Acridine orange is a fluorescent dye that is cell-permeable and nucleic acid selective, which allows it to enter the cell and intercalate or bind with the nucleic acid present in an organism. On interaction with the nucleic acid, acridine orange fluoresces emitting different colors that enable researchers to differentiate cellular organelles. It emits green fluorescence when bound to double-stranded DNA and red fluorescence when bound to RNA or single-stranded DNA. 

Acridine orange is also cationic, enabling it to enter acidic compartments such as lysosomes, where it emits orange light in low pH conditions.