I have isolated mitochondrial DNA from liver mitochondria and then run it through a polymyxin B column to remove any endotoxin, however the DNA seems to have been retained in the column. I have done this previously with total genomic DNA and had no problem. Any suggestions on how to elute the DNA?
PMB is cationic and binds the phosphate on lipid A. Since mitochondrial DNA is not protected by histones, it may be for this reason its phosphates unexpectedly interact with PMB.
According to my organic chemist labmate, one way to disrupt such interaction is by lowering the pH (but not too low! very low pH causes DNA to degrade on its own).
methanol-acetic acid mix at some ratio has been reported as a solution for extracting DNA. See:
http://scialert.net/fulltext/?doi=pjbs.2013.1823.1825&org=11
Acetic acid itself is pH2 when pure, which may be too acidic for your purpose.
http://www.sciencedirect.com/science/article/pii/0014482778902963
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