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Here, we describe allosteric ribozymes, which are activated by the addition of a short regulator oligonucleotide. The allosteric hammerhead ribozyme, which contains a single-stranded loop instead of stem II, exhibited minimal cleavage of the target RNA; however, it becomes active by the addition of oligonucleotides that bind to the ribozyme. We have also carried out in vitro selection to obtain an allosteric hairpin ribozyme, which is activated with a short oligonucleotide. The ribozyme contains the characteristic hairpin loop with the structure that changes upon regulator oligonucleotide binding. Since both regulations are sequence-specific, ribozymes containing different sequences can be positively and independently controlled by a specific oligonucleotide. Furthermore, these allosteric hairpin loops have the ability to control the activities of other functional RNAs.
