Cell biology 

Ethidium monoazide bromide (EMA) is a fluorescent nucleic acid stain with a photoaffinity label. The dye, after photolysis, binds covalently to nucleic acids.The dye has been used to footprint drug binding sites on DNA, to modify plasmid DNA and for labeling yeast cells for leukocyte phagocytosis assays. A particularly useful application of the dye is to label dead cells in a mixed population of live and dead cells. Because EMA is relatively impermeant to live cells, it selectively binds DNA in dead cells. Photolysis renders the dead cell DNA covalently labeled with the dye. One can then wash and fix the cell preparation for analysis by microscopy, fluorescence plate reader or flow cytometry. The major advantage of this method is that researchers can avoid extensive manipulation of live pathogenic organisms.

EMA has been used to differentiate between viable and dead bacteria by 5′-nuclease PCR.

• Ex (pH 3) = 458 nm
• λ_Ex/λ_Em (after photocrosslinking to nucleic acid) = 510/600 nm
• Orange solid soluble in DMF, or ethanol
• Store desiccated at 4^oC or -20^oC and protect from light, especially in solution
• C₂₁H₁₈BrN₅
• MW: 420