Broyde S

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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
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
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)
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
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
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
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
Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion.	Broyde S	2006	PLoS Biol
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
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
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
Altering DNA polymerase incorporation fidelity by distorting the dNTP binding pocket with a bulky carcinogen-damaged template.	Broyde S	2004	Biochemistry
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
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
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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Broyde S

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