Solution Conformation of the (+)-trans-anti-[BPh]dA Adduct opposite dT in a DNA Duplex: Intercalation of the Covalently Attached Benzo[c]phenanthrene to the 5′-Side of the Adduct Site without Disruption of the Modified Base Pair

Benzo[c]phenanthrene diol epoxide can covalently bind to the exocyclic amino group of deoxyadenosine to generate [BPh]dA adducts where the polycyclic aromatic hydrocarbon is attached to the major groove edge of DNA. This paper reports on NMR-energy minimization structural studies of the (+)-trans-anti-[BPh] dA adduct positioned opposite dT in the sequence context d(C5-[BPh]A6-C7) d-(G16-T17-G18) at the 11-mer duplex level. The exchangeable and nonexchangeable protons of the benzo[c]phenanthrenyl moiety and the nucleic acid were assigned following analysis of two-dimensional NMR data sets in H₂O and D₂O solution. The solution structure of the (+)-trans-anti-[BPh]dA dT 11-mer duplex has been determined by incorporating intramolecular and intermolecular proton-proton distances defined by upper and lower bounds deduced from NOESY data sets as restraints in energy minimization computations. The covalently attached benzo[c]phenanthrene ring intercalates to the 5′-side of the [BPh]-dA6 lesion site without disruption of the flanking Watson-Crick dC5 dG18 and [BPh] dA6 dT 17 base pairs. The observed buckling of the intercalation cavity reflects the selective overlap of the intercalated phenanthrenyl ring with dT17 and dG18 bases on the unmodified strand. The structure provides new insights into how a polycyclic aromatic hydrocarbon covalently attached to the major groove edge of deoxyadenosine can still unidirectionally intercalate into the helix without disruption of the modified base pair. Our study establishes that among the contributing factors are a propeller-twisted [BPh]dA6 dT17 base pair, displacement of the carcinogen-DNA linkage bond from the plane of the dA6 base, the specific pucker adopted by the benzylic ring, and the propeller-like nonplanar geometry for the aromatic phenanthrenyl ring system. Our combined experimental-computational studies to date have now identified three structural motifs adopted by covalent polycyclic aromatic hydrocarbon-DNA adducts with their distribution determined by the chiral characteristics of individual stereoisomers and by whether the covalent adducts are generated at the minor or the major groove edge of the helix.