Hi,

I want to study the structure of the DNA-protein complex using AFM. The problem is I don't have purified protein with me. So, as an alternative, I am planning to incubate the DNA fragment with the whole cell extract of a strain that expresses the protein of interest. As a control, I will take a strain that does not express the protein of interest. The problem is, how to get rid of the whole DNA that will come in the whole cell extract. Usually the DNA is removed by DNAse digestion and then purification of the protein. Since I want to do the same thing without purifying the protein, I am not sure how the DNAse treatment will be done and how the DNAse will be removed prior to subsequent DNA incubation. Any suggestion/protocol is appreciated.

Thanks