A process for preparing phosphorothioate oligonucleotides utilizes S-(alkaryl or aryl) phosphorothioate compounds as intermediates suitable for use in the solution phase. A dinucleotide is prepared from a nucleoside intermediate that has been phosphitylated with an S-(alkaryl or aryl) alkyl phosphorothioate diester salt. The alkyl ester group is removed and the resulting nucleotide diester is reacted with a further nucleoside having a free 5'-hydroxyl group. Nucleotide units are linked together to yield compounds of the structure: ##STR1## where X is H, a first blocking group, a nucleoside, a nucleotide or an oligonucleotide; Y is H, a second blocking group, a nucleoside, a nucleotide or an oligonucleotide; R is an alkaryl or aryl group; n is an integer greater than 0; and Bx is a heterocyclic base. Deblocking of the S-alkaryl or S-aryl moiety yields a phosphorothioate oligonucleotide.