Understanding and predicting RNA structure
Abstract/Contents
- Abstract
- RNA is an important biological macromolecule that carries out a variety of roles in the cell. To function, RNA needs to fold into precise three-dimensional structures. Different physical forces like entropy, base-pairing and stacking interactions, tertiary contacts and electrostatics affect this folding process. In the first part of this thesis, we focus on nucleic acid electrostatics; RNA molecules have negatively charged backbones that require counterions to neutralize charge-repulsion and facilitate folding. We discuss the ion conditions necessary for a riboswitch (gene-regulating RNA found on 5' or 3' ends of messenger RNA) folding, studied how the flexibility of single stranded DNA is affected by the presence of different amounts of counterions and present a benchmark experimental dataset that can be used for direct comparison to electrostatic theories. The second part of the thesis deals with computational and analysis tools developed to model and understand nucleic acid systems with the ultimate goal of being able to predict RNA structure. Since RNA typically folds hierarchically, we devised a general hierarchical sampling protocol that naturally explores RNA three-dimensional conformational space efficiently and can be used in concert with any force field, such as an RNA knowledgebased potential that we also discuss in this thesis. Additionally, we examined a clustering method that can assist analysis of structural models. Lastly, we applied our modeling techniques to study simple two-way RNA junctions with all-atom representation, and probed the modeled effects of sterics, chain connectivity and sequence on dynamic RNA behavior.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2012 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Sim, Yen Ling Adelene |
|---|---|
| Associated with | Stanford University, Department of Applied Physics |
| Primary advisor | Doniach, S |
| Primary advisor | Levitt, Michael, 1947- |
| Thesis advisor | Doniach, S |
| Thesis advisor | Levitt, Michael, 1947- |
| Thesis advisor | Herschlag, Daniel |
| Advisor | Herschlag, Daniel |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Yen Ling Adelene Sim. |
|---|---|
| Note | Submitted to the Department of Applied Physics. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2012. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2012 by Yen Ling Adelene Sim
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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