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Ethidium Bromide is also used during DNA fragment separation by agarose gel electrophoresis. It is added to running buffer and binds by intercalating between DNA base pairs. When the agarose gel is illuminated using UV light, DNA bands become visible. Intercalation of EtBr can alter properties of the DNA molecule, such as charge, weight, conformation, and flexibility. Since the mobilities of DNA molecules through the agarose gel are measured relative to a molecular weight standard, the effects of EtBr can be critical to determining the sizes of molecules.

Sigmon, J. and Larcom, L. L. (1996), The effect of ethidium bromide on mobility of DNA fragments in agarose gel electrophoresis. ELECTROPHORESIS, 17: 1524–1527. doi:10.1002/elps.1150171003