The key to measuring mitochondrial DNA damage is to first make sure you have a clean preparation of mitochondria from which to analyze the nucleic acid. If not, the results are quite difficult to discern from nuclear DNA. Many people use 8-oxo-dG as a measure of oxidative DNA damage in the mitochondria, but there are other methods. I will refer you to a presentation by Scott Ballinger at the Society for Free Radical Biology and Medicine meeting in 2009. I hope it will be helpful and a useful contact for you in the event you need further guidance.

http://www.sfrbm.org/frs/Ballinger.pdf

Good luck,

~Adam

The histone H2AX is marker of exactly Single and Double Strand breaks and it is useful for study capacity for repair those kind of damage and it is not only characteristic for nucleus DNA. If you want to quickly check the level of DNA damage you can simply do the gel electrophoresis and observe a "ladder" on the gel. But first you need to know what kind of damage want to analyzed and depends on you should treat your mitochondria sample the enzyme which cutting in the site of damage., if you want to some more information feel free to contact me.

What kind of mtDNA damage are you wanting to look at? Alkylation damage, Hydrolytic damage, Formation of adducts, Mismatched bases, DNA strand breaks or Oxidative damage?

Here is a link to a review which elucidates the different types of damage and current knowledge: http://www.ncbi.nlm.nih.gov/pubmed/23637283

Since you Mentioned g-H2AX (nDNA Strand breaks) I could suggest you look into 53BP1 as a marker for mtDNA damage. However if you plan to image mitochondria for their damage, as can be done with H2AX you will need some high resolution microscopy, a STED for example.

If you come across other options or have already found a solution i would be very glad if you would share it here.

Alternatively maybe use qRT-PCR http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-973-7:183

Dear Dr. Bolanos-Vilegas,

53BP1 is a protein involved in the regulation of double strand DNA break response. The accumulation of 53BP1 leads to H2AX foci formation in the nucleus.

(http://www.jbc.org/content/278/22/19579.long)

After much reading into mitochondrial DNA damage markers in the last week I would like to revise my suggestion about 53BP1. Although Strand breaks (Single and Double) occur in the mitochondria and can be repaired according to current reviews, there seems to be no evidence for 53BP1 accumulating in the mitochondria in the same way that it does in the nucleus.

mtDNA is more vulnerable to damage than DNA housed in the nucleus due to structural variations and location.

I would imagine markers for autophagy could potentially be a good marker for damage in mtDNA.

Attached is methods for measuring mitochondrial DNA damage:

http://www.sfrbm.org/frs/Ballinger.pdf