Analysis of the conformational space and dynamics of RNA helicases by single-molecule FRET in solution and on...

RNA helicases are a diverse group of enzymes that catalyze the unwinding of RNA duplex regions in an ATP-dependent reaction. Both the helicase itself and its RNA substrate undergo conformational changes during the reaction, which are amenable to Förster resonance energy transfer (FRET) studies. Single-molecule FRET studies in solution by confocal microscopy and on surfaces by total internal reflection microscopy provide information on different conformers present, their fractional populations in equilibrium, and the rate constants of their inter-conversion. Collectively, the information gained can be integrated into a kinetic and thermodynamic framework that quantitatively describes the conformational dynamics of the helicase studied. FRET experiments also provide distance information to map and model the structures of individual conformational states. The integrated model provides a comprehensive description of the structure and dynamics of the helicase, which can be linked to its biological function. Single-molecule FRET studies have tremendous potential to define the relationship between structure, function and dynamics of RNA helicases and to understand the mechanistic basis for their broad range of biological functions. The focus of this chapter is on providing guidance in the design of single-molecule FRET experiments and on the interpretation of the data obtained. Selected examples illustrate important considerations when analyzing single-molecule experiments, as well as their limitations and possible pitfalls.