TBI-Preprint 03-nagel

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Titel:
The Refolding Mechanism of the Metastable Structure at the 5′-end of the hok mRNA of Plasmid R1

Author(s):
J.H.A. Nagel, J. Møller-Jensen, C. Flamm, K.J. Öistämö, J. Besnard, I.L. Hofacker, A.P. Gultyaev, M.H. de Smit, P.K. Schuster, K. Gerdes and C.W.A. Pleij

submitted to:
Proc. Natl. Acad. Sci. USA, (2003)

Abstract:
It has previously been shown that premature translation of the plasmid-encoded Hok toxin during transcription of the hok mRNA is prevented by the formation of metastable hairpins at the 5′-end. Here, the refolding pathway from this metastable structure to the stable conformation in the 5′-leader of the hok mRNA is experimentally monitored in vitro. Refolding kinetics and a mutational analysis on the 5′-end 74 nucleotide hok fragment and the hok mRNA show that the refolding mechanism starts by forming an interaction of the extreme 5′- and 3′-end nucleotides, followed by a gradual zippering into the stable conformation at the expense of the metastable one. A prediction of the refolding pathway, including the saddle-point structure, could be experimentally verified, allowing a detailed description of the secondary structural refolding in the hok mRNA. Moreover, the integration of these new experimental results with the existing in silico, in vitro and in vivo data, provides a unique insight into the dynamics of a self-induced structural switch in a biologically active RNA.

Keywords:
RNA structure, RNA folding kinetics, RNA folding pathway, F-factors, RNA metastable structure

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Last modified: 2003-03-21 16:12:19 www