Nuclear Magnetic Resonance Solution Structure of an Undecanucleotide Duplex with a Complementary Thymidine Base opposite a 10R Adduct Derived from Trans Addition of a Deoxyadenosine N⁶-Amino Group to (-)-(7R,8S,9R,10S)-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene

The solution structure of a modified undecamer duplex containing (-)-(7R,8S,9R,10S)-7,8- dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene covalently bonded through trans ring opening at C10 of the epoxide by the N⁶-amino group of deoxyadenosine (dA) was studied. This diol epoxide 1 diastereomer has the benzylic 7-hydroxyl group and the epoxide oxygen cis. The modified nucleotide residue has R chirality at C10 of the hydrocarbon (10R adduct). The undecamer duplex d(C₁G₂G₃T₄C₅A*₆C₇G₈A₉G₁₀G₁₁).d(C₁₂C₁₃T₁₄C₁₅G₁₆T₁₇G₁₈A₁₉C₂₀C₂₁G₂₂) has a complementary T opposite the modified dA (dA*6 is the modified dA). Exchangeable and nonexchangeable proton assignments were made using 2D TOCSY, NOESY, and water/NOESY NMR spectroscopy. The hybrid complete relaxation matrix program MORASS was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations. The refined structure showed the hydrocarbon intercalated from the major groove between dA*6-T17 and dC5-dG18 base pairs. The modified dA*6 was in the normal anti configuration and showed Watson-Crick base pairing to T17 opposite. The chemical shifts of the hydrocarbon protons and the unusual shifts of sugar protons were accounted for by the intercalated orientation of the hydrocarbon.