Synthetic Catalytic Oligonucleotides Based on the Hammerhead Ribozyme

Abstract

The discovery that certain small RNA molecules found in nature, viz. plant viroids, virusoids, and satellite RNAs, undergo spontaneous self-cleavage, has led to the design of short oligoribonucleotides that are able to function in trans as specific endoribonucleases (Uhlenbeck 1987; Haseloff and Gerlach 1988). The naturally occurring self-cleavage reaction plays a central role in the rolling circle replication of these pathogenic RNAs (Symons 1989). The so-called hammerhead model was proposed for the secondary structure of the self-cleaving domain consistent with many of these cleavage sites (Forster and Symons 1987), and is illustrated in Fig. 1 with the now standard numbering system (Hertel et al. 1992). The structure consists of three helices and a singlestanded loop of highly conserved residues (Keese and Symons 1987). Cleavage occurs after a NUX triplet, where N can be A, C, G, or U and X is not G, to generate a sequence terminating in the 2′,3′-cyclic phosphate of the X residue plus the 5′-hydroxy form of the second sequence. The trans cleaving structure can be formed from two RNA strands in a number of ways. The Uhlenbeck design in which the hammerhead motif is split through helices I and II (Uhlenbeck 1987), and the Haseloff and Gerlach design in which the motif is split between helices I and III as illustrated in Fig. 1 (Haseloff and Gerlach 1988). However, the Uhlenbeck style ribozymes have been shown to cleave substrates less efficiently than the Haseloff and Gerlach versions (Ruffner et al. 1989).KeywordsHuman Immunodeficiency Virus TypeCatalytic CoreHammerhead RibozymeTriethylene GlycolHexaethylene GlycolThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.