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Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion
Stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases. Expand
The Chemical Biology of DNA Damage
Preface. List of Contributors. PART ONE Chemistry and Biology of DNA Lesions. 1 Introduction and Perspectives on the Chemistry and Biology of DNA Damage (Nicolas E. Geacintov and Susan Broyde). 1.1Expand
Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery
Investigation of site specifically modified oligonucleotides containing single, well‐defined polycyclic aromatic hydrocarbon (PAH) diol epoxide‐adenine adducts suggests differences in the thermodynamic properties and thermal stabilities are associated with differences in distortions to the DNA induced by the lesions. Expand
Solution conformation of the major adduct between the carcinogen (+)-anti-benzo[a]pyrene diol epoxide and DNA.
The solution structure centered about the BP covalent adduct site in the (BP)G.C 11-mer duplex is determined by incorporating intramolecular and intermolecular proton-proton distance bounds deduced from the NMR data sets as constraints in energy minimization computations. Expand
Structural basis for the recognition of diastereomeric 5′,8-cyclo-2′-deoxypurine lesions by the human nucleotide excision repair system
The locally impaired stacking interaction energies correlate with relative NER incision efficiencies, and explain these results on a structural basis in terms of differences in dynamic perturbations of the DNA backbone imposed by the R and S covalent 5′,8 bonds. Expand
Solution structure of the 2-amino-1- methyl-6-phenylimidazo[4,5-b]pyridine C8-deoxyguanosine adduct in duplex DNA
This study contributes the first structural information on the biologically relevant HA class to a growing body of knowledge about how conformational similarities and differences for a variety of types of lesions can influence protein interactions and ultimately biological outcome. Expand
Mechanism of error-free and semi-targeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4
It is shown that Dpo4 catalyzes elongation from a correct 3′-terminal cytosine opposite [AF]G in a nonrepetitive template sequence with low efficiency, which leads to cognate full-length product, as well as mis-elongated products containing base mutations and deletions. Expand
Nucleotide excision repair of 2-acetylaminofluorene- and 2-aminofluorene-(C8)-guanine adducts: molecular dynamics simulations elucidate how lesion structure and base sequence context impact repair
The greater NER efficiencies of the dG-C8-AAF adduct are correlated with greater extents of base sequence-dependent local untwisting and minor groove opening together with weaker stacking interactions. Expand