u need to first isolate the mitochondria from your cells and then remove the nuclear DNA by DNAse treatment then procees for DNA isolation from mitochondiral cells by any method for cells
I have isolated mitochondrial DNA from isect tissue but never tried on rat muscles. I have notice the princicple is almost he same and with a litlle modificaiton you can achieve success and u can find the compositon of the buffers here..
http://ableweb.org/volumes/vol-22/4-oxford.pdf
I can say that do not used nitrogen to grind your tissue It will burst open the mitochondria and DNA will de degraded.