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
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