Abstract
The (2-acetoxyphenoxy)ethyl (APOE) group could be an alternative to the conventional 2-cyanoethyl group for phosphate protection in solid-phase oligonucleotide synthesis to circumvent DNA alkylation by acrylonitrile generated under basic condition. This group is stable during oligonucleotide synthesis and can be removed under mild conditions using aqueous ammonium hydroxide. Multiple phosphorothioate oligodeoxyribonucleotides and 2‘-O-methoxyethyl-modified oligoribonucleotide chimera were synthesized and characterized extensively. The deprotection of this group follows an intramolecular attack on the α-carbon adjacent to phosphate oxygen to liberate the oligonucleotide and an innocuous cyclic ether as side product. No modification of nucleobases was observed during deprotection of this group.
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