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Beard WA

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Publications:

Title Authors Year Journal
A review of recent experiments on step-to-step "hand-off" of the DNA intermediates in mammalian base excision repair pathways. Beard WA Molekuliarnaia biologiia
Understanding the loss-of-function in a triple missense mutant of DNA polymerase β found in prostate cancer. Beard WA 2013 International journal of oncology
Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction. Beard WA 2013 Journal of the American Chemical Society
Insights into the Conformation of Aminofluorene-dG Adduct in a DNA Polymerase Active Site. Beard WA 2013 The Journal of biological chemistry
Observing a DNA polymerase choose right from wrong. Beard WA 2013 Cell
Inhibition of HIV-1 Reverse Transcriptase-Catalyzed Synthesis by Intercalated DNA Benzo[a]Pyrene 7,8-Dihydrodiol-9,10-Epoxide Adducts. Beard WA 2013 PloS one
DNA Polymerase β Gap-filling Translesion DNA Synthesis. Beard WA 2012 Chemical research in toxicology
DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion. Beard WA 2012 Nucleic acids research
Effect of β,γ-CHF- and β,γ-CHCl-dGTP Halogen Atom Stereochemistry on the Transition State of DNA Polymerase β Beard WA 2012 Biochemistry
Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Beard WA 2012 Structure (London, England : 1993)
Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms. Beard WA 2012 Theoretical chemistry accounts
Metal-induced DNA translocation leads to DNA polymerase conformational activation. Beard WA 2011 Nucleic acids research
Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion. Beard WA 2011 Proceedings of the National Academy of Sciences of the United States of America
Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. Beard WA 2011 The Journal of biological chemistry
DNA polymerase beta ribonucleotide discrimination: insertion, misinsertion, extension, and coding. Beard WA 2010 The Journal of biological chemistry
DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine. Beard WA 2010 Mutation research
Substrate channeling in mammalian base excision repair pathways: passing the baton. Beard WA 2010 The Journal of biological chemistry
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Beard WA 2010 Proceedings of the National Academy of Sciences of the United States of America
Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. Beard WA 2010 Journal of the American Chemical Society
Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site. Beard WA 2010 Nature structural & molecular biology
Base excision repair and design of small molecule inhibitors of human DNA polymerase beta. Beard WA 2010 Cell Mol Life Sci
A real-time fluorescence method for enzymatic characterization of specialized human DNA polymerases. Beard WA 2009 Nucleic acids research
DNA polymerase beta and PARP activities in base excision repair in living cells. Beard WA 2009 DNA repair
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function. Beard WA 2009 Org Lett
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". Beard WA 2009 The Journal of biological chemistry
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. Beard WA 2008 J Med Chem
DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. Beard WA 2008 Biochemistry
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Beard WA 2008 Proteins
Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta. Beard WA 2008 Proceedings of the National Academy of Sciences of the United States of America
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Beard WA 2008 Molecular cell
Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. Beard WA 2007 Biochemistry
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. Beard WA 2007 Biophys J
The X family portrait: structural insights into biological functions of X family polymerases. Beard WA 2007 DNA repair
Coordination of steps in single-nucleotide base excision repair mediated by apurinic/apyrimidinic endonuclease 1 and DNA polymerase beta. Beard WA 2007 The Journal of biological chemistry
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. Beard WA 2007 Journal of molecular biology
(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. Beard WA 2007 Journal of the American Chemical Society
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. Beard WA 2006 Biochemistry
Determination of lysine pK values using [5-13C]lysine: application to the lyase domain of DNA Pol beta. Beard WA 2006 Journal of the American Chemical Society
Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features. Beard WA 2006 Proceedings of the National Academy of Sciences of the United States of America
Energy analysis of chemistry for correct insertion by DNA polymerase beta. Beard WA 2006 Proceedings of the National Academy of Sciences of the United States of America
Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Beard WA 2006 Structure (London, England : 1993)
Structure and mechanism of DNA polymerase Beta. Beard WA 2006 Chem Rev
Activities and mechanism of DNA polymerase beta. Beard WA 2006 Methods in enzymology
DNA polymerase beta and flap endonuclease 1 enzymatic specificities sustain DNA synthesis for long patch base excision repair. Beard WA 2005 The Journal of biological chemistry
DNA polymerase lambda mediates a back-up base excision repair activity in extracts of mouse embryonic fibroblasts. Beard WA 2005 The Journal of biological chemistry
Syn-full behavior by T7 DNA polymerase. Beard WA 2005 Structure (London, England : 1993)
A thymine isostere in the templating position disrupts assembly of the closed DNA polymerase beta ternary complex. Beard WA 2005 Biochemistry
Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity. Beard WA 2005 Biochemistry
Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Beard WA 2005 Structure (London, England : 1993)
Structural insight into the DNA polymerase beta deoxyribose phosphate lyase mechanism. Beard WA 2005 DNA repair
High-level expression and purification of untagged and histidine-tagged HIV-1 reverse transcriptase. Beard WA 2004 Protein expression and purification
Dynamic characterization of a DNA repair enzyme: NMR studies of [methyl-13C]methionine-labeled DNA polymerase beta. Beard WA 2004 Biochemistry
Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. Beard WA 2004 Journal of the American Chemical Society
Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates. Beard WA 2004 The Journal of biological chemistry
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. Beard WA 2004 Biophys J
Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity. Beard WA 2004 Structure (London, England : 1993)
Localization of the deoxyribose phosphate lyase active site in human DNA polymerase iota by controlled proteolysis. Beard WA 2003 The Journal of biological chemistry
Rapid segmental and subdomain motions of DNA polymerase beta. Beard WA 2003 The Journal of biological chemistry
Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Beard WA 2003 Structure (London, England : 1993)
Structural insights into the origins of DNA polymerase fidelity. Beard WA 2003 Structure (London, England : 1993)
Efficiency of correct nucleotide insertion governs DNA polymerase fidelity. Beard WA 2002 The Journal of biological chemistry
Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity. Beard WA 2002 The Journal of biological chemistry
Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. Beard WA 2002 Journal of molecular biology
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. Beard WA 2002 Journal of molecular biology
DNA lesion bypass polymerases open up. Beard WA 2001 Structure (London, England : 1993)
DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase beta. Implication for the identity of the rate-limiting conformational change. Beard WA 2001 The Journal of biological chemistry
Vertical-scanning mutagenesis of a critical tryptophan in the "minor groove binding track" of HIV-1 reverse transcriptase. Major groove DNA adducts identify specific protein interactions in the minor groove. Beard WA 2000 The Journal of biological chemistry
DNA polymerase beta and mammalian base excision repair. Beard WA 2000 Cold Spring Harbor symposia on quantitative biology
Structural design of a eukaryotic DNA repair polymerase: DNA polymerase beta. Beard WA 2000 Mutation research
Minor groove interactions at the DNA polymerase beta active site modulate single-base deletion error rates. Beard WA 2000 The Journal of biological chemistry
Residues in the alphaH and alphaI helices of the HIV-1 reverse transcriptase thumb subdomain required for the specificity of RNase H-catalyzed removal of the polypurine tract primer. Beard WA 1999 The Journal of biological chemistry
Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove. Beard WA 1999 The Journal of biological chemistry
Uniquely altered DNA replication fidelity conferred by an amino acid change in the nucleotide binding pocket of human immunodeficiency virus type 1 reverse transcriptase. Beard WA 1999 The Journal of biological chemistry
The fidelity of DNA polymerase beta during distributive and processive DNA synthesis. Beard WA 1999 The Journal of biological chemistry
Interactions between DNA polymerase beta and the major covalent adduct of the carcinogen (+)-anti-benzo[a]pyrene diol epoxide with DNA at a primer-template junction. Beard WA 1998 Biochemistry
Vertical-scanning mutagenesis of a critical tryptophan in the minor groove binding track of HIV-1 reverse transcriptase. Molecular nature of polymerase-nucleic acid interactions. Beard WA 1998 The Journal of biological chemistry
Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism. Beard WA 1998 The Journal of biological chemistry
Functional analysis of the amino-terminal 8-kDa domain of DNA polymerase beta as revealed by site-directed mutagenesis. DNA binding and 5'-deoxyribose phosphate lyase activities. Beard WA 1998 The Journal of biological chemistry
Structural insights into DNA polymerase beta fidelity: hold tight if you want it right. Beard WA 1998 Chemistry & biology
Mammalian abasic site base excision repair. Identification of the reaction sequence and rate-determining steps. Beard WA 1998 The Journal of biological chemistry
Subunits of human replication protein A are crosslinked by photoreactive primers synthesized by DNA polymerases. Beard WA 1998 Nucleic acids research
A minor groove binding track in reverse transcriptase. Beard WA 1997 Nat Struct Biol
Probing structure/function relationships of HIV-1 reverse transcriptase with styrene oxide N2-guanine adducts. Beard WA 1997 The Journal of biological chemistry
dNTP binding to HIV-1 reverse transcriptase and mammalian DNA polymerase beta as revealed by affinity labeling with a photoreactive dNTP analog. Beard WA 1996 The Journal of biological chemistry
Enzyme-DNA interactions required for efficient nucleotide incorporation and discrimination in human DNA polymerase beta. Beard WA 1996 The Journal of biological chemistry
dNTP binding site in rat DNA polymerase beta revealed by controlled proteolysis and azido photoprobe cross-linking. Beard WA 1996 Biochemistry
Role of the "helix clamp" in HIV-1 reverse transcriptase catalytic cycling as revealed by alanine-scanning mutagenesis. Beard WA 1996 The Journal of biological chemistry
Specific inhibition of DNA polymerase beta by its 14 kDa domain: role of single- and double-stranded DNA binding and 5'-phosphate recognition. Beard WA 1995 Nucleic acids research
Purification and domain-mapping of mammalian DNA polymerase beta. Beard WA 1995 Methods in enzymology
Human immunodeficiency virus type 1 reverse transcriptase. 3'-Azidodeoxythymidine 5'-triphosphate inhibition indicates two-step binding for template-primer. Beard WA 1995 The Journal of biological chemistry
Reduced frameshift fidelity and processivity of HIV-1 reverse transcriptase mutants containing alanine substitutions in helix H of the thumb subdomain. Beard WA 1995 The Journal of biological chemistry
DNA damage-induced transcriptional activation of a human DNA polymerase beta chimeric promoter: recruitment of preinitiation complex in vitro by ATF/CREB. Beard WA 1995 Biochemistry
Structure/function studies of human immunodeficiency virus type 1 reverse transcriptase. Alanine scanning mutagenesis of an alpha-helix in the thumb subdomain. Beard WA 1994 The Journal of biological chemistry
Site-directed mutagenesis of HIV reverse transcriptase to probe enzyme processivity and drug binding. Beard WA 1994 Current opinion in biotechnology
Studies of gapped DNA substrate binding by mammalian DNA polymerase beta. Dependence on 5'-phosphate group. Beard WA 1994 The Journal of biological chemistry
Expression and purification of the HIV-1 reverse transcriptase using the baculovirus expression vector system. Beard WA 1993 Protein expression and purification
HIV-1 reverse transcriptase: inhibition by 2',5'-oligoadenylates. Beard WA 1993 Biochemistry
Structure/function studies of HIV-1(1) reverse transcriptase: dimerization-defective mutant L289K. Beard WA 1993 Biochemistry
Kinetic analysis of template.primer interactions with recombinant forms of HIV-1 reverse transcriptase. Beard WA 1993 Biochemistry

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