Kinetic solvent deuterium isotope effect in transesterification of RNA models

• Published in: Journal of physical organic chemistry 2005-05, Vol.18 (5), p.385-397
• Main Authors: Virtanen, Noora, Polari, Lauri, Välilä, Maria, Mikkola, Satu
• Format: Article
• Language: English
• Subjects: phosphodiester bonds; RNA; solvent isotope effect; transesterification
• ISSN: 0894-3230; 1099-1395
• DOI: 10.1002/poc.883

2‐Methylbenzimidazole ribonucleoside arylphosphates (1a,b) and alkylphosphates (2a,b) were synthesized as RNA model compounds containing a minimised number of exchangeable protons. Intramolecular transesterification of these substrates was studied in H2O and D2O solutions over a wide pL range and apparent kinetic solvent deuterium isotope effects of the alkaline cleavage of both substrates and of the cleavage and isomerisation of 2a under neutral and acidic conditions were determined. The observed k H 2O/k D 2O of 4.9 obtained for the alkaline cleavage of the arylphosphate 1b can be primarily attributed to the ΔpK of the attacking nucleophile. The alkyl leaving group in 2a brings about an additional 1.5‐fold isotope effect (k H 2O/k D 2O of 7.1 observed), which, considering the pL–dependence of the reaction, can not be explained by a process involving a proton transfer. Differences in solvation of the transition state are tentatively suggested as a source of the difference. In contrast to alkaline cleavage, under neutral and acidic conditions the cleavage and isomerisation of 2a showed no apparent solvent isotope effect. Several examples found in the literature show that intramolecular proton transfer from phosphate to the leaving group in pre‐equilibria may not necessarily result in an observable solvent isotope effect. This may also explain the results obtained in the present work, since intramolecular proton transfer processes take place in transesterification reactions of 2a under neutral and acidic conditions. Relevance of the results obtained in the base catalysed cleavage to hammerhead ribozyme reaction is briefly discussed. Copyright © 2004 John Wiley & Sons, Ltd. Alkaline cleavage of nucleoside aryl and alkyl phosphates are characterized by a large apparent solvent isotope effect, whereas under acidic and neutral conditions no significant effects were observed.