Quinacrine mustard dihydrochloride is primarily used in research applications, particularly in the field of molecular biology and genetics. It is known for its ability to bind to DNA, making it a useful tool in studies involving chromosome staining and fluorescence microscopy. Researchers utilize it to visualize and analyze chromosomal structures, aiding in the identification of genetic abnormalities and the study of chromosomal behavior during cell division. Additionally, it has been explored for its potential in studying mutagenesis and DNA repair mechanisms due to its DNA-binding properties. While its use in clinical applications is limited, it remains a valuable compound in laboratory settings for advancing genetic and biochemical research.