Excessive foaming during electrophoresis

Hi all! We’ve been trying to run electrophoresis but are facing up some challenges. We use roughly the same set up (same chamber size, same electrodes size, shape and distance between them) with perfusion pump fluid circulation (ETC buffer temp started 37C after some time reached 50C). We do not have a power supply that would give us more than 150 mA. With this amperage the maximum voltage we can set is around 7-8V. Not too much. We use Hoefer SX250 Power Supply (max amp is 200 mV). We run electrophoresis for around 5 days and the brain just started to be a bit transparent and swollen. Yet this is not the biggest concern as with this value we observe quite decent electrophoresis. Too decent I would say – our chamber is full of bubbles. SDS foams like mad. We had to make some hole in chamber cover so as to release some gas. Still, we cannot leave apparatus for too long on as the foam is getting too abundant. We checked the buffer (pH, also did two separate buffers) and it seems it is not a problem. Then what? Do you have any suggestions? Also, as per electrophoresis condition, what seems to be the problem when comes to max voltage we can get? Thanks in advance for your feedback and suggestions


  • The best suggestion I could give you : don't use a perfusion pump ! Those are too slow, and can't clear the chamber fast enough. You will have the temperature building up in the chamber as well, as you noticed. Try a faster pump (eg aquarium pump?), you want to have around 5 L/min of flow.
  • marzenamarzena Posts: 3
    Thank you. That's one of the options we took into consideration. It seems the flow is indeed too low.
  • I use a flow rate of about 150 ml/min, which clears the bubbles well. I tried a couple perfusion pumps in the lab and they only ran at 25-50 ml/min. The chamber became too hot and cooked my brain.
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