Acridine Orange hydrochloride is widely used in biological and medical research for its ability to fluoresce under specific wavelengths, making it a valuable tool for staining and microscopy. It is particularly effective in distinguishing between DNA and RNA in cells, as it binds to nucleic acids and emits different fluorescence colors—green for DNA and red for RNA. This property makes it useful for studying cell cycles, apoptosis, and the differentiation of cell types. Additionally, it is employed in microbiology to detect and analyze bacteria and other microorganisms, aiding in the identification of live and dead cells. Its application extends to flow cytometry, where it helps in sorting and analyzing cell populations based on nucleic acid content.