Internal Standard for cytoplasmatic DNA

[Little Chris]

Hello,

for my studies with viral DNA in cell cultures i need to seperate the cytoplasmatic and the nuclear DNA to analyse the viral DNA concentration just in the cytoplasmatic fraction. The problem is now to find an appropriate housekeeping gene to normalize my data. Is mitochondrial DNA a possible solution? Thanks a lot for answers!

[Aga]

I think that there's a danger in using mitochondrial DNA genes as housekeeping.
A single cell can contain many mitochondria, but if you're studying one cell line you can possibly have an average number of mitochondria per cell. However, in a body different kind of cells contain different numbers of mitochondria, and so muscle cells or hepatocyte are different from e.g. epithelial cells, as far as mitochondria number is concerned.
Number of mitochondria per cell, IMO, depends on cell metabolism. If you analyse viral DNA in different tissues I think mitochondrial gene as housekeeping is not an answer.

Correct me if I'm wrong.