Developing and testing a reconstitution model for RNA folding

Placeholder Show Content


One of the most fascinating phenomena in biology is the folding of macromolecules into complex three-dimensional shapes that carry out all biological functions. Critical to the efficacy of these molecules is their capacity to fold on timescales relevant to biology and form specific and stable (but not too stable) structures. For decades, scientists have been studying how the physical properties of each macromolecule are utilized to combat the entropy of countless alternative conformations to form a native state. The function of structured RNAs is critical at every level of gene-expression regulation, thus developing a predictive model for how these molecules fold is of fundamental importance as it holds the promise of therapeutic design and control. Previous studies of RNA structure have determined that the architecture of RNA is structurally modular, therefore we posit that we can harness this feature of RNA to simplify the folding process into separate energetic contributions that are additive to predict the kinetic and thermodynamic behavior of structure RNA, i.e. energetic "Reconstitution". These energetic contributions are the conformational entropy due to the dynamics of the helices and junctions that connect them, the electrostatic penalty for bringing these RNA elements together, and the free energy of formation of tertiary contacts. Using, smFRET I provide support for energetic independence of these contributions from comparisons of measurements of rate and equilibrium constants for the effects of mutations in the tertiary contacts of the P4-P6 RNA, which found these energetics were the same over a range of conditions and structural contexts. To further test this reconstitution hypothesis and determine other simplifying and predictive rules for RNA building blocks, we utilized a simple RNA tertiary system, the tectoRNA, in concert with RNA-array technology to assess variations in ~ 100,000 variants. The number of variants provided by this approach and the simplicity of this system allowed us to address multiple open questions in the field of RNA folding regarding the conformational preferences of RNA helical sequences, junctions, and tertiary contacts. This thesis represents a step towards testing and developing a quantitative and predictive model for RNA folding.


Type of resource text
Form electronic; electronic resource; remote
Extent 1 online resource.
Publication date 2015
Issuance monographic
Language English


Associated with Bisaria, Namita
Associated with Stanford University, Department of Biochemistry.
Primary advisor Herschlag, Daniel
Thesis advisor Herschlag, Daniel
Thesis advisor Das, Rhiju
Thesis advisor Straight, Aaron, 1966-
Advisor Das, Rhiju
Advisor Straight, Aaron, 1966-


Genre Theses

Bibliographic information

Statement of responsibility Namita Bisaria.
Note Submitted to the Department of Biochemistry.
Thesis Thesis (Ph.D.)--Stanford University, 2015.
Location electronic resource

Access conditions

© 2015 by Namita Bisaria
This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).

Also listed in

Loading usage metrics...