Electrophilic Assistance to the Cleavage of an RNA Model Phopshodiester via Specific and General Base-Catalyzed Mechanisms

摘要

Kinetics of transesterification of the RNA model substrate 2-nhydroxypropyl 4-nitrophenyl phosphate promoted by Mg2+ and Ca2+, the mostncommon biological metals acting as cofactors for nuclease enzymes and ribozymes, asnwell as by Co(NH3)6n3+, Co(en)3n3+, Li+, and Na+ cations, often employed as mechanisticnprobes, was studied in 80% v/v (50 mol %) aqueous DMSO, a medium that allows onento discriminate easily specific base (OH−-catalyzed) and general base (buffer-catalyzed)nreaction paths. All cations assist the specific base reaction, but only Mg2+ and Na+ assistnthe general base reaction. For Mg2+-assisted reactions, the solvent deuterium isotopeneffects are 1.23 and 0.25 for general base and specific base mechanisms, respectively.nRate constants for Mg2+-assisted general base reactions measured with different bases fitnthe Brønsted correlation with a slope of 0.38, significantly lower than the slope for thenunassisted general base reaction (0.77). Transition state binding constants for catalystsnin the specific base reaction (K⧧nOH) both in aqueous DMSO and pure water correlatenwith their binding constants to 4-nitrophenyl phosphate dianion (KNPP) used as a minimalist transition state model. It was foundnthat K⧧nOH ≈ KNPP for “protic” catalysts (Co(NH3)6n3+, Co(en)3n3+, guanidinium), but K⧧nOH ≫ KNPP for Mg2+ and Ca2+ acting asnLewis acids. It appears from results of this study that Mg2+ is unique in its ability to assist efficiently the general base-catalyzedntransesterification often occurring in active sites of nuclease enzymes and ribozymes.