Watching single RNA molecules respond to local application of mechanical force

Abstract

We have recently developed a molecular handle consisting of DNA that permits one to manipulate single RNA molecules using an optical trap. We are now using these handles to grab individual molecules of the P5abc subdomain of the T. Thermophila ribozyme, and investigate how P5abc, as well as several other closely related RNAs, respond to local application of mechanical force. We discovered that certain RNA molecules behave like ideal two-state systems when subject to constant external forces: they hop between two states (folded and unfolded) and the kinetics and thermodynamics of such hopping depends on the magnitude of the applied external force. We encountered a serious problem in these RNA folding-unfolding experiments. In particular, many biologically relevant RNA molecules were seen to have very slow unfolding kinetics, and this made it impossible to unfold them reversibly and determine key thermodynamic properties such as the equilibrium free energy of folding. We subsequently asked whether a recent advance in theoretical statistical mechanics could be used to solve the fundamental problem of recovering equilibrium information from nonequilibrium experiments. In 1997 C. Jarzynski proved an equality relating the irreversible work to the equilibrium free energy difference, 4G. This remarkable theoretical result states that it is possible to obtain equilibrium thermodynamic parameters from processes carried out arbitrarily far from equilibrium. We tested Jarzynski's equality by mechanically stretching a single molecule of RNA reversibly and irreversibly between two conformations. Consistent with our hopes, we found that it was possible to recover the equilibrium 4G profile of the stretching process from the nonequilibrium experiments. This work thus extends the thermodynamic analysis of single molecule manipulation data beyond the context of equilibrium experiments.