Transesterification of an RNA model in buffer solutions in H2O and D2O

Abstract

AbstractTransesterification of a phosphodiester bond of RNA models has been studied in various buffer solutions, under neutral and slightly alkaline conditions in H2O and D2O. The results show that imidazole is the only buffer system where a clear buffer catalysis on the cleavage of a phosphodiester bond is observed. The rate enhancement in sulphonic acid buffers is smaller, and a sulphonate base, particularly, is inactive as a catalyst. The rate‐enhancing effect of imidazole is, however, catalytic, and the catalytic inactivity of sulphonate buffers can be attributed to their structure and/or charge. The catalysis by imidazole is a complex system which, in addition to first‐order reactions, involves a process that shows a second‐order dependence in imidazole concentration. The latter reaction becomes significant in acidic imidazole buffers (pH < pKa), as the buffer concentration increases. The kinetic solvent deuterium isotope effect kH/kD, referring to first‐order catalysis by imidazole base, is 2.3 ± 0.3. That referring to second‐order catalysis is most probably much larger, but an accurate value could not be obtained. Copyright © 2007 John Wiley & Sons, Ltd.