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Journal/Book: ACS Chem. Biol.
Published: 2010
Pages: 753-765
Volume: 5
Issue: 8
Accession no.: 189
Publisher:
ISBN:

Probing mechanism and transition state of RNA refolding

Boris Fürtig, Philipp Wenter, Stefan Pitsch, Harald Schwalbe
Abstract:
Kinetics and the atomic detail of RNA refolding are only poorly understood. It has been proposed that conformations with transient base pairing interaction are populated during RNA refolding but a detailed description of those states is lacking. By NMR and CD spectroscopy, we examined the refolding of a bistable RNA and the influence of urea, Mg2+ and spermidine on its refolding kinetics. The bistable RNA serves as a model system and exhibits two almost equally stable groundstate conformations. We designed a photolabile caged RNA to selectively stabilize one of the two groundstate conformations and trigger RNA refolding by in-situ light irradiation in the NMR spectrometer. We can show that the refolding kinetics of the bistable RNA is modulated by urea, Mg2+ and spermidine by different mechanisms. From a statistical analysis based on elementary rate constants, we deduce the required number of base pairs that need to be destabilized during the refolding transition and propose a model for the transition state of the folding reaction.
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Prof. Dr. Harald Schwalbe
Institut für Organische Chemie und Chemische Biologie
Johann Wolfgang Goethe Universität
Max-von-Laue-Str. 7
D-60438 Frankfurt am Main
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