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I have been layering my running SDS-PAGE gels with water-saturated
isobutanol for the last 15 years, I never had problems. I guess the trick
is not to add too much, I would just add 500ul for a regular 30-35ml gel
and wash it thorougly with deionized water after polymerization. It is a
good practice to wipe off the extra droplets of water before making the
stacking gel. Isopropyl may serve as a good alternative.
If anybody has problems with running their gels I would be more than happy
to run their samples--let's talk.