If I keep peptide constant, in what ratio should I add DNA for titration so that I can get a good plot for binding constant calculation?
It will depend on your binding constant. You need to perform a first "blind" titration to find out that. I would start at 0,5 micromolar peptide and DNA from 0 to 10, and then modify according to the shape of your curve.
There are a number of good references that describe the process:
[1] K. Hirose, J. Incl. Phenom. Macro. Chem. 2001, 39, 193–209.
[2] P. Thordarson, Chem. Soc. Rev. 2011, 40, 1305–1323.
[3] X. Qu, J. B. Chaires, Methods Enzymol. 2000, 321, 353–369.
We have done this with small molecules, the procedure is the same as with peptides
[1] M. I. Sánchez, O. Vazquez, J. Martinez-Costas, M. E. Vazquez, J. L. Mascareñas, Chem. Sci. 2012, 3, 2383–2387.
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