Effect of a Stem I Substitution on the Self-Cleavage Rate of a Hammerhead Ribozyme

Abstract

Hammerhead ribozymes have been the focus of much research including therapeutics against cancer and viral infection. Hammerhead ribozymes are small self-cleaving RNAs characterized by a hammerhead motif – three short helices flanking a central catalytic core of conserved nucleotides. The central catalytic core is highly conserved in all hammerhead ribozymes, however the double stranded stems are variable between species with some capped and some not. Since RNA has limited chemical diversity, in many cases RNA molecules must rely on dynamics, highly complex multistep conformational transitions, for their functioning. Much of the research conducted thus far has studied the affect of peripheral loop-loop interactions on the cleavage efficiency of the hammerhead ribozyme. The present study attempts to answer whether we can see effects from specific helical sequences in the absence of loops. Specifically this study is attempting test Olke Uhlenbeck’s hypothesis that the anticodon stem from E. coli tRNA alanine in place of stem I of a hammerhead ribozyme will increase its cleavage efficiency. He believes the uracil-adenine base pairs present in this stem near the catalytic core increase catalytic activity as suggested by previous research.