Figure 1. The chemical mechanism of the nucleolytic ribozymes, showing catalysis by general acid–base catalysis.

The cleavage reaction is left to right and the ligation reaction right to left. The central phosphorane structure will be close to the transition state in the reaction trajectory. In the cleavage reaction, B ⁻ acts as a general base to deprotonate the O2′ nucleophile, and the general acid AH ⁺ protonates the 5′-oxyanion leaving group.