Characterization of high molecular weight impurities in synthetic phosphorothioate oligonucleotides

Phosphorothioate oligonucleotides manufactured by standard phosphoramidite techniques using nucleoside-loaded supports contain high molecular weight impurities of the type shown. These impurities are avoided if a novel universal solid support is used. Phosphorothioate oligonucleotides manufactured by standard phosphoramidite techniques using 2′-deoxyadenosine- or 2′- O-(2-methoxyethyl)-5-methylcytosine-loaded solid supports contain branched impurities consisting of two chains linked through the exocyclic amino group of the 3′-terminal nucleoside of one chain and the 3′-terminal hydroxyl group of another via a P(O)SH group. These impurities are not produced when a universal, non-nucleoside derivatized support is used.