Finite-enthalpy model parameters from DNA melting temperatures

Peyrard-Bishop (PB) models are used for the study of denaturation in DNA. Unfortunately, there is little connection of these models to linear nearest-neighbour models which are extensively used for the calculation of melting temperatures in biochemistry. Here we use the Joyeux-Buyukdagli (JB) model, a variant of the PB model which incorporates stacking enthalpies, and carry out a fitting procedure to experimental melting temperatures where we let the enthalpies vary freely. We start out with a single value for the enthalpy for all combinations of base pairs and after the fitting we obtain a new set of enthalpies which correlate very strongly with the measured enthalpies. This result provides the needed support for the use of experimental enthalpies in the JB/PB model