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Nucleic Acids Research Advance Access originally published online on May 5, 2009
Nucleic Acids Research 2009 37(12):4043-4054; doi:10.1093/nar/gkp297
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Nucleic Acids Research, 2009, Vol. 37, No. 12 4043-4054
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin

Loussiné Zargarian, Igor Kanevsky, Ali Bazzi, Jonathan Boynard, Françoise Chaminade, Philippe Fossé and Olivier Mauffret*

Laboratoire de Biotechnologies et Pharmacologie génétique Appliquée (LBPA), UMR 8113 CNRS, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan cedex, France

*To whom correspondence should be addressed. Tel: +33 1 47 40 77 33; Fax: +33 1 47 40 76 71; Email: olivier.mauffret{at}lbpa.ens-cachan.fr

Received September 23, 2008. Revised March 17, 2009. Accepted April 15, 2009.

First strand transfer is essential for HIV-1 reverse transcription. During this step, the TAR RNA hairpin anneals to the cTAR DNA hairpin; this annealing reaction is promoted by the nucleocapsid protein and involves an initial loop–loop interaction between the apical loops of TAR and cTAR. Using NMR and probing methods, we investigated the structural and dynamic properties of the top half of the cTAR DNA (mini-cTAR). We show that the upper stem located between the apical and the internal loops is stable, but that the lower stem of mini-cTAR is unstable. The residues of the internal loop undergo slow motions at the NMR time-scale that are consistent with conformational exchange phenomena. In contrast, residues of the apical loop undergo fast motions. The lower stem is destabilized by the slow interconversion processes in the internal loop, and thus the internal loop is responsible for asymmetric destabilization of mini-cTAR. These findings are consistent with the functions of cTAR in first strand transfer: its apical loop is suitably exposed to interact with the apical loop of TAR RNA and its lower stem is significantly destabilized to facilitate the subsequent action of the nucleocapsid protein which promotes the annealing reaction.


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