Maximizing RNA folding rates: a balancing act.
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.
Thirumalai
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Department of Chemistry and Institute for Physical Sciences and Technology, University of Maryland, College Park 20742-2021, USA. thirum@glue.umd.edu
Woodson
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SA
D000818:Animals; D007700:Kinetics; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D016053:RNA, Protozoan / Q000737:chemistry* / Q000378:metabolism*; D013768:Tetrahymena / Q000201:enzymology*
D016337:RNA, Catalytic; D016053:RNA, Protozoan