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Nucleic Acids Research 2006 34(9):2607-2617; doi:10.1093/nar/gkl347
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Published online 17 May 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@oxfordjournals.org

Article

Thermodynamic characterization of an engineered tetracycline-binding riboswitch

Michael Müller, Julia E. Weigand, Oliver Weichenrieder1 and Beatrix Suess*

Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg Staudtstrasse 5, 91058 Erlangen, Germany 1 The Netherlands Cancer Institute, Department of Molecular Carcinogenesis Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +49 9131 852 88 18; Fax: +49 9131 852 80 82; Email: bsuess{at}biologie.uni-erlangen.de

*Correspondence may also be addressed to Oliver Weichenrieder. Tel: +31 20 512 1951; Fax: +31 20 512 1954; Email: o.weichenrieder{at}nki.nl

Received March 27, 2006. Revised April 12, 2006. Accepted April 19, 2006.

Riboswitches reflect a novel concept in gene regulation that is particularly suited for technological adaptation. Therefore, we characterized thermodynamically the ligand binding properties of a synthetic, tetracycline (tc)-binding RNA aptamer, which regulates gene expression in a dose-dependent manner when inserted into the untranslated region of an mRNA. In vitro, one molecule of tc is bound by one molecule of partially pre-structured and conformationally homogeneous apo-RNA. The dissociation constant of 770 pM, as determined by fluorimetry, is the lowest reported so far for a small molecule-binding RNA aptamer. Additional calorimetric analysis of RNA point mutants and tc derivatives identifies functional groups crucial for the interaction and including their respective enthalpic and entropic contributions we can propose detailed structural and functional roles for certain groups. The conclusions are consistent with mutational analyses in vivo and support the hypothesis that tc-binding reinforces the structure of the RNA aptamer, preventing the scanning ribosome from melting it efficiently.


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