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

Probing mechanism and transition state of RNA refolding

Boris Fürtig, Philipp Wenter, Stefan Pitsch, Harald Schwalbe
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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