Microwave assisted rapid deprotection of oligodeoxyribonucleotides

Abstract

A novel method for the deprotection of oligodeoxyribonucleotides under microwave irradiation has been developed. The oligodeoxynucleotides having base labile, phenoxyacetyl (pac), protection for exocyclic amino functions were fully deprotected in 0.2 M sodium hydroxide (methanol:water :: 1:1, v/v) = A and 1 M sodium hydroxide (methanol:water :: 1:1, v/v) = B using microwaves in 4 and 2 min, respectively. The deprotection of oligodeoxyribonucleotides carrying conventional protecting groups, dA(bz), dC(bz) and dG(pac), for exocyclic amino functions was achieved in 4 min in B without any side product formation. The deprotected oligonucleotides were compared with the oligomers deprotected using standard deprotection conditions (29% aq. ammonia, 16 h, 55°C) with respect to their retention time on HPLC and biological activity.