Probing RNA folding through electrostatic and coarse-grained simulations
Abstract/Contents
- Abstract
- The discovery by Cech and coworkers that structured RNA molecules could catalyze specific reactions has revolutionized our understanding of RNA's role and place in the biological machinery of life. The notion of understanding RNA folding from a biophysical perspective means understanding the formation of RNA structure in terms of the basic physical forces at play. This thesis describes the the use of electrostatic and coarse grain simulations and associated experiments to investigate different features of RNA folding. Chapter 1 gives an brief introduction to RNA folding, the primary physical forces that influence its formation, and a review of recent advances in our understanding of structure formation in RNA. Chapters 2 and 3 comprise the next section of the thesis and detail advances in our understanding of electrostatic effects around nucleic acids, a topic of great importance in RNA folding. Specifically, chapter 2 presents the development of a size-modified Poisson-Boltzmann theory to help account for the effects of ionic size while chapter 3 presents a critical assessment of the Poisson-Boltzmann description of electrostatic relaxation in tethered duplex model systems. Chapter 4 highlights a general theoretical framework for understanding the combined effects of electrostatics and junction topology on RNA folding stability and specificity. The last section focuses on the use of coarse grained simulation to understand the role of junction topology in shaping the allowed conformational space of the Transactivation Response (TAR) element from the genome of the Human Immunodeficiency Virus (HIV). Though the last section is not, strictly speaking, a study of RNA folding, understanding RNA conformational motion is of critical importance to the question of structure acquisition in RNAs.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Copyright date | 2010 |
| Publication date | 2009, c2010; 2009 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Chu, Vincent Bangping | |
|---|---|---|
| Associated with | Stanford University, Department of Applied Physics | |
| Primary advisor | Doniach, S | |
| Thesis advisor | Doniach, S | |
| Thesis advisor | Herschlag, Daniel | |
| Thesis advisor | Pande, Vijay | |
| Advisor | Herschlag, Daniel | |
| Advisor | Pande, Vijay |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Vincent Bangping Chu. |
|---|---|
| Note | Submitted to the Department of Applied Physics. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2010. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2010 by Vincent Bangping Chu
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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