Netropsin dihydrochloride is primarily used in molecular biology and biochemistry research due to its ability to bind selectively to the minor groove of DNA, particularly at AT-rich sequences. This property makes it a valuable tool for studying DNA structure and function. It is often employed in experiments to investigate DNA-protein interactions, as it can inhibit the binding of certain proteins to DNA by occupying specific sites. Additionally, it is used in chromatin research to explore the role of DNA conformation in gene regulation. Its application extends to the development of novel therapeutic agents, as its DNA-binding mechanism provides insights into designing molecules that can target specific DNA sequences for medical purposes.