Self-cleaving RNAs                                          

A number of small RNAs pathogenic to plants and animals undergo a site-specific autocatalysed cleavage reaction in vitro .

These catalytic RNAs are classified into four main groups:

1. the VIROIDS (independently replicating, circular, rod-shaped plant pathogens);
2. VIRUSOIDS (encapsidated viroid-like satellite RNAs, which require a helper virus for replication);
3. linear satellite RNAs (similar to virusoids but encapsidated as linear molecules); and
4. HEPATITIS DELTA VIRUS (an animal pathogen that requires a helper virus for replication).

These RNAs probably replicate by a ROLLING CIRCLE mechanism. The multimeric linear molecules that are produced are thought to be processed into unit-size progeny by the self-cleavage reaction in vivo. In addition, the RNA transcript of the newt Notophthalmus viridescens satellite II DNA (not directly related to the pathogenic satellite RNAs) undergoes a self-cleavage reaction in vitro.

The most common structural motif contains 13 conserved nucleotides that are present within a secondary structure domain of ~30 nucleotides, which is known as a hammerhead . This domain is necessary and sufficient for catalytic activity in vitro.

The self-cleaving domain derived from the genomic and antigenomic RNA from hepatitis delta virus consists of an 85-nucleotide region that can be folded into a PSEUDOKNOT -like structure. The minus strand of tobacco ringspot virus satellite RNA contains a catalytic domain of 50 nucleotides, known as a HAIRPIN structure, and a 14-nucleotide substrate domain.

The catalytic and substrate domains base-pair together to form two short intramolecular stems. Another self-cleaving RNA has been identified from the mitochondrial plasmid transcibe of Neurospora (VS RNA). The catalytic motif is unknown but it appears to be unrelated to the other self-cleaving RNAs. All the self-cleaving RNAs undergo a one-step reaction that involves the nucleophilic attack of the 2 hydroxyl on the ribose ring at the phosphodiester bond to be cleaved to form products with 5 hydroxyls and 2,3-cyclic phosphates. No cofactors or energy source are required. In some cases the reverse reaction has been demonstrated.

The intramolecular autocatalytic cleavage reaction can be converted into an intermolecular enzymatic reaction by providing the enzymatic activity and substrate (the sequence to be cleaved) as two separate RNA molecules that hybridize to form the catalytically active structure .

Each enzyme unit remains intact after the reaction and consequently is able to cleave multiple units of substrate. This ribozyme can also be engineered to make a highly specific restriction endoribonuclease.