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Structure of the 1,N2-Ethenodeoxyguanosine Adduct Opposite Cytosine in Duplex DNA: Hoogsteen Base Pairing at pH 5.2

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journal contribution
posted on 16.12.2015 by Ganesh Shanmugam, Ivan D. Kozekov, F. Peter Guengerich, Carmelo J. Rizzo, Michael P. Stone
The exocyclic 1,N2-ethenodeoxyguanosine (1,N2-ϵdG) adduct, arising from the reaction of vinyl halides and other vinyl monomers, including chloroacetaldehyde, and lipid peroxidation products with dG, was examined at pH 5.2 in the oligodeoxynucleotide duplex 5′-d(CGCATXGAATCC)-3′·5′-d(GGATTCCATGCG)-3′ (X = 1,N2-ϵdG). Previously, X(anti)·C(anti) pairing was established in this duplex, containing the 5′-TXG-3′ sequence context, at pH 8.6 [Shanmugam, G., Goodenough, A. K., Kozekov, I. D., Harris, T. M., Guengerich, F. P., Rizzo, C. J., and Stone, M. P. (2007) Chem. Res. Toxicol. 20, 1601−1611]. At pH 5.2, the 1,N2-ϵdG adduct decreased the thermal stability of the duplex by ∼13 °C. The 1,N2-ϵdG adduct rotated about the glycosyl bond from the anti to the syn conformation. This resulted in the observation of a strong nuclear Overhauser effect (NOE) between the imidazole proton of 1,N2-ϵdG and the anomeric proton of the attached deoxyribose, accompanied by an NOE to the minor groove A20 H2 proton from the complementary strand. The syn conformation of the glycosyl bond at 1,N2-ϵdG placed the exocyclic etheno moiety into the major groove. This resulted in the observation of NOEs between the etheno protons and the major groove protons of the 5′-neighboring thymine. The 1,N2-ϵdG adduct formed a Hoogsteen pair with the complementary cytosine, characterized by downfield shifts of the amino protons of the cytosine complementary to the exocyclic adduct. The pattern of chemical shift perturbations indicated that the lesion introduced a localized structural perturbation involving the modified base pair and its 3′- and 5′-neighbor base pairs. A second conformational equilibrium was observed, in which both the modified base pair and its 3′-neighboring G·C base pair formed tandem Hoogsteen pairs. The results support the conclusion that at neutral pH, in the 5′-TXG-3′ sequence, the 1,N2-ϵdG adduct exists as a blend of conformations in duplex DNA. These involve the interconversion of the glycosyl torsion angle between the anti and the syn conformations, occurring at an intermediate rate on the NMR time scale.