Biophysical characterization of non-coding regions of viral RNAs
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University of Lethbridge. Faculty of Arts and Science
Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry
Throughout the last few decades, it has emerged that the genomic organization of organisms is not simple, easily laid out, or straightforward. Long gone are the days of the central dogma, where DNA is transcribed to RNA, and RNA is translated to proteins. Non-coding RNA has emerged as an essential biological regulator of numerous cellular processes. These non-coding RNA are not simply a chain of ribonucleotides conferring function through the primary sequence; rather, functions of non-coding RNA are also related to the tertiary structure or 3-dimensional arrangement. This thesis focuses on the core theme of biophysical characterization of non-coding RNA structure and interactions with chapters and on four specific biophysical techniques I have used; multi-angle light scattering, microscale thermophoresis, small-angle X-ray scattering, and analytical ultracentrifugation. Using these techniques and others, we investigated non-coding RNA regions of different RNA-based viruses. We compared Murray Valley Encephalitis and Powassan virus’, 5’ and 3’ TR atomic structures. We showed Japanese Encephalitis virus and Zika virus 5’ TRs direct interaction with DDX3X human helicase and DDX17’s direct interaction and unwinding of Rift Valley Fever virus’ S-segment non-coding RNAs. Lastly, we characterized the cyclization interaction of the 5’ and 3’ TR of Japanese encephalitis using biophysical and computational methods. Taken together, this thesis demonstrates that many biophysical techniques can be used to investigate viral non-coding RNA structure and non-coding RNA interactions to uncover and validate meaningful biologically relevant interactions in vitro.
non-coding RNA structure , viral RNA , biophysical characterization , RNA-based viruses