Working on this project:
In this project, we use pulsed EPR methods with rigid paramagnetic spin labels to investigate the structure and the conformational flexibility of RNA motives. Orientation-selective pulsed EPR ex-periments allow determining the distance and the orientation between two spin labels attached to the RNA molecule. This information can be used (alone or in combination with other spectroscopic and computational methods) to obtain a detailed picture on the tertiary structure and the conforma-tional flexibility of the RNA molecule under various conditions (ligand or protein binding, ion con-centration). In the 3rd funding period, we will determine the intrinsic dynamics of double-stranded RNA molecules and combine and compare our results and the results from other spectroscopic techniques with MD simulations. Additionally, we will use the same methodology to investigate structure and dynamics of several RNA aptamers and other small RNA motives. The influence and importance of specific Mg2+ binding sites to the tertiary structure and flexibility of RNA motives will be investigated with spin labels as well as by substituting the diamagnetic Mg2+ with paramagnetic Mn2+. We will compare/combine our EPR results with results obtained from other spectroscopic or computational methods on the same systems within this CRC. Further, we will explore the potential to perform such kind of EPR measurements at room temperature and in cells.