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UBC Theses and Dissertations

Physical evidence for a universal cloverleaf structure for 5S RNA and 5.8S RNA Luoma, Gregory Allan


A number of structures had been previously proposed for prokaryotic 5S RNA, eukaryotic 5S RNA and eukaryotic 5.8S RNA based on a minimal amount of experimental evidence. None of the models could be adapted to all 5S RNA and 5.8S RNA species, although experimental evidence suggested similar structures. Therefore, a cloverleaf structure was proposed, based on laser Raman evidence (G.A. Luoma, M. Sc. Thesis). This structure could be adapted to E. coli 5S RNA, S. cerevisiae 5S RNA and S. cerevisiae 5.8S RNA while satisfying the limited amount of experimental evidence. To increase the experimental structural data, ultraviolet spectroscopy, circular dichroism spectroscopy, low field proton nuclear magnetic resonance spectroscopy and electron spin resonance spectroscopy were performed on S. cerevisiae 5S RNA, E. coli 5S RNA and wheat germ 5S RNA. Also, 5-fluorouracil was incorporated into S. cerevisiae 5S RNA to attempt to obtain further structural evidence. Finally, the presence of multiple conformations in the 5S RNA species was determined. This substantial physical characterisation is in total support of the cloverleaf model for these 5S RNA species. The cloverleaf model has also been adapted to all known sequences of 5S RNA and 5.8S RNA. For eukaryotic 5S RNA, the cloverleaf can explain the evolution of the various species. For prokaryotic 5S RNA, the cloverleaf can explain the inter-conversion of the native and B-form conformers. Finally, for 5.8S RNA, the cloverleaf model can explain the ability of yeast 5.8S RNA and E. coli 5S RNA to bind the same ribosomal proteins.

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