Ethidium bromide

Biological Activity

Ethidium bromide is an embedded dye used for fluorescent labeling (nucleic acid staining) in molecular biology laboratory science, such as agarose gel electrophoresis. 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. 

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. 

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.

Chemical Information

Molecular Weight	394.32
Formula	C21H20BrN3
CAS Number	1239-45-8
Form	Solid
Solubility (25°C)	H2O ≥ 100 mg/mL DMSO 25 mg/mL
Storage	4°C, protect from light, dry, sealed

References

[1] Rodrigo Galindo-Murillo et al. Nucleic Acids Res. Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations

[2] En Xie et al. Chemosphere. Mechanisms and pathways of ethidium bromide Fenton-like degradation by reusable magnetic nanocatalysts

[3] Ali Fakhri. Ecotoxicol Environ Saf. Assessment of Ethidium bromide and Ethidium monoazide bromide removal from aqueous matrices by adsorption on cupric oxide nanoparticles

[4] Alexey Petrov et al. Methods Enzymol. RNA purification by preparative polyacrylamide gel electrophoresis

[5] J Sigmon et al. Electrophoresis. The effect of ethidium bromide on mobility of DNA fragments in agarose gel electrophoresis