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AAT Bioquest

What reagents are used in agarose gel electrophoresis?

Posted July 17, 2024


Answer

Reagents used in agarose gel electrophoresis include: 

Ethidium Bromide (EtBr)
Ethidium bromide (EtBr) is the most widely used reagent for dyeing DNA in agarose gels. EtBr is an intercalating dye that binds to DNA and fluoresces under UV light. On binding to DNA, EtBr fluoresces orange, enabling researchers to visualize the DNA, which otherwise invisible to the naked eye. 

Because ethidium bromide binds to DNA in a concentration-dependent manner, the intensity of the bands increases with higher DNA concentrations, enabling estimation of DNA quantity based on band intensity. 

Buffer

Buffer facilitates the flow of electric current through the gel. The buffer used in agarose gel electrophoresis may be either TBE (Tris/Boric acid/EDTA) or TAE (Tris/Acetic acid/EDTA).

Tracking Dye

The sample is mixed with a tracking dye, such as xylene cyanol, orange dye, or bromophenol blue. Tracking dyes enhance the visibility of the loaded sample. They also act as markers for the progress of electrophoresis.

Additional resources

The effect of ethidium bromide on mobility of DNA fragments in agarose gel electrophoresis

Gel Electrophoresis

Helixyte™ Green Nucleic Acid Gel Stain *10,000X DMSO Solution*

Gel Electrophoresis Annotator