Chromomycin A₃ is primarily used in molecular biology and cytogenetics as a fluorescent dye for staining DNA. It binds specifically to GC-rich regions of DNA, making it a valuable tool for chromosome banding techniques, such as G-banding, which helps in identifying chromosomal abnormalities and studying genetic disorders. Additionally, it has been explored for its potential in cancer research due to its ability to inhibit RNA synthesis by interacting with DNA, showing promise as an antitumor agent. Its fluorescent properties also make it useful in flow cytometry and fluorescence microscopy for analyzing cellular DNA content and studying cell cycle dynamics.