Exploring tertiary folding in RNA : novel structural motifs in HDV and TYMV RNA studied by NMR spectroscopy

Contains fulltext : 18663.pdf (publisher's version ) (Open Access)RNA molecules lie at the basis of many cellular processes. They serve as a carrier of information, but can also form intricate complexes with proteins and other RNAs, and can even have catalytic activity, in which case they are called ribozymes. This versatility of RNA function relates to a wide range of structural properties. Apart from the tRNA structure (1973), however, the number of high-resolution structures have long remained very low. Presently, in the midst of a surge of RNA structures derived from NMR spectroscopy and X-ray crystallography, many observations and predictions from the past on higher order folding in RNA are being confirmed and reproduced. Yet, the understanding of RNA structure has also greatly been expanded by numerous novel features discovered in the recent past. This thesis describes several of these new properties, as found in the genomic RNAs of hepatitis delta virus (HDV) and turnip yellow mosaic virus (TYMV). The catalytic RNA found in HDV constitutes a distinct class of the ribozymes found thus far. Using NMR spectroscopy, we have succeeded in obtaining a high-resolution structure of the central loop of the ribozyme (chapter 2) which indicates that it has some degree of preformation for folding into a mature catalytic RNA. The next chapters all deal with the structural properties of the pseudoknot in the aminoacyl acceptor domain of the tRNA-like structure in TYMV. RNA pseudoknots are found in virtually all classes of RNA and play key roles in a variety of biological processes. Chapters 3 and 5 describe the structural and dynamical properties of the TYMV pseudoknot in detail. Base stacking, novel loop-helix interactions and a preformed hairpin loop structure are the prime stabilizing features of the molecule. Finally, new NMR approaches in resonance assignment and the determination of torsion angles are described in chapter 4110 p