Design and Optimization of Sequence-Specific Hairpin Ribozymes

The hairpin ribozyme belongs to a group of small catalytic RNAs that have been extensively used to trans -cleave RNA molecules. Many efforts have been made to elucidate its reaction mechanism, and there is great interest in designing hairpin ribozymes with improved catalytic activity for use in the development of agents that specifically inactivate RNA molecules. This chapter summarizes the general principles in the design of hairpin ribozymes for targeting purposes, and provides a brief overview of the well-characterized modifications of the ribozyme sequences and structural domains that are necessary for optimal activity. The main features of the target sequence are also examined and other procedures or modifications of interest are also discussed.