Studying RNA sequence and structure using solid-state and hybrid biomimetic nanopores

of Dissertation Nanopores have garnered much attention for their ability to act as single-molecule DNA sequencers; despite their biological importance, much less work has been reported on the study of RNA molecules. Much like DNA, the direct sequencing of single RNA molecules is a topic of great importance as it would enable comprehensive and bias free transcriptome analysis. In addition, the secondary and tertiary structures formed by relatively short RNA fragments are a topic of equal biological importance as they pertain to non-coding RNAs and their function within the cell. Nanopores are unique tools that can allow local forces to be applied to single charged molecules, and at the same time monitor the presence and/or structure of the same molecule in solution. Nanopores have demonstrated extreme sensitivity to variations in sequence as well as structure. Here we explore the ability of solid-state SiN nanopores to probe the landscape of tertiary and quaternary states that are adopted by the mitochondrial leucine tRNA (UUR), a tRNA that is the target of many pathogenic mutations which effect its structure. We explore a novel point mutation that causes dimerization as well as misfolding of the tRNA and attempt to develop a platform capable of rapidly assessing tRNA conformational states. In addition, we develop a novel platform which may allow for monitoring ion transport through carbon nanotube porins (CNTPs). This system may find use as a platform to monitor the DNA/RNA sequencing capabilities of these CNTPs.