Insights into the sequence-structure-function relationship of the GLMS ribozyme from single-molecule force spectroscopy and massively-parallel biochemistry of sequence variants
Abstract/Contents
- Abstract
- Structured RNAs play a range of essential roles in the cell, including central functions in protein synthesis and gene regulation. These important RNAs include ribozymes, which catalyze chemical reactions, and riboswitches, mRNA elements which modulate gene expression in response to metabolite ligands. Structured RNAs ultimately enact their function by folding from linear sequences into elaborate three-dimensional conformations with specific biochemical properties. A mechanistic understanding of the relationships between RNA sequence, folding, and function should allow for increasingly sophisticated engineering of RNAs with desired functions, as well as the design of drugs targeting naturally occurring RNAs. In my PhD thesis research, I delved into these relationships in the context of the glmS ribozyme riboswitch. This widespread bacterial riboswitch regulates the production of an essential cell wall precursor, glucosamine 6-phosphate (GlcN6P), making it a compelling target for antibiotic development efforts. The key step for gene regulation is a self-cleavage reaction performed by the ribozyme riboswitch only when GlcN6P is bound in its active site. I investigated this structured RNA using two powerful and complementary approaches: (1) single-molecule force spectroscopy using a high-resolution optical tweezers apparatus to study folding, ligand binding, and catalysis, and their interrelationship; and (2) massively-parallel biochemistry on an RNA array to systematically dissect the sequence-dependence of self-cleavage activity and mutational interactions between residues.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2018; ©2018 |
| Publication date | 2018; 2018 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Savinov, Andrew |
|---|---|
| Degree supervisor | Block, Steven M |
| Thesis advisor | Block, Steven M |
| Thesis advisor | Das, Rhiju |
| Thesis advisor | Moerner, W. E. (William Esco), 1953- |
| Degree committee member | Das, Rhiju |
| Degree committee member | Moerner, W. E. (William Esco), 1953- |
| Associated with | Stanford University, Biophysics Program. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Andrew Savinov. |
|---|---|
| Note | Submitted to the Biophysics Program. |
| Thesis | Thesis Ph.D. Stanford University 2018. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2018 by Andrew Savinov
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