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Broyde S

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Publications:

Title Authors Year Journal
Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion. Broyde S 2012 Nucleic acids research
Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Broyde S 2010 Nature structural & molecular biology
Influence of local sequence context on damaged base conformation in human DNA polymerase iota: molecular dynamics studies of nucleotide incorporation opposite a benzo[a]pyrene-derived adenine lesion. Broyde S 2009 Nucleic acids research
Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing? Broyde S 2009 Biochemistry
Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase. Broyde S 2009 Biochemistry
Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases. Broyde S 2009 Structure (London, England : 1993)
Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase. Broyde S 2009 Journal of molecular biology
Lesion processing: high-fidelity versus lesion-bypass DNA polymerases. Broyde S 2008 Trends in biochemical sciences
The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions. Broyde S 2008 Nucleic acids research
Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism. Broyde S 2008 Biochemistry
A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. Broyde S 2007 Journal of the American Chemical Society
Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase. Broyde S 2007 The Journal of biological chemistry
Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. Broyde S 2007 Nucleic acids research
Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies. Broyde S 2006 Nucleic acids research
A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Broyde S 2006 Nucleic acids research
Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. Broyde S 2006 PLoS Biol
Accommodation of a 1S-(-)-benzo[c]phenanthrenyl-N6-dA adduct in the Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations. Broyde S 2005 Chemical research in toxicology
Molecular dynamics of a food carcinogen-DNA adduct in a replicative DNA polymerase suggest hindered nucleotide incorporation and extension. Broyde S 2005 Chemical research in toxicology
Altering DNA polymerase incorporation fidelity by distorting the dNTP binding pocket with a bulky carcinogen-damaged template. Broyde S 2004 Biochemistry
The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches. Broyde S 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. Broyde S 2004 Biophys J
Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. Broyde S 2002 Journal of molecular biology
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. Broyde S 2002 Journal of molecular biology
Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen. Broyde S 2001 Journal of molecular biology
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. Broyde S 1998 Biochemistry
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