Chemical. CAS 65-61-2. Formula C17H19N3 . HCl. MW 301.81. Acridine Orange hydrochloride salt is a cell-permeable metachromatic fluorescent dye that stains DNA and RNA. It is used as a nucleic acid-selective fluorescent cationic dye useful for cell cycle determination and staining dead cells. Being cell-permeable, it interacts with DNA and RNA by intercalation or electrostatic attractions respectively. When bound to DNA, it is very similar spectrally to fluorescein, with an excitation maximum at 502nm and an emission maximum at 525nm green. When acridine orange associates with RNA, the excitation maximum shifts to 460nm blue, and the emission maximum shifts to 650nm red. Acridine orange will also enter acidic compartments such as lysosomes where it becomes protonated and sequestered. At low pH inside the organelles, it will emit an orange fluorescence peak at 590nm and for optimal endosome visualization a blue light excitation 475nm is used.