"Hairpin" and "hammerhead" ribozymes directed towards the mumps virus nucleocapsid RNA: specific cleavage of a small synthetic RNA substrate and full-length mRNA

Synthetic hammerhead ribozymes as tools in gene expression

The assessment of genetic controls for sequential developmental processes such as tooth formation and biomineralization is often difficult in transgenic "knockout" models, where phenotypes reflect only the permanent eradication of a gene, and reveal little about the dynamic range of expression for the gene(s) involved. One promising strategy to overcome this problem is through the use of ribozymes, a class of metalloenzymes made entirely of ribonucleic acid (RNA), that are capable of cleaving other RNA molecules in a catalytic fashion. Their activity can be targeted against specific mRNAs by selection of unique sequences flanking a conserved catalytic motif. In synthetic ribozymes, specificity, stability, and cell permeability can be dramatically improved by the incorporation of chemically modified ribonucleotides. This review focuses on the design and application of hammerhead ribozymes, the best-known and most widely used class of RNA-based enzymes. So far, except for a few conserved structures at the catalytic core, no one particular model or superior ribozyme design has been identified. It may well be that each cell, tissue, and organism has different requirements for the uptake, activity, and stability of hammerhead ribozymes. However, designed ribozymes can be highly effective agents for timed and localized elimination of gene products. As the 3D structures of active hammerhead molecules are revealed, more effective ribozymes will be developed. Today, developments in ribozyme-mediated sequence-specific blocking of gene expression hold great promise for active RNA enzymes as tools in biomolecular research and for eliminating unwanted gene expression in human diseases.

Ribozyme-mediated decrease in mumps virus nucleocapsid mRNA level and progeny in infected vero cells

The effects of endogenously expressed ribozymes directed to the mumps virus nucleocapsid (NP) mRNA were studied during viral infection. To this end, eukaryotic expression vectors encoding ribozymes or controls of passive hybridization effects were constructed and used to transfect mumps permissive Vero cells. Transcripts spanning trans-acting ribozymes of the hammerhead and hairpin types were designed to hydrolyze the first 5'GUC-3' sequence downstream from the initiation site and to hybridize to a 16 base sequence containing the putative cleavage site. Control vectors encoded mutated and catalytically inactive forms of the ribozymes or a 16 base antisense version of the target sequence. When stably expressed in cells, both ribozymes and passive control RNAs reduced viral yields. A ribozyme-mediated effect on viral growth was, however, observed, as both ribozyme types reduced viral titers by approximately 80%, well above the highest inhibition level of approximately 35% found when noncatalytic RNAs were expressed. In addition, levels of NP mRNA were generally lower in cells expressing catalytic RNAs, supporting the observed inhibition of viral growth. Although cleavage in vitro of a synthetic analog of the NP mRNA was demonstrated using RNAs isolated from ribozyme-expressing cells, in vivo cleavage products were not detectable despite the use of sensitive methods, possibly because of degradation phenomena. We also suggest here that additional controls should be conducted when semicompetitive RT-PCR methods are used to evaluate intracellular cleavage by ribozymes, as the results may depend on the initial target RNA concentration.

Tailing cDNAs with terminal deoxynucleotidyl transferase in RT-PCR assays to identify ribozyme cleavage products

Polytailing a cDNA with terminal deoxynucleotidyltransferase (TdT) results in the addition of a homopolymeric sequence at its 3'-end. Here we describe the use of tailing in competitive RT-PCR assays to evaluate cleavage efficiency of ribozymes. Using a system that perfectly mimics intracellular cleavage, we were able to detect as few as 1% of cleaved moieties. Furthermore, employing primers overlapping the junction between tails and the cleaved RNA moiety in non-competitive assays, the sensitivity of the method could be improved to <10 fg. Using the latter protocol and reactions employing a trans -acting hairpin ribozyme targeting the nucleocapsid mRNA of the mumps virus, we were able to demonstrate ribozyme-induced cleavage.