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â¢ Mitochondrial DNA is found inside the mitochondria while nuclear DNA is found inside the nucleus of a cell. â¢ One cell contains approximately 99.75% of nuclear DNA and 0.25% of mitochondrial DNA.â¢ The mutation rate of mitochondrial DNA is nearly twenty times faster than that of nuclear DNA.he uniqueness of mitochondrial DNA is that it is maternally inherited as a linked set of genes, passed on to progeny in the cytoplasm of the egg cell; thus no recombination between maternal and paternal genomes occurs.
When looking at the structure, it is easily visible that nuclear DNA are in linear molecules, while mtDNA are in closed circular molecules. Also, nuclear DNA contains a nuclear genome while mtDNA contains a mitochondrial genome.Genome is the complete set of genetic material of an organism. One final difference in the structure is nuclear DNA contains three-billion nucleotides, and mtDNA only contains 16,569 nucleotides.Nucleotides are the building blocks of DNA, they are made of a nucleoside linked to a phosphate group.ne final difference in the structure is nuclear DNA contains three-billion nucleotides, and mtDNA only contains 16,569 nucleotides. Nucleotides are the building blocks of DNA, they are made of a nucleoside linked to a phosphate group.