I am running hand cast 12% bis-tris gels using MES buffer (novex formulations) at 100v. Every so often, towards the end of the run I notice a warping of the gel at the bottom corners which progresses upwards and distorts the migration of bands running towards the bottom. It's not a problem as long as I stop the gel in time, but if i let it run to the bottom it ruins the run.
Sometimes the running buffer is cold, sometimes RT. I have run on ice, I have run at higher and lower voltages and always with fresh running buffer. The amps are not doing anything funny from run to run. Gels from the same batch are not consistent with regards to warping, some do, some don't. Storing gels in the refrigerator (in heat sealed pouches with some buffer and sodium azide) for a few days or using them immediately has no affect on whether the gel warps or not. It is completely by a roll of the dice whether or not the gel will do this.
The only thing that I notice is that it begins at the very bottom of the gel, progressing upwards from the exact place where the foot of the core assembly of my mini-protean gel box holds the gel on both sides. If you look at this assembly the feet have been hollowed out to allow for maximum buffer exposure so as not to block off any current etc. Is it possible that this space is becoming acidic during the run? It seems as though some ions are actually migrating upwards causing these warped areas. In fact when the blue dye front reaches a warped area it turns yellow indicating a pH drop. What the heck is causing this? Has anyone else noticed this ever or is my gel box simply possessed?
Hm. I saw this in tris-glycine-sds system (home-made), with a completly new internal part. 13.5% hand-made gels. Two, but only one showed the things during the same run. Thanks to you, i stopped the run. I have no idea about it.
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