NMR studies of A.C mismatches in DNA dodecanucleotides at acidic pH. Wobble A(anti).C(anti) pair formation.

Two-dimensional proton NMR studies were undertaken on the d(C-G-A-G-A-A-T-T-C-C-C-G) duplex (designated A.C 12-mer) where the A at the mismatch site is flanked by G residues and the d(C-G-C-G-A-A-T-T-C-A-C-G) duplex (designated C.A 12-mer) where the A at the mismatch site is flanked by C residues in an attempt to elucidate the role of flanking base pairs on the structure of the A.C mismatch. The exchangeable and nonexchangeable proton spectra of these two dodecanucleotides have been completely characterized by two-dimensional nuclear Overhauser enhancement (NOE) experiments in H2O and D2O solution at acidic pH. The NOE distance connectivities demonstrate that both A and C at the mismatch site are stacked into a right-handed helix between flanking G.C base pairs and exhibit anti-glycosidic torsion angles. The proton chemical shifts and NOE patterns are consistent with Wobble A.C pairing for the A.C 12-mer and C.A 12-mer duplexes in solution and demonstrate that the A.C mismatches introduce local conformational perturbations that do not extend to the central AATT segment. We detect that amino protons of adenosine (approximately 9.2 ppm) but not of cytidine at the A.C mismatch site in both duplexes on lowering the pH below 6.