You can run a few µl of your sample on a native gel or agarose gel and
visualise co-purified DNA by ethidium bromide/gel red staining.
If your protein is stable at high salt concentrations (and a lot of DNA-binding
proteins are) you can use a high salt concentration (like 1 M) in the lysis
buffer.
Ion exchange is also a good way to get rid of DNA, in my experience.
Lisa
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