Activation of the H-ras protooncogene in rats by methylating carcinogens results from a G-to-A transition mutation at the second position of codon 12 (GGA), presumably due to formation of an O6-methylguanine (m6G) at this position. A similar transition at the first position of codon 12 appears not to occur in vivo. To study the possible structural basis for this bias in mutation, we synthesized a series of 11-base H-ras sequences [e.g., 5'-d(CGCTG*G*AGGCG)-3' and two complementary strands] containing an m6G at the first, second, or both positions of codon 12 (i.e., G* = m6G). The results of solution chemical studies indicated that the individual strands formed stable hairpin structures among which that containing m6G at the second position of codon 12 was most stable. Further, the DNA duplex with m6G at the second position was significantly more stable than that with m6G at the first position, and under certain conditions, it was more stable than the unmodified duplex as well. It is possible that such a difference in stability might lead to more ready recognition of an m6G at the first position by repair proteins, and this could contribute to the apparent site specificity of mutation by methylating carcinogens at codon 12 of the H-ras gene.