The present invention discloses novel methods for the synthesis of
oligonucleotides with nucleoside phosphoramidites on solid supports. The
methods comprise the stepwise chain assembly of oligonucleotides on
supports with 5'-acyl phosphoramidites. The synthesis cycles consist of a
front end deprotection step which is conducted with a solution of a
primary amine or a phenolate, a phosphoramidite coupling step with a
5'-acyl nucleoside phosphoramidite in the presence of an activator, a
phosphite oxidation step and an optional capping step. The novel methods
improve the quality of synthetic oligonucleotides due to the
irreversibility of the front end deprotection step, which prevents the
formation of deletion sequences, and due to the avoidance of acidic
reagents in the synthesis cycles, which prevent the formation of
depurination side products. The invention further discloses novel
nucleoside phosphoramidite compositions wherein the phosphoramidites
carry acyl front end protective groups which are cleavable with primary
amines or phenolates. The invention is applicable to the synthesis of
oligodeoxyribonucleotides, oligoribonucleotides and oligonucleotides with
modifications in their sugar or phosphate groups.