SCHEME 1.

General in-line monoanionic mechanism (top) and G8-assisted dianionic general base catalysis mechanism (bottom) of phosphodiester cleavage transesterification catalyzed by the hairpin ribozyme. In the in-line monoanionic mechanism, the first proton transfer (PT1), the nucleophilic attack (Nu), and the exocyclic cleavage (Cl) steps are shown. For the uncatalyzed model reaction in solution, the O_1P and O_2P pathways are energetically equivalent. In the G8-assisted dianionic general base catalysis mechanism, the deprotonated G8 acts as a general base to activate 2′-hydroxyl group, and the reaction proceeds to the product without forming INT₂.