title: Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models.
abstract: RNA molecules form three-dimensional structures via base pairing that determine the function and biochemical activity of the molecule. Here we introduce a structure-based method for studying the folding dynamics of RNA secondary structures. The approach focuses on native contacts that are parametrized with standard empirical free energies. Kinetic Monte Carlo simulations for free folding of simple hairpins and complex structures such as a tRNA as well as for folding in the presence of an external force show good agreement with experimental data. A systematic comparison of simulated and experimental folding rates for various structures shows a strong correlation, indicating that the approach can predict folding rates within about an order of magnitude.
authors: Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.
authors: Michael
authors: M
authors: Faber
authors: Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.
authors: Stefan
authors: S
authors: Klumpp
mesh_terms: D020029:Base Pairing; D055029:Inverted Repeat Sequences; D007700:Kinetics; D008958:Models, Molecular; D009010:Monte Carlo Method; D059370:RNA Folding; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics
chemical_list: D012343:RNA, Transfer