Conformational transitions in RNA probed in riboswitch systems [electronic resource]
- Mona Ali.
- Physical description
- 1 online resource.
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|3781 2011 A||In-library use|
- Ali, Mona.
- Doniach, S. primary advisor.
- Das, Rhiju advisor.
- Pande, Vijay advisor.
- Stanford University. Department of Applied Physics
- Conformational transitions are a key phenomenon in biological processes; proteins and nucleic acids require structural malleability that not only enables them to adopt specific three-dimensional structures that impart activity, but also accommodates conformational transitions that enhance their functions and allow them to communicate with their surrounding environment. Protein conformational transitions have been extensively studied for a large number of systems, but RNA conformational transitions are less well understood. In this dissertation, I have studied conformational transitions in RNA occurring at the levels of both secondary and tertiary structure. A thiamine pyrophosphate and an adenine riboswitch have been used to follow the folding of RNA from an ensemble of partially structured heterogeneous conformers in the ligand-free state to fully folded native states in the ligand-bound state. Small angle X-ray scattering and two-dimensional chemical footprinting have been used as the primary experimental techniques to query the conformational transitions occurring in these two RNA systems. Being solution techniques, these methods are particularly suitable for probing heterogeneous ensembles of RNA structures that exist at thermodynamic equilibrium in variable salt and ligand concentrations. The results provide detailed characterization of partially folded RNA structures and the conformational transitions that mediate their conversion to natively folded forms.
- Publication date
- Submitted to the Department of Applied Physics.
- Thesis (Ph.D.)--Stanford University, 2011.
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