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Transesterification of an RNA model in buffer solutions in H 2 O and D 2 O
Author(s) -
Virtanen Noora,
Nevalainen Ville,
Lehtinen Taru,
Mikkola Satu
Publication year - 2007
Publication title -
journal of physical organic chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.325
H-Index - 66
eISSN - 1099-1395
pISSN - 0894-3230
DOI - 10.1002/poc.1130
Subject(s) - chemistry , phosphodiester bond , imidazole , catalysis , transesterification , medicinal chemistry , kinetic isotope effect , solvent , base (topology) , deuterium , inorganic chemistry , stereochemistry , organic chemistry , rna , biochemistry , physics , quantum mechanics , gene , mathematical analysis , mathematics
Transesterification of a phosphodiester bond of RNA models has been studied in various buffer solutions, under neutral and slightly alkaline conditions in H 2 O and D 2 O. 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 < p K a ), as the buffer concentration increases. The kinetic solvent deuterium isotope effect k H / k D , 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.