It won't force James Watson to retitle the Double Helix, but new research suggests that the three-stranded stretches that frequently turn up in mitochondrial DNA (mtDNA) aren't junk. Instead, the triple-stranded forms might provide a scaffold for a protein that helps mitochondria organize their DNA, as He et al. show on page .
Researchers have known for more than 30 years that one section of mtDNA often carries an additional strand, creating a displacement loop, or D-loop. However, the conventional wisdom held that D-loops were nonfunctional leftovers of incomplete replication. He et al. began to doubt that explanation after “we found a protein that is in love with D-loops,” says team leader Ian Holt. Other researchers had previously identified the protein, ATAD3, but knew nothing about its job in mitochondria.
The researchers discovered that ATAD3 prefers to latch onto D-loops, even in solutions where double-stranded DNA is 1,000 times more abundant. ATAD3 also helps stabilize complexes with multiple copies of mtDNA. When the scientists tracked ATAD3 down in the mitochondria, they learned that it often hangs out in the clusters of mtDNA called nucleoids. ATAD3 may either help mtDNA copies segregate from each other or cluster multiple copies of them into nucleoids. Herding mtDNA into nucleoids might offer the strands protection from the reactive oxygen species that are prevalent in mitochondria or allow the cell to control the number of mtDNA copies. 
