Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme

Abstract

An unique catalytic strategy was recently reported for the glmS ribozyme [ Bingaman et al., Nat. Chem. Biol. 2017, 13, 439-445 ] that involves promotion of productive hydrogen bonding of the O2′ nucleophile to facilitate its activation. We provide broad evidence of this strategy in the hammerhead, pistol, and VS ribozymes and 8-17 DNAzyme, enabled by a functionally important divalent metal ion that interacts with the scissile phosphate and disrupts nonproductive competitive hydrogen bonding with the O2′ nucleophile. This strategy, designated tertiary gamma (3°γ) catalysis, illustrates an additional role for divalent ions in ribozyme catalysis.