problems with PCR from chIP material - double band PCR from chIP material (Oct/12/2006 )

Hi,
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!!

V

-veronicaalej-

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.

-pcrman-

QUOTE (pcrman @ Oct 18 2006, 09:42 PM)

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...
Thank you

-veronicaalej-