Nope, there is no such marker as the supercoiling differs in circular DNA and hence the electrophoretic mobility. You can use a restriction enzyme to linearize and confirm the size with standard DNA ladders.

If the goal is to obtain intact circular mtDNA, you MIGHT get lucky by using a normal size standard and then take several plugs where you 'guess' the mtDNA should be... but this sounds like a very 'dirty' approach. Personally, I would try CsCl ultracentrifugation to separate circular from linear DNA (providing you have enough starting tissue).

Hi Mangal, thank you. would you know of an enzyme that would linearize mtDNA but leave the nuclear one intact (no fragmentation of it that would contaminiate the mtDNA)?

Thanks

Hi Rex,

I gladly would, but have no ultracentrifuge, hence the "workaround" I'm trying to do... Our centrifuge has a max of 16 000xg

Thanks though :)

Hi Gunes-Helene,

Here is a paper by Rudolf J. Wiesner, my former boss in Köln, Germany. He describes a method to isolate mtDNA from total DNA on agarose gel, but this requires a southern blot step to identify where the relaxed mtDNA form migrates:

Article Purification of mitochondrial DNA from total cellular DNA of...

Hope this helps!

Thank you Olivier Baris! Sorry to have missed you answer, but it's still relevant for me to read more! :)