1,N²-Etheno-2′-deoxyguanosine Adopts the syn Conformation about the Glycosyl Bond When Mismatched with Deoxyadenosine

The oligodeoxynucleotide 5′-CGCATXGAATCC-3′·5′-GGATTCAATGCG-3′ containing 1,N²-etheno-2′-deoxyguanosine (1,N²-εdG) opposite deoxyadenosine (named the 1,N²-εdG·dA duplex) models the mismatched adenine product associated with error-prone bypass of 1,N²-εdG by the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) and by Escherichia coli polymerases pol I exo^– and pol II exo^–. At pH 5.2, the T_m of this duplex was increased by 3 °C as compared to the duplex in which the 1,N²-εdG lesion is opposite dC, and it was increased by 2 °C compared to the duplex in which guanine is opposite dA (the dG·dA duplex). A strong NOE between the 1,N²-εdG imidazole proton and the anomeric proton of the attached deoxyribose, accompanied by strong NOEs to the minor groove A²⁰ H2 proton and the mismatched A¹⁹ H2 proton from the complementary strand, establish that 1,N²-εdG rotated about the glycosyl bond from the anti to the syn conformation. The etheno moiety was placed into the major groove. This resulted in NOEs between the etheno protons and T⁵ CH₃. A strong NOE between A²⁰ H2 and A¹⁹ H2 protons established that A¹⁹, opposite to 1,N²-εdG, adopted the anti conformation and was directed toward the helix. The downfield shifts of the A¹⁹ amino protons suggested protonation of dA. Thus, the protonated 1,N²-εdG·dA base pair was stabilized by hydrogen bonds between 1,N²-εdG N1 and A¹⁹ N1H⁺ and between 1,N²-εdG O⁹ and A¹⁹ N⁶H. The broad imino proton resonances for the 5′- and 3′-flanking bases suggested that both neighboring base pairs were perturbed. The increased stability of the 1,N²-εdG·dA base pair, compared to that of the 1,N²-εdG·dC base pair, correlated with the mismatch adenine product observed during the bypass of 1,N²-εdG by the Dpo4 polymerase, suggesting that stabilization of this mismatch may be significant with regard to the biological processing of 1,N²-εdG.