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DNA–DNA hybridization

January 01, 1970

This article is about the specific use in genomics. For the general phenomenon, see Nucleic acid thermodynamics § Hybridization.

In genomics, DNA–DNA hybridization is a molecular biology technique that measures the degree of genetic similarity between DNA sequences. It is used to determine the genetic distance between two organisms and has been used extensively in phylogeny and taxonomy.[1]

Method edit

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 require more energy to separate them: i.e. they separate when heated at a higher temperature than dissimilar sequences, a process known as "DNA melting".[2][3][4]

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 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.[5]

One method was introduced for hybridizing large numbers of DNA samples against large numbers of DNA probes on a single membrane. These samples would have to be separated in their own lanes inside the membranes and then the membrane would have to be rotated to a different angle where it would result in simultaneous hybridization with many different DNA probes.[6]

Uses edit

When several species are compared, similarity values allow organisms to be arranged in a phylogenetic tree; it is therefore one possible approach to carrying out molecular systematics.[citation needed]

In microbiology edit

DNA–DNA hybridization (DDH) is used as a primary method to distinguish bacterial species as it is difficult to visually classify them accurately.[7] 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 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.[8][9][10] In 2014, a threshold of 79% similarity has been suggested to separate bacterial subspecies.[11]

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 processed.[12] This new DDH technique became the standard for bacterial taxonomy.[13]

In zoology edit

Charles Sibley and Jon Ahlquist, pioneers of the technique, used DNA–DNA hybridization to examine the phylogenetic relationships of avians (the Sibley–Ahlquist taxonomy) and primates.[14][15]

In radioactivity edit

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.[16]

Replacement by genome sequencing edit

Critics argue that the technique is inaccurate for comparison of closely related species, as any attempt to measure differences between orthologous sequences between organisms is overwhelmed by the hybridization of paralogous sequences within an organism's genome.[17][better source needed][better source needed] 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.[18]

In silico methods edit

The modern approach is to carry out DNA–DNA hybridization in silico utilizes completely or partially sequenced genomes.[19] The GGDC and TYGS developed at DSMZ are the most accurate known tools for calculating DDH-analogous values.[19] 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 Escherichia coli, Bacillus cereus group, and Aeromonas.[20] The Judicial Commission of International Committee on Systematics of Prokaryotes has admitted dDDH as taxonomic evidence.[21]

See also edit

References edit

  1. ^ Erko Stackebrandt (8 September 2010). Molecular Identification, Systematics, and Population Structure of Prokaryotes. Springer Science & Business Media. ISBN 978-3-540-31292-5.
  2. ^ Sinden, Richard R. (1994). DNA structure and function. San Diego: Academic Press. pp. 37–45. ISBN 0-12-645750-6. OCLC 30109829.
  3. ^ Tools and techniques in biomolecular science. Aysha Divan, Janice Royds. Oxford: Oxford University Press. 2013. ISBN 978-0-19-969556-0. OCLC 818450218.{{cite book}}: CS1 maint: others (link)
  4. ^ Forster, A. C.; McInnes, J. L.; Skingle, D. C.; Symons, R. H. (1985-02-11). "Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin". Nucleic Acids Research. 13 (3): 745–761. doi:10.1093/nar/13.3.745. ISSN 0305-1048. PMC 341032. PMID 2582358.
  5. ^ Hood, D. W.; Dow, C. S.; Green, P. N. (1987). "DNA:DNA hybridization studies on the pink-pigmented facultative methylotrophs". Journal of General Microbiology. 133 (3): 709–720. doi:10.1099/00221287-133-3-709. ISSN 0022-1287. PMID 3655730.
  6. ^ Socransky, S. S.; Smith, C.; Martin, L.; Paster, B. J.; Dewhirst, F. E.; Levin, A. E. (October 1994). ""Checkerboard" DNA-DNA hybridization". BioTechniques. 17 (4): 788–792. ISSN 0736-6205. PMID 7833043.
  7. ^ Auch, Alexander F.; von Jan, Mathias; Klenk, Hans-Peter; Göker, Markus (2010). "Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison". Standards in Genomic Sciences. 2 (1): 117–134. doi:10.4056/sigs.531120. ISSN 1944-3277. PMC 3035253. PMID 21304684.
  8. ^ Brenner DJ (1973). "Deoxyribonucleic acid reassociation in the taxonomy of enteric bacteria". International Journal of Systematic Bacteriology. 23 (4): 298–307. doi:10.1099/00207713-23-4-298.
  9. ^ 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). "Report of the ad hoc committee on reconciliation of approaches to bacterial systematics". International Journal of Systematic Bacteriology. 37 (4): 463–464. doi:10.1099/00207713-37-4-463.
  10. ^ Tindall BJ, Rossello-Mora R, Busse H-J, Ludwig W, Kampfer P (2010). "Notes on the characterization of prokaryote strains for taxonomic purposes". International Journal of Systematic and Evolutionary Microbiology. 60 (Pt 1): 249–266. doi:10.1099/ijs.0.016949-0. hdl:10261/49238. PMID 19700448.
  11. ^ 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). "Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy". Standards in Genomic Sciences. 9: 2. doi:10.1186/1944-3277-9-2. PMC 4334874. PMID 25780495.
  12. ^ 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". Systematic and Applied Microbiology. 27 (6): 689–695. doi:10.1078/0723202042369875. ISSN 0723-2020. PMID 15612626.
  13. ^ Huang, Chien-Hsun; Li, Shiao-Wen; Huang, Lina; Watanabe, Koichi (2018). "Identification and Classification for the Lactobacillus casei Group". Frontiers in Microbiology. 9: 1974. doi:10.3389/fmicb.2018.01974. ISSN 1664-302X. PMC 6113361. PMID 30186277.
  14. ^ Genetic Similarities: Wilson, Sarich, Sibley, and Ahlquist
  15. ^ C.G. Sibley & J.E. Ahlquist (1984). "The Phylogeny of the Hominoid Primates, as Indicated by DNA–DNA Hybridization". Journal of Molecular Evolution. 20 (1): 2–15. Bibcode:1984JMolE..20....2S. doi:10.1007/BF02101980. PMID 6429338. S2CID 6658046.
  16. ^ 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.
  17. ^ Marks, Jonathan (2007-05-09). . Archived from the original on 2007-05-09. Retrieved 2019-06-02.
  18. ^ 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". Oral Microbiology and Immunology. 19 (6): 352–362. doi:10.1111/j.1399-302x.2004.00168.x. PMID 15491460.
  19. ^ a b Meier-Kolthoff JP, Auch AF, Klenk HP, Goeker M (2013). "Genome sequence-based species delimitation with confidence intervals and improved distance functions". BMC Bioinformatics. 14: 60. doi:10.1186/1471-2105-14-60. PMC 3665452. PMID 23432962.
  20. ^ Riojas, Marco A.; McGough, Katya J.; Rider-Riojas, Cristin J.; Rastogi, Nalin; Hazbón, Manzour Hernando (1 January 2018). "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". International Journal of Systematic and Evolutionary Microbiology. 68 (1): 324–332. doi:10.1099/ijsem.0.002507. PMID 29205127.
  21. ^ 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". International Journal of Systematic and Evolutionary Microbiology. 72 (12). doi:10.1099/ijsem.0.005708. hdl:10261/295959. PMID 36748499.

Further reading edit

  • Graur, D. & Li, W-H. 1991 (2nd ed. 1999). Fundamentals of Molecular Evolution.

January 01, 1970
hybridization, this, article, about, specific, genomics, general, phenomenon, nucleic, acid, thermodynamics, hybridization, this, article, multiple, issues, please, help, improve, discuss, these, issues, talk, page, learn, when, remove, these, template, messag. This article is about the specific use in genomics For the general phenomenon see Nucleic acid thermodynamics Hybridization This article has multiple issues Please help improve it or discuss these issues on the talk page Learn how and when to remove these template messages This article needs attention from an expert in Molecular and Cell Biology The specific problem is article is inexpert in historical and conceptual scope and sourcing WikiProject Molecular and Cell Biology may be able to help recruit an expert June 2019 This article s factual accuracy may be compromised due to out of date information Please help update this article to reflect recent events or newly available information June 2019 This article relies excessively on references to primary sources Please improve this article by adding secondary or tertiary sources Find sources DNA DNA hybridization news newspapers books scholar JSTOR June 2019 Learn how and when to remove this message This article needs additional citations for verification Please help improve this article by adding citations to reliable sources Unsourced material may be challenged and removed Find sources DNA DNA hybridization news newspapers books scholar JSTOR June 2019 Learn how and when to remove this message Learn how and when to remove this message In genomics DNA DNA hybridization is a molecular biology technique that measures the degree of genetic similarity between DNA sequences It is used to determine the genetic distance between two organisms and has been used extensively in phylogeny and taxonomy 1 Contents 1 Method 2 Uses 2 1 In microbiology 2 2 In zoology 2 3 In radioactivity 3 Replacement by genome sequencing 3 1 In silico methods 4 See also 5 References 6 Further readingMethod editThe 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 require more energy to separate them i e they separate when heated at a higher temperature than dissimilar sequences a process known as DNA melting 2 3 4 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 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 5 One method was introduced for hybridizing large numbers of DNA samples against large numbers of DNA probes on a single membrane These samples would have to be separated in their own lanes inside the membranes and then the membrane would have to be rotated to a different angle where it would result in simultaneous hybridization with many different DNA probes 6 Uses editThis section has multiple issues Please help improve it or discuss these issues on the talk page Learn how and when to remove these template messages This section s factual accuracy may be compromised due to out of date information Please help update this article to reflect recent events or newly available information June 2019 This section relies excessively on references to primary sources Please improve this section by adding secondary or tertiary sources Find sources DNA DNA hybridization news newspapers books scholar JSTOR June 2019 Learn how and when to remove this message This section needs expansion with full up to date secondary source based overview You can help by adding to it June 2019 Learn how and when to remove this message When several species are compared similarity values allow organisms to be arranged in a phylogenetic tree it is therefore one possible approach to carrying out molecular systematics citation needed In microbiology edit DNA DNA hybridization DDH is used as a primary method to distinguish bacterial species as it is difficult to visually classify them accurately 7 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 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 8 9 10 In 2014 a threshold of 79 similarity has been suggested to separate bacterial subspecies 11 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 processed 12 This new DDH technique became the standard for bacterial taxonomy 13 In zoology edit Charles Sibley and Jon Ahlquist pioneers of the technique used DNA DNA hybridization to examine the phylogenetic relationships of avians the Sibley Ahlquist taxonomy and primates 14 15 In radioactivity edit 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 16 Replacement by genome sequencing editThis section relies excessively on references to primary sources Please improve this section by adding secondary or tertiary sources Find sources DNA DNA hybridization news newspapers books scholar JSTOR June 2019 Learn how and when to remove this message Critics argue that the technique is inaccurate for comparison of closely related species as any attempt to measure differences between orthologous sequences between organisms is overwhelmed by the hybridization of paralogous sequences within an organism s genome 17 better source needed better source needed 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 18 In silico methods edit The modern approach is to carry out DNA DNA hybridization in silico utilizes completely or partially sequenced genomes 19 The GGDC and TYGS developed at DSMZ are the most accurate known tools for calculating DDH analogous values 19 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 Escherichia coli Bacillus cereus group and Aeromonas 20 The Judicial Commission of International Committee on Systematics of Prokaryotes has admitted dDDH as taxonomic evidence 21 See also editDNA melting Temperature gradient gel electrophoresisReferences edit Erko Stackebrandt 8 September 2010 Molecular Identification Systematics and Population Structure of Prokaryotes Springer Science amp Business Media ISBN 978 3 540 31292 5 Sinden Richard R 1994 DNA structure and function San Diego Academic Press pp 37 45 ISBN 0 12 645750 6 OCLC 30109829 Tools and techniques in biomolecular science Aysha Divan Janice Royds Oxford Oxford University Press 2013 ISBN 978 0 19 969556 0 OCLC 818450218 a href Template Cite book html title Template Cite book cite book a CS1 maint others link Forster A C McInnes J L Skingle D C Symons R H 1985 02 11 Non radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent photobiotin Nucleic Acids Research 13 3 745 761 doi 10 1093 nar 13 3 745 ISSN 0305 1048 PMC 341032 PMID 2582358 Hood D W Dow C S Green P N 1987 DNA DNA hybridization studies on the pink pigmented facultative methylotrophs Journal of General Microbiology 133 3 709 720 doi 10 1099 00221287 133 3 709 ISSN 0022 1287 PMID 3655730 Socransky S S Smith C Martin L Paster B J Dewhirst F E Levin A E October 1994 Checkerboard DNA DNA hybridization BioTechniques 17 4 788 792 ISSN 0736 6205 PMID 7833043 Auch Alexander F von Jan Mathias Klenk Hans Peter Goker Markus 2010 Digital DNA DNA hybridization for microbial species delineation by means of genome to genome sequence comparison Standards in Genomic Sciences 2 1 117 134 doi 10 4056 sigs 531120 ISSN 1944 3277 PMC 3035253 PMID 21304684 Brenner DJ 1973 Deoxyribonucleic acid reassociation in the taxonomy of enteric bacteria International Journal of Systematic Bacteriology 23 4 298 307 doi 10 1099 00207713 23 4 298 Wayne LG Brenner DJ Colwell RR Grimont PD Kandler O Krichevsky MI Moore LH Moore WEC Murray RGE Stackebrandt E Starr MP Truper HG 1987 Report of the ad hoc committee on reconciliation of approaches to bacterial systematics International Journal of Systematic Bacteriology 37 4 463 464 doi 10 1099 00207713 37 4 463 Tindall BJ Rossello Mora R Busse H J Ludwig W Kampfer P 2010 Notes on the characterization of prokaryote strains for taxonomic purposes International Journal of Systematic and Evolutionary Microbiology 60 Pt 1 249 266 doi 10 1099 ijs 0 016949 0 hdl 10261 49238 PMID 19700448 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 Goker M 2013 Complete genome sequence of DSM 30083T the type strain U5 41T of Escherichia coli and a proposal for delineating subspecies in microbial taxonomy Standards in Genomic Sciences 9 2 doi 10 1186 1944 3277 9 2 PMC 4334874 PMID 25780495 Mehlen Andre 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 Systematic and Applied Microbiology 27 6 689 695 doi 10 1078 0723202042369875 ISSN 0723 2020 PMID 15612626 Huang Chien Hsun Li Shiao Wen Huang Lina Watanabe Koichi 2018 Identification and Classification for the Lactobacillus casei Group Frontiers in Microbiology 9 1974 doi 10 3389 fmicb 2018 01974 ISSN 1664 302X PMC 6113361 PMID 30186277 Genetic Similarities Wilson Sarich Sibley and Ahlquist C G Sibley amp J E Ahlquist 1984 The Phylogeny of the Hominoid Primates as Indicated by DNA DNA Hybridization Journal of Molecular Evolution 20 1 2 15 Bibcode 1984JMolE 20 2S doi 10 1007 BF02101980 PMID 6429338 S2CID 6658046 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 Marks Jonathan 2007 05 09 DNA hybridization in the apes Technical issues Archived from the original on 2007 05 09 Retrieved 2019 06 02 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 Oral Microbiology and Immunology 19 6 352 362 doi 10 1111 j 1399 302x 2004 00168 x PMID 15491460 a b Meier Kolthoff JP Auch AF Klenk HP Goeker M 2013 Genome sequence based species delimitation with confidence intervals and improved distance functions BMC Bioinformatics 14 60 doi 10 1186 1471 2105 14 60 PMC 3665452 PMID 23432962 Riojas Marco A McGough Katya J Rider Riojas Cristin J Rastogi Nalin Hazbon Manzour Hernando 1 January 2018 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 International Journal of Systematic and Evolutionary Microbiology 68 1 324 332 doi 10 1099 ijsem 0 002507 PMID 29205127 Arahal David R Bull Carolee T Busse Hans Jurgen Christensen Henrik Chuvochina Maria Dedysh Svetlana N Fournier Pierre Edouard Konstantinidis Konstantinos T Parker Charles T Rossello Mora Ramon Ventosa Antonio Goker Markus 27 April 2023 Judicial Opinions 123 127 International Journal of Systematic and Evolutionary Microbiology 72 12 doi 10 1099 ijsem 0 005708 hdl 10261 295959 PMID 36748499 Further reading editGraur D amp Li W H 1991 2nd ed 1999 Fundamentals of Molecular Evolution Retrieved from https en wikipedia org w index php title DNA DNA hybridization amp oldid 1209508694, wikipedia, wiki, book, books, library,

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