Local cooperativity mechanism in the DNA melting
We propose a statistical mechanics model for the melting transition of DNA. Base pairing and stacking aretreated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set oflocal rules which mimic the geometrical constraints in the real molecule. This microscopic mechanism intrinsicallyaccounts for the cooperativity related to the free energy penalty of bubble nucleation. The modeldescribes both the unpairing and unstacking parts of the spectroscopically determined experimental meltingcurves. Furthermore, the model explains the observed temperature dependence of the effective thermodynamicparameters used in models of the nearest neighbor type. We compute the partition function for the modelthrough the transfer matrix formalism, which we also generalize to include nonlocal chain entropy terms.