William A. Beard Laboratory of Structural Biology NIEHS, National Institutes of Health Biography Publications Institution JoVE Articles William A. Beard has not added a biography. If you are William A. Beard and would like to personalize this page please email our Author Liaison for assistance. Publications Understanding the Loss-of-function in a Triple Missense Mutant of DNA Polymerase β Found in Prostate Cancer International Journal of Oncology. Oct, 2013 | Pubmed ID: 23877444 Observing a DNA Polymerase Choose Right from Wrong Cell. Jul, 2013 | Pubmed ID: 23827680 Insights into the Conformation of Aminofluorene-deoxyguanine Adduct in a DNA Polymerase Active Site The Journal of Biological Chemistry. Aug, 2013 | Pubmed ID: 23798703 Amino Acid Substitution in the Active Site of DNA Polymerase β Explains the Energy Barrier of the Nucleotidyl Transfer Reaction Journal of the American Chemical Society. May, 2013 | Pubmed ID: 23647366 DNA Polymerase Minor Groove Interactions Modulate Mutagenic Bypass of a Templating 8-oxoguanine Lesion Nucleic Acids Research. Feb, 2013 | Pubmed ID: 23267011 Perspective: Pre-chemistry Conformational Changes in DNA Polymerase Mechanisms Theoretical Chemistry Accounts. Nov, 2012 | Pubmed ID: 23459563 DNA Polymerase β Gap-filling Translesion DNA Synthesis Chemical Research in Toxicology. Dec, 2012 | Pubmed ID: 23121263 Effect of β,γ-CHF- and β,γ-CHCl-dGTP Halogen Atom Stereochemistry on the Transition State of DNA Polymerase β Biochemistry. Oct, 2012 | Pubmed ID: 23043620 DNA Sequence Context Effects on the Glycosylase Activity of Human 8-oxoguanine DNA Glycosylase The Journal of Biological Chemistry. Oct, 2012 | Pubmed ID: 22989888 Structures of DNTP Intermediate States During DNA Polymerase Active Site Assembly Structure (London, England : 1993). Nov, 2012 | Pubmed ID: 22959623 Stereospecific Formation of a Ternary Complex of (S)-α,β-fluoromethylene-dATP with DNA Pol β Chembiochem : a European Journal of Chemical Biology. Mar, 2012 | Pubmed ID: 22315190 Binary Complex Crystal Structure of DNA Polymerase β Reveals Multiple Conformations of the Templating 8-oxoguanine Lesion Proceedings of the National Academy of Sciences of the United States of America. Jan, 2012 | Pubmed ID: 22178760 Metal-induced DNA Translocation Leads to DNA Polymerase Conformational Activation Nucleic Acids Research. Apr, 2012 | Pubmed ID: 22169953 Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion The Journal of Biological Chemistry. Sep, 2011 | Pubmed ID: 21733843 Substrate Channeling in Mammalian Base Excision Repair Pathways: Passing the Baton The Journal of Biological Chemistry. Dec, 2010 | Pubmed ID: 20952393 Base Excision Repair and Design of Small Molecule Inhibitors of Human DNA Polymerase β Cellular and Molecular Life Sciences : CMLS. Nov, 2010 | Pubmed ID: 20844920 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. Sep, 2010 | Pubmed ID: 20724659 DNA Polymerase Structure-based Insight on the Mutagenic Properties of 8-oxoguanine Mutation Research. Nov, 2010 | Pubmed ID: 20696268 Mutagenic Conformation of 8-oxo-7,8-dihydro-2'-dGTP in the Confines of a DNA Polymerase Active Site Nature Structural & Molecular Biology. Jul, 2010 | Pubmed ID: 20526335 DNA Polymerase Beta Ribonucleotide Discrimination: Insertion, Misinsertion, Extension, and Coding The Journal of Biological Chemistry. Aug, 2010 | Pubmed ID: 20519499 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. Jun, 2010 | Pubmed ID: 20465217 DNA Polymerase Beta Substrate Specificity: Side Chain Modulation of the "A-rule" The Journal of Biological Chemistry. Nov, 2009 | Pubmed ID: 19759017 DNA Polymerase Beta and PARP Activities in Base Excision Repair in Living Cells DNA Repair. Nov, 2009 | Pubmed ID: 19748837 A Real-time Fluorescence Method for Enzymatic Characterization of Specialized Human DNA Polymerases Nucleic Acids Research. Oct, 2009 | Pubmed ID: 19684079 Coordination Between Polymerase Beta and FEN1 Can Modulate CAG Repeat Expansion The Journal of Biological Chemistry. Oct, 2009 | Pubmed ID: 19674974 Alpha,beta-difluoromethylene Deoxynucleoside 5'-triphosphates: a Convenient Synthesis of Useful Probes for DNA Polymerase Beta Structure and Function Organic Letters. May, 2009 | Pubmed ID: 19351147 Alpha,beta-methylene-2'-deoxynucleoside 5'-triphosphates As Noncleavable Substrates for DNA Polymerases: Isolation, Characterization, and Stability Studies of Novel 2'-deoxycyclonucleosides, 3,5'-cyclo-dG, and 2,5'-cyclo-dT Journal of Medicinal Chemistry. Oct, 2008 | Pubmed ID: 18811136 Structures of DNA Polymerase Beta with Active-site Mismatches Suggest a Transient Abasic Site Intermediate During Misincorporation Molecular Cell. May, 2008 | Pubmed ID: 18471977 Negligible Impact of Pol Iota Expression on the Alkylation Sensitivity of Pol Beta-deficient Mouse Fibroblast Cells DNA Repair. Jun, 2008 | Pubmed ID: 18434259 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. Apr, 2008 | Pubmed ID: 18391201 DNA Polymerase Beta Fidelity: Halomethylene-modified Leaving Groups in Pre-steady-state Kinetic Analysis Reveal Differences at the Chemical Transition State Biochemistry. Jan, 2008 | Pubmed ID: 18161950 Exploring the Role of Large Conformational Changes in the Fidelity of DNA Polymerase Beta Proteins. Jan, 2008 | Pubmed ID: 17671961 (R)-beta,gamma-fluoromethylene-dGTP-DNA Ternary Complex with DNA Polymerase Beta Journal of the American Chemical Society. Dec, 2007 | Pubmed ID: 18031037 The X Family Portrait: Structural Insights into Biological Functions of X Family Polymerases DNA Repair. Dec, 2007 | Pubmed ID: 17631059 Coordination of Steps in Single-nucleotide Base Excision Repair Mediated by Apurinic/apyrimidinic Endonuclease 1 and DNA Polymerase Beta The Journal of Biological Chemistry. May, 2007 | Pubmed ID: 17355977 Differing Conformational Pathways Before and After Chemistry for Insertion of DATP Versus DCTP Opposite 8-oxoG in DNA Polymerase Beta Biophysical Journal. May, 2007 | Pubmed ID: 17293403 Modifying the Beta,gamma Leaving-group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase Beta Biochemistry. Jan, 2007 | Pubmed ID: 17209556 Magnesium-cationic Dummy Atom Molecules Enhance Representation of DNA Polymerase Beta in Molecular Dynamics Simulations: Improved Accuracy in Studies of Structural Features and Mutational Effects Journal of Molecular Biology. Feb, 2007 | Pubmed ID: 17174326 Regulation of DNA Repair Fidelity by Molecular Checkpoints: "gates" in DNA Polymerase Beta's Substrate Selection Biochemistry. Dec, 2006 | Pubmed ID: 17176036 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. Nov, 2006 | Pubmed ID: 17079493 Energy Analysis of Chemistry for Correct Insertion by DNA Polymerase Beta Proceedings of the National Academy of Sciences of the United States of America. Sep, 2006 | Pubmed ID: 16938895 Activities and Mechanism of DNA Polymerase Beta Methods in Enzymology. 2006 | Pubmed ID: 16793365 Determination of Lysine PK Values Using [5-13C]lysine: Application to the Lyase Domain of DNA Pol Beta Journal of the American Chemical Society. Jun, 2006 | Pubmed ID: 16787052 Magnesium-induced Assembly of a Complete DNA Polymerase Catalytic Complex Structure (London, England : 1993). Apr, 2006 | Pubmed ID: 16615916 Structure and Mechanism of DNA Polymerase Beta Chemical Reviews. Feb, 2006 | Pubmed ID: 16464010 A Thymine Isostere in the Templating Position Disrupts Assembly of the Closed DNA Polymerase Beta Ternary Complex Biochemistry. Nov, 2005 | Pubmed ID: 16285726 Syn-full Behavior by T7 DNA Polymerase Structure (London, England : 1993). Nov, 2005 | Pubmed ID: 16271879 Mismatch-induced Conformational Distortions in Polymerase Beta Support an Induced-fit Mechanism for Fidelity Biochemistry. Oct, 2005 | Pubmed ID: 16201758 Structural Insight into the DNA Polymerase Beta Deoxyribose Phosphate Lyase Mechanism DNA Repair. Dec, 2005 | Pubmed ID: 16172026 Nucleotide-induced DNA Polymerase Active Site Motions Accommodating a Mutagenic DNA Intermediate Structure (London, England : 1993). Aug, 2005 | Pubmed ID: 16084394 DNA Polymerase Lambda Mediates a Back-up Base Excision Repair Activity in Extracts of Mouse Embryonic Fibroblasts The Journal of Biological Chemistry. May, 2005 | Pubmed ID: 15749700 DNA Polymerase Beta and Flap Endonuclease 1 Enzymatic Specificities Sustain DNA Synthesis for Long Patch Base Excision Repair The Journal of Biological Chemistry. Feb, 2005 | Pubmed ID: 15561706 Structural Insights into DNA Polymerase Beta Deterrents for Misincorporation Support an Induced-fit Mechanism for Fidelity Structure (London, England : 1993). Oct, 2004 | Pubmed ID: 15458631 Dynamic Characterization of a DNA Repair Enzyme: NMR Studies of [methyl-13C]methionine-labeled DNA Polymerase Beta Biochemistry. Jul, 2004 | Pubmed ID: 15248749 Critical Role of Magnesium Ions in DNA Polymerase Beta's Closing and Active Site Assembly Journal of the American Chemical Society. Jul, 2004 | Pubmed ID: 15238001 Highly Organized but Pliant Active Site of DNA Polymerase Beta: Compensatory Mechanisms in Mutant Enzymes Revealed by Dynamics Simulations and Energy Analyses Biophysical Journal. Jun, 2004 | Pubmed ID: 15189842 Influence of DNA Structure on DNA Polymerase Beta Active Site Function: Extension of Mutagenic DNA Intermediates The Journal of Biological Chemistry. Jul, 2004 | Pubmed ID: 15145936 High-level Expression and Purification of Untagged and Histidine-tagged HIV-1 Reverse Transcriptase Protein Expression and Purification. Mar, 2004 | Pubmed ID: 14766302 Localization of the Deoxyribose Phosphate Lyase Active Site in Human DNA Polymerase Iota by Controlled Proteolysis The Journal of Biological Chemistry. Aug, 2003 | Pubmed ID: 12777390 Structural Insights into the Origins of DNA Polymerase Fidelity Structure (London, England : 1993). May, 2003 | Pubmed ID: 12737815 Structure of DNA Polymerase Beta with the Mutagenic DNA Lesion 8-oxodeoxyguanine Reveals Structural Insights into Its Coding Potential Structure (London, England : 1993). Jan, 2003 | Pubmed ID: 12517346 Rapid Segmental and Subdomain Motions of DNA Polymerase Beta The Journal of Biological Chemistry. Feb, 2003 | Pubmed ID: 12458221 Efficiency of Correct Nucleotide Insertion Governs DNA Polymerase Fidelity The Journal of Biological Chemistry. Dec, 2002 | Pubmed ID: 12370169 Polymerase Beta Simulations Suggest That Arg258 Rotation is a Slow Step Rather Than Large Subdomain Motions Per Se Journal of Molecular Biology. Apr, 2002 | Pubmed ID: 11955015 Loss of DNA Polymerase Beta Stacking Interactions with Templating Purines, but Not Pyrimidines, Alters Catalytic Efficiency and Fidelity The Journal of Biological Chemistry. Mar, 2002 | Pubmed ID: 11756435 Steady-state, Pre-steady-state, and Single-turnover Kinetic Measurement for DNA Glycosylase Activity Akira Sassa1, William A. Beard1, David D. Shock1, Samuel H. Wilson1 1Laboratory of Structural Biology, NIEHS, National Institutes of Health JoVE 50695 Chemistry
Steady-state, Pre-steady-state, and Single-turnover Kinetic Measurement for DNA Glycosylase Activity Akira Sassa1, William A. Beard1, David D. Shock1, Samuel H. Wilson1 1Laboratory of Structural Biology, NIEHS, National Institutes of Health JoVE 50695 Chemistry