A vital tool of the molecular biologist and geneticist, ethidium bromide (EtBr) is used to stain DNA molecules in procedures such as polyacrylamide gel electrophoresis (PAGE) and southern blotting. EtBr molecules are flat and have similar dimensions to the purine-pyrimidine base pairs found in DNA - i.e. the C-G and A-T pairs that form the "rungs of the ladder" of a DNA molecule. This structure allows the EtBr molecules to intercalate between the base pairs (the "rungs").



        
        H    H          H    H
        |    |          |    |
        C == C          C == C
       /      \        /      \       
      /        \      /        \     
H2N--C          C -- C         C --NH2
      \\      //      \\      //     
       \\    //        \\    //       
        C -- C          C -- C
        |     \        /     |
        H      \     +/      H
                C == N   Br-
        H      /      \ 
        |     /        \
        C -- C          C2H5
      //      \\        
     //        \\       
  H--C          C--H
      \        /
       \      /
        C == C
        |    |
        H    H

The chemical structure of Ethidium Bromide, a charged polycyclic aromatic compound.

Upon binding to DNA an increase in fluorescence under UV light is observed. This increase in fluorescence allows the detection of molecules of DNA when placed under a UV light source. So when a scientist separates DNA molecules by electrophoresis (which uses an electric current to pull molecules through a gel in which different sizes of molecule will travel at different speeds) the gel is first stained with EtBr so that DNA can be detected in the gel afterwards. Forgetting to add EtBr to your gel can potentially ruin your experiment as certain people have and most probably shall learn through experience.

This molecule is not without its downsides though. EtBr is a potent carcinogen due to its ability to intercalate into DNA molecules and thus disrupt DNA replication which in turn can cause mutations involving the insertion of a nucleotide at points at which it intercalates. As such it must not be allowed to contact skin and is generally treated with great respect in laboratories in which it is used. A certain amount of trust is required in your colleagues in the hope that they clean equipment properly after use and don't use gloves that may have contacted EtBr to open doors, use computers, or touch any other such communal equipment. Even so, I do find myself in paranoid moments checking for new growths on my skin...


References:

Voet D, Voet J G Biochemistry (2nd edition), John Wiley & Sons, Inc., 1995.

Turner P C et al., Instant Notes in Molecular Biology, Bios Scientific Publishers Ltd., 2000

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