Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters.

We calculate the nearest-neighbour enthalpies and entropies at 5 salt concentrations of 18 RNA sequences, each for at least 9 different species concentrations, totalling 757 melting temperatures, using a melting temperature optimization method. These new parameters do not need to be salt-corrected and are shown to provide overall improved melting temperature predictions. They show a marked quadratic dependence with salt concentrations which are compensated to form linear Gibbs free energies. Two different parameter schemes were tested, with fixed or variable initial parameters. We have found that using variable initial parameters provides better predictive results than using salt correction factors and that the prediction uncertainty is considerably reduced for a validation set of independent sequences. An interpolation scheme is introduced to generate model parameters for arbitrary salt concentrations which performs better against a validation set than predictions using salt corrections.