I think the best thing is to isolate first mitochondria, then treat these intact mitochondria with DNases to get rid of any nuclear DNA on the outersurface and then extract mit genome
Why do you want to remove the nuclear DNA? If you are diligent with your primer designs and you test for pseudo gene amplification using Rho0 cells then the genomic DNA should not be a problem for most applications.
Hello Andrew i am not using any primers here,i'm facing this problem while cloning restriction digested Mt-DNA in to the vector where most of the times i'm seeing nuclear contamination