1,<i>N</i><sup>2</sup>-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><sup>2</sup>-etheno-2′-deoxyguanosine (1,<i>N</i><sup>2</sup>-εdG) opposite deoxyadenosine (named the 1,<i>N</i><sup>2</sup>-εdG·dA duplex) models the mismatched adenine product associated with error-prone bypass of 1,<i>N</i><sup>2</sup>-εdG by the <i>Sulfolobus solfataricus</i> P2 DNA polymerase IV (Dpo4) and by <i>Escherichia coli</i> polymerases pol I <i>exo</i><sup><i>–</i></sup> and pol II <i>exo</i><sup><i>–</i></sup>. At pH 5.2, the <i>T</i><sub>m</sub> of this duplex was increased by 3 °C as compared to the duplex in which the 1,<i>N</i><sup>2</sup>-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><sup>2</sup>-εdG imidazole proton and the anomeric proton of the attached deoxyribose, accompanied by strong NOEs to the minor groove A<sup>20</sup> H2 proton and the mismatched A<sup>19</sup> H2 proton from the complementary strand, establish that 1,<i>N</i><sup>2</sup>-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 T<sup>5</sup> CH<sub>3</sub>. A strong NOE between A<sup>20</sup> H2 and A<sup>19</sup> H2 protons established that A<sup>19</sup>, opposite to 1,<i>N</i><sup>2</sup>-εdG, adopted the <i>anti</i> conformation and was directed toward the helix. The downfield shifts of the A<sup>19</sup> amino protons suggested protonation of dA. Thus, the protonated 1,<i>N</i><sup>2</sup>-εdG·dA base pair was stabilized by hydrogen bonds between 1,<i>N</i><sup>2</sup>-εdG N1 and A<sup>19</sup> N1H<sup>+</sup> and between 1,<i>N</i><sup>2</sup>-εdG <i>O</i><sup>9</sup> and A<sup>19</sup> <i>N</i><sup>6</sup>H. 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><sup>2</sup>-εdG·dA base pair, compared to that of the 1,<i>N</i><sup>2</sup>-εdG·dC base pair, correlated with the mismatch adenine product observed during the bypass of 1,<i>N</i><sup>2</sup>-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><sup>2</sup>-εdG.