Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters
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Universidade Federal de Minas Gerais
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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.
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RNA stability, Nearest-neighbour model, Melting temperature calculation
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https://www.sciencedirect.com/science/article/pii/S0301010418311200?via%3Dihub