Very Stable Mismatch Duplexes: Structural and Thermodynamic Studies on Tandem G·A Mismatches in DNA

We have used ultraviolet melting techniques to compare the stability of several DNA duplexes containing tandem G·A mismatches to similar duplexes containing tandem A·G, L·A, and T·A base pairs. We have found that tandem G-A mismatches in 5ʹ-Y-G-A-R-3ʹ duplexes are more stable than their I-A counterparts and that they are sometimes more stable than tandem 5ʹ-Y-T-A-R-3ʹ sequences. This is not the case for tandem G-A mismatches in other base stacking environments, and it suggests that tandem G-A mismatches in 5ʹ-Y-G-A-R-3ʹ sequences have a unique configuration. In contrast to tandem 5ʹ-G-A-3ʹ mismatches, tandem 5ʹ-A-G-3ʹ mismatches were found to be unstable in all cases examined.