Cooperative binding of effecters by an allosteric ribozyme

An allosteric ribozyme that requires two different effecters 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 effecters are present, this 'binary' RNA switch self-cleaves with a rate enhancement of similar to 300-fold over the rate observed in the absence of effecters. 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 effecters reveals a level of structural and functional complexity for RNA that is similar to that observed with allosteric proteins.