The final deprotection step in oligonucleotide synthesis is reduced to a mild and rapid ammonia treatment by using labile base-protecting groups.
Phenoxyacetyl (pac) and methoxyacetyl (mac) for adenine and guanine, isobutyryl for cytosine, were successfully applied as amino protecting groups both in phosphotriester and phosphoramidite approaches. As shown by N.M.R. and H.P.L.C. analysis, they are completely deblocked in less than four hours in 29% ammonia at room temperature allowing the preparation of modified DNA containing alkali labile bases such as saturated pyrimidines. The stability of N6-phenoxyacetyl-deoxyadenosine versus depurination in acidic conditions used in the detritylation step was favorably compared with that of the classic N6-benzoyl protected adenine.
D000641:Ammonia; D002851:Chromatography, High Pressure Liquid; D007202:Indicators and Reagents; D009682:Magnetic Resonance Spectroscopy; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis*
D007202:Indicators and Reagents; D009838:Oligodeoxyribonucleotides; D000641:Ammonia