William A. Beard

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 26	2013

Other Publications

Article	Year
Observing a DNA polymerase choose right from wrong. Cell\| PubMed ID: 23827680	2013
Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity. The Journal of biological chemistry\| PubMed ID: 11756435	2002
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. Journal of molecular biology\| PubMed ID: 11955015	2002
Efficiency of correct nucleotide insertion governs DNA polymerase fidelity. The Journal of biological chemistry\| PubMed ID: 12370169	2002
Rapid segmental and subdomain motions of DNA polymerase beta. The Journal of biological chemistry\| PubMed ID: 12458221	2003
Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure (London, England : 1993)\| PubMed ID: 12517346	2003
Structural insights into the origins of DNA polymerase fidelity. Structure (London, England : 1993)\| PubMed ID: 12737815	2003
Localization of the deoxyribose phosphate lyase active site in human DNA polymerase iota by controlled proteolysis. The Journal of biological chemistry\| PubMed ID: 12777390	2003
High-level expression and purification of untagged and histidine-tagged HIV-1 reverse transcriptase. Protein expression and purification\| PubMed ID: 14766302	2004
Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates. The Journal of biological chemistry\| PubMed ID: 15145936	2004
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. Biophysical journal\| PubMed ID: 15189842	2004
Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. Journal of the American Chemical Society\| PubMed ID: 15238001	2004
Dynamic characterization of a DNA repair enzyme: NMR studies of [methyl-13C]methionine-labeled DNA polymerase beta. Biochemistry\| PubMed ID: 15248749	2004
Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity. Structure (London, England : 1993)\| PubMed ID: 15458631	2004
DNA polymerase beta and flap endonuclease 1 enzymatic specificities sustain DNA synthesis for long patch base excision repair. The Journal of biological chemistry\| PubMed ID: 15561706	2005
DNA polymerase lambda mediates a back-up base excision repair activity in extracts of mouse embryonic fibroblasts. The Journal of biological chemistry\| PubMed ID: 15749700	2005
Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Structure (London, England : 1993)\| PubMed ID: 16084394	2005
Structural insight into the DNA polymerase beta deoxyribose phosphate lyase mechanism. DNA repair\| PubMed ID: 16172026	2005
Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity. Biochemistry\| PubMed ID: 16201758	2005
Syn-full behavior by T7 DNA polymerase. Structure (London, England : 1993)\| PubMed ID: 16271879	2005
A thymine isostere in the templating position disrupts assembly of the closed DNA polymerase beta ternary complex. Biochemistry\| PubMed ID: 16285726	2005
Structure and mechanism of DNA polymerase Beta. Chemical reviews\| PubMed ID: 16464010	2006
Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure (London, England : 1993)\| PubMed ID: 16615916	2006
Determination of lysine pK values using [5-13C]lysine: application to the lyase domain of DNA Pol beta. Journal of the American Chemical Society\| PubMed ID: 16787052	2006
Activities and mechanism of DNA polymerase beta. Methods in enzymology\| PubMed ID: 16793365	2006
Energy analysis of chemistry for correct insertion by DNA polymerase beta. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16938895	2006
Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17079493	2006
Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational ef... Journal of molecular biology\| PubMed ID: 17174326	2007
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. Biochemistry\| PubMed ID: 17176036	2006
Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. Biochemistry\| PubMed ID: 17209556	2007
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. Biophysical journal\| PubMed ID: 17293403	2007
Coordination of steps in single-nucleotide base excision repair mediated by apurinic/apyrimidinic endonuclease 1 and DNA polymerase beta. The Journal of biological chemistry\| PubMed ID: 17355977	2007
The X family portrait: structural insights into biological functions of X family polymerases. DNA repair\| PubMed ID: 17631059	2007
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Proteins\| PubMed ID: 17671961	2008
(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. Journal of the American Chemical Society\| PubMed ID: 18031037	2007
DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. Biochemistry\| PubMed ID: 18161950	2008
Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18391201	2008
Negligible impact of pol iota expression on the alkylation sensitivity of pol beta-deficient mouse fibroblast cells. DNA repair\| PubMed ID: 18434259	2008
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Molecular cell\| PubMed ID: 18471977	2008
Alpha,beta-methylene-2'-deoxynucleoside 5'-triphosphates as noncleavable substrates for DNA polymerases: isolation, characterization, and stability studies of novel 2'-deoxycyclonucleosides,... Journal of medicinal chemistry\| PubMed ID: 18811136	2008
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function. Organic letters\| PubMed ID: 19351147	2009
Coordination between polymerase beta and FEN1 can modulate CAG repeat expansion. The Journal of biological chemistry\| PubMed ID: 19674974	2009
A real-time fluorescence method for enzymatic characterization of specialized human DNA polymerases. Nucleic acids research\| PubMed ID: 19684079	2009
DNA polymerase beta and PARP activities in base excision repair in living cells. DNA repair\| PubMed ID: 19748837	2009
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". The Journal of biological chemistry\| PubMed ID: 19759017	2009
Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. Journal of the American Chemical Society\| PubMed ID: 20465217	2010
DNA polymerase beta ribonucleotide discrimination: insertion, misinsertion, extension, and coding. The Journal of biological chemistry\| PubMed ID: 20519499	2010
Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site. Nature structural & molecular biology\| PubMed ID: 20526335	2010
DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine. Mutation research\| PubMed ID: 20696268	2010
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20724659	2010
Base excision repair and design of small molecule inhibitors of human DNA polymerase Î². Cellular and molecular life sciences : CMLS\| PubMed ID: 20844920	2010
Substrate channeling in mammalian base excision repair pathways: passing the baton. The Journal of biological chemistry\| PubMed ID: 20952393	2010
Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. The Journal of biological chemistry\| PubMed ID: 21733843	2011
Metal-induced DNA translocation leads to DNA polymerase conformational activation. Nucleic acids research\| PubMed ID: 22169953	2012
Binary complex crystal structure of DNA polymerase Î² reveals multiple conformations of the templating 8-oxoguanine lesion. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22178760	2012
Stereospecific formation of a ternary complex of (S)-Î±,Î²-fluoromethylene-dATP with DNA pol Î². Chembiochem : a European journal of chemical biology\| PubMed ID: 22315190	2012
Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure (London, England : 1993)\| PubMed ID: 22959623	2012
DNA sequence context effects on the glycosylase activity of human 8-oxoguanine DNA glycosylase. The Journal of biological chemistry\| PubMed ID: 22989888	2012
Effect of Î²,Î³-CHF- and Î²,Î³-CHCl-dGTP halogen atom stereochemistry on the transition state of DNA polymerase Î². Biochemistry\| PubMed ID: 23043620	2012
DNA polymerase Î² gap-filling translesion DNA synthesis. Chemical research in toxicology\| PubMed ID: 23121263	2012
DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion. Nucleic acids research\| PubMed ID: 23267011	2013
Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms. Theoretical chemistry accounts\| PubMed ID: 23459563	2012
Amino acid substitution in the active site of DNA polymerase Î² explains the energy barrier of the nucleotidyl transfer reaction. Journal of the American Chemical Society\| PubMed ID: 23647366	2013
Insights into the conformation of aminofluorene-deoxyguanine adduct in a DNA polymerase active site. The Journal of biological chemistry\| PubMed ID: 23798703	2013
Understanding the loss-of-function in a triple missense mutant of DNA polymerase Î² found in prostate cancer. International journal of oncology\| PubMed ID: 23877444	2013