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Duplex-single strand denaturing transition in DNA oligomers

We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics model, and we find that the so-called zipper model, where denaturing proceeds through opening of the duplex at the ends describes well the temperature dependence of the average number of open base pairs. Analysis of the length dependence of the transition parameters however suggest that bubble formation is important and that the transition, in the thermodynamic limit, is continuous, albeit close to first order.