Conformational dynamics of RNA

Two projects are presented in this thesis, showcasing the application of PELDOR spectroscopy, and, more specifically, orientation-selective PELDOR spectroscopy to the study of the conformational variety of two small RNA molecules. By combining orientation-selective PELDOR with other experimental and computational methods, the conformational ensemble and the conformational dynamics of these small RNA molecules were assessed. In the first project, the conformational variety of a small 20 base-pair duplex RNA was investigated. The duplex RNA is used as an almost model-like system which is representative for double-helical regions in larger RNA molecules. The comparison to previously published results on duplex DNA was also of great interest due to the differences in helix geometries of DNA and RNA. A set of eight samples was investigated where the position of one of the two Çm spin labels was fixed to the same nucleotide and the position of the second Çm spin label was varied throughout the helix, covering almost a full turn of the helix. The rigidity of Çm allowed us to record orientation-selective PELDOR data at different frequencies. These data provided very precise distances in the nanometer range. In addition, the data encode information about the orientations of the spin labels, which are directly linked to the conformational variety of the duplex RNA. 19F ENDOR experiments performed on three singly-Çm, singlyfluorine- labeled RNA constructs, yielded additional information on the local structure and dynamics of the RNA duplex. The experimental orientation-selective PELDOR and 19F ENDOR data were quantitatively compared to data from MD simulations. An excellent agreement was observed between the experimental data and MD simulations using the OL3 force field and explicitly modeled Çm labels in the simulations. The MD simulations show the degree of dynamics which is present even in these small duplexes. The agreement between the MD simulations and the experimental data confirms that the frozen ensemble of our measurements captures structures which cover the full structural variety of the RNA duplex obtained from simulations at physiological temperatures. In a direct comparison of MD simulations with and without the labels, it became clear that the introduction of the Çm spin label causes some small structural rearrangements, which are confined to a region of ±2 base pairs around the spin-labeled site. Also, smallscale dynamics of Çm were observed over the course of the MD trajectory. Such small rearrangements are likely to occur for other spin labels as well, but are usually not resolved. We are able to resolve these small-scale dynamics and the structural rearrangements of the helix only because the RNA is very well-behaved - although it is also dynamic - and because of the use of the rigid Çm spin label. With the approach presented here, it was possible to gain comprehensive insights into the structure of the RNA and its variety on the global scale, using PELDOR spectroscopy, and on the local scale, using 19F ENDOR spectroscopy. In the second project, the orientation-selective PELDOR methodology was applied to the TMR-3 aptamer, which holds the potential for being a riboswitch for the regulation of gene expression. The structural changes of the aptamer upon binding to the ligand 5-TAMRA were explored. Due to the higher complexity of the system as compared to the RNA duplex and the accompanied complexity of correctly parameterizing the RNA-ligand interaction, it was decided not to take the same route using MD simulations as in the first project. Instead, a large bundle of structures was generated by combining EPR data with previously published NMR data. From this large bundle, a subset was selected by iteratively and globally fitting to the orientation-selective PELDOR data recorded at Xand G-band for three Çm-labeled constructs simultaneously. This yields a subset of structures which represent the structural variety of the TMR-3 aptamer. We were able to obtain a bundle of structures for the ligand-bound state of the TMR-3 aptamer to 5-TAMRA and, for the first time, a structure bundle for the ligand-unbound state of TMR-3 was obtained. The structures in the ensemble of the ligand-bound state confirm the large-scale features, which were previously derived from liquid-state NMR data. Additionally, conclusions about the dynamics of the aptamer-ligand complex can be drawn from the structural variety in the bundle. The three-way junction of the aptamer-ligand complex is retained in the structures derived from NMR and EPR restraints. All three helices exhibit a significant degree of structural diversity, comparable to the duplex RNA in the first project. Our data reflects a twisting motion of one of the helices. The previously inaccessible unbound state of the TMR-3 aptamer is much more structurally diverse compared to the ligand-bound state.