Do other people using the same electrophoresis rig experience the same problems, or is this something that only happens with your samples/buffers?

We started having issue like that with our poured gels. We tried out some precast gels and it fixed the problem. Is it possible one of the solutes used to make the gels has expired? When we were having issues we realized our APS was expired as well as a few other things. That could have unwanted effects.

Hi Caroline, the color of the leading edge tells me that there is a pH difference between samples. pH differences of samples will seriously screw up SDS-PAGE. The leading edge should be uniform blue, but there are yellow lanes.

Bromophenol blue is yellow below pH 5. You should have seen this when adding SDS sample buffer to your samples.

There are 2 quick ways of dealing with this 1) increase the pH of your samples. 2) process your samples with spin columns to get rid of the low pH buffer.

Hello Caroline,

The bands that run unevenly are yellow in color, which suggests that pH of some sample was incorrect. Your markers look fine so do the bands that retained blue front. When you mixed your samples with loading buffer and boiled, were they blue in color? or they turned to yellow during the electrophoresis?

If the dye front turned to yellow during the run, that suggests that glycine is degrading. However, because this phenomena is not uniform, I am ruling out the possibility that your buffers containing glycine have gone bad, though trying out freshly prepared buffers wont harm.

Another thing, trivial it may sound but just check for the presence of bubbles at the bottom of the gel that might have trapped between the gel and the buffer. Please make sure that there are no bubbles and the gel is uniformly in contact with the buffer.

I agree with the above comments.  The color yellow is an indication that the pH is to acidic. 

Best,

Evelyn

I also think that this is a result of nonoptimal pH in your setting (esp. buffers).