Mismatches and bubbles in DNA

Single mismatches in the DNA double helix form nucleation sites for bubbles. Although the overall melting temperature of the duplex is affected to different degrees depending on the probe length, the statistical weights of the bubble states around the defect are always strongly affected. Here we show experimentally that a single mismatch has indeed a dramatic effect on the distribution of intermediate (bubble) states in the melting transition of DNA oligomers. For probe lengths in the range 20-40 bases, the mismatch transforms a transition with many intermediates into a nearly two-state transition. One surprising consequence is the existence of a regime where the sensitivity of a mismatch detection assay based on monitoring intermediate states would increase with probe length. Our results provide experimental constraints on how mismatches should be implemented in models of DNA melting, such as the widely used thermodynamic nearest neighbor model, to which we compare our data.