Unraveling RNA by Mechanical Unzipping

Abstract: We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying experimental conditions. Energy measurements permit us to characterize the thermodynamics of RNA hybridization (base pairing and stacking), the dynamics of the formation of native and kinetic (intermediates and misfolded) molecular states, and interactions with metallic ions. This paper introduces basic concepts and reviews recent developments related to RNA force thermodynamics, native and barrier RNA energy landscapes, and RNA folding dynamics. We emphasize the implications of mechanical unzipping experiments to understand non-coding RNAs and RNAs in extreme environments.