Investigating the dynamics of tRNA protein complexes by single molecule fluorescence spectra

Most of the more than hundred nucleoside modifications discovered to date in RNA [1] are thought to sustain and optimize the functional conformation of tRNA. Single molecule Fluorescence Resonance Energy Transfer (sm-FRET) has proven to be a valuable tool to investigate tRNA dynamics. Even transient conformations could be resolved by observation of the distance between two fluorescent dyes [2]. Furthermore it could be shown, that the conformational equilibrium of tRNA depends on the concentration of the counterion (Mg²⁺, Ca²⁺,...) [3]. An ongoing investigation of tRNA dynamics implies an expansion onto tRNA-protein-complexes, since a conformational change in protein binding and after processing is very likely. In our group it could be shown that pseudouridine synthase 1 forms a reversible complex with tRNA containing 5-fluorouracil without turnover of the substrate [4]. The goal of this work is to elucidate whether this complex is also present in reversible form for the Uridine-containing substrate. This is done by measurement of single molecule fluorescence spectra of a tRNA before, during and after modification. Observation on the single molecule level is necessary here, because it reveals populations, which are normally hidden in the ensemble due to their low lifetime and abundance. Doing this by the means of single molecule fluorescence spectra provides the potential to unambiguously identify changes in structure and environment of the tRNA during enzymatic turnover.