Dynamics of DNA duplexes containing internal G.T, G.A, A.C, and T.C pairs: hydrogen exchange at and adjacent to mismatch sites

We have undertaken high-resolution NMR studies to elucidate the conformation and dynamics of the d(C1-G2-C3-G4-A5-A6-T6-T5-C4-G3-C2-G1) 12-mer duplex and its analogs where the symmetrically related dG.dC base pairs in position 3 are replaced by dG.dT, dG.dA, dA.dC, and dT.dC mismatch pairs. The pairing schemes for the dG.dA and dA.dC mismatch interactions have been elucidated from intra- and inter-base pair nuclear Overhauser effect measurements. The replacement of two dG.dC pairs by two dG.dA or two dG.dT pairs results in an approximately 20 C destabilization of the 12-mer; replacement by two dA.dC or two dT.dC pairs results in an approximately 30 C destabilization of the 12-mer. The hydrogen exchange kinetics of the resolved and assigned imino protons in the 12-mer duplex and its mismatch analogs in 0.1 M phosphate have been monitored by saturation recovery measurements. We observe kinetic destabilization at dG.dC base pair 4 adjacent to the mismatch site, which increases in the order 12-mer less than 12-mer GT less than 12-mer GA less than 12-mer AC less than 12-mer TC. By contrast, the kinetic destabilization at dA.dT base pairs 5 and 6 increases in the order 12-mer approximately 12-mer GT approximately 12-mer GA less than 12-mer AC less than 12-mer TC. These results demonstrate that the introduction of dG.dT and dG.dA mismatches results in dynamic perturbations that are localized at the adjacent base pairs, whereas introduction of dA.dC and dT.dC mismatches results in perturbations that extend several base pairs into the duplex. Both base pair opening and preequilibrium pathways contribute to the imino proton hydrogen exchange rates in the 12-mer GA, 12-mer AC, and 12-mer TC duplexes, which is in contrast to earlier studies that demonstrated that the imino proton hydrogen exchange rates were a direct measure of the base pair opening rates in the 12-mer and 12-mer GT duplexes.