Abstract:In RNA secondary structure prediction, nearest-neighbor parameters are used to determine the stability of a given structure. We derived the nearest-neighbor parameters for RNAs containing inosinecytosine pairs. For parameter derivation, we developed a method that combines UV adsorption measurement experiments with free-energy calculations using molecular dynamics simulations. The method provides fast drop-in parameters for modified bases. Derived parameters were compared and found to be consistent with existin… Show more
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