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Nucleic Acids Research 2005 33(6):1970-1981; doi:10.1093/nar/gki346
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Published online 6 April 2005

© The Author 2005. 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{at}oupjournals.org

Article

Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase

Jean-Guillaume Renisio, Sylvain Cosquer, Ilham Cherrak, Saïd El Antri, Olivier Mauffret and Serge Fermandjian*

Centre National de la Recherche Scientifique Unité Mixte de Recherche 8113, Laboratoire de Biotechnologies et Pharmacologie génétique Appliquée, Ecole Normale Supérieure de Cachan 94235 Cachan, France and Institut Gustave Roussy, 94805 Villejuif Cedex, France

*To whom correspondence should be addressed. Tel: +33 1 42 11 4985; Fax: +33 1 42 1151 76; Email: sfermand{at}igr.fr

Received February 22, 2005. Revised March 21, 2005. Accepted March 21, 2005.

The integration of the human immunodeficiency virus type 1 DNA into the host cell genome is catalysed by the viral integrase (IN). The reaction consists of a 3'-processing [dinucleotide released from each 3' end of the viral long terminal repeat (LTR)] followed by a strand transfer (insertion of the viral genome into the human chromosome). A 17 base pair oligonucleotide d(GGAAAATCTCTAGCAGT), d(ACTGCTAGAGATTTTCC) reproducing the U5-LTR extremity of viral DNA that contains the IN attachment site was analysed by NMR using the classical NOEs and scalar coupling constants in conjunction with a small set of residual dipolar coupling constants (RDCs) measured at the 13C/15N natural abundance. The combination of these two types of parameters in calculations significantly improved the DNA structure determination. The well-known features of A-tracts were clearly identified by RDCs in the first part of the molecule. The binding/cleavage site at the viral DNA end is distinguishable by a loss of regular base stacking and a distorted minor groove that can aid its specific recognition by IN.

Present addresses: Jean-Guillaume Renisio, Institut de Biologie et Chimie des Protéines, Unité Propre de Recherche du CNRS, 69367 Lyon, France

Saïd El Antri, Laboratoire de Chimie Bioorganique et Analytique, Faculté des Sciences et Techniques, BP 146, Mohamedia, Maroc, France

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

PDB accession no. 1TQR


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