EFFECT OF MISMATCHED COMPLEMENTARY STRANDS AND 5'-CHANGE IN SEQUENCE CONTEXT ON THE THERMODYNAMICS AND STRUCTURE OF BENZO[A]PYRENE-MODIFIEDOLIGONUCLEOTIDES

Benzo[rr]pyrene (B[a]P) is a well-studied environmental carcinogen tha t when activated can react with DNA to form four major adducts: (+)-tr ans-, (-)-trans-, (+)-cis-, and (-)-cis-anti-B[a]P-dG. In this study, two oligonucleotides (5'-dCCATT-G(B[a]P)-CTACC-3' and 5'-dCCATC-G(B[a] P)-CTACC-3') were prepared, each containing the four isomeric adducts, and these were hybridized to either complementary sequences or to seq uences containing an A, G, or T opposite the adducted guanine. Thermal melting curves, CD, and UV spectra of each duplex were measured and c ompared with the unmodified counterpart. The raw and relative thermody namic measurements were then compared which indicated that differences occur that are both adduct and sequence dependent. These differences were next compared with the in vitro DNA polymerase incorporation data and were found to be strikingly correlated. Most significantly, for a ll four B[a]P isomers a mismatch of an A across from the adduct result ed in the least amount of relative destabilization, while the Watson-C rick complement C showed the most; in vitro studies showed that A is t he preferred base incorporated across from each isomer, while C was in corporated least often. This observed correlation suggests that one fa ctor contributing to misincorporation at an adduct site is the thermod ynamic stability of the incorporated base. Structurally, the effect of sequence context and mismatched complementary strands were also compa red, suggesting that all adducts tend to intercalate within the helix when they are complemented with a mismatched complementary strand. In addition, the level of this intercalation seems to be both sequence an d stereoisomer dependent.