Regarding to the protocol of pouring SDS-Polyacrylamide gels, at the step of "pour the acrylamide solution into the gap between the glass plates". We leave sufficient
space for the stacking gel (the length of the teeth of the comb plus 1 cm). Then we use a Pasteur pipette to overlay the acrylamide solution carefully with water, or 0.1% SDS (for gels containing ~8% acrylamide) or isobutanol (for gels containing ~10% acrylamide).
I just know the alcohol-overlaying, but I guess Water or SDS are for the same reason: When you pour a gel, the surface is bumpy and sometimes you have bubbles on the surface. After adding a bit of alcoholic solution, the bubbles are gone and the surface becomes even, the gel solidifies with an even surface. Due to different densities the alcohol will stay on top of your gel.
It's also a good idea to put some water in your isobutanol to saturate it, otherwise it will quickly evaporate.
Don't forget to remove the overlaying solution carefully (!) with a paper towel of rest of whatman paper before pouring the stacking gel, otherwise it might disturb your run.
The purpose of 0.1% SDS and isobutanol is to create an anaerobic environment to allow the gel to polymerize. Oxygen radicals inhibit acrylamide polymerization (the reason for adding ammonium persulfate to the mix). I've seen protocols using 0.1% SDS for gels with 8% acrylamide and isobutanol for gels of 10% acrylamide. I don't really understand why. I've used a 1:1 isobutanol:water mixture irrespective of acrylamide percentage and it always worked.
Khalil Ardat, yes I also did but no different. I just worry if there is something related to molecular weight of the solution. thank you
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