ethidium

Ethidium, commonly encountered as ethidium bromide, is a fluorescent dye used in molecular biology as a DNA intercalator. It is a phenanthridinium salt that becomes highly fluorescent when bound between base pairs. In solution it has weak fluorescence, but DNA-bound ethidium emits a bright orange-red light when excited by ultraviolet or blue light.

In agarose gel electrophoresis, gels are stained with dilute ethidium bromide so that DNA fragments fluoresce under UV transilluminators or blue-light devices, enabling visualization of migration patterns. It is valued for simplicity, speed, and cost, though sensitivity is comparable to other dyes.

Ethidium bromide is mutagenic and hazardous. It should be handled with gloves, eye protection, and in a well-ventilated area or fume hood. Spills should be cleaned with proper absorbent materials and sodium hypochlorite; waste is treated as hazardous chemical waste.

Because of safety concerns, several non-mutagenic alternatives have been developed, such as SYBR Safe and GelRed. These dyes may require different imaging settings. Ethidium bromide waste requires institutional disposal according to local regulations; solutions can be decontaminated before disposal.

Ethidium bromide commonly appears as the bromide salt; standard stock solutions are water-based and stored away from light.