RNA Dynamics Probed by Single-Molecule Fluorescence Resonance Energy Transfer Studies

In combination with single-molecule fluorescence resonance energy transfer (FRET) measurements with a nanosecond time resolution for a pair of dye molecules attached to a RNA molecule, fluorescence intensity correlation functions contain information about photophysical and conformational dynamics. In this work, we have simulated photon emission from single coupled dye molecules in a FRET model, where a FRET pair resides on a diffusive RNA molecule, with the goal to understand how the dynamics of the RNA molecule is reflected in the observed photoemission statistics, and to test the utility and the validity of the simple analysis procedure to fluorescence intensity correlation method based on separation of the time scales. The results demonstrate that the present complete simulation of photon statistics of the system, by combining these diffusive chain dynamics with the distance-dependent stochastic photon emission from the FRET-coupled dye pair, provides a full view of the RNA dynamics, and holds a great promising benchmark for probing the folding kinetics of RNA molecules.