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We obtained the first experimental measurements of§the length of the§denaturation bubble appearing in the DNA melting§transition. This is§achieved by working with short oligomers which can§form only one bubble§per molecule. Using a quenching technique to trap the§bubble states, we§could measure the length of the bubble and the§relative weights of the§bubble states as a function of temperature. We found§that the average§bubble size grows for increasing temperature, but§reaches a plateau at a§length of order B (the length of the AT region).§After the plateau, the§average bubble length jumps to 1. This jump of the§order parameter is a§signature of a discontinuous transition, one where§the bubble size remains§finite up to critical temperature of strand§separation. For a§bubble flanked by double-stranded regions, the§nucleation size is around 3§bases. For bubbles opening at the ends of the§molecule there is no§nucleation threshold. For the first time we show§experimentally that a§single mismatch transforms a transition with many§intermediates into a§nearly two-state transition for oligomer length in§the range of 20 to 40§bases.
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