Ethidium bromide (EtBr) is the most commonly used nucleic acid stain for PAGE or agarose gel electrophoresis. The fluorescence of EtBr increases 21-fold upon binding to double-stranded RNA and 25-fold on binding double-stranded DNA so that destaining the background is not necessary with a low stain concentration (10 μg/ml). Ethidium bromide has been used in a number of fluorimetric assays for nucleic acids. It has been shown to bind to single-stranded DNA (although not as strongly) and triple-stranded DNA. Because of its ability to bind to DNA, EtBr is an inhibitor of DNA polymerase.
Ethidium bromide intercalates double-stranded DNA and RNA and acts as a frameshift mutagen. It can also be used in conjunction with acridine orange to differentiate between viable, apoptotic and necrotic cells.
For staining a gel after electrophoresis, dilute a sample of the stock solution to 0.5 μg/ml with water and incubate the gel for 15-30 min. Destaining is usually not needed but can be carried out in water for 15 min if decreased background is necessary. The DNA bands can then be detected on a UV light box (254 nm wavelength). Ethidium bromide can also be incorporated into the gel and running buffer at 0.5 μg/ml and visualized immediately after electrophoresis.