My question pertains to the generation of polyclonal antibodies from synthetic peptides, such as those provided by GenScript, for use in ChIP-Seq. I recognize a potential problem in submitting a single peptide for antibody generation: that the specific protein epitope recognized by the antibody and represented by the synthetic peptide will not be exposed after formaldehyde cross-linking of the protein-DNA complex. Would it therefore be possible to obtain a polyclonal antibody by inoculating rabbits with two synthetic peptides from the same protein, such that more than one epitope may be recognized by the antibody?
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I don't think the 2-peptide strategy will work because each of the peptide will be independently displayed by the immune system. I know of a few companies that are trying this approach (with a single peptide) and are having marginal success.
If you are married to using a peptide antigen, you may want to try raising a monoclonal so you can screen for the desired properties (recognizing DNA-bound protein). Here though, the major challenge is having target to use in your screening.
Another thought would be to try a genetic immunization approach (like SDI). I've never tried them, but it looks look on paper...
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