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Nucleic Acids Research 2006 34(2):593-605; doi:10.1093/nar/gkj458
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Published online 30 January 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{at}oxfordjournals.org

Article

Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins

Margareta Cruceanu1, Maria A. Urbaneja2, Catherine V. Hixson2, Donald G. Johnson2, Siddhartha A. Datta3, Matthew J. Fivash4, Andrew G. Stephen5, Robert J. Fisher5, Robert J. Gorelick2, Jose R. Casas-Finet6, Alan Rein3, Ioulia Rouzina7 and Mark C. Williams1,8,*

1Department of Physics, Northeastern University 111 Dana Research Center, 110 Forsyth Street, Boston, MA 02115, USA 2AIDS Vaccine Program, SAIC-Frederick, Inc. NCI at Frederick, Frederick, MD 21702, USA 3HIV Drug Resistance Program, NCI-Frederick Frederick, MD 21702-1201, USA 4Data Management Services, Inc. NCI-Frederick, Frederick, MD 2170, USA 5Protein Chemistry Laboratory, SAIC Frederick, Inc. NCI at Frederick, Frederick, MD 2170, USA 6MedImmune, Inc. 35 W. Watkins Mill Road, Gaithersburg, MD 20878, USA 7Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota 6-155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA 8Center for Interdisciplinary Research on Complex Systems, Northeastern University 111 Dana Research Center, 110 Forsyth Street, Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: 1 617 373 7323; Fax: 1 617 373 2943; Email: mark{at}neu.edu

Received December 5, 2005. Revised January 5, 2006. Accepted January 5, 2006.

The Gag polyprotein of HIV-1 is essential for retroviral replication and packaging. The nucleocapsid (NC) protein is the primary region for the interaction of Gag with nucleic acids. In this study, we examine the interactions of Gag and its NC cleavage products (NCp15, NCp9 and NCp7) with nucleic acids using solution and single molecule experiments. The NC cleavage products bound DNA with comparable affinity and strongly destabilized the DNA duplex. In contrast, the binding constant of Gag to DNA was found to be ~10-fold higher than that of the NC proteins, and its destabilizing effect on dsDNA was negligible. These findings are consistent with the primary function of Gag as a nucleic acid binding and packaging protein and the primary function of the NC proteins as nucleic acid chaperones. Also, our results suggest that NCp7's capability for fast sequence-nonspecific nucleic acid duplex destabilization, as well as its ability to facilitate nucleic acid strand annealing by inducing electrostatic attraction between strands, likely optimize the fully processed NC protein to facilitate complex nucleic acid secondary structure rearrangements. In contrast, Gag's stronger DNA binding and aggregation capabilities likely make it an effective chaperone for processes that do not require significant duplex destabilization.

Correspondence may also be addressed to Ioulia Rouzina. Tel: 1 612 624 7468; Fax: 1 612 624 5121; Email: rouzina{at}cbs.umn.edu


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