We have carried out molecular dynamics (MD) simulations to elucidate how lesion structure and dynamics may impact lesion access to the nucleotide excision repair (NER) machinery in the context of the nucleosome. NER assays, involving studies of the extent of dual incisions of the modified strand in standard HeLa cell extracts, performed either with S or R 5'-8-cyclo-2'-deoxypurines or the bulky (+)-cis-B[a]P-N2-dG lesion, showed that the cyclo-lesions are not repaired, while the (+)-cis-B[a]P-N2-dG is repair-susceptible. In free DNA in solution, the cyclo-lesions with R stereochemistry are better substrates of NER than the S isomers, while the (+)-cis-B[a]P-N2-dG adduct is characterized by the highest efficiency of NER dual incisions. Our MD results show that the (+)-cis-B[a]P-N2-dG adduct in the nucleosome has dynamic and structural properties that would more readily lead to lesion access than either S or R cyclo-lesions. Furthermore, there are inherent differences in structure and dynamics between the S and R cyclo-stereoisomers in solution (Kropachev et al, 2014, Nucleic Acids Res. doi: 10.1093/nar/gku162), and these differences persist in nucleosomes; hence, once access is achieved, stereospecific dual incision NER efficiencies could manifest themselves. (Supported by NIH Grants CA-28038 and CA-75449 to S.B., ES-011589 to V.S., and CA-099194 to N.E.G.)

Access of the NER machinery for lesion repair in nucleosomes is impacted by lesion structure and dynamics

248th National Meeting (2014)

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