De Novo Folding of RNA Hairpins by Temperature Replica Exchange

Abstract

Describing folding and thermodynamic behaviors of small RNA hairpins is a key step in elucidating the folding processes of larger RNA macromolecules. Experimental methods have been used to describe a wide range of dynamical behavior in RNA hairpins including the dynamics of loop residue interactions and folding rates of stems, but many questions surrounding the detailed mechanism of RNA hairpin formation remain unanswered. The order and directionality of stem nucleation and stem base-pair formation remains open for debate, as well as the effects of stem-length on the rate of hairpin formation and the frequency of base mismatches. All-atom molecular dynamics offers a methodology for analyzing heterogeneous, multiple-pathway folding processes and how they contribute to the overall thermodynamic behaviors of RNA hairpins. To that end, we analyzed the equilibrium folding of a hyperstable tetraloop with a four base-pair stem, r(ggccGCAAggcc), using recently published RNA parameters. Using microsecond-timescale temperature replica-exchange molecular dynamics simulations we are able to sample a large ensemble of conformational states adopted by RNA hairpins and describe the thermodynamic processes involved in hairpin formation. The results give us insights into the biophysical driving forces of RNA folding.