Fig. 3
From: Secondary structure of the human mitochondrial genome affects formation of deletions
Integral scheme of the origin of mtDNA deletions. The parental heavy strand is marked by a gray line, while the parental light strand is marked by a black line. Daughter strands are indicated by dotted lines. Direct nucleotide repeats are marked by red arrows, and inverted nucleotide repeats are marked by green arrows. The origin of replication of the heavy strand (OH) and the origin of replication of the light strand (OL) are labeled. A At the start of replication, the daughter heavy strand (dotted gray line) is replicated on the template of the parental light strand (black line), and the replication fork begins to move from OH towards OL. B During this time, the parental heavy strand remains single-stranded (ssDNA) for a significant amount of time, and different types of microhomology, including inverted repeats (green arrows), can fold the spatial structure. C Once the first replication fork reaches OL, the second one begins replicating the daughter’s light strand (dotted back line) on the template of the parental heavy strand. D The second replication fork stalls near the stem initiated by the inverted repeats. If the stalling time is sufficiently long and the spatial structure of ssDNA cannot be resolved, the new-synthesized daughter chain dissociates partially and re-aligns with the second arm of the direct repeat. If ssDNA forms a stem, it may rotate (as indicated by the black arrow), potentially bringing direct repeats even closer together. E This allows the replication fork to continue replication. F Replication of the daughter light strand is finished, and the ssDNA loop region disappears either in the second round of mtDNA replication (see Fig. 5f in [28]) or when mtDNA with deletions is repaired, and ssDNA is degraded