Working on this project:
Our project aims at developing and characterizing spectroscopic probes and/or triggers to initiate and report conformational dynamics in specifically tailored RNA systems using time-resolved optical and IR spectroscopy. We propose to apply the developed systems and methodologies to obtain a time- and site-resolved picture of the functional dynamics of various regulatory RNAs. In particular, we will develop new bifunctional labels. Beyond this, we will establish a dual-label strategy for FRET analyses, which will be compared to PELDOR measurements (Aim I). Furthermore we will continue to monitor RNA folding and hybridization dynamics with specific IR-spectroscopic labels. Here we will focus on the influence of cations on the RNA folding dynamics (Aim II). Additionally, we will develop photoswitchable RNA-ligand-systems based on azobenzene units or circularized RNAs (Aim III). With this approach we will gain a spatial and temporal resolution of ligand-binding processes. Furthermore, with photoswitchable RNA we will overcome the time-resolution limitations of the stopped-flow method for the studies of binding dynamics.