1,<i>N</i>²-Etheno-2′-deoxyguanosine Adopts the <i>syn</i> Conformation about the Glycosyl Bond When Mismatched with Deoxyadenosine

The oligodeoxynucleotide 5′-CGCAT<u>X</u>GAATCC-3′·5′-GGATTC<u>A</u>ATGCG-3′ containing 1,<i>N</i>²-etheno-2′-deoxyguanosine (1,<i>N</i>²-εdG) opposite deoxyadenosine (named the 1,<i>N</i>²-εdG·dA duplex) models the mismatched adenine product associated with error-prone bypass of 1,<i>N</i>²-εdG by the <i>Sulfolobus solfataricus</i> P2 DNA polymerase IV (Dpo4) and by <i>Escherichia coli</i> polymerases pol I <i>exo</i>^<i>–</i> and pol II <i>exo</i>^<i>–</i>. At pH 5.2, the <i>T</i>_m of this duplex was increased by 3 °C as compared to the duplex in which the 1,<i>N</i>²-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,<i>N</i>²-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,<i>N</i>²-εdG rotated about the glycosyl bond from the <i>anti</i> to the <i>syn</i> 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,<i>N</i>²-εdG, adopted the <i>anti</i> conformation and was directed toward the helix. The downfield shifts of the A¹⁹ amino protons suggested protonation of dA. Thus, the protonated 1,<i>N</i>²-εdG·dA base pair was stabilized by hydrogen bonds between 1,<i>N</i>²-εdG N1 and A¹⁹ N1H⁺ and between 1,<i>N</i>²-εdG <i>O</i>⁹ and A¹⁹ <i>N</i>⁶H. 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,<i>N</i>²-εdG·dA base pair, compared to that of the 1,<i>N</i>²-εdG·dC base pair, correlated with the mismatch adenine product observed during the bypass of 1,<i>N</i>²-εdG by the Dpo4 polymerase, suggesting that stabilization of this mismatch may be significant with regard to the biological processing of 1,<i>N</i>²-εdG