Utilization of properties of natural catalytic RNA to design and synthesize functional ribozymes

Abstract

Publisher Summary The unexpected discovery that the RNA molecule has catalytic properties has led to a plethora of interest in the identification and utilization of the variety of catalytic RNA molecules, or ribozymes, that occur in nature. Naturally occurring catalytic RNA motifs can be classified broadly into two groups based on their catalytic activity. The hammerhead, hairpin, and hepatitis delta virus ribozymes can be characterized by their ability to self-cleave a target phospodiester bond, as opposed to the group I and group II intron ribozymes, which can be characterized by their ability to self-splice by a two-step cleavage and ligation mechanism. The former group of small ribozyme motifs is found typically in viral or viroid RNAs, whereas the latter, larger ribozymes are found in bacteria and lower eukaryores. The detailed analysis of the structure and properties of these ribozymes has identified their potential as molecular tools. In particular, the hammerhead ribozyme, by virtue of its small size and ability to be designed to cleave virtually any target RNA, has been widely touted for the therapy of both genetic and infectious diseases. More recently, the group I intron ribozyme has similarly been proposed as a therapeutic tool by virtue of its potential to repair a defective target RNA. This chapter outlines the methods by which the hammerhead and group I intron ribozyme motifs can be utilized to design and construct synthetic ribozymes as potential molecular tools.