Mitochondrial DNA Stability and Gene Expression: Protein Target Identification and Oligonucleotide Approaches

Mitochondria are organelles of bacterial origin that are involved in energy production and other cellular processes. They have their DNA, known as mitochondrial DNA (mtDNA), which encodes essential respiratory chain proteins and is distinct from and independent of nuclear DNA. Since these molecules localize close to the electron transport chain (ETC), mtDNA is prone to damage. To confront this, mitochondria have specialized antioxidants and DNA repair systems. However, mtDNA damage can lead to mitochondrial dysfunction when the damage surpasses the functioning of those scavenging and repair mechanisms. This can result in several mitochondrial diseases like cancer or neurodegenerative diseases. Mitochondrial health maintenance also depends on the proper functioning of gene expression and regulation machinery. Even if significant discoveries in the field of mitochondrial genetics have been made in the last few years, there are many unanswered questions and treatments for mitochondrial diseases are still focused on the relief of the symptoms. Therefore, a deeper understanding of mitochondrial genetics is needed to face mitochondrial-related diseases effectively. This dissertation investigates cutting-edge techniques for studying mitochondrial genetics and examines a few protein targets and their possible medical applications. We present a new approach to quantifying oxidative mtDNA damage. We also introduce an oligonucleotide-based approach to disrupt mtDNA stability, which could be used in vivo as a therapeutic approach against cancer. In addition to studying mtDNA stability, this work displays a novel method to study proteins interacting with mtDNA and mtRNA to understand gene expression and regulation better. Finally, we validated Cyclophilin D (CyPD), one of the protein targets found in the nucleic acid interactome screening. In the future, this protein might be used as a therapeutic target. The work presented, paves the way for further research into better understanding the mechanisms involved in mitochondrial gene expression and towards developing treatments for mitochondrial-related illnesses.