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Nucleic Acids Research 2005 33(11):3447-3454; doi:10.1093/nar/gki626
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Published online 16 June 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

Monitoring tat peptide binding to TAR RNA by solid-state 31P–19F REDOR NMR

Greg L. Olsen, Thomas E. Edwards1, Pritilekha Deka, Gabriele Varani, Snorri Th. Sigurdsson2 and Gary P. Drobny*

Department of Chemistry, University of Washington Seattle, WA 98195-1700, USA 1Division of Basic Sciences, Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, Seattle, WA 98109, USA 2Science Institute, University of Iceland Dunhaga 3, IS-107 Reykjavik, Iceland

*To whom correspondence should be addressed. Tel: +1 206 685 2052; Fax: +1 206 685 8665; Email: drobny{at}chem.washington.edu

Received February 24, 2005. Revised May 13, 2005. Accepted May 13, 2005.

Complexes of the HIV transactivation response element (TAR) RNA with the viral regulatory protein tat are of special interest due in particular to the plasticity of the RNA at this binding site and to the potential for therapeutic targeting of the interaction. We performed REDOR solid-state NMR experiments on lyophilized samples of a 29 nt HIV-1 TAR construct to measure conformational changes in the tat-binding site concomitant with binding of a short peptide comprising the residues of the tat basic binding domain. Peptide binding was observed to produce a nearly 4 Å decrease in the separation between phosphorothioate and 2'F labels incorporated at A27 in the upper helix and U23 in the bulge, respectively, consistent with distance changes observed in previous solution NMR studies, and with models showing significant rearrangement in position of bulge residue U23 in the bound-form RNA. In addition to providing long-range constraints on free TAR and the TAR–tat complex, these results suggest that in RNAs known to undergo large deformations upon ligand binding, 31P–19F REDOR measurements can also serve as an assay for complex formation in solid-state samples. To our knowledge, these experiments provide the first example of a solid-state NMR distance measurement in an RNA–peptide complex.


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