I have performed EMSA on 2% agarose in 0.25 TBE. I can not rid of some unspecific band which is present in whole gel but much stronger in 2 and 3 lanes and its not a shit (shift is on the top of 2 lane). 1 lane is a control of labelled DNA, 2 lane is a DNA plus protein and 3 lane is a DNA labelled and unlabelled (300 times more than labelled) plus protein. I used labelled DNA after gel elution to get rid of HEX-labelled primers but nothing changed. In the kit that I use is also poly dI-dC which may interact with some reagents however its not an explenation why the band is present everywhere. I am attaching the photo of the gel.
Check this link..it may be helpful.
https://www.sciencedirect.com/science/article/pii/S1056871910000456
If you have seen the non specific band in all wells even the one you didn't load anything in it, that suggests that you have a contamination which could be from preparing the gel or running buffer. Good luck
There seems to be a faint band visible all across the gel which makes me think that something is moving up the gel and stopping the sample from moving through the gel , One possibility for this is that the buffer has become depleted during electrophoresis and the pH of the buffer and hence the in the gel has changed and will not allow movement of dna so it all ends up in the same place looking like a band. If you think this might be the case then make up new buffer and check its concentration and pH. If the result happens again check the pH of the buffer after the run to make sure it has not changed too much
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