Oligos bearing the 6-chloro-2-methoxyacridine molecule at either terminus or within their sequence have the ability to intercalate efficiently into a double helix. Covalent binding of MeO-Cl-Acridine therefore increases hybrid stability by providing additional binding energy. Acridine-labelled oligos can thus be used in applications where increased stability of oligonucleotide hybrids is crucial. Adding the dye to the 3’terminus also protects the oligo from exonuclease degradation.
These oligos also possess the ability to form triplex helices, and, due to their relative hydrophobicity, to pass through membranes more easily than unmodified oligonucleotides.