STRUCTURE OF DAMAGED DNA

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DESCRIPTION: (Applicant's Description) The long-term goal of this research is to establish three-dimensional structures of DNA adducts and related lesions, and to correlate structural features of selectively-damaged DNA with its thermodynamic properties and with biological processes, including mutagenesis and DNA repair. Supported by a minority supplement, we have utilized high-resolution NMR spectroscopy and molecular dynamics to establish solution structures of DNA duplexes containing exocyclic lesions and abasic sites, determining their global structural features, lesion-containing base alignments, and perturbations at or near the lesion site. Our future studies encompass three areas: (i) novel DNA adducts, (ii) DNA abasic sites, and (iii) damaged DNA/repair protein complexes. We will perform studies on lesion-containing DNA duplexes focusing on etheno-, acrolein-, and FaPy-dG, adducts resulting from oxidative DNA damage and lipid peroxidation. The structure of these lesions paired with canonical Watson-Crick partners and mutagenic intermediates will be established. We will extend our studies of abasic sites by establishing correlations between sugar configuration, C1, hydrogen bonding, and the intra- or extrahelical position of the abasic site. In addition, we will characterize bistrand abasic site lesions to evaluate the effects of sequence context, mismatch formation, and directionality in DNA duplexes. We also will determine the three-dimensional structure of a putative "flipped-out" DNA intermediate that forms when MutY binds to a non-cleavable DNA substrate, and will establish a solution structure for the C-terminal domain MutY protein.