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).

Hope this helps, and good luck !

I would try:

20-50 mM HEPES pH 6.5-8.0

50-150 mM NaCl or KCl

0,1 - 2 mM MgCl2

TCEP/DTT/B-ME if necessary

tRNA or BSA to avoid nonspecific binding

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.

Hope you good luck!

Ok. Thanks.