Synthesis of a new photoisomerizable linker for connecting two oligonucleotide segments

Synthesis of a photoisomerizable linker containing an azobenzene unit for connecting oligonucleotide segments has been described 4,4'-Azobenzene dicarbonyl chloride was converted to the fully protected diol by treatment with the O-sily protected aminopentanol. Partial deprotection of the silyl group afforded the monoprotected diol, which was protected by a dimethoxytrityl group. Then the remaining silyl protecting group was removed to afford the alcohol. The hydroxy function was converted to the phosphoramidite. The amidite can be used for joining two oligonucleotides via the 5'-terminal hydroxyl group of one oligomer and the 3'-terminal oxygen of the other.