we add Etbr within the agarose gel but we do not add Etbr directly in native PAGE ?when we make agarose gel, we add Etbr before its solidification but we do not add Etbr when the native PAGE gel is in liquid form, why ?

  • $\begingroup$ The fact that EtBr is a potent mutagen is why it is not commonly used in liuquid solutions as it is hazardous. So this way it's in liuquid form for the least amount of time resulting in less human exposure. $\endgroup$ – Technetium Nov 27 '15 at 11:04
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    $\begingroup$ Perhaps EtBr inhibits the polymerization reaction (by absorbing, or quenching, the free radicals required to initiate the reaction)? That is just a guess. While some people prefer to stain, and then destain the gel afterwards, since the EtBr is positively charged you can just add some to the running buffer in the anode chamber and the dye will enter the gel. $\endgroup$ – mdperry Nov 27 '15 at 11:49
  • $\begingroup$ In the long PAGE runs, EtBr will run out of the gel. $\endgroup$ – WYSIWYG Nov 27 '15 at 14:55
  • $\begingroup$ Actually, my friend added EtBr to acrylamide solution and polymerized it. It was polymerized. In addition DNA was detectable. One of potential problems could be migration of EtBr opposite DNA. You could not detect DNA the bottom of gel unless you supply EtBr. And I guess a slight difference between gel and running buffer may cause shift of migration speed at the boundary. Because resolution in PAGE is higher than agarose, shift of migration speed might be problematic. $\endgroup$ – 243 Nov 28 '15 at 5:20

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