D-loop



In molecular biology, a displacement loop or D-loop is a 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".[1]

(An unrelated use of the term D-loop, but not displacement loop, is for the loop of transfer RNA molecule.)

D-loops occur in a number of particular situations, including in circular DNA molecules.

In mitochondria

Researchers at Cal Tech discovered in 1971 that the circular mitochondrial DNA from growing cells included a short segment of three strands which they called a displacement loop.[1] 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.[2] 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.[3] 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.[3][4]

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.[5] The region contains RNA from the two strands of mitochondrial DNA immediately adjacent to the D-loop structure that is associated with initiation of DNA replication.[6]

The function of the D-loop which occurs in mitochondrial DNA is not yet clear, but recent research suggests that it participates in the organization of the mitochondrial nucleoid.[7][8]

In telomeres

In 1999 it was reported that telomeres, which cap the end of chromosomes, terminate in a lariat-like structure termed a t-loop.[9] This is a loop of both strands of the chromosome which are joined to an earlier point in the double-stranded DNA by the 3' strand end invading the strand pair to form a D-loop; a special protein stabilizes the joint. The t-loop which is completed by the D-loop splice protects the end of the chromosome from damage.[10]

In DNA repair

When a double-stranded DNA molecule has suffered a break in both strands, one repair mechanism available in diploid eukaryotic cells is homologous recombination repair. This makes use of the intact chromosome homologous to the broken one as a template to bring the two double-stranded pieces into correct alignment for rejoining. Early in this process, one strand of one piece is matched to a strand of the intact chromosome and that strand is used to form a D-loop at that point, displacing the intact chromosome's other strand. Various ligation and synthesis steps follow to effect the rejoining.[11]

In humans, the protein RAD51 is central to the homologous search and formation of the D-loop. In the bacterium Escherichia coli, a similar function is performed by the protein RecA.[12]

See also

References

  1. ^ a b Kasamatsu, H et al. (1971), "A novel closed-circular mitochondrial DNA with properties of a replicating intermediate", Proc Natl Acad Sci USA' (1971 Sep) 68(9):2252-7. PubMed
  2. ^ Doda, JN et al. (1981), "Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences", Proc Natl Acad Sci USA (1981 Oct) 78(10):6116-20. PubMed
  3. ^ a b Fish, J et al. (2004), "Discovery of a major D-loop replication origin reveals two modes of human mtDNA synthesis", Science (2004 Dec 17) 306(5704):2098-101. PubMed
  4. ^ Holt IJ et al. (2000), "Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA". Cell 100:515–524. PubMed
  5. ^ Larizza A et al. (2002), "Lineage Specificity of the Evolutionary Dynamics of the mtDNA D-Loop Region in Rodents", J Mol Evol. (2002 Feb) 54(2):145-55. PubMed
  6. ^ Chang, DD et al. (1985), "Priming of human mitochondrial DNA replication occurs at the light-strand promoter", Proc Natl Acad Sci USA (1985 Jan) 82(2):351-5. PubMed
  7. ^ He, Jiuya et al. (2007), "The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization", J Cell Biol. 2007 January 15; 176(2): 141–146. doi:10.1083/jcb.200609158
  8. ^ Leslie, Mitch (2007), "Thrown for a D-loop", J Cell Biol. 2007 January 15; 176(2): 129. doi:10.1083/jcb.1762iti3
  9. ^ Griffith, JD et al. (1999), "Mammalian telomeres end in a large duplex loop", Cell (1999 May 14) 97(4):503-14. PubMed
  10. ^ Greider, CW (1999), "Telomeres do D-loop-T-loop", Cell (1999 May 14) 97(4):419-22. PubMed
  11. ^ Hartl, Daniel L. and Jones, Elizabeth W. (2005), Genetics: Analysis of Genes and Genomes (Jones & Bartlett Publishers), p. 251.
  12. ^ Shibata, T et al. (2001), "Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material", Proc Natl Acad Sci USA (2001 Jul 17) 98(15):8425-32. PubMed
 
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