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In eukaryotes, two primary models for how homologous recombination repairs double-strand breaks in DNA are the double-strand break repair (DSBR) pathway (sometimes called the ''double Holliday junction model'') and the synthesis-dependent strand [[Annealing (biology)|annealing]] (SDSA) pathway.<ref name="Sung">{{Cite journal | last1=Sung | first=P | last2=Klein | first2=H | title=Mechanism of homologous recombination: mediators and helicases take on regulatory functions | journal=Nature Reviews Molecular Cell Biology | volume=7 | issue=10 | pages=739–750 | date=October 2006 | doi=10.1038/nrm2008 | pmid=16926856}}</ref> In the case of double strand breakage, the 3' end is degraded and the longer 5' end invades the contiguous sister chromatid, forming a replication bubble. As this bubble nears the broken DNA, the longer 5' antisense strand again invades the sense strand of this portion of DNA, transcribing a second copy. When replication ends, both tails are reconnected to form two Holliday Junctions, which are then cleaved in a variety of patterns by proteins.<ref name="hartel">{{cite book | last1=Hartel | first1=Daniel L. | first2=Elizabeth W. | last2=Jones | title=Genetics: Analysis of Genetics and Genomes | year=2009 | publisher=Jones & Bartlett | location=Burlington | chapter=Chapter 6: Molecular Biology of DNA Replication and Recombination | chapter-url=https://books.google.com/books?id=cfvILxY9tCIC&pg=PA190}}</ref> An animation of this process can be seen [http://web.mit.edu/engelward-lab/animations/DSBR.html here].<ref>{{cite web | last=Helleday | first=T. | title=Double-Strand Break Repair via Double Holliday Junctions (Szostak Model) | url=http://web.mit.edu/engelward-lab/animations/DSBR.html | work=Animation | publisher=MIT}}</ref>
Double-strand DNA breaks in bacteria are repaired by the [[RecBCD]] pathway of homologous recombination. Breaks that occur on only one of the two DNA strands, known as single-strand gaps, are thought to be repaired by the [[Homologous recombination#RecF pathway|RecF pathway]]. Both the RecBCD and RecF pathways include a series of reactions known as ''[[branch migration]]'', in which single DNA strands are exchanged between two intercrossed molecules of duplex DNA, and ''resolution'', in which those two intercrossed molecules of DNA are cut apart and restored to their normal double-stranded state.<ref>{{Cite journal | title=Comparative and evolutionary analysis of the bacterial homologous recombination systems | journal=PLoS Genetics | last=Rocha | first=EPC | date=August 2005 | volume=1 | issue=2 | page=e15 | doi=10.1371/journal.pgen.0010015 | pmid=16132081 | pmc=1193525 | last2=Cornet | first2=E | last3=Michel | first3=B}} {{open access}}</ref> Homologous recombination occurs in several [[Viral classification|groups]] of viruses. In [[DNA virus]]es such as [[herpesvirus]], recombination occurs through a break-and-rejoin mechanism like in bacteria and eukaryotes.<ref name="Fleischmann_1996">{{cite book | title=Medical Microbiology | year=1996 | publisher=University of Texas Medical Branch at Galveston | isbn=0-9631172-1-1 | last=Fleischmann Jr | first=WR | chapter=Chapter 43 | edition=4th | url=
There is evidence for recombination in some [[RNA virus]]es, specifically [[positive-sense ssRNA virus]]es like [[retrovirus]]es, [[picornavirus]]es, and [[coronavirus]]es. There is controversy over whether homologous recombination occurs in [[negative-sense ssRNA virus]]es like [[influenza]].<ref name="Boni_2010">{{cite journal | title=Guidelines for identifying homologous recombination events in influenza a virus | editor1-first=Darren P. | journal=PLoS ONE | date=3 May 2010 | editor1-last=Martin | volume=5 | first5=Darren P. | issue=5 | page=e10434 | last1=Boni | last5=Martin | first1=MF | last2=de Jong | first2=MD | last3=van Doorn | first3=HR | last4=Holmes | first4=EC | pmid=20454662 | pmc=2862710 | doi=10.1371/journal.pone.0010434}} {{open access}}</ref>
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