AA mismatched DNAs with a single base difference exhibit a large structural change and a propensity for the parallel-stranded conformation

AA mismatches in DNA with different nearest-neighbor sequences were studied to understand the structural changes that accompany base-pair mismatches and the associated thermodynamics. Two synthesized duplexes, , 5' -d(CGACAATTGACG) (called AA1) and 5' -d(CGAGAATTCACG) (called AA2) as a palindrome sequences, had different nearest-neighbor sequences to the AA mismatches. This study focused on elucidating the structural and thermodynamic differences between these two molecules. A hydrogen bond between the mismatched adenines in AA1 was found, while no hydrogen bond in AA2. Both of the mismatched adenines in AA1 were stacked in the helix, while the mismatched adenine in AA2 surrounded by guanines was partially out of the helix and the other mismatched adenine surrounded by cytosines was stacked in the helix. Thermodynamically, AA1 was more stable than AA2. The melting temperature of the internal bases of AA1 was about 7 degree higher than that of AA2. The standard Gibbs free energy change for the duplex formation of AA1 was 1.30 Kcal/mol smaller than that of AA2. These thermal properties could be ascribed to the formation of the hydrogen bond. The conformational changes of these molecules at low pH were also investigated and compared. AA1 unambiguously assumed a parallel-stranded duplex at pH 4, while AA2 existed as a mixture of anti-parallel and parallel duplexes below pH 5.