CONFORMATION OF AMINE-MODIFIED DNA - 2-AMINOFLUORENE-MODIFIED AND 2-(ACETYLAMINO)FLUORENE-MODIFIED DEOXYDINUCLEOSIDE MONOPHOSPHATES WITH ALL POSSIBLE NEAREST NEIGHBORS - A COMPARISON OF SEARCH AND OPTIMIZATIONMETHODS

Although a significant part of the replication fork exists as single-s tranded DNA, little is known about the effect of carcinogens and mutag ens on single-strand conformation. Large-scale conformational searches with potential energy minimization, using the torsion angle space mol ecular mechanics program DUPLEX, were employed to explore the conforma tion of all 16 deoxydinucleoside monophosphates bearing 2-aminofluoren e (AF) or 2-(acetylamino)fluorene (AAF) modification on guanine. We ha ve thus examined the effect of 3' versus 5' modification, the presence or absence of the acetyl group, and the effect of four different neig hbors in each case. The principal effect of the acetyl group appeared to be the destabilization of anti (and, to a lesser degree, borderline anti) conformations for modified guanine. This mattered little in the 5'-substituted dimers, where one conformational type predominated in the low-energy structures for the adducts of both AAF and AF: It was r ight-handed, with syn-guanine, imperfect base-base stacking, and fluor ene to 3'-sugar contacts. Greater divergence was seen in the 3'-substi tuted series. The AAF-substituted 3'-adducts primarily displayed good base-fluorene stacking, with syn-guanine in contact with the 5'-sugar. The AF-substituted 3'-adducts displayed a variety of structures which included base-base and carcinogen-base stacked forms. Two novel forms were encountered [global minima for d(ApG-AF) and d(GpG-AF)], whose u nusual structures suggest mutagenic capability. In order to address th e multiple minimum problem, we conducted our searches of conformation space using two alternative optimization methods that also employ diff ering search strategies. We used the Powell algorithm, BOTM, with star ting conformations that are selected combinations of rotamers, and the method of simulated annealing (SA), with random or arbitrary starting conformations. While both approaches were effective in defining the m ost important structures, SA was more successful than BOTM in locating the