Synthesis and Binding Properties of Oligonucleotides Covalently Linked to an Acridine Derivative: New Study of the Influence of the Dye Attachment Site

2-Methoxy-6-chloro-9-aminoacridine has been coupled via a polymethylene linker to various positions of an oligonucleotide chain:  the 3‘-position, using a new universal support, the 5‘-position, and both 5‘- and 3‘-positions via a phosphate. The intercalating agent was also linked to the oligonucleotide chain via an internucleotide phosphorothiolate. The mixture of diastereoisomers was obtained as well as each pure Rp and Sp isomer. Finally, the acridine moiety was introduced to the 5-position of the deoxyuridine. The binding properties of these oligonucleotide−acridine conjugates with their DNA counterparts have been studied by absorption spectroscopy.