D-loop

In molecular biology, a displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. The third strand has a base sequence which is complementary to one of the main strands and pairs with it, thus displacing the other complementary main strand in the region. Within that region the structure is thus a form of triple-stranded DNA. A diagram in the paper introducing the term illustrated the D-loop with a shape resembling a capital "D", where the displaced strand formed the loop of the "D".

D-loops occur in a number of particular situations, including in DNA repair, in telomeres, and as a semi-stable structure in molecules.

Researchers at Caltech discovered in 1971 that the circular mitochondrial DNA from growing cells included a short segment of three strands which they called a displacement loop. They found the third strand was a replicated segment of the heavy strand (or H-strand) of the molecule, which it displaced, and was hydrogen bonded to the light strand (or L-strand). Since then, it has been shown that the third strand is the initial segment generated by a replication of the heavy strand that has been arrested shortly after initiation and is often maintained for some period in that state. The D-loop occurs in the main non-coding area of the mitochondrial DNA molecule, a segment called the control region or D-loop region.

Replication of the mitochondrial DNA can occur in two different ways, both starting in the D-loop region. One way continues replication of the heavy strand through a substantial part (e.g. two-thirds) of the circular molecule, and then replication of the light strand begins. The more recently reported mode starts at a different origin within the D-loop region and uses coupled-strand replication with simultaneous synthesis of both strands.

Certain bases within the D-loop region are conserved, but large parts are highly variable and the region has proven to be useful for the study of the evolutionary history of vertebrates. The region contains promoters for the transcription of RNA from the two strands of mitochondrial DNA immediately adjacent to the D-loop structure that is associated with initiation of DNA replication. D-loop sequences are also of interest in the study of cancers.

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