VS ribozyme

The Varkud satellite (VS) ribozyme is an RNA enzyme that carries out the cleavage of a phosphodiester bond.

When these 2 domains are synthesized in vitro separately, they can perform the self-cleavage reaction by trans-acting[5] The substrate binds into a cleft which is made by two helices.

The A730 loop and A756 nucleotide are critical to its function since they participate in the phosphoric transfer chemistry activity of the ribozyme[6] VS RNA is transcribed as a multimeric transcript from VS DNA.

VS RNA self-cleaves at a specific phosphodiester bond to produce a monomeric and few multimeric transcripts.

The base bulges of the ribozyme, helices II and IV have very important structural roles since replacing them with other nucleotides does not affect their activity.

[9] The active sites of the ribozyme can be found in the helical junctions, the bulges and the lengths of the critical helices those being III and V. There is one important area found in the internal loop of helix VI called A730, a single base change in this loop would lead to decreased loss of cleavage activity but no significant changes in the folding of the ribozyme occur.

[11] The way that both of these reactions are facilitated is by general acid-base catalysis which strengthen the oxygen nucleophile by removing bonded proteins and stabilizing the oxyanion leaving groups through protonation.

Another proposed catalytic strategy is the stabilization of a pentavalent phosphate of the reaction transition state.

Very high concentration of bivalent and monovalent cation increase the efficiency of the cleavage reaction.

The cations' role is considered to be charge neutralizing in the folding of RNA rather than acting as a catalyst.

A molecular fossil of RNA world which has retained both cleavage and ligation functions.