A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate

We describe a novel and general strategy for controlling the activity of RN A-cleaving nucleic acid enzymes (ribozymes and DNAzymes) via the use of RNA and DNA effecters. Whereas in conventional heteroallosteric enzymes (inclu ding ribozymes) control of catalysis is achieved by the binding of effector molecules to the enzyme, in our strategy DNA and RNA regulators bind to bo th the enzyme and the substrate. The design of this system permits the cont rol of catalysis even in the absence of a detailed knowledge of the seconda ry and tertiary structure of the relevant ribozyme or DNAzyme. Here, we uti lize the ability of RNA and DNA to form branched three-way junctions to reg ulate the RNA-cleaving activity of the in vitro selected "10-23" DNAzyme by three orders of magnitude. Control is exercised by the ability of a DNA or RNA "regulator" to induce formation of stable and catalytically competent "three-way" enzyme-substrate-regulator complexes, relative to otherwise uns table and catalytically poor enzyme-substrate complexes. Such expansively r egulated "three-way" ribozyme/DNAzyme systems might find utility in vivo to bring about the catalyzed destruction of one RNA transcript contingent on the presence in its immediate environment of another gene transcript. (C) 2 001 Academic Press.