Patent ID: 6858715

Claim:
A method for deprotecting a phosphate-linked oligonucleotide, said oligonucleotide having a plurality of protected phosphorus linkages of formula: wherein: each X is O or S; R t is a phosphorus protecting group of the formula: —C(R 10 ) 2 —C(R 10 ) 2 —W or —C(R 10 ) 2 —(CH═CH) P —C(R 10 ) 2 —W each R 10 is independently H or lower alkyl; W is an electron withdrawing group; p is 1 or 3; comprising: providing a sample containing a plurality of said phosphate linked oligonucleotides; and contacting said oligonucleotides with a deprotecting reagent for a time and under conditions sufficient to remove substantially all of said R 1 groups from said oligonucleotides to form a plurality of deprotected oligomers, said deprotecting reagent containing at least one aliphatic amine, the conjugate acid of said amine having a pKa of from about 8 to about 11, said deprotecting reagent further comprises a scavenger, wherein said scavenger is a purine, a pyrimidine, inosine, a pyrrole, an imidazole, a triazole, a mercaptam, a beta amino thiol, a phosphine, a phosphite, a diene, urea, a thiourea, an amide, an imide, a cyclic imide, a ketone, a polymer having free thiol groups, or a polymer having free amino groups; said deprotecting reagent optionally further comprising one or more solvents selected from the group consisting of aliphatic, haloaliphatic, cyanoaliphatic, aromatic and alkylaromatic solvents.