Defining Optimum Reaction Conditions for Hammerhead Ribozymes

Hammerhead ribozymes, in their trans -cleaving form catalyze the cleavage of complementary RNA strands, which contain the UX sequence (where X is A, U, or C) Immediately 5′ to the site of cleavage, although not all such sequences are cleaved with the same efficiency (1 ,2 ). The reactivity of the hammerhead ribozyme is assumed to follow the model outlined in Scheme 1 , i.e., ribozyme and substrate anneal, cleavage takes place, and then dissociation of the two products occurs independently. The in vitro study of hammerhead activity allows manipulation of the reaction conditions in order to gain insight into the detail of the cleavage reaction.