Mitochondrial DNA deletions are associated with non-B DNA conformations

Mitochondrial DNA (mtDNA) deletions are a primary cause of mitochondrial disease and are believed to contribute to the aging process and to various neurodegenerative diseases.Despite strongobserva-tional and experimental evidence, themolecular basis of the deletion process remainsobscure. In this study, we test the hypothesis that the primary cause of mtDNA vulnerability to breakage resides in the forma-tion of non-B DNA conformations, namely hairpin, cruciform and cloverleaf-like elements. Using the largest database of human mtDNA deletions built thus far (753 different cases), we show that site-specific breakage hotspots exist in the mtDNA. Furthermore, we discover that the most frequent deletion breakpoints occur within or near predicted structures, a result that is supported by data from transgenic mice with mitochondrial disease. There is also a significant association between the folding energy of an mtDNA region and the number of break-points that it harbours. In particular, two clusters of hairpins (near theD-loop 30-terminus and the L-strand origin of replication) are hotspots for mtDNA breakage. Consistent with our hypothesis, the highest number of 50- and 30-breakpoints per base is found in thehighly structured tRNAgenes.Overall, the data presented in this study suggest that non-B DNA conformations are a key element of the mtDNA deletion process