Ribozyme

[1] The most common activities of natural or in vitro evolved ribozymes are the cleavage (or ligation) of RNA and DNA and peptide bond formation.

[4] Attempts have been made to develop ribozymes as therapeutic agents, as enzymes which target defined RNA sequences for cleavage, as biosensors, and for applications in functional genomics and gene discovery.

In 1967, Carl Woese, Francis Crick, and Leslie Orgel were the first to suggest that RNA could act as a catalyst.

In 1989, Thomas R. Cech and Sidney Altman shared the Nobel Prize in chemistry for their "discovery of catalytic properties of RNA".

[8] In the 1980s, Thomas Cech, at the University of Colorado Boulder, was studying the excision of introns in a ribosomal RNA gene in Tetrahymena thermophila.

After much work, Cech proposed that the intron sequence portion of the RNA could break and reform phosphodiester bonds.

Many ribozymes have either a hairpin – or hammerhead – shaped active center and a unique secondary structure that allows them to cleave other RNA molecules at specific sequences.

Despite having only four choices for each monomer unit (nucleotides), compared to 20 amino acid side chains found in proteins, ribozymes have diverse structures and mechanisms.

In comparison, RNase A, a protein that catalyzes the same reaction, uses a coordinating histidine and lysine to act as a base to attack the phosphate backbone.

For example, pancreatic ribonuclease A and hepatitis delta virus (HDV) ribozymes can catalyze the cleavage of RNA backbone through acid-base catalysis without metal ions.

[13] Ribozyme can also catalyze the formation of peptide bond between adjacent amino acids by lowering the activation entropy.

[14] In a model system, there is no requirement for divalent cations in a five-nucleotide RNA catalyzing trans-phenylalanation of a four-nucleotide substrate with 3 base pairs complementary with the catalyst, where the catalyst/substrate were devised by truncation of the C3 ribozyme.

According to this scenario, at the origin of life, all enzymatic activity and genetic information encoding was done by one molecule: RNA.

[30] The RNA polymerase ribozyme (RPR) called tC9-4M was able to polymerize RNA chains longer than itself (i.e. longer than 177 nt) in magnesium ion concentrations close to physiological levels, whereas earlier RPRs required prebiotically implausible concentrations of up to 200 mM.

The only factor required for it to achieve this was the presence of a very simple amino acid polymer called lysine decapeptide.

In a subsequent study, the researchers began with the 38-6 ribozyme and applied another 14 rounds of selection to generate the '52-2' ribozyme, which compared to 38-6, was again many times more active and could begin generating detectable and functional levels of the class I ligase, although it was still limited in its fidelity and functionality in comparison to copying of the same template by proteins such as the T7 RNA polymerase.

Reverse transcription capability could have arisen as a secondary function of an early RNA-dependent RNA polymerase ribozyme.

[37] A short 20-nucleotide RNA variant ribozyme was identified that self-reproduces via template directed ligation of two 10 nucleotide oligomers.

[38] Sexual reproduction might have been present in the RNA world that preceded DNA cellular life forms.

Lincoln and Joyce used in vitro evolution to develop ribozyme ligases capable of self-replication in about an hour, via the joining of pre-synthesized highly complementary oligonucleotides.

[42] Although not true catalysts, the creation of artificial self-cleaving riboswitches, termed aptazymes, has also been an active area of research.

Riboswitches are regulatory RNA motifs that change their structure in response to a small molecule ligand to regulate translation.

In the presence of the ligand, in these cases theophylline, the regulatory RNA region is cleaved off, allowing the ribosome to bind and translate the target gene.

One major challenge of using RNA-based enzymes as a therapeutic is the short half-life of the catalytic RNA molecules in the body.