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Maximizing RNA folding rates: A balancing act

Published online by Cambridge University Press:  01 June 2000

D. THIRUMALAI
Affiliation:
Department of Chemistry and Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742-2021, USA
SARAH A. WOODSON
Affiliation:
T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218-2685, USA
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Abstract

Large ribozymes typically require very long times to refold into their active conformation in vitro, because the RNA is easily trapped in metastable misfolded structures. Theoretical models show that the probability of misfolding is reduced when local and long-range interactions in the RNA are balanced. Using the folding kinetics of the Tetrahymena ribozyme as an example, we propose that folding rates are maximized when the free energies of forming independent domains are similar to each other. A prediction is that the folding pathway of the ribozyme can be reversed by inverting the relative stability of the tertiary domains. This result suggests strategies for optimizing ribozyme sequences for therapeutics and structural studies.

Type
PERSPECTIVE
Copyright
2000 RNA Society

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