Exact Folding Dynamics of RNA Secondary Structures

Barrier trees consisting of local minima and their connecting saddle points imply a natural coarse-graining for the description of the energy landscape of RNA secondary structures. Here we show that, based on this approach, it is possible to predict the folding behavior of RNA molecules by numerical integration. Comparison with stochastic folding simulations shows reasonable agreement of the resulting folding dynamics and a drastic increase in computational efficiency that makes it possible to investigate the folding dynamics of RNA of at least tRNA size. Our approach is readily applicable to bistable RNA molecules and promises to facilitate studies on the dynamic behavior of RNA switches. § To whom correspondence should be addressed