Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects

The stability of a DNA double helix of-any particular sequence is conventio nally estimated as the average of the stabilities of the 10 different neare st-neighbor (NN) base pair doublets that it contains. Therefore, much effor t has been devoted to the experimental characterization and tabulation of t he enthalpy, entropy, and free energy of melting for each of the NN doublet s. Although data from different research groups generally agree for the NN free energies and melting temperatures, there are major disagreements for t he enthalpies and entropies. The largest differences are between the parame ters obtained on oligomeric relative to polymeric DNA. This disagreement in terferes with the practical application of NN thermodynamic parameters. It also raises doubts regarding several fundamental assumptions about DNA melt ing, such as the absence of longer range interaction, the length dependence of DNA melting parameters per base pair, the applicability of polyelectrol yte theory to the description of salt effects on oligomers, and the purely enthalpic difference between NN doublets. Here we show that if one takes in to account the significant heat capacity increase associated with DNA melti ng, all of the above assumptions are self-consistently reconciled with expe riment.