Two-dimensional proton NMR studies are reported on the complementary d(C-A-T-G-T-G- T-A-C)·d(G-T-A-C-eA-C-A-T-G) nonanucleotide duplex (designated ϵdA·dT 9-mer duplex) containing 1,N6ethenodeoxyadenosine (ϵdA), a carcinogen-DNA adduct, positioned opposite thymidine in the center of the helix. Our NMR studies have focused on the conformation of the ϵdA·dT 9-mer duplex at neutral pH with emphasis on defining the alignment at the dT5·ϵdA14 lesion site. The through-space NOE distance connectivities establish that both dT5 and ϵdA14 adopt anti glycosidic torsion angles, are directed into the interior of the helix, and stack with flanking Watson-Crick dG4·dC15 and dG6·dC13 pairs. Furthermore, the d(G4-T5-G6)·d(C13-ϵA14-C15) trinucleotide segment centered about the dT5·ϵdA14 lesion site adopts a right-handed helical conformation in solution. Energy minimization computations were undertaken starting from six different alignments of dT5(anti) and ϵdA14(anti) at the lesion site and were guided by distance constraints defined by lower and upper bounds estimated from NOESY data sets on the ϵdA·dT 9-mer duplex. Two families of energy-minimized structures were identified with the dT5 displaced toward either the flanking dG4·dC15 or the dG6·dC13 base pair. These structures can be differentiated on the basis of the observed NOEs from the imino proton of dT5 to the imino proton of dG4 but not dG6 and to the amino protons of dC15 but not dC13 that were not included in the constraints data set used in energy minimization. Our NMR data are consistent with a nonplanar alignment of edA14(anti) and dT5(anti) with dT5 displaced toward the flanking dG4·dC15 base pair within the d(G4-T5-G6)·d(C13-ϵA14-C15) segment of the ϵdA·dT 9-mer duplex.
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