I expressed an enzyme in DH5 with PUC vector and purified it by dialysis method. By what method and protocol can I remove DNA contamination from the protein purified?
What exactly do you mean by the "dialysis method"?
In general, you need an extra step in your protocol to separate the DNA out. This can either be through anion exchange at a pH at which your protein will not bind to the resin or, at the very least, separate differentially from the resin-bound DNA. As suggested above by Dominique Liger , chromatography with a heparin column is also widely used. I would also suggest performing these steps in the presence of high salt concentration (even as high as 1 M) to dissociate the DNA from your protein.