The hairpin ribozyme is a naturally occurring RNA that catalyzes sequence-specific cleavage and ligation of RNA. It has been the subject of extensive biochemical and structural studies, perhaps the most detailed for any catalytic RNA to date. Comparison of the structures of its constituent domains free and fully assembled demonstrates that the RNA undergoes extensive structural rearrangement. This rearrangement results in a distortion of the substrate RNA that primes it for cleavage. This ribozyme is known to achieve catalysis employing exclusively RNA functional groups. Metal ions or other catalytic cofactors are not used. Current experimental evidence points to a combination of at least four mechanistic strategies by this RNA: (1) precise substrate orientation, (2) preferential transition state binding, (3) electrostatic catalysis, and (4) general acid base catalysis.
Copyright 2003 Wiley Periodicals, Inc. Biopolymers 73: 71-78, 2004