Stem–loop formation drives RNA folding in mechanical unzipping experiments

Abstract

Significance Understanding how complementary RNA single strands anneal to form the native structure requires accurate knowledge of the energetics of hybridization and the kinetics driving the hairpin fold. The annealing dynamics are highly complex for RNA, where multiple long-lived intermediate states occur along the folding pathway. In this framework, single-molecule experiments allow us to derive the thermodynamics and kinetics of RNA folding and the characterization of the intermediates along the folding pathway. We mechanically unzip a 2-kbp RNA hairpin with optical tweezers in sodium and magnesium, deriving the 10 RNA nearest-neighbor free energies and modeling the hybridization kinetics in a barrier energy landscape of stem–loop secondary structures. Our study contributes to a better understanding of the RNA folding problem.