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Updated: Oct 4, 2026

Chemical Triphosphorylation of Oligonucleotides
Published on: June 2, 2022
Quinone methide phosphodiester alkylations under aqueous conditions
1Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
Abstract:
A detailed analysis of the alkylation of phosphodiesters with a p-quinone methide under aqueous conditions has been accomplished. The relative rates of phosphodiester alkylation and hydrolysis have been examined by (1)H NMR analysis of the reaction of 2,6-dimethyl-p-quinone methide in a buffered diethyl phosphate/acetonitrile solution (1:9 v/v, pH 4.0). The rate of hydrolysis of the quinone methide was confirmed by UV analysis in 28.5% solutions of aqueous inorganic phosphate in acetonitrile at pH 4.0 and 7.0. Similarly, the rate of phosphodiester alkylations by the quinone methide was also confirmed by UV analysis in 28.5% solutions of aqueous dibenzyl, dibutyl, or diethyl phosphate in acetonitrile at pH 4.0 and 7.0. These kinetic studies further establish that the phosphodiester alkylation reactions are acid-catalyzed, second-order processes. The rate constant for phosphodiester alkylation was found to range from approximately 370-3700 times the rate constant of quinone methide hydrolysis with diethyl and dibenzyl phosphate, respectively (pH 4.0, 28.5% aqueous acetonitrile).
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