Selective phosphate protection: a novel synthesis of double-labeled oligonucleotides

[structure: see text] A novel, selective labeling of oligonucleotides with two different reporter groups is described. The oligonucleotide is synthesized using a stable 2-(4-methoxybenzamido)ethyl protection for a selected internucleosidic thiophosphate (PS) and a labile 2-(N-isopropyl-4-methoxybenzamido)ethyl for the 3'-terminal PS and internucleosidic phosphates. The latter group and the base protection are removed, and the 3'-terminal PS is labeled. The former protection is then cleaved by a prolonged ammonolysis, and the second reporter is introduced at the internucleosidic PS.