Characterization of functional nucleic acid structure in translation, reverse transcription, and electronics applications
Abstract/Contents
- Abstract
- Ribonucleic acid (RNA) actively regulates all stages of genetic expression from transcription to translation. Actions performed by RNA molecules are made possible by the ability of RNA to fold into unique tertiary structures. Messenger RNA (mRNA) structure enables alternative translational pathways, such as frameshifting and bypassing, that recode the protein sequence. Transfer RNA (tRNA) structure is highly evolved for interfacing with the ribosome to maximize translational fidelity, but can be repurposed by retroviruses to act as a primer during reverse transcription. Ribosomal RNA (rRNA) is a majority component of the ribosome by mass and catalyzes amide bond formation between amino acids in a peptide chain. This work examines RNA structure in four systems: Escherichia coli rRNA, T4 bacteriophage mRNA, human tRNA, and synthetic conductive nanowires. Mutations in E. coli rRNA structure, as well as the effects of treatment with macrolide antibiotics, were probed by a novel quantitative fluorescent translation assay using the SNAPf reporter protein to evaluate changes in ribosomal processivity. The solution NMR structure of the T4 bacteriophage Gene 60 mRNA 5' stem-loop was solved, and the terminal loop sequence was determined to be important for the mechanism of translational bypassing. Human tRNALys3 in complex with HIV genomic RNA was also studied by solution NMR to reveal a unique structure adopted by the complex during HIV reverse transcription initiation. Finally, the thermal and chemical stability of Ag(I)-intercalated polycytosine nanowire structures was evaluated by enzymatic, spectrophotometric, and biophysical assays. These projects not only reflect the deep importance of RNA structure to all aspects of genetic expression but also highlight some of the applications of nucleic acid structure in bioengineering.
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 | Capece, Mark Christopher |
|---|---|
| Degree supervisor | Khosla, Chaitan, 1964- |
| Degree supervisor | Puglisi, Joseph D |
| Thesis advisor | Khosla, Chaitan, 1964- |
| Thesis advisor | Puglisi, Joseph D |
| Thesis advisor | Solomon, Edward I |
| Degree committee member | Solomon, Edward I |
| Associated with | Stanford University, Department of Chemistry. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Mark Christopher Capece. |
|---|---|
| Note | Submitted to the Department of Chemistry. |
| Thesis | Thesis Ph.D. Stanford University 2018. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2018 by Mark Christopher Capece
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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