Examples include the following:
- RNase P
- Group I introns (includes intron of pre‑rRNA in Tetrahymena)
- Group II introns
- RNA: peptide bond formation
Viroids and virusoids have a self-cleaving activity that localized to a 58 nucleotide structure illustrated in Figure 3.3.15. The mechanism differs in some respects from the phosphoester transfer. A divalent metal hydroxide binds in the active site, and abstracts a proton from the 2' OH of the nucleotide at the cleavage site. This now serves as a nucleophile to attack the 3' phosphate and cleave the phosphodiester bond, generating a 2',3' cyclic phosphate and a 5' OH on the ends of the cleaved RNA.
One application currently being explored is the use of designed hammerheads to cleave a particular mRNA, thereby turning off expression of a particular gene. If over-expression or ectopic expression of a defined gene were the cause of some pathology (e.g. some form of cancer), then reducing its expression could have therapeutic value.
Other RNAs possibly involved in catalysis, such as the snRNAs involved in splicing pre-mRNA.
Even though RNAs can be sufficient for catalysis, sometimes they are assisted by proteins to improve efficiency. For instance, group I introns are capable of splicing introns by themselves in a cell-free reaction. However, some are not very efficient in this process, and in the cell they are assisted by proteins that themselves are not catalytic but they enhance the reaction. Examples are maturases, which are proteins that assist in the splicing of some group I introns found in yeast mitochondria.