I am doing SDS-PAGE using an 8% resolving gel and 5% stacking gel with a Tris-glycine running buffer. During electrophoresis, I get a smeared/tailing dye front which is totally opposite with the dye front we observe everytime we run Native-PAGE. Any suggestion on what causes this and any recommendation so that we can fix this problem? I have included an image of the dye front.
SDS-PAGE electrophoresis relies on a discontinuous buffer system where the ionic strength and pH of the different buffers (electrode, stacking gel, lower gel and sample buffer have to be matched correctly. Asssuming that you followed the established recipe correctly (Lämmli 1970. Nature 227,680-685), your gels should run fine, unless your samples are grossly off the mark with respect to pH and salt concentration. Something to be aware of is that SDS can decompose, particularly if heated for too long and generate sulfuric acid monosodium salt, which could alter the pH of the sample buffer.
However, I wouldn't worry too much about the smearing of the tracking dye, as long as the protein pattern looks fine after staining the gel.
Did you use some detergents in sample buffer like SDS and DTT or 2-mercapthoethanol?
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