Theoretical studies of RNA catalytic activity.
2010-08
Loading...
View/Download File
Persistent link to this item
Statistics
View StatisticsJournal Title
Journal ISSN
Volume Title
Title
Theoretical studies of RNA catalytic activity.
Authors
Published Date
2010-08
Publisher
Type
Thesis or Dissertation
Abstract
RNA possess a diverse ensemble of conformations that interchange on time scales
that range from femtoseconds to milliseconds. This conformational variability has a profound
effect on RNA function, and has been exploited in RNA molecules such as aptamers,
aptazymes, and riboswitches that have been engineered to be allosterically controlled.
Central to this work is the questions of how RNA conformational variability affects
with its catalytic activity. We employ a set of diverse theoretical and simulation tools, such
as molecular dynamics, free energy calculations, and path sampling that greatly extend the
capability of structural and molecular biology experiments to reveal atomic level details of
RNA energetics and dynamics.
Our systems of interest are two prototypical catalytic RNA systems: L1 ligase and
Hammerhead ribozymes, both of which are postulated to reach their catalytically active
states through complex mechanisms that involve large domains movements, change in base
pairing patterns and direct participation of divalent metal ions. In the case of L1 ligase, we
reveal the structural basis of its allosteric control that involves an 80 angstrom swing of one
of its stems, as well as the role of a flexible active site toward providing catalytic selectivity.
In the case of Hammerhead ribozyme, we characterize the conformation and dynamics of
several constructs in different ionic environments that lead to catalysis.
Description
University of Minnesota Ph.D. dissertation. August 2010. Major: Chemistry. Advisor: Darrin M. York. 1 computer file (PDF); viii, 104 pages.
Related to
Replaces
License
Collections
Series/Report Number
Funding information
Isbn identifier
Doi identifier
Previously Published Citation
Suggested citation
Giambasu, George M˘ad˘alin. (2010). Theoretical studies of RNA catalytic activity.. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/116673.
Content distributed via the University Digital Conservancy may be subject to additional license and use restrictions applied by the depositor. By using these files, users agree to the Terms of Use. Materials in the UDC may contain content that is disturbing and/or harmful. For more information, please see our statement on harmful content in digital repositories.