Ethidium homodimer is generally used as a DNA stain for dead cells. Due the positive charge of ethidium bromide, it has low membrane permeability and can only penetrate a cell membrane after it is damaged. Once inside the cell, the dye then fluoresces upon binding to DNA.

Dihydroethidium, which is a reduced form of ethidium bromide, is commonly used an indicator for ROS (reactive oxygen species), mainly superoxide. Once within the cell, dihydroethidium, which initially has a blue color, fluoresces red when oxidized. Due to the dye’s affinity for DNA, the nucleus is stained red.