Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides.

ABSTRACT: The most popular RNA secondary structure prediction programs utilize free energy (ΔG°37) minimization and rely upon thermodynamic parameters from the nearest neighbor (NN) model. Experimental parameters are derived from a series of optical melting experiments; however, acquiring enough melt data to derive accurate NN parameters with modified base pairs is expensive and time consuming. Given the multitude of known natural modifications and the continuing use and development of unnatural nucleotides, experimentally characterizing all modified NNs is impractical. This dilemma necessitates a computational model that can predict NN thermodynamics where experimental data is scarce or absent. Here, we present a combined molecular dynamics/quantum mechanics protocol that accurately predicts experi

SUBMITTER: Hopfinger MC 

PROVIDER: S-EPMC7498315 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature