Synthesis and binding properties of perylene-oligo-2′-deoxyribonucleotide conjugates

Perylene has been covalently linked, via polymethylene tethers, to the 5′- and the 3′-ends of an oligopyrimidine sequence. The presence of the polycyclic ligand stabilizes the duplexes and the triplexes formed by the modified oligonucleotides and their single- and double-stranded DNA targets as compared to those formed with the parent unmodified oligonucleotide used as reference. Stabilization of the triplex is at its highest when perylene is linked to the 5′-end of the oligonucleotide via a nine-atom size linker. Stabilization of the duplexes is nearly equivalent whatever the position of the substitution (5′ or 3′) and the linker size used to tether both entities.