I am trying to get pure cytoplasmic and nuclear fractions from mammalian cells after infection, for further viral DNA quantification. After fractionation and DNA extraction, I quantified mitochondrial DNA in both fractions ( as what I have are DNA extracts) to validate my fractionation, but I got mitochondrial DNA in the nuclear fraction. Perhaps some cytoplasmic structures are pelleted with nuclei. Does anyone have a protocol to get pure cytoplasmic and nuclear fractions, and how to validate it on the DNA level (as I am looking for DNA extraction, not protein, and if there is a better control other than mitochondrial DNA)? Thanks

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