problems with PCR from chIP material - double band PCR from chIP material (Oct/12/2006 )
I'm looking for help about one intriguing subject. I'm performing chIPs assays using an specific pair of primers for a promoter region which give me a clear nice band when I use the input material for the PCR. I get the same nice band when I immunoprecipitate against one transcription factor, but when I immunoprecipitate against a different protein I get my band and a second band of approximately double size of my specific product! I'm trying to figure out how can it be possible and I don't find an answer, since the PCR seems to work fine and it doesn't seem to be a problem of the setup of the PCR reaction.
Thanks for your help in advance!!
Is it possible that your primers also bind to some other region of the genome which was co-ChIPed with the fragment of your interest? Try an in silco PCR search using your primer sequence.
Well, I wouldn't say that's the case, because in the input material I never see that band and the input is supposed to have every fragment of DNA. Yeah, and I also tried the virtual PCR and it only gave me one band...
So, the mistery remains...