DNA-Protein interactions

How to perform the interactions if you donot know the active and passive residues of both DNA and protein

without more information on your system, I’m afraid we cannot really help you.

If you do not know anything about the interaction, the first lead would be to look at the electrostatic and solvation properties of your protein, assuming the conformational changes are mild upon interactions. Phosphate groups are negatively charged and give DNA molecules a negative charge, therefore look up for positive patches on your protein surface …