Disappearing protein MWM marker - (Jan/12/2009 )
Hi, I'm having a bizarre problem. Running 6% gels with prestained MWM, 200V. The marker initially separates and I can see all the bands, but by the time the dye front reached the bottom of the gel, only the low MW bands are visible in the gel, and the high MW bands are gone!? When I saw this the first time i continued with the transfer and did a ponceau, which showed smears of protein in all the other lanes where it should be, but I could not detect my protein of interest with a western (and it is highly overexpressed and usually get very strong signal). I prepared fresh gels, checked Tris pH, made fresh running buffer, loaded more MWM, and still my marker disappears...?
It is my first western after the holiday so maybe something has gone off??
Thanks for any suggestions!
It is my first western after the holiday so maybe something has gone off??
Thanks for any suggestions!
Was is the size of your protein? 8% gel is already good enough to separate high MW proteins. A low % of gel will lead to smearing of the protein. Also your voltage might be too high, usually 120 to 150V should be okay (even for 10% gel). So your marker proteins are still there but smeared, the color become paler as you continue the run