DNA–DNA hybridization

DNA–DNA hybridization generally refers to a molecular biology technique that measures the degree of genetic similarity between pools of DNA sequences. It is usually used to determine the genetic distance between two organisms. This has been used extensively in phylogeny and taxonomy.

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

Method

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".

To assess the melting profile of the hybridized DNA, the double-stranded DNA is bound to a column and the mixture is heated in small steps. At each step, the column is washed; sequences that melt become single-stranded and wash off the column. The temperatures at which labelled DNA comes off the column 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.

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.[1]

Uses

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.

In microbiology

DNA–DNA hybridization was once used as a primary method to distinguish bacterial species; a similarity value greater than 70% and ≤ 5 ºC in ΔTm in the stability of the heteroduplex is described as indicating that the compared strains belonged to distinct species.[2][3][4] In 2014, a threshold of 79% similarity has been suggested to separate bacterial subspecies.[5] DNA–DNA hybridization has not been tested much worldwide because it could take years to get results and it's not always that easy to perform in routine laboratories. However in 2004, there has been a new method tested out by digesting melting profiles with Sau3A in microplates in order to get a faster DNA–DNA hybridization test result.[6]

In zoology

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.[7][8]

In radioactivity

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.[9]

Replacement by genome sequencing

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.[10] 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.[11]

In silico methods

The modern approach is to carry out DNA–DNA hybridization in silico using completely or partially sequenced genomes.[12] The GGDC developed at DSMZ is the most accurate known tool for calculating DDH-analogous values.[12] Among other algorithmic improvements, it solves the problem with paralogous sequences by carefully filtering them from the matches between the two genome sequences.

See also

References
  1. 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.
  2. 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.
  3. 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. PMID 3213314.
  4. 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. PMID 19700448.
  5. 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.
  6. 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.
  7. Genetic Similarities: Wilson, Sarich, Sibley, and Ahlquist
  8. 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.
  9. 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.
  10. Marks, Jonathan (2007-05-09). "DNA hybridization in the apes—Technical issues". Archived from the original on 2007-05-09. Retrieved 2019-06-02.
  11. 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.
  12. 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.

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