Dear Sivaraman, it might be difficult if the DNA binding is an intrinsic property of your protein and important for the function. But you can try of course to degrade the DNA using DNAseI and hope that the resulting small pieces and nucleotides will not bind to your protein, I use sometimes streptomycine sulfate to precipitate the DNA before the protein purification. If the protein is just soluble with DNA you could try also addional additive like Arg or more glycerol (10% is still O.K.) to prevent precipitation after the removal of the DNA. Good luck with your protein
Best regards Christian
