Length and Statistical Weight of Bubbles in DNA Melting

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Abstract
We present measurements of the length of the bubble versus temperature in the melting transition of DNA oligomers. The sequences are clamped at the ends of GC pairs (strong binding), and have AT rich (weaker binding) middle regions of variable length B relative to the molecule size. We use a quenching technique to trap intermediate states. We find that the average relative bubble size grows from zero for increasing temperature, but reaches a plateau at a length of order B, producing a discontinuous transition with finite bubble size. The statistical weight of the bubble states decreases as B is reduced, the transition becoming more cooperative.