EFFICIENT IMPROVEMENT OF HAMMERHEAD RIBOZYME MEDIATED CLEAVAGE OF LONG SUBSTRATES BY OLIGONUCLEOTIDE FACILITATORS

Hammerhead ribozymes were found to be not very efficient in cleaving l ong RNA substrates in trans. Oligonucleotide facilitators, capable of affecting hammerhead ribozymes by interacting with the substrate at th e termini of the ribozyme, may improve this reaction. We determined in vitro the effects of 18 DNA and RNA oligonucleotide facilitators on t hree substrates containing 39, 452, and 942 nucleotides, respectively, by estimating the facilitator influences on association between riboz yme and substrate and on the cleavage step. The effects increase with the length of the substrates. With the 39mer substrate a maximal 4-fol d enhancement of the ribozyme activity could be detected, the reaction with the 942mer substrate was accelerated up to 115-fold by facilitat or addition: In long, structured substrates the facilitators have the potential to preform the substrate for the ribozyme attack. Due to thi s preforming effect, the rate of ribozyme-substrate association was in creased as well as the rate of the cleavage step. 3'-End facilitators accelerate both of these rates, largely independent on the facilitator length. The rate of the cleavage step is raised as a result of a favo rable activation energy gain by these facilitators. With all substrate s, the 5'-end facilitators increase the association rate between riboz yme and substrate in dependence on their length. With the 39mer substr ate the 5'-end facilitators decrease the rate of the cleavage step. Wi th the long substrates 5'-end facilitators partially increase the rate of the cleavage step due to their preforming potential with these sub strates. In some examples, combinations of several 5'-end and 3'-end f acilitators provide an additional improvement over single facilitators in both the association between ribozyme and substrate and the cleava ge step. Results suggest that even short facilitators may be efficient effecters enhancing hammerhead ribozyme mediated cleavage of long sub strates.