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In a gel electrophoresis, let's assume an SDS-PAGE, I understand that the sample is loaded on a cuboidal well and the electric field is straight downward. It is easy to assume that the sample is going to run straight in the gel. Like it does here.

Image of an SDS-PAGE

But when I observed the apparatus in my lab, the anode was all throughout the base - looking something like this (cathode not shown here and the anode is insulated on the side - so effectively present at the base of the gel).

Schematic of apparatus electrodes

What makes the sample run in the gel only in a straight line? You may say that the forces cancel out on the either sides but what about the well that's at one end? It's being pulled downwards and also the other end.

So how does this work?

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  • $\begingroup$ It's a very good question and I have no idea what the answer is. The only thing is, I am just not sure whether it belongs here... Fundamentally this is a physics question about a biological technique. $\endgroup$
    – orthocresol
    Jun 25, 2016 at 23:04
  • $\begingroup$ Should it be migrated? since cross posting isnt allowed right? $\endgroup$
    – Polisetty
    Jun 25, 2016 at 23:16
  • $\begingroup$ Please don’t add electrochemistry to electrophoresis questions, since that tag is meant for chemical reactions occuring with the help of or to produce electricity. $\endgroup$
    – Jan
    Jun 25, 2016 at 23:30

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What you are trying to achieve in the electrophoresis experiment is a homogenous electric field. If the electric field points downward homogenously, then the greatest force will be exercised in a downwards direction which will lead to a downwards movement of your charged sample.

While not being exactly equivalent, you can show a similar feature (homogenous field) with a horseshoe magnet. If you place a piece of paper or cardboard over the top of it and then sprinkle iron filings onto that, they should arrange themselves in a linear fashion between the magnet’s poles.

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  • $\begingroup$ Oh right! Simple Gauss Law. Thanks :) High school physics. Now I understand why all that we learnt was important! $\endgroup$
    – Polisetty
    Jun 29, 2016 at 10:28
  • $\begingroup$ But still, wasn't that for an infinitely long charged wire? How do we manage to generate a homogenous field in this case? $\endgroup$
    – Polisetty
    Jun 29, 2016 at 10:29
  • $\begingroup$ @Polisetty It’s homogenous enough for the sake of the experiment ;) $\endgroup$
    – Jan
    Jun 29, 2016 at 12:20

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