Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models

摘要

RNAmolecules form three-dimensional structures via base pairing that determine the function and biochemicalnactivity of the molecule. Here we introduce a structure-based method for studying the folding dynamics of RNAnsecondary structures. The approach focuses on native contacts that are parametrized with standard empiricalnfree energies. Kinetic Monte Carlo simulations for free folding of simple hairpins and complex structures suchnas a tRNA as well as for folding in the presence of an external force show good agreement with experimentalndata. A systematic comparison of simulated and experimental folding rates for various structures shows a strongncorrelation, indicating that the approach can predict folding rates within about an order of magnitude.