Nitromethane as a scavenger of acrylonitrile in the deprotection of synthetic oligonucleotides

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 NH₃. The 2-cyanoethylation of thymidine was inhibited effectively in the presence of nitromethane.