NMR studies of exocyclic 1,N2-propanodeoxyguanosine adducts (X) opposite purines in DNA duplexes: protonated X(syn).cntdot.A(anti) pairing (acidic pH) and X(syn).cntdot.G(anti) pairing (neutral pH) at the lesion site

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Abstract
Proton and phosphorus two-dimensional NMR studies are reported for the complementary d(Cl-A2-T3-G4-X5-G6-T7-A8-C9).cntdot.d(G10-T11-A12-C13-A14-C15-A16-T17-G18) nonanucleotide duplex (designated X.cntdot.A 9-mer) that contains a 1,N2-propanodeoxyguanosine exocyclic adduct, X5, opposite deoxyadenosine A14 in the center of the helix. The NMR studies detect a pH-dependent conformational transition; this paper focuses on the structures present at pH 5.8. The two-dimensional NOESY studies of the X.cntdot.A 9-mer duplex in H2O and D2O solution establish that X5 adopts a syn orientation while A14 adopts an anti orientation about the glycosidic bond at the lesion site. The large downfield shift of the amino protons of A14 demonstrates protonation of the deoxyadenosine base at pH 5.8 such that the protonated X5(syn) .cntdot.A14(anti)pair is stabilized by two hydrogen bonds at low pH. At pH 5.8, the observed NOE between the H8 proton of X5 and the H2 proton of A14 in the X.cntdot.A 9-mer duplex demonstrates unequivocally the formation of the protonated X5(syn).cntdot.A14(anti)pair. The 1,N2-propano bridge of X5(syn) is located in the major groove. Selective NOEs from the exocyclic methylene protons of X5 to the major groove H8 proton of flanking G4 but not G6 of the G4-X5-G6 segment provide additional structural constraints on the local conformation at the lesion site. A perturbation in the phosphodiester backbone is detected at the C13-A14 phosphorus located at the lesion site by 31P NMR spectroscopy. The two-dimensional NMR studies have been extended to the related complementary X.cntdot.G 9-mer duplex that contains a central X5.cntdot.G14 lesion in a sequence that is otherwise identical with the X.cntdot.A 9-mer duplex. The NMR experimental parameters are consistent with formation of a pH-independent X5(syn).cntdot.G14(anti) pair stabilized by two hydrogen bonds with the 1,N2-propano exocyclic adduct of X5(syn) located in the major groove.

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