Will sonication occationally destroy an epitode (e.g Histone 3 dimethylated Lys - (Oct/21/2007 )
Will sonication occationally destroy an epitode (e.g Histone 3 dimethylated Lys 4) so that antibody can not recognize? And this explain why immunoprecipitation after sonication is not 100% pulling down every piece of target chromatin DNA? Thank you.
I would say formaldehyde fixation (over fixation) is more likely to mask the epitope than sonication breaking the histone tails.
if your protease inhibitors are not working properly you would get the same effect.