Abstract Setting the Stage for Replacement of Mitochondrial Genes The goal of this project is to perform required pre-clinical investigations in a novel approach to reduce the levels of disease-causing mutant mtDNA in cells from patients with mitochondrial diseases. We will use mitochondrial-targeted TAL-effector nucleases (mitoTALENs) as novel gene therapy tools to specifically eliminate selected mtDNA haplotypes. This approach was successful in cultured cells and now we to use mitoTALENs in novel ways to alter mtDNA heteroplasmy in mouse tissues, focusing on expression from rAAV2/9 in limb muscles, extra-ocular muscles and the retina. In addition, we will optimize a mitoTALEN that we hope can be used in human patients in the near future.