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Nucleic Acids Research, 2001, Vol. 29, No. 7 1631-1637
© 2001 Oxford University Press

Cooperative binding of effectors by an allosteric ribozyme

Antony M. Jose, Garrett A. Soukup and Ronald R. Breaker*

Department of Molecular, Cellular and Developmental Biology, KBT 452, Yale University, PO Box 208103, New Haven, CT 06520-8103, USA

An allosteric ribozyme that requires two different effectors to induce catalysis was created using modular rational design. This ribozyme construct comprises five conjoined RNA modules that operate in concert as an obligate FMN- and theophylline-dependent molecular switch. When both effectors are present, this ‘binary’ RNA switch self-cleaves with a rate enhancement of ~300-fold over the rate observed in the absence of effectors. Kinetic and structural studies implicate a switching mechanism wherein FMN binding induces formation of the active ribozyme conformation. However, the binding site for FMN is rendered inactive unless theophylline first binds to its corresponding site and reorganizes the RNA structure. This example of cooperative binding between allosteric effectors reveals a level of structural and functional complexity for RNA that is similar to that observed with allosteric proteins.

* To whom correspondence should be addressed. Tel: +1 203 432 9389; Fax: +1 203 432 5713; Email: ronald.breaker{at}yale.edu Present address: Garrett A. Soukup, Department of Biomedical Sciences, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA


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