Abstract
A novel deprotection procedure for synthetic oligonucleotides was developed to prevent nucleobase alkylation. Acrylonitrile, a side product of the deprotection of a 2-cyanoethyl phosphate protecting group and which causes nucleobase alkylation, was found to be trapped by the addition of some acidic compounds, which generate a carbanion species under the conventional deprotection conditions using aqueous NH 3. The 2-cyanoethylation of thymidine was inhibited effectively in the presence of nitromethane.
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