Thermodynamic comparison of the base pairs formed by the carcinogenic lesion O6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs.

A set of 10 non-self-complementary nonadeoxyribonucleoside octaphosphates, d(GGTTXTTGG) and d(CCAAYAACC), where X and Y are A, C, G, T, or O6MeG, has been synthesized by a large-scale, automated, phosphoramidite procedure. Purification was effected by reversed-phase HPLC, and the base composition was verified by analytical HPLC after enzymatic degradation to the constituent deoxynucleosides. This set of molecules was designed to allow evaluation of the nearest-neighbor dependence of each base pair. The thermal stability, expressed as Tmax, of each duplex containing one of the O6MeG base pairs, a Watson-Crick pair, or one of the mismatches possible with this set of molecules was determined over a concentration range of 5.7-200 microM. From these data the delta H degree, delta S degree, and delta G degree of each combination were calculated. In general, the relative thermal stabilities observed for the O6-methylguanine combinations confirm our previous findings that the most stable base pair is formed with cytosine rather than thymine and that all O6MeG pairs are much weaker than Watson-Crick base pairs [Kuzmich, S., Marky, L. A., & Jones, R. A. (1983) Nucleic Acids Res. 11, 3393-3404; Gaffney, B. L., Marky, L. A., & Jones, R. A. (1984) Biochemistry 23, 5686-5691]. Moreover, the nine combinations containing O6-methylguanine are all of similar thermal stability, cover a much smaller range in Tmax than do the mismatches, and show little sequence dependence.