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D-loop replication
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'''D-loop replication''' is a proposed process by which circular DNA like [[chloroplast]]s and [[mitochondria]] replicate their genetic material. An important component of understanding [[D-loop]] replication is that many [[chloroplast]]s and [[mitochondria]] have a single circular [[chromosome]] like [[bacterium|bacteria]] instead of the linear [[chromosome]]s found in [[eukaryote]]s. However, many [[chloroplasts]] and [[mitochondria]] have a linear chromosome, and D-loop replication is not important in these organelles. Also, not all circular genomes use D-loop replication as the process of replicating its genome.<ref>Russell, P. J. 2002. ''iGenetics.''Benjamin Cummings, San Francisco</ref> In many organisms, one strand of [[DNA]] in the [[plasmid]] comprises heavier [[nucleotide]]s (relatively more [[purine]]s: [[adenine]] and [[guanine]]). This strand is called the [[Heavy strand|H (heavy) strand]]. The [[Light strand|L (light) strand]] comprises lighter nucleotides ([[pyrimidine]]s: [[thymine]] and [[cytosine]]). Replication begins with replication of the heavy strand starting at the [[D-loop]] (also known as the [[mtDNA control region|control region]]). A D-loop is a short portion in circular DNA that has three strands instead of two. The middle strand, which is complementary to the light strand, displaces the heavy strand and forms a displacement loop (D-loop).<ref name=":0">{{cite journal | last1 = Kasamatsu | first1 = Harumi | last2 = Robberson | first2 = Donald L. | last3 = Vinograd | first3 = Jerome | year = 1971 | title = A novel closed-circular mitochondrial DNA with properties of a replicating intermediate | journal = Proceedings of the National Academy of Sciences | volume = 68 | issue = 9| pages = 2252β2257 | doi=10.1073/pnas.68.9.2252| pmid = 5289384 | pmc = 389395 | bibcode = 1971PNAS...68.2252K | doi-access = free }}</ref> Circular DNA is stable with this small D-loop and can remain in this formation, but the middle strand, or the displacing strand, is replaced frequently due to its short half-life, and is very energetically expensive to the cell.<ref name=":1">{{cite journal | last1 = Nicholls | first1 = Thomas J. | last2 = Minczuk | first2 = Michal | year = 2014 | title = In D-loop: 40 years of mitochondrial 7S DNA | journal = Experimental Gerontology | volume = 56 | pages = 175β181 | doi=10.1016/j.exger.2014.03.027| pmid = 24709344 | s2cid = 140205074 }}</ref><ref name=":2">{{cite journal | last1 = Doda | first1 = Jackie N. | last2 = Wright | first2 = Catharine T. | last3 = Clayton | first3 = David A. | year = 1981 | title = Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences | journal = Proceedings of the National Academy of Sciences | volume = 78 | issue = 10| pages = 6116β6120 | doi=10.1073/pnas.78.10.6116| pmid = 6273850 | pmc = 348988 | bibcode = 1981PNAS...78.6116D | doi-access = free }}</ref> When diagramed, the resulting structure looks like the letter D. The D-loop was first discovered in 1971 when researchers noticed that many DNA in the mitochondria they were examining under microscope contained a short segment that was tripled stranded.<ref name=":0" />
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