Bubbles on the marker after transfer - (Feb/17/2011 )
I was running 4% SDS-PAGE BT gel. The marker that I used, developed spots on it after transfer. It looks as if the air bubbles were not removed properly but I had ensured that it has been removed before transfer. Also, the marker I used was frozen at -20C. I guess it was not thawed properly. I do not know if that is the reason. Please help!!
Did you use a prestained MWM? If so, were the "air bubbles" seen within the marker prior to transfer. If they weren't, my thought would be air bubbles somewhere in the western device. Sometimes very small bubbles remain that are not easily seen and cause major problems for transfer. My suggestion would be to repeat with a Prestained MWM paying particular attention to smoothing out all of the air bubbles from between the gels and the membrane.
I don't think it is a freeze/thaw situation with your MWM. I would only consider this if you saw the "air bubbles" within the marker prior to transfer.
Hope this helps.
Thanks for your reply. I would know the result today. I hope it has affected just the marker and not my samples.