I have recently purchased a new electrophoresis unit. On electrophoresis in 1 and 2% agarose, gel bands of same size on the electrode side move slowly giving the whole thing a slanting look. The unit had been properly leveled before. Can any body tell me the reason for that?
A picture would help. Are you seeing a "smile" - both sides slanting up, even in the middle ? Are you running samples with high salt in the samples (eg ppted DNA). Overloading can cause a problem. Make sure the electrodes are well covered if using a min-gel. Running a gel at too high a voltage can sometimes cause problems with resolution.
Thanks Ian. No, I am not seeing a smile. The left side of the gel is slanting down while right side is slanting up just like a staircase. The gel is run at 100V. Other parameters will be taken care of and then I will come back to you.
Sure sounds like you're not getting current flowing equally from all points at the "top" and "bottom". A picture really would help - does this unit have a wire or bar of exposed metal that "extends" the electrodes so that they run the full width of the apparatus? If the electrode simply go into the buffer on one side, you'll definitely get a stronger current flow on the side containing the electrodes - the charge needs to be distributed equally.
The electrodes in my mini gel which go into the buffer on one side were not fully covered by the buffer. Covering the buffer has helped but to be fully sure that this is the cause, I will repeat my experiment few more times.
Thank you all for your suggestions.
Oh, that would definitely cause what you are seeing!!! That seems like a bad design - the electrode should always be lower than the "top" of the gel so that it enforces full coverage. What brand/model is that unit?
Covering the electrodes with buffer has not helped much. Any other way to rectify the problem?
I agree, picture would really help. If electrodes are fully covered with buffer, and you can actually "see" the current as small bubbles running, I can suggest checking 1st if agarose tray is placed horizontally and if there is any source of heat/cold near the tray during polymerization process. This can cause unequal agarose net and difference in fragments' speed. Temperature can also cause this kind of problem, when you have a heat/cold source near the unit. Simply touch the unit while running to see if the temperature on both sides of the unit is equal. You should check the reagents too; buffer, ddH2O...
And that brings up another question - is the gel covered entirely with buffer - are the ends fully exposed to the buffer or is something blocking them? Gulnaz, take a photo of the apparatus and post it if you can; we'd need to see the electrodes and the gel itself....
I am sending the photo of the apparatus and the gel picture as an attachment.
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