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Nucleic Acids Research 2005 33(14):4395-4403; doi:10.1093/nar/gki741
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Published online 2 August 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

Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein

Besik I. Kankia*, George Barany and Karin Musier-Forsyth

Department of Chemistry, University of Minnesota Minneapolis, MN 55455, USA

*To whom correspondence should be addressed. Tel: +1 612 624 5954; Fax: +1 612 626 7431; Email: bkankia{at}umn.edu

Received April 15, 2005. Revised June 3, 2005. Accepted July 11, 2005.

The human immunodeficiency virus type 1 nucleocapsid protein (NC) is a nucleic acid chaperone that catalyzes the rearrangement of nucleic acids into their thermodynamically most stable structures. In the present study, a combination of optical and thermodynamic techniques were used to characterize the influence of NC on the secondary structure, thermal stability and energetics of monomolecular DNA quadruplexes formed by the sequence d(GGTTGGTGTGGTTGG) in the presence of K+ or Sr2+. Circular dichroism studies demonstrate that NC effectively unfolds the quadruplexes. Studies carried out with NC variants suggest that destabilization is mediated by the zinc fingers of NC. Calorimetric studies reveal that NC destabilization is enthalpic in origin, probably owing to unstacking of the G-quartets upon protein binding. In contrast, parallel studies performed on a related DNA duplex reveal that under conditions where NC readily destabilizes and unfolds the quadruplexes, its effect on the DNA duplex is much less pronounced. The differences in NC's ability to destabilize quadruplex versus duplex is in accordance with the higher {Delta}G of melting for the latter, and with the inverse correlation between nucleic acid stability and the destabilizing activity of NC.

DDBJ/EMBL/Genbank accession no. NC_002572


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