF 2011 Journal of bacteriology
An Abridged Transition State Model To Derive Structure, Dynamics, and Energy Components of DNA Polymerase β Fidelity. Goodman MF 2011 Biochemistry
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Goodman MF 2010 Proceedings of the National Academy of Sciences of the United States of America
Modifications to the dNTP triphosphate moiety: from mechanistic probes for DNA polymerases to antiviral and anti-cancer drug design. Goodman MF 2010 Biochimica et biophysica acta
Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. Goodman MF 2010 Journal of the American Chemical Society
DNA polymerase fidelity: comparing direct competition of right and wrong dNTP substrates with steady state and pre-steady state kinetics. Goodman MF 2010 Biochemistry
A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Goodman MF 2010 Crit Rev Biochem Mol Biol
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function. Goodman MF 2009 Org Lett
Translesion DNA polymerases remodel the replisome and alter the speed of the replicative helicase. Goodman MF 2009 Proceedings of the National Academy of Sciences of the United States of America
A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases. Goodman MF 2009 Biochemistry
The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP. Goodman MF 2009 Nature
Replication bypass of interstrand cross-link intermediates by Escherichia coli DNA polymerase IV. Goodman MF 2008 The Journal of biological chemistry
DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. Goodman MF 2008 Biochemistry
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Goodman MF 2008 Proteins
A dynamic polymerase exchange with Escherichia coli DNA polymerase IV replacing DNA polymerase III on the sliding clamp. Goodman MF 2008 The Journal of biological chemistry
Replication bypass of the acrolein-mediated deoxyguanine DNA-peptide cross-links by DNA polymerases of the DinB family. Goodman MF 2008 Chemical research in toxicology
Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. Goodman MF 2007 Biochemistry
Lessons from 50 years of SOS DNA-damage-induced mutagenesis. Goodman MF 2007 Nature reviews. Molecular cell biology
Steric and electrostatic effects in DNA synthesis by the SOS-induced DNA polymerases II and IV of Escherichia coli. Goodman MF 2007 Biochemistry
DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength. Goodman MF 2007 FEBS letters
(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. Goodman MF 2007 Journal of the American Chemical Society
Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta. Goodman MF 2006 Biochemistry
Purification and characterization of Escherichia coli DNA polymerase V. Goodman MF 2006 Methods in enzymology
Roles of DNA polymerase V and RecA protein in SOS damage-induced mutation. Goodman MF 2006 Chem Rev
RecA acts in trans to allow replication of damaged DNA by DNA polymerase V. Goodman MF 2006 Nature
DNA polymerase V and RecA protein, a minimal mutasome. Goodman MF 2005 Molecular cell
Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases. Goodman MF 2005 Proceedings of the National Academy of Sciences of the United States of America
Lyase activities intrinsic to Escherichia coli polymerases IV and V. Goodman MF 2005 DNA repair
A biochemically defined system for mammalian nonhomologous DNA end joining. Goodman MF 2004 Molecular cell
In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR. Goodman MF 2004 BMC clinical pathology
Error-prone replication for better or worse. Goodman MF 2004 Trends Microbiol
To slip or skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases. Goodman MF 2004 The Journal of biological chemistry
Increased dNTP binding affinity reveals a nonprocessive role for Escherichia coli beta clamp with DNA polymerase IV. Goodman MF 2004 The Journal of biological chemistry
Mechanism of loading the Escherichia coli DNA polymerase III beta sliding clamp on DNA. Bona fide primer/templates preferentially trigger the gamma complex to hydrolyze ATP and load the clamp. Goodman MF 2003 The Journal of biological chemistry
Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. Goodman MF 2003 Journal of the American Chemical Society
Escherichia coli DNA polymerase V subunit exchange: a post-SOS mechanism to curtail error-prone DNA synthesis. Goodman MF 2003 The Journal of biological chemistry
Computer simulation studies of the fidelity of DNA polymerases. Goodman MF 2003 Biopolymers
Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair. Goodman MF 2003 The EMBO journal
Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis. Goodman MF 2002 Proceedings of the National Academy of Sciences of the United States of America
Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Goodman MF 2002 Annu Rev Biochem
Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment. Goodman MF 2002 The Journal of biological chemistry
Weak strand displacement activity enables human DNA polymerase beta to expand CAG/CTG triplet repeats at strand breaks. Goodman MF 2002 The Journal of biological chemistry
Resolving a fidelity paradox: why Escherichia coli DNA polymerase II makes more base substitution errors in AT- compared with GC-rich DNA. Goodman MF 2002 The Journal of biological chemistry
Human DNA polymerase iota promiscuous mismatch extension. Goodman MF 2001 The Journal of biological chemistry
A model for SOS-lesion-targeted mutations in Escherichia coli. Goodman MF 2001 Nature
Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Goodman MF 2001 Nat Struct Biol
Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli. Goodman MF 2001 Proceedings of the National Academy of Sciences of the United States of America
Coping with replication 'train wrecks' in Escherichia coli using Pol V, Pol II and RecA proteins. Goodman MF 2000 Trends in biochemical sciences
A model for Escherichia coli DNA polymerase III holoenzyme assembly at primer/template ends. DNA triggers a change in binding specificity of the gamma complex clamp loader. Goodman MF 2000 The Journal of biological chemistry
Base stacking and even/odd behavior of hairpin loops in DNA triplet repeat slippage and expansion with DNA polymerase. Goodman MF 2000 The Journal of biological chemistry
The biochemical basis and in vivo regulation of SOS-induced mutagenesis promoted by Escherichia coli DNA polymerase V (UmuD'2C). Goodman MF 2000 Cold Spring Harbor symposia on quantitative biology
The expanding polymerase universe. Goodman MF 2000 Nat Rev Mol Cell Biol
Fidelity of eucaryotic DNA polymerase delta holoenzyme from Schizosaccharomyces pombe. Goodman MF 2000 The Journal of biological chemistry
Visualization of two binding sites for the Escherichia coli UmuD'(2)C complex (DNA pol V) on RecA-ssDNA filaments. Goodman MF 2000 Journal of molecular biology
Molecular mechanism and energetics of clamp assembly in Escherichia coli. The role of ATP hydrolysis when gamma complex loads beta on DNA. Goodman MF 2000 The Journal of biological chemistry
"Action-at-a-distance" mutagenesis. 8-oxo-7, 8-dihydro-2'-deoxyguanosine causes base substitution errors at neighboring template sites when copied by DNA polymerase beta. Goodman MF 1999 The Journal of biological chemistry
Division of labor--sequential ATP hydrolysis drives assembly of a DNA polymerase sliding clamp around DNA. Goodman MF 1999 The EMBO journal
A phenotype for enigmatic DNA polymerase II: a pivotal role for pol II in replication restart in UV-irradiated Escherichia coli. Goodman MF 1999 Proceedings of the National Academy of Sciences of the United States of America
UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V. Goodman MF 1999 Proceedings of the National Academy of Sciences of the United States of America
Abasic template lesions are strong chain terminators for DNA primase but not for DNA polymerase alpha during the synthesis of new DNA strands. Goodman MF 1999 Biochemistry
On the wagon--DNA polymerase joins "H-bonds anonymous". Goodman MF 1999 Nat Biotechnol
Pre-steady state analysis of the assembly of wild type and mutant circular clamps of Escherichia coli DNA polymerase III onto DNA. Goodman MF 1998 The Journal of biological chemistry
Stopped-flow fluorescence study of precatalytic primer strand base-unstacking transitions in the exonuclease cleft of bacteriophage T4 DNA polymerase. Goodman MF 1998 Biochemistry
DNA polymerase fidelity: from genetics toward a biochemical understanding. Goodman MF 1998 Genetics
Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4 DNA polymerase. Goodman MF 1998 Biochemistry
The proofreading pathway of bacteriophage T4 DNA polymerase. Goodman MF 1998 The Journal of biological chemistry
Analysis of strand slippage in DNA polymerase expansions of CAG/CTG triplet repeats associated with neurodegenerative disease. Goodman MF 1998 The Journal of biological chemistry
The Escherichia coli polB locus is identical to dinA, the structural gene for DNA polymerase II. Characterization of Pol II purified from a polB mutant. Goodman MF 1997 The Journal of biological chemistry
Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity. Goodman MF 1997 Proceedings of the National Academy of Sciences of the United States of America
Abasic translesion synthesis by DNA polymerase beta violates the "A-rule". Novel types of nucleotide incorporation by human DNA polymerase beta at an abasic lesion in different sequence contexts. Goodman MF 1997 The Journal of biological chemistry
Fidelity of Escherichia coli DNA polymerase III holoenzyme. The effects of beta, gamma complex processivity proteins and epsilon proofreading exonuclease on nucleotide misincorporation efficiencies. Goodman MF 1997 The Journal of biological chemistry
Escherichia coli DNA polymerase II catalyzes chromosomal and episomal DNA synthesis in vivo. Goodman MF 1997 Proceedings of the National Academy of Sciences of the United States of America
NMR study of the conformation of the 2-aminopurine:cytosine mismatch in DNA. Goodman MF 1996 Biochemistry
Dynamics of loading the beta sliding clamp of DNA polymerase III onto DNA. Goodman MF 1996 The Journal of biological chemistry
Purification and properties of DNA polymerase II from Escherichia coli. Goodman MF 1995 Methods in enzymology
Enthalpy-entropy compensation in DNA melting thermodynamics. Goodman MF 1995 The Journal of biological chemistry
Gel kinetic analysis of DNA polymerase fidelity in the presence of proofreading using bacteriophage T4 DNA polymerase. Goodman MF 1995 The Journal of biological chemistry
Proofreading-defective DNA polymerase II increases adaptive mutation in Escherichia coli. Goodman MF 1995 Proceedings of the National Academy of Sciences of the United States of America
Purification and properties of wild-type and exonuclease-deficient DNA polymerase II from Escherichia coli. Goodman MF 1995 The Journal of biological chemistry
Nucleotide insertion and primer extension at abasic template sites in different sequence contexts. Goodman MF 1994 Annals of the New York Academy of Sciences
Crystallization of DNA polymerase II from Escherichia coli. Goodman MF 1994 Journal of molecular biology
Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 3'-exonuclease activity of bacteriophage T4 DNA polymerase. Goodman MF 1994 Biochemistry
Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation. Goodman MF 1994 J Bacteriol
Ionization of bromouracil and fluorouracil stimulates base mispairing frequencies with guanine. Goodman MF 1993 The Journal of biological chemistry
Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase. Goodman MF 1993 The Journal of biological chemistry
Effect of a template-located 2',2'-difluorodeoxycytidine on the kinetics and fidelity of base insertion by Klenow (3'-->5'exonuclease-) fragment. Goodman MF 1993 Cancer research
Influence of 5'-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment. Goodman MF 1993 Biochemistry
Biochemical basis of DNA replication fidelity. Goodman MF 1993 Crit Rev Biochem Mol Biol
Absence of a role for DNA polymerase II in SOS-induced translesion bypass of phi X174. Goodman MF 1993 J Bacteriol
Base mispair extension kinetics. Binding of avian myeloblastosis reverse transcriptase to matched and mismatched base pair termini. Goodman MF 1992 The Journal of biological chemistry
Activity of the purified mutagenesis proteins UmuC, UmuD', and RecA in replicative bypass of an abasic DNA lesion by DNA polymerase III. Goodman MF 1992 Proceedings of the National Academy of Sciences of the United States of America
Comparison of HIV-1 and avian myeloblastosis virus reverse transcriptase fidelity on RNA and DNA templates. Goodman MF 1992 The Journal of biological chemistry
Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR. Goodman MF 1992 Nucleic acids research
Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins. Goodman MF 1992 The Journal of biological chemistry
A comparison of the fidelity of copying 5-methylcytosine and cytosine at a defined DNA template site. Goodman MF 1992 Nucleic acids research
Specificity and enzymatic mechanism of the editing exonuclease of Escherichia coli DNA polymerase III. Goodman MF 1991 The Journal of biological chemistry
Kinetics of extension of O6-methylguanine paired with cytosine or thymine in defined oligonucleotide sequences. Goodman MF 1991 Biochemistry
DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli. Goodman MF 1990 Proceedings of the National Academy of Sciences of the United States of America
Base mispair extension kinetics. Comparison of DNA polymerase alpha and reverse transcriptase. Goodman MF 1990 The Journal of biological chemistry
Comparative efficiency of forming m4T.G versus m4T.A base pairs at a unique site by use of Escherichia coli DNA polymerase I (Klenow fragment) and Drosophila melanogaster polymerase alpha-primase complex. Goodman MF 1990 Biochemistry
Nearest neighbor influences on DNA polymerase insertion fidelity. Goodman MF 1989 The Journal of biological chemistry
Effect of 3' flanking neighbors on kinetics of pairing of dCTP or dTTP opposite O6-methylguanine in a defined primed oligonucleotide when Escherichia coli DNA polymerase I is used. Goodman MF 1989 Proceedings of the National Academy of Sciences of the United States of America
Kinetic analysis of base substitution mutagenesis by transient misalignment of DNA and by miscoding. Goodman MF 1989 The Journal of biological chemistry
Comparison of polymerase insertion and extension kinetics of a series of O2-alkyldeoxythymidine triphosphates and O4-methyldeoxythymidine triphosphate. Goodman MF 1989 Biochemistry
Spontaneous and UV-induced mutations in Escherichia coli K-12 strains with altered or absent DNA polymerase I. Goodman MF 1989 Journal of bacteriology
The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme. Goodman MF 1988 Nucleic acids research
Purification and characterization of an inducible Escherichia coli DNA polymerase capable of insertion and bypass at abasic lesions in DNA. Goodman MF 1988 The Journal of biological chemistry
Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Goodman MF 1988 Proceedings of the National Academy of Sciences of the United States of America
Nucleotide insertion kinetics opposite abasic lesions in DNA. Goodman MF 1987 The Journal of biological chemistry
DNA polymerase insertion fidelity. Gel assay for site-specific kinetics. Goodman MF 1987 The Journal of biological chemistry
Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine. Goodman MF 1986 Nucleic acids research
Synthesis and properties of oligonucleotides containing 2'-deoxynebularine and 2'-deoxyxanthosine. Goodman MF 1986 Nucleic acids research
Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity. Goodman MF 1986 Proceedings of the National Academy of Sciences of the United States of America
Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity. Goodman MF 1985 The Journal of biological chemistry
A fidelity assay using "dideoxy" DNA sequencing: a measurement of sequence dependence and frequency of forming 5-bromouracil X guanine base mispairs. Goodman MF 1985 Proceedings of the National Academy of Sciences of the United States of America
Ribonucleoside and deoxyribonucleoside triphosphate pools during 2-aminopurine mutagenesis in T4 mutator-, wild type-, and antimutator-infected Escherichia coli. Goodman MF 1985 The Journal of biological chemistry
On the fidelity of DNA replication. The accuracy of T4 DNA polymerases in copying phi X174 DNA in vitro. Goodman MF 1984 The Journal of biological chemistry
On the molecular basis of transition mutations. Frequency of forming 2-aminopurine-cytosine base mispairs in the G X C----A X T mutational pathway by T4 DNA polymerase in vitro. Goodman MF 1984 The Journal of biological chemistry
The biochemical basis of 5-bromouracil-induced mutagenesis. Heteroduplex base mispairs involving bromouracil in G x C----A x T and A x T----G x C mutational pathways. Goodman MF 1984 The Journal of biological chemistry
On the enzymatic basis for mutagenesis by manganese. Goodman MF 1983 The Journal of biological chemistry
Kinetic measurement of 2-aminopurine X cytosine and 2-aminopurine X thymine base pairs as a test of DNA polymerase fidelity mechanisms. Goodman MF 1982 Proceedings of the National Academy of Sciences of the United States of America
On the molecular basis of transition mutations: frequencies of forming 2-aminopurine.cytosine and adenine.cytosine base mispairs in vitro. Goodman MF 1981 Proceedings of the National Academy of Sciences of the United States of America
Evidence for the absence of DNA proofreading in HeLa cell nuclei. Goodman MF 1981 The Journal of biological chemistry
Error induction and correction by mutant and wild type T4 DNA polymerases. Kinetic error discrimination mechanisms. Goodman MF 1979 The Journal of biological chemistry
2-Aminopurine-induced mutagenesis in T4 bacteriophage: a model relating mutation frequency to 2-aminopurine incorporation in DNA. Goodman MF 1977 Proceedings of the National Academy of Sciences of the United States of America
Adriamycin interactions with T4 DNA polymerase. Two modes of template-mediated inhibition. Goodman MF 1977 The Journal of biological chemistry
Studies on the biochemical basis of spontaneous mutation. III. Rate model for DNA polymerase-effected nucleotide misincorporation. Goodman MF 1974 Journal of molecular biology
Studies on the biochemical basis of spontaneous mutation. II. The incorporation of a base and its analogue into DNA by wild-type, mutator and antimutator DNA polymerases. Goodman MF 1974 Journal of molecular biology
Adriamycin and daunorubicin inhibition of mutant T4 DNA polymerases. Goodman MF 1974 Proceedings of the National Academy of Sciences of the United States of America

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