Abstract
The ability of RNA to sample multiple conformations allows it to fulfill a myriad of biological roles. The folding pathways that RNA takes to achieve these conformations are not intuitive, and there is a pressing need to predictively model this folding behavior. The GTPase center (GAC) of the large subunit of the prokaryotic ribosome, is a well-studied 58mer that exhibits ion-dependent tertiary folding. By substituting the fluorescent base analog 2-aminopurine (2AP), 15N labeled bases, or 13C labeled bases in to specific loop and bulge regions we are able to monitor local changes that occur during Mg2+ induced tertiary folding. Being able to contrast the results from stopped flow kinetics, NMR dynamics and structural studies, we can see how local interactions make up tertiary folding. This work was funded by the NIH R01-GM098102 to KBH. Labeled RNA molecules were contributed by Agilent and NMR studies were supported by Agilent.
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