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DNA–DNA hybridization

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To assess the melting profile of the hybridized DNA, the double-stranded DNA is bound to a column or filter and the mixture is heated in small steps. At each step, the column or filter is washed; sequences that melt become single-stranded and wash off. The temperatures at which labelled DNA comes off
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are the most accurate known tools for calculating DDH-analogous values. Among other algorithmic improvements, it solves the problem with paralogous sequences by carefully filtering them from the matches between the two genome sequences. The method has been used for resolving difficult taxa such as
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DNA–DNA hybridization (DDH) is used as a primary method to distinguish bacterial species as it is difficult to visually classify them accurately. This technique is not widely used on larger organisms where differences in species are easier to identify. In the late 1900s, strains were considered to
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DDH is a common technique for bacteria, but it is labor intensive, error-prone, and technically challenging. In 2004, a new DDH technique was described. This technique utilized microplates and colorimetrically labelled DNA to decrease the time needed and increase the amount of samples that can be
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The DNA of one organism is labelled, then mixed with the unlabelled DNA to be compared against. The mixture is incubated to allow DNA strands to dissociate and then cooled to form renewed hybrid double-stranded DNA. Hybridized sequences with a high degree of similarity will bind more firmly, and
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Arahal, David R.; Bull, Carolee T.; Busse, Hans-Jürgen; Christensen, Henrik; Chuvochina, Maria; Dedysh, Svetlana N.; Fournier, Pierre-Edouard; Konstantinidis, Konstantinos T.; Parker, Charles T.; Rossello-Mora, Ramon; Ventosa, Antonio; Göker, Markus (27 April 2023). "Judicial Opinions 123–127".
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A method was introduced to hybridize a large number of DNA samples against numerous DNA probes on a single membrane. The samples would need to be separated into individual lanes within the membrane, which would then be rotated to allow simultaneous hybridization with multiple DNA probes.
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In 1969, one such method was performed by Mary Lou Pardue and Joseph G. Gall at the Yale University through radioactivity where it involved the hybridization of a radioactive test DNA in solution to the stationary DNA of a cytological preparation, which is identified as autoradiography.
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belong to the same species if they had a DNA–DNA similarity value greater than 70% and their melting temperatures were within 5 °C of each other. In 2014, a threshold of 79% similarity has been suggested to separate bacterial subspecies.
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sequences within an organism's genome. DNA sequencing and computational comparisons of sequences is now generally the method for determining genetic distance, although the technique is still used in microbiology to help identify bacteria.
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Meier-Kolthoff JP, Hahnke RL, Petersen JP, Scheuner CS, Michael VM, Fiebig AF, Rohde CR, Rohde MR, Fartmann BF, Goodwin LA, Chertkov OC, Reddy TR, Pati AP, Ivanova NN, Markowitz VM, Kyrpides NC, Woyke TW, Klenk HP, Göker M (2013).
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Mehlen, André; Goeldner, Marcia; Ried, Sabine; Stindl, Sibylle; Ludwig, Wolfgang; Schleifer, Karl-Heinz (November 2004). "Development of a fast DNA-DNA hybridization method based on melting profiles in microplates".
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reflects the amount of similarity between sequences (and the self-hybridization sample serves as a control). These results are combined to determine the degree of genetic similarity between organisms.
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S.S. Socransky; A.D. Haffajee; C. Smith; L. Martin; J.A. Haffajee; N.G. Uzel; J. M. Goodson (2004). "Use of checkerboard DNA–DNA hybridization to study complex microbial ecosystems".
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Pardue, Mary Lou, and Joseph G Hall. “Molecular Hybridization of Radioactive DNA to the DNA of Cytological Preparations.” Kline Biology Tower, Yale University, 13 Aug. 1969.
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Wayne LG, Brenner DJ, Colwell RR, Grimont PD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987).
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Socransky, S. S.; Smith, C.; Martin, L.; Paster, B. J.; Dewhirst, F. E.; Levin, A. E. (October 1994). ""Checkerboard" DNA-DNA hybridization".
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require more energy to separate them: i.e. they separate when heated at a higher temperature than dissimilar sequences, a process known as "
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Critics argue that the technique is inaccurate for comparison of closely related species, as any attempt to measure differences between
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Riojas, Marco A.; McGough, Katya J.; Rider-Riojas, Cristin J.; Rastogi, Nalin; Hazbón, Manzour Hernando (1 January 2018).
1046:"Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin" 774: 560: 299: 197: 1529:
C.G. Sibley & J.E. Ahlquist (1984). "The Phylogeny of the Hominoid Primates, as Indicated by DNA–DNA Hybridization".
31: 972: 825: 666: 611: 475: 368: 350: 248: 70: 642: 1187:"Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison" 715:, pioneers of the technique, used DNA–DNA hybridization to examine the phylogenetic relationships of avians (the 467: 288: 62: 799: 585: 324: 222: 1811: 1030: 498: 135: 1657:"Genome sequence-based species delimitation with confidence intervals and improved distance functions" 1517: 863: 752: 538: 277: 175: 684: 1538: 8: 1277:"Report of the ad hoc committee on reconciliation of approaches to bacterial systematics" 679:
When several species are compared, similarity values allow organisms to be arranged in a
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Please help update this article to reflect recent events or newly available information.
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Please help update this article to reflect recent events or newly available information.
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This article is about the specific use in genomics. For the general phenomenon, see
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Auch, Alexander F.; von Jan, Mathias; Klenk, Hans-Peter; Göker, Markus (2010).
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Molecular Identification, Systematics, and Population Structure of Prokaryotes
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processed. This new DDH technique became the standard for bacterial taxonomy.
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Forster, A. C.; McInnes, J. L.; Skingle, D. C.; Symons, R. H. (1985-02-11).
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Huang, Chien-Hsun; Li, Shiao-Wen; Huang, Lina; Watanabe, Koichi (2018).
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article is inexpert in historical and conceptual scope, and sourcing.
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Tindall BJ, Rossello-Mora R, Busse H-J, Ludwig W, Kampfer P (2010).
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sequences between organisms is overwhelmed by the hybridization of
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International Journal of Systematic and Evolutionary Microbiology
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International Journal of Systematic and Evolutionary Microbiology
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International Journal of Systematic and Evolutionary Microbiology
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needs attention from an expert in Molecular and Cell Biology
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Genetic Similarities: Wilson, Sarich, Sibley, and Ahlquist
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The modern approach is to carry out DNA–DNA hybridization
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Meier-Kolthoff JP, Auch AF, Klenk HP, Goeker M (2013).
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between two organisms and has been used extensively in
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International Committee on Systematics of Prokaryotes
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Technique used to measure similarity in DNA sequences
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Springer Science & Business Media. 901:has admitted dDDH as taxonomic evidence. 826:Learn how and when to remove this message 667:Learn how and when to remove this message 612:Learn how and when to remove this message 369:Learn how and when to remove this message 351:Learn how and when to remove this message 249:Learn how and when to remove this message 1268: 916:Temperature gradient gel electrophoresis 401:sequences. It is used to determine the 14: 1804: 960: 934:Erko Stackebrandt (8 September 2010). 762:Please improve this section by adding 548:Please improve this section by adding 393:technique that measures the degree of 185:Please improve this article by adding 103:may be able to help recruit an expert. 101:WikiProject Molecular and Cell Biology 1797:Fundamentals of Molecular Evolution. 850: 735: 623: 521: 482: 441: 289:adding citations to reliable sources 260: 158: 119: 77: 36: 1418:Systematic and Applied Microbiology 722: 24: 1789: 690: 25: 1828: 862:utilizes completely or partially 457:This section has multiple issues. 52:This article has multiple issues. 1631:10.1111/j.1399-302x.2004.00168.x 1619:Oral Microbiology and Immunology 740: 732:Replacement by genome sequencing 628: 526: 487: 446: 265: 163: 124: 82: 41: 1740: 1699: 1610: 1584: 1573: 1522: 1511: 1452: 1408: 1107:Journal of General Microbiology 465:or discuss these issues on the 276:needs additional citations for 60:or discuss these issues on the 1591:Marks, Jonathan (2007-05-09). 1531:Journal of Molecular Evolution 1178: 1143: 1094: 1037: 989: 954: 13: 1: 1370:Standards in Genomic Sciences 1191:Standards in Genomic Sciences 921: 897:. 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Index

DNA–DNA hybridisation
Nucleic acid thermodynamics § Hybridization
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WikiProject Molecular and Cell Biology
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"DNA–DNA hybridization"
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