Optimized Transcription of a Stem I Substitution in the Hammerhead Ribozyme and the Potential for Gene Therapy

Abstract

Ribonucleic acid, or RNA, is widely recognized to be a vital molecule to life. The central dogma of biology recognizes RNA as the messenger between DNA and protein, in reference to mRNA. It is common knowledge that RNA is a very versatile molecule. Gilber’s RNA world hypothesis makes the case for RNA being the precursor to life relying on two assumptions; RNA is capable of storing genetic information and RNA is capable of self-replication. Being a DNA messenger, RNA was seen as capable for storing genetic information, but it was not until 1981 in a study by Cech et al. that confirmed that RNA was cutting introns and ligating exons completely in the absence of proteins. These strands of seemingly “enzymatic” RNA came to be known as ribozymes. Several types of ribozyme have been discovered, each with specific biochemical functionality. The most prevalent ribozymes known today are ribosomal RNA (rRNA), the hairpin ribozyme, and the hammerhead ribozyme. The hammerhead ribozyme is named after its RNA tertiary structure motifs, being composed of a central catalytic core, and three “double stranded” helical stems, stem I, II, and III. The specific cleavage reaction catalyzed by the hammerhead ribozyme is a trans-esterification of the phosphodiester bond that produces two fragments, the downstream fragment containing a 5’hydroxyl and the upstream fragment containing a 2’,3’-cyclic phosphate. While the role of the catalytic core is clear, the dynamics of the stems are thought to have an effect on the kinetic activity of the ribozyme. The current study is based on previous research and will work to successfully perform a large scale transcription of wild type and stem I substituted HH8 ribozymes as well as find further research for the therapeutic potential of hammerhead ribozymes.