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Nucleic Acids Research 2006 34(9):2618-2633; doi:10.1093/nar/gkl240
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Published online 17 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Analysis of hepatitis C virus RNA dimerization and core–RNA interactions

Roland Ivanyi-Nagy, Igor Kanevsky1, Caroline Gabus, Jean-Pierre Lavergne2, Damien Ficheux2, François Penin2, Philippe Fossé1 and Jean-Luc Darlix*

LaboRetro, Unité INSERM de Virologie Humaine, Ecole Normale Supérieure de Lyon IFR 128 Biosciences Lyon-Gerland, 69364 Lyon Cedex 07, France 1 CNRS-UMR 8113, LBPA-Alembert, Ecole Normale Supérieure de Cachan 94235 Cachan Cedex, France 2 Institut de Biologie et Chimie des Protéines, CNRS-UMR 5086, Université Claude Bernard Lyon I IFR 128 Biosciences Lyon-Gerland, 69367 Lyon Cedex 07, France

*To whom correspondence should be addressed. Tel: +33 4 72 72 81 69; Fax: +33 4 72 72 87 77; Email: Jean-Luc.Darlix{at}ens-lyon.fr

Received January 16, 2006. Revised February 8, 2006. Accepted March 29, 2006.

The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3'-untranslated region (3'-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623–2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3'-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus.


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R. Ivanyi-Nagy, J.-P. Lavergne, C. Gabus, D. Ficheux, and J.-L. Darlix
RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae
Nucleic Acids Res., February 11, 2008; 36(3): 712 - 725.
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