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Novel bis-acridine orange (1) was synthesized from Fmoc-Lys(Boc)-OH and Fmoc-Lys(AO)-OH (AO: acridine orange), with the 9-position of acridine orange (AO) linked to the epsilon-amino moiety of lysine, on the peptide synthesizer. Bis-acridine orange (1) yielded a very weak fluorescence in an aqueous media due to the intramolecular stacking, but its fluorescence was enhanced over 200-times upon binding to double-stranded DNA, irrespective of the DNA sequences. Circular dichroism (CD) spectra showed that 1 binds to double stranded DNA in its stacked conformation, concomitant with fluorescence enhancement.

Fluoreometric behavior of a novel bis-acridine orange bound to double stranded DNA