Synthesis and hybridization properties of oligonucleotide perylene conjugates: influence of the conjugation parameters on triplex and duplex stabilities

We report here the synthesis of oligo-2'-deoxyribonucleotides (ODNs) conjugated with perylene. Introduction of perylene, coupled either directly or via a propyl linker to the anomeric position of a 2'-deoxyribose residue, induces the formation of two anomers. Single incorporations of each pure anomer of these sugar perylene units have been performed at either the 5'-end or an internal position of a pyrimidic pentadecamer. The binding properties of these modified ODNs with their single- and double-stranded DNA targets were studied by absorption spectroscopy. Double incorporations of the sugar perylene unit most efficient at stabilizing the triplex and duplex structures (the beta-anomer involving the propyl linker) have been performed at both the 5'-end and at an internal position (or both the 5'- and 3'-ends) of the ODN chain. Comparison has been made with ODN perylene conjugates involving either one or two perylenes attached via a longer polymethylene chain to either the 5'- or 3'- (or both the 5'- and 3'-) terminal phosphate groups. The ODNs involving two perylenes are more efficient at stabilizing the triplex and the duplex structures than the ODNs involving only one perylene and, among these, the ODN perylene conjugate involving two sugar perylene units attached at both termini is the most efficient. The results of the fluorescence studies have shown an important increase in the intensity of the fluorescent signal upon hybridization of the ODNs involving two perylenes with either the single- or the double-stranded targets. This increase in the intensity of the fluorescent signal could be used as proof of the hybridization.