Torque spectroscopy of DNA
Abstract/Contents
- Abstract
- Cellular processes such as transcription and replication are regulated by torque in supercoiled DNA. Torque affects the kinetics of DNA-associated enzymes and can favor localized unwinding and other structural transitions of the double helix. High-resolution methods for direct measurement and control of DNA torque are needed in order to understand the sequence-dependent energetics and dynamics of torsionally strained DNA. I have developed a single-molecule magnetic tweezers method for torque measurement and feedback, enabling investigations of DNA under biologically relevant mechanical perturbations. My colleagues and I characterized the overall response of DNA to torque, the sequence-dependent energetics of strand separation and Z-DNA formation, and the physical properties of DNA mismatches. We analyzed the results using an equilibrium model for cooperative structural transitions that quantitatively describes our observations. I have further explored the dynamics of strand separation, and showed how my measurements can be explained using a drag-limited model in which the observed single-molecule dynamics depend only on parameters measured in equilibrium. The results contribute to our understanding of non-canonical DNA conformations, provide general lessons for studying transition dynamics in tethered systems, and enable future studies of mechanochemistry in molecular machines at the heart of biology.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2014 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Fernandes, Louis Edward |
|---|---|
| Associated with | Stanford University, Biophysics Program. |
| Primary advisor | Bryant, Zev David |
| Thesis advisor | Bryant, Zev David |
| Thesis advisor | Kirkegaard, Karla |
| Thesis advisor | Puglisi, Joseph D |
| Advisor | Kirkegaard, Karla |
| Advisor | Puglisi, Joseph D |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Louis Edward Fernandes. |
|---|---|
| Note | Submitted to the Program in Biophysics. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2014. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2014 by Louis Edward Fernandes
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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