I have someone here at Columbia who wants to do a two steps staining for a DNA adduct with a 1' monoclonal antibody and a 2' FITC conjugated antibody. The major problem we have is that they have to isolate the nucleus from cells with a nuclear isolation buffer, then treat the isolated nucleus with 2N HCL to unfold the DNA in order to expose the adduct. At last, they do the staining to look for presence of the adduct in those HCL treated nucleus (the nucleus most likely are lysed already with only DNA remaining). Does anyone have any recommendation in doing FACS with this type of DNA staining (FACSing only DNA, that is not confined within a nucleus/cells). I would expect the size of the DNA to be smaller than debris, so what should I do with the FSC/SSC. And, how should I interpret the data, since I don't even know whether I am looking at debris or DNA.
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