I want to perform a quantitative measurement of the binding of a protein( say X ) to DNA in three different experimental conditions. Will this help if I perform ChIP with a specific antibody against the protein X and then measure the CD spectra of the protein X bound to DNA in the three different samples??
CD spectra is used for examining the structure of proteins in solution. In proteins, the chromophores of interest include the peptide bond or aromatic amino acid side chains or disulphide bonds and also non-protein cofactors can absorb over a wide spectral range. So the secondary structure composition or tertiary structure fingerprint can be predicted. So you can perform the experiment with a proper control (i.e. in respect with DNA or protein). But I rather want to say that you should also perform the fluorescence experiment for knowing the binding affinity as well.
Ok I do not get this. What exactly do you want to accomplish. You want to do ChIP and then do CD. On what? Presumably you precipitate it (IP) how are you going to measure the CD of a precipitate?
CD CAN detect changes in DNA conformation and protein conformation if you have an interaction. In your case you have a lot of DNA present that is not affected by binding and also a lot of signal from the antibody.
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