Mechanism of general acid–base catalysis in transesterification of an RNA model phosphodiester studied with strongly basic catalysts

Abstract

Using 80% vol aqueous DMSO as the reaction medium for transesterification of an RNA model substrate 2-hydroxypropyl 4-nitrophenyl phosphate allows one to observe catalysis in buffer mixtures composed of highly basic components such as guanidines, amidines or alkylamines, which provide up to 10³-fold accelerations over the background reaction in the 0.01–0.1 M concentration range. The rate law k_obs = k₁[B] + k₂[B][BH⁺] was established indicating contributions from both simple general base catalysis and the reaction involving concerted action of neutral (B) and protonated (BH⁺) forms of the buffer. The catalytic efficiency of guanidinium and amidinium cations is 10 times larger than that of more acidic ammonium cations. Rate constants k₁ and k₂ obey the Brønsted equations with the slopes 0.77 and 0.69 respectively. Proton inventory for k₂ (B = guanidine) in D₂O/H₂O mixtures gives two fractionation factors ϕ₁ = 0.48 and ϕ₂ = 1.26 for normal and inverse isotope effects respectively. The former results from the proton transfer to B and the latter from the binding of guanidinium cation to the phosphate group as follows from observation of an inverse solvent isotope effect for the binding of guanidinium and amidinium cations to a phosphodiester anion. The results of kinetic studies together with analysis of transition state stabilization free energies for guanidinium and amidinium cations show that the protonated buffer component acts via electrostatic transition state stabilization rather than proton transfer, which may be possible for a guanidinium assisted hydroxide catalyzed reaction.