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Alkylation of the N3-position of thymidine by acrylnitrile, which is liberated during ß-elimination of the cyanoethyl group from the phosphates, is a well-known side reaction during simultaneous cleavage of the protecting groups and the oligonucleotide from the support.
This side reaction can be avoided by use of diethylamine or t-butylamine in acetonitrile for the ß-elimination. The oligonucleotide is subsequently cleaved from the support using any standard cleavage conditions.
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