Nucleic Acids Research Advance Access originally published online on September 20, 2006
Nucleic Acids Research 2006 34(18):5032-5038; doi:10.1093/nar/gkl613
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Nucleic Acids Research, 2006, Vol. 34, No. 18 5032-5038
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes
Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
*To whom correspondence should be addressed. Tel: +49 6221 54 48 53; Fax: +49 6221 54 64 30; Email: jaeschke{at}uni-hd.de
Received June 22, 2006. Revised August 3, 2006. Accepted August 7, 2006.
Allosteric mechanisms are widely used in nature to control the rates of enzymatic reactions, but little is known about RNA catalysts controlled by these principles. The only natural allosteric ribozyme reported to date catalyzes an RNA cleavage reaction, and so do almost all artificial systems. RNA has, however, been shown to accelerate a much wider range of chemical reactions. Here we report that RNA catalysts for organic reactions can be put under the stringent control of effector molecules by straight-forward rational design. This approach uses known RNA sequences with catalytic and ligand-binding properties, and exploits weakly conserved sequence elements and available structural information to induce the formation of alternative, catalytically inactive structures. The potential and general applicability is demonstrated by the design of three different systems in which the rate of a catalytic carbon–carbon bond forming reaction is positively regulated up to 2100-fold by theophylline, tobramycin and a specific mRNA sequence, respectively. Although smaller in size than a tRNA, all three ribozymes show typical features of allosteric metabolic enzymes, namely high rate acceleration and tight allosteric regulation. Not only do these findings demonstrate RNA's power as a catalyst, but also highlight on RNA's capabilities as signaling components in regulatory networks.