SOLUTION PROPERTIES AND COMPUTATIONAL ANALYSIS OF AN OLIGODEOXYNUCLEOTIDE CONTAINING N-(DEOXYGUANOSIN-8-YL)-1-AMINOPYRENE

An oligodeoxyribonucleotide 5'-d(CTCATG(AP)ATTCC), in which G(AP) deno tes N-(guanin-8-yl)-1-aminopyrene, the CS-guanine adduct of reductivel y activated 1-nitropyrene, was synthesized and characterized by polyac rylamide gel electrophoresis, absorption and fluorescence spectroscopy , circular dichroism, and thermal melting studies, Polyacrylamide gel electrophoresis showed slower mobility of the adducted oligonucleotide in single-stranded form compared to its unmodified counterpart, as ex pected. In duplex form, however (with a deoxycytidine opposite the add uct), the adducted 11mer migrated faster than the parent duplex, Absor ption and fluorescence studies indicated significant interaction of th e aminopyrene residue with the DNA bases in the modified 11mer, The sp ectroscopic data also suggested the presence of one or more conformers in which the aminopyrene residue is quasi-intercalative, as well as o ne(s) in which the aminopyrene is externally bound, Thermodynamic para meters for the helix-to-coil transitions for the 11mer duplex were det ermined, The difference in free energy (Delta Delta G degrees) between the unmodified and modified sequences was relatively small (similar t o 1.2 kcal/mol), Circular dichroism spectra indicated the presence of essentially B-form DNA, The energy minimizations suggested that the mo st stable conformers shared a common feature: displacement of the modi fied guanine from the double helix, In the global minimum, the aminopy rene residue was inserted in the helix in the site of displaced guanin e. In other low energy structures, the aminopyrene was also displaced towards the minor groove (in addition to guanine), or partly inserted and partly in the groove, More conventional structures were also encou ntered, with anti-guanine within the helix and aminopyrene in the majo r groove, or syn-guanine within the helix, and aminopyrene in the mino r groove, Such structures were 12-20 kcal/mol less stable than the glo bal minimum, however, The C8-guanine adduct of aminopyrene thus appear s to perturb the B-DNA structure to a greater extent than do the adduc ts of less bulky amines such as aminofluorene and 4-aminobiphenyl.