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[dgmashek]

I am using chemical cross-linkers to test if two proteins (each with unique epitope tags) are interacting. I am using DSS or BS3 cross-linkers added to cell homogenates transfected with my tagged protein. As I increase the concentration of my cross-linkers from 0 to 2 mM I see my protein band (~75kd )disappear. However, I do not see a concurrent increase in any larger bands! So where are my proteins going? I have stained the gel with Comassie and did see a slight increase in protein remaining in the well as I increase the concentration of cross-linker, but this is not always the case. Any help from someone with cross-linking experience would be greatly appreciated!!!

[guru]

This is probably due to polymerization of protein, which is common with homobifunctional crosslinkers like DSS or BS3.