Structural studies of the O6meG.cntdot.T interaction in the d(C-G-T-G-A-A-T-T-C-O6meG-C-G) duplex

Abstract

High-resolution proton and phosphorus NMR studies are reported on the self-complementary d(C1-G2-T3-G4-A5-A6-T7-T8-C9-O6meG10-C11-G12) duplex (henceforth called O6meG.cntdot.T 12-mer), which contains T3.cntdot.O6meG10 interactions in the interior of the helix. The imino proton of T3 is observed at 9.0 ppm, exhibits a temperature-independent chemical shift in the premelting transition range, and broadens out at the same temperature as the imino proton of the adjacent G2.cntdot.C11 toward the end of the helix at pH 6.8. We observed inter base pair nuclear Overhauser effects (NOEs) between the base protons at the T3.cntdot.O6meG10 modification site and the protons of flanking G2.cntdot.C11 and G4.cntdot.C11 and G4.cntdot.C9 base pairs, indicative of the stacking of the T3 and O6meG10 bases into the helix. Two-dimensional correlated (COSY) and nuclear Overhauser effect (NOESY) studies have permitted assignment of the base and sugar H1'', H2'', and H2" nonexchangeable protons in the O6meG.cntdot.T 12-mer duplex. The observed NOEs demonstrate an anti conformation about all the glycosidic bonds, and their directionality supports formation of a right-handed helix in solution. The observed NOEs between the T3.cntdot.O6meG10 interaction and the adjacent G2.cntdot.C11 and G4.cntdot.C9 base pairs at the modification site exhibit small departures from patterns for a regular helix in the O6meG.cntdot.T 12-mer duplex. The phosphorus resonances exhibit a 0.5 ppm spectral dispersion indicative of an unperturbed phosphodiester backbone for the O6meG.cntdot.T 12-mer duplex. We propose a model for pairing of T3 and O6meG10 at the modification site in the O6meG.cntdot.T 12-mer duplex. This study compares the NMR parameters of the O6meG.cntdot.T 12-mer duplex with those of the G.cntdot.T 12-mer duplex, which contains a T3.cntdot.G10 mismatch at the same site in the helix.