11 Small Ribozymes

Abstract

Often referred to as “small” ribozymes, the hammerhead (Forster and Symons 1987a), hairpin (Buzayan et al. 1986), hepatitis delta virus (HDV) (Kuo et al. 1988), and Neurospora VS ribozymes (Saville and Collins 1990) all cleave a RNA phosphodiester backbone to yield a 5′ hydroxyl and a 2′, 3′ cyclic phosphodiester as product). Since the reaction produces a cyclic phosphodiester, but does not hydrolyze it (thereby undergoing only the first step of a classic ribonuclease reaction and approximately conserving the substrate bond energy in the products), these ribozymes can also ligate the products to re-form a phosphodiester. Each of these ribozymes has been derived from a self-cleavage activity of linear RNA intermediates in the rolling circle replication cycle of small satellite RNAs, or in the case of the Neurospora VS ribozyme, of the mitochondrial Varkud satellite plasmid. The native function of these catalytic motifs is to cleave a linear RNA having multiple tandem (plus or minus) copies of the satellite sequence into segments of unit length prior to their ligation into circles. Given such a biological function, the activity is required to be precise with regard to site of cleavage and to yield a product whose ends can readily be ligated, but it is not required to be kinetically rapid. In the discussions below, it will become apparent that cleavage-site specificity is often achieved through Watson-Crick base-pairing between RNA sequences flanking the target phosphodiester bond and those flanking the catalytic “core” of the ribozyme (although the Neurospora VS ribozyme appears to...