DAPI (4′,6-Diamidino-2-Phenylindole, Dihydrochloride) is a nucleic acid stain that binds to A-T rich regions of DNA along the minor groove. DAPI is predominantly impermeant to live cells, allowing it to be used as a viability dye in unfixed cells to discriminate intact from membrane-compromised cells. Note, however, that high concentrations of the dye may still enter intact cells. Additionally, DAPI may be used to analyze DNA content in fixed cells, or as a nuclear counterstain in imaging or flow cytometry.

When bound to double-stranded DNA, DAPI has an excitation wavelength maximum of 358 nm and an emission maximum of 461 nm. DAPI is also well excited by the violet laser line (eg, 405 nm). Note that DAPI also binds RNA. Under these conditions, DAPI emits maximally at 500 nm, but with less intensity than when bound to double-stranded DNA.