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usually the DNA doesn't get digested by restriction enzymes if the DNA is denatured as already suggested by Nick or due to purification of not so clean DNA. particularly in your case as the DNA is quite big. so i suggest you purify the DNA using quiakit or give phenol-chloroform extraction again of your DNA.
hope this helps
to answer your questions, you can try adding a reducing agent like 2-mercaptoethanol to your cells. this may help the dissociation of heavy and light chains and weaken the interaction of the antibody with the antigen. alternately, antigen-antibody interactions are dissociated at high magnesium chloride concentrations (2-4M). In am sure that eukaryotic cells can be grown in 2-mercaptoethanol and so shouldn't harm your cells. But I am not sure about Magnesium chloride.
the effect of the antibody on the cells depends on the antigen to which the antibody was bound. that requires literature search. Or you can test the viability of your antibody bound cells at regular intervals
all the best