Varani, GabrieleSun, Yi-Ting2023-01-212023-01-212023-01-212022Sun_washington_0250E_24918.pdfhttp://hdl.handle.net/1773/49632Thesis (Ph.D.)--University of Washington, 2022RNA structures are involved in many biological processes and the progression of human disease, making them potential targets for therapeutic development. The first chapter introduces topics relevant to targeting RNA structures and to the subsequent chapters of this thesis: disease-associated RNA classes, the characteristics of RNA-binding ligands of different sizes (e.g., small molecules, peptides, engineered proteins), and NMR-based methods for RNA structure determination.Chapter 2 describes the strategy and result of my research on designing cyclic β-hairpin peptidomimetics targeting pre-microRNA-20b (pre-miR-20b). Small cyclic peptidomimetics were rationally designed based on the sequence of β2-β3 hairpin of Rbfox2 protein, that recognize the terminal loop of precursor miR-20b. I identified a peptide with low µ-molar affinity for the miR-20b precursor and specifically targets the apical loop of pre-miR-20b. This work demonstrates that it is possible to mimic RNA-binding proteins with a minimal structurally pre-organized peptide, which provide a starting point for designing or evolving small peptide mimetics of RNA-binding proteins. Chapter 3 describes the results of structural analysis of a 70 nucleotides stem-loop RNA structure (called SLA) from Dengue virus serotype 1 (DENV1), which functions as the promoter for viral replication. NMR structure of a monomeric DENV1 SLA is assembled to high-resolution from independently folded structural elements, and SAXS modeling is used for independent validation. Both NMR structure determination and SAXS modeling result in an L-shape of RNA structure. It is very likely that the three-dimensional structure of SLA is conserved among flaviviruses because the sequence is highly conserved among different flavivirus genomes. This work establishes RNA structural features involved in Dengue replication and provides a foundation for the discovery of new antiviral drugs that target this essential replicative step.application/pdfen-USnoneDengue virusDrug DiscoveryNMRPeptideRNAStructural biologyChemistryChemistryThesis