I want to check whether or not my protein binds to DNA. At this stage, I am not using any labeling. I want to see if there is any DNA-protein interaction. Please suggest the ideal binding buffer and conditions.
Sorry, but the "ideal binding buffer" for all of the DNA binding proteins doesn't exist, because it depends really on your particular protein. So as a first attempt to test DNA-protein interaction, I would advise you to use a buffer in which your protein behaves well (not aggregating...). Second, DNA-protein interactions is mostly driven by interactions with phosphates, and therefore you need to avoid having too much salt in your buffer if you don't want to break these interactions (ideally about 150mM NaCl, and not more than 300-400mM NaCl).
I agree with Yann-Vai, this universal buffer does not exist. But you can still try to start with 100-200 mM NaCl or KCl, 1 mM MgCl2, 0.1-0.5 mM EDTA, 1 mM DTT, 20 mM Hepes or 10 mM Tris for the binding buffer. Sometimes EGTA is also important for certain protein to bind to DNA. And oligo dT, salmon sperm DNA and BSA can be used for removing the nonspecific binding.