RNA molecules that are capable of catalyzing endonucleolytic cleavage reactions are called “ribozymes.” They have the potential to create phenotypic mutants or to inhibit viral gene expression, as has been shown for antisense genes. In nature, some viroids, virusoids, and satellite RNAs of plant viruses perform self-cleavage reactions. The nucleotide region directing the catalysis of the cleavage reaction can by physically separated from the region where cleavage occurs. In principle, the recognition of any target RNA could be envisaged by linking the complementary nucleotide sequences of the regions flanking the cleavage site to the catalytic domain. As a consequence, ribozymes may catalyze cleavage reactions in trans and may be directed to many different target RNAs. This chapter outlines the approach used in the laboratory to design ribozymes. This involves the computer simulation of the RNA secondary structure and the predicted bimolecular ribozyme-target RNA interaction. © 1995, Academic Press, Inc.
