Ethidium bromide

Ethidium bromide is a polyaromatic fluorescent small molecule and nucleic acid intercalator widely used as a stain in DNA and RNA electrophoresis. Upon intercalation into the hydrophobic region between nucleic acid base pairs, fluorescence-quenching water molecules associated to the Ethidium bromide structure are displaced and the bound Ethidium bromide then fluoresces very strongly compared to free Ethidium bromide (~25 fold increase in dsDNA). Intercalation distorts the ribonucleic acid structure and impedes natural DNA interactions, presenting a powerful mutagen effect associated with Ethidium bromide. This imposition on DNA structure also makes Ethidium bromide an inhibitor of DNA polymerase.