Effect of a Stem I Substitution on the Self-Cleavage Rate of a Hammerhead Ribozyme
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RNA is a significant fixture in important biological processes. It serves a diverse array of functions, such as a catalyst in chemical reactions and a role in gene regulation. RNAs that catalyze chemical reactions are more commonly referred to as ribozymes. Hammerhead ribozymes are one type of ribozyme. A hammerhead ribozyme is a small, trans-RNA-cleaving class of ribozyme first discovered in plant pathogenic viroids and virusoids in the late 1980's. Since then it has garnered the attention of many studies as a possible therapeutic for cancer and viral infections and is well characterized. Many of these studies found them to be too inefficient for use against viruses and cancer. However research has identified that the structure of the hammerhead will affect its cleavage rates. Therefore changing the structure of a hammerhead may lead to more efficient ribozymes and a renewed effort to better understand the relationship between structure, dynamics, and cleavage efficiency is underway. With a better understanding of the relationship between these three aspects of a hammerhead ribozyme, one could theoretically design much more efficient hammerhead ribozymes that would be a viable option for therapeutic treatments. Olke Uhlenbeck has suggested that the substitution of the anticodon stem of E. coli tRNA alanine for stem I of a hammerhead ribozyme may speed up the rate of its RNA cleaving. In this study we investigate this claim on the HH8 hammerhead ribozyme through designing and testing via activity assays. Due to setbacks caused by faulty transcription buffer, the activity assays could not be performed in the time of this study, so no conclusions could be made as to the cleavage efficiency of the ribozyme. However, once complete this study may provide useful incite into the effect of helical sequences on cleavage efficiency of hammerhead ribozymes.