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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
878:
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
695:
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
699:
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
421:
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
1747:
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".
433:
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.
727:
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.
1708:"Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii are later heterotypic synonyms of Mycobacterium tuberculosis"
696:
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.
846:
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.
1359:
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).
1415:
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".
430:
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.
1617:
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".
1580:
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).
100:
1150:
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:
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475:
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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
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62:
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1657:"Genome sequence-based species delimitation with confidence intervals and improved distance functions"
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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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1103:"DNA:DNA hybridization studies on the pink-pigmented facultative methylotrophs"
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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.
641: with: full, up-to-date, secondary source-based overview. You can help by
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1310:"Notes on the characterization of prokaryote strains for taxonomic purposes"
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Forster, A. C.; McInnes, J. L.; Skingle, D. C.; Symons, R. H. (1985-02-11).
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1244:"Deoxyribonucleic acid reassociation in the taxonomy of enteric bacteria"
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Huang, Chien-Hsun; Li, Shiao-Wen; Huang, Lina; Watanabe, Koichi (2018).
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1461:"Identification and Classification for the Lactobacillus casei Group"
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article is inexpert in historical and conceptual scope, and sourcing.
1358:
1308:
Tindall BJ, Rossello-Mora R, Busse H-J, Ludwig W, Kampfer P (2010).
1001:. Aysha Divan, Janice Royds. Oxford: Oxford University Press. 2013.
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1362:"Complete genome sequence of DSM 30083, the type strain (U5/41) of
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sequences between organisms is overwhelmed by the hybridization of
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1366:, and a proposal for delineating subspecies in microbial taxonomy"
1750:
International
Journal of Systematic and Evolutionary Microbiology
1712:
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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683:; it is therefore one possible approach to carrying out
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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
27:
Technique used to measure similarity in DNA sequences
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291:. Unsourced material may be challenged and removed.
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501:may be compromised due to out-of-date information
138:may be compromised due to out-of-date information
1803:
1593:"DNA hybridization in the apes—Technical issues"
1281:International Journal of Systematic Bacteriology
1248:International Journal of Systematic Bacteriology
32:Nucleic acid thermodynamics § Hybridization
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1795:Graur, D. & Li, W-H. 1991 (2nd ed. 1999).
1101:Hood, D. W.; Dow, C. S.; Green, P. N. (1987).
967:. San Diego: Academic Press. pp. 37–45.
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998:Tools and techniques in biomolecular science
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476:Learn how and when to remove these messages
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901:has admitted dDDH as taxonomic evidence.
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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
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916:Temperature gradient gel electrophoresis
401:sequences. It is used to determine the
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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.
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1619:Oral Microbiology and Immunology
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1531:Journal of Molecular Evolution
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1370:Standards in Genomic Sciences
1191:Standards in Genomic Sciences
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961:Sinden, Richard R. (1994).
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95:. The specific problem is:
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1120:10.1099/00221287-133-3-709
964:DNA structure and function
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1465:Frontiers in Microbiology
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1261:10.1099/00207713-23-4-298
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1478:10.3389/fmicb.2018.01974
1430:10.1078/0723202042369875
717:Sibley–Ahlquist taxonomy
1674:10.1186/1471-2105-14-60
775:"DNA–DNA hybridization"
561:"DNA–DNA hybridization"
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1050:Nucleic Acids Research
1029:: CS1 maint: others (
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387:DNA–DNA hybridization
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1062:10.1093/nar/13.3.745
285:improve this article
1543:1984JMolE..20....2S
1242:Brenner DJ (1973).
1203:10.4056/sigs.531120
1661:BMC Bioinformatics
1551:10.1007/BF02101980
395:genetic similarity
1812:Molecular biology
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1537:(1): 2–15.
1337:10261/49238
911:DNA melting
891:group, and
840:orthologous
424:DNA melting
1806:Categories
1603:2019-06-02
922:References
844:paralogous
786:newspapers
753:references
704:In zoology
572:newspapers
539:references
462:improve it
311:newspapers
209:newspapers
176:references
57:improve it
1487:1664-302X
1438:0723-2020
1211:1944-3277
1164:0736-6205
1129:0022-1287
1070:0305-1048
1025:cite book
1017:818450218
894:Aeromonas
860:in silico
852:In silico
816:June 2019
650:June 2019
602:June 2019
511:June 2019
468:talk page
407:phylogeny
341:June 2019
239:June 2019
148:June 2019
109:June 2019
63:talk page
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1471:: 1974.
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1229:21304684
983:30109829
905:See also
411:taxonomy
397:between
383:genomics
1684:3665452
1567:6658046
1559:6429338
1539:Bibcode
1496:6113361
1393:4334874
1220:3035253
1172:7833043
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1088:2582358
854:methods
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876:DSMZ
872:TYGS
870:and
868:GGDC
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438:Uses
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1817:DNA
1766:hdl
1758:doi
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