This technique might be interesting for you:

http://www.biotechniques.com/BiotechniquesJournal/2013/September/Fast-mitochondrial-DNA-isolation-from-mammalian-cells-for-next-generation-sequencing/biotechniques-346265.html

In addition there are a number of kits for isolation of mitochondrial DNA, like http://www.biovision.com/mitochondrial-dna-isolation-kit-2835.html and http://www.abcam.com/mitochondrial-dna-isolation-kit-ab65321.html.

However, there is no easy way to remove mtDNA from a total (genomic and mtDNA) preparation.

Cheers, Christian

Thank you, Christian!

It is possible to amplify mitochondrial DNA by PCR  using mitochondrial sequence specific primers and total genomic DNA as a template.

Thank you, Jyothisri, but I cannot use PCR ampification because I am looking for unnatural nucleotide insertions in mtDNA that would be lost after PCR.

Jyothisri, do have sequences for good primers to assess mtDNA release (and also primers for DNA as control) ? Thanks