EtBr binds to SDS? - (Sep/30/2015 )
I came across to very strange thing while doing some experiment. I wanted to see if there is any nucleic acid , that is binding to my protein. I denatured protein with 4X loading dye and saw a very thick band on agarose gel. To rule out if the band is specific nucleic acid or some contamination, I loaded only dye and SDS on agarose gel. To my surprise I saw the same thick band in SDS . I thought may be the sds is not pure enough. Then I loaded ultrapure SDS from invitrogen on gel, but the band is still there . I don't understand, whats happening? Does EtBr binds to SDS? Please see the picture attached
SDS has a strong negative charge, EtBr positive, so it might be. How large or better small is the band? Such molecules should be very small (compared to macromolecules) and fast moving.
You should put some SDS and Etbr in a tube and see if it's similar strong fluorescing.
If not (and a larger band than the molecules should have) then perhaps other contaminants e.g. in loading dye or EtBr directly.
The band runs at very low molecular weight only. Refer to the gel picture I have attached. May be you are right that due to its high negative charge, SDS binds to EtBr. There should not be any contaminant in this SDS as I used the ultrapure one, which is used for mass spectrometry.