Conformational searches elucidate effects of stereochemistry on structures of deoxyadenosine covalently bound to tumorigenic metabolites of benzo[C] phenanthrene.

Remarkably different conformations can result when DNA binds with stereoisomeric compounds containing differing absolute configurations of substituents about chiral carbon atoms. Furthermore, the biochemical functions of covalent adducts with DNA are strongly affected by the stereochemistry of the ligands. Such stereochemical effects are manifested by DNA covalent adducts derived from metabolites of the non-planar fjord region environmental chemical carcinogen benzo[c]phenanthrene. To analyze these phenomena, an extensive conformational investigation for R and S stereoisomeric adducts to deoxyadenosine, derived from trans addition of enantiomeric anti diol epoxide metabolites of benzo[c]phenanthrene, has been carried out. We have surveyed the potential energy surface of the two adducts by varying systematically at 5 degree intervals in combination, the three important torsion angles that govern conformational flexibility of the carcinogen bulk with respect to the linked nucleoside. We carried out a grid search by creating 373, 248 structures for each isomer, and evaluated their molecular mechanical energies. This has permitted us to map the potential energy surface of each adduct in these three variables, and to delineate their low energy regions. The maps have a symmetric relationship which stems from the near mirror-image stereochemistry in the R and S isomers. This produces near mirror-image low energy structures in the nucleoside adducts. The limited sets of stereoisomer-dependent conformational domains delineated are determined by steric effects. Moreover, these features have been experimentally demonstrated to play governing structural roles in such carcinogen-damaged DNA duplexes: opposite orientations in the stereoisomer pairs computed for the nucleosides are observed by high-resolution NMR in the similarly modified DNA double helices, and are likely to play important roles in their interactions with enzymes involved in DNA transactions, and hence their biological activities.