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Nucleic Acids Research 2006 34(1):334-342; doi:10.1093/nar/gkj435
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Published online 12 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

Stabilities of HIV-1 DIS type RNA loop–loop interactions in vitro and in vivo

Christina Lorenz, Nicolas Piganeau and Renée Schroeder*

Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna Dr Bohrgasse 9/5, A-1030 Vienna, Austria

*To whom correspondence should be addressed. Tel: +43 1 4277 54690; Fax: +43 1 4277 9528; Email: renee.schroeder{at}univie.ac.at

Received September 7, 2005. Revised December 21, 2005. Accepted December 21, 2005.

RNA loop–loop interactions are a prevalent motif in the formation of tertiary structure and are well suited to trigger molecular recognition between RNA molecules. We determined the stabilities of several loop–loop interactions with a constant 6 bp core sequence and varying unpaired flanking nucleotides and found that the flanking bases have a strong influence on the stability and ion dependence of the kissing complex. In general, the stabilities determined in 1 M Na+ are equivalent to those in the presence of near physiological Mg2+ concentrations. Therefore we further tested whether the stabilities determined in vitro and within yeast cells correlate, using a recently developed yeast RNA-hybrid system. For the majority of the loop types analyzed here, the melting temperatures determined in vitro are in good agreement with the relative ß-galactosidase activity in yeast cells, showing that data derived from in vitro measurements reflect in vivo properties. The most stable interactions are the naturally occurring HIV-1 DIS MAL and LAI derived loops with the motif (5' AA/GN6A 3'), emphasizing the crucial role of stable kissing complexes in HIV genome dimerization.


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