"Phantom" GFP bands - (Nov/08/2006 )
Has anyone ever run across the problem of "phantom" GFP bands appearing in an agarose gel? I have cut a plasmid with 2 different sets of enzymes, and both times there appeared a faint band at about 500 bp. My boss says that he has come across this before, and it is some sort of enigma associated with fluorescent protein vectors
Do you work with the Clontech pEGFPC vector? If you do, I know exactly what you're talking about. The mysterious band is always there no matter what. Good news is that this band does not affect the cloning or GFP-tagged protein expression. We weren't able to figure out neither its meaning nor origin (my friend was even trying to sequence this little bastard - no luck though). Right now I work with the same backbone vector but instead of GFP I have monomeric YFP (we simply exchanged the colors) and the band is not there, so it has to be somehow related to EGFP sequence. I suppose.
Good luck with your experiments.
Yep, that's the vector!
Good luck with your stuff too.