Conformation of the deoxydinucleoside monophosphate dCpdG modified at carbon 8 of guanine with 2-(acetylamino)fluorene.

Minimized conformational potential energy calculations were performed for dCpdG modified with the carcinogen 2-(acetylamino)fluorene (AAF). The major adduct, linked via a covalent bond between guanine C-8 and N-2 of AAF, was investigated. The 12 variable torsion angles and both deoxyribose puckers were independent flexible parameters in the energy minimizations. Three categories of low-energy conformers were calculated in which the guanine was syn and nearly perpendicular to the plane of the fluorene: (1) forms in which fluorene is stacked with cytidine (included among these is the global minimum energy conformation); (2) conformers which preserve guanine-cytidine stacking while placing the fluorene in a base-pair obstructing position; (3) conformers which maintain guanine-cytidine stacking and place the fluorene at the helix exterior, without interfering with base pairing. The Z form is important in this group. In addition, a low-energy conformation with guanine anti, but still nearly perpendicular to fluorene, was computed. Molecular models were constructed for the most important conformations incorporated into larger polymers. These indicated that the fluorene-cytidine stacked forms induce a severe kink in the B helix. Conformers with guanine-cytidine stacking and AAF in a base-pair obstructing position place the AAF at the B-type helix interior with little distortion in the helix direction. Conformers with the guanine-cytidine stack in which AAF does not affect base pairing place the fluorene at the Z or alternate helix exterior. It is suggested that base sequence, extent of modification, and external conditions such as salt concentration determine which of a number of possible conformational effects is actually induced by AAF. The variety of observed experimental results with AAF-modified DNA may reflect there various conformational possibilities.