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

The oligodeoxynucleotide 5'-CGCATXGAATCC-3' center dot 5'-GGATTCAATGCG-3' containing 1,N-2-etheno-2'-deoxyguanosine (1,N-2-epsilon dG) opposite deoxyadenosine (named the 1,N-2-epsilon dG.dA duplex) models the mismatched adenine product associated with error-prone bypass of 1,N-2-epsilon dG 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 degrees C as compared to the duplex in which the 1,N-2-epsilon dG lesion is opposite dC, and it was increased by 2 degrees C compared to the duplex in which guanine is opposite dA (the dG.dA duplex). A strong NOE between the 1,N-2-epsilon dG imidazole proton and the anomeric proton of the attached deoxyribose, accompanied by strong NOEs to the minor groove A(20) H2 proton and the mismatched A(19) H2 proton from the complementary strand, establish that 1,N-2-epsilon dG 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 T-5 CH3. A strong NOE between A(20) H2 and A(19) H2 protons established that A(19), opposite to 1,N-2-epsilon dG, adopted the anti conformation and was directed toward the helix. The downfield shifts of the A(19) amino protons suggested protonation of dA. Thus, the protonated 1,N-2-epsilon dG.dA base pair was stabilized by hydrogen bonds between 1,N-2-epsilon dG N1 and A(19) N1H(+) and between 1,N-2-epsilon dG O-9 and A(19) (NH)-H-6. 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,N-2-epsilon dG.dA base pair, compared to that of the 1,N-2-epsilon dG.dC base pair, correlated with the mismatch adenine product observed during the bypass of 1,N-2-epsilon dG by the Dpo4 polymerase, suggesting that stabilization of this mismatch may be significant with regard to the biological processing of 1,N-2-epsilon dG.