Mutagenesis (molecular biology technique)

In molecular biology, mutagenesis is an important laboratory technique whereby DNA mutations are deliberately engineered to produce mutant genes, proteins, strains of bacteria, or other genetically modified organisms. The various constituents of a gene, as well as its regulatory elements and its gene products, may be mutated so that the functioning of a genetic locus, process, or product can be examined in detail. The mutation may produce mutant proteins with interesting properties or enhanced or novel functions that may be of commercial use. Mutant strains may also be produced that have practical application or allow the molecular basis of a particular cell function to be investigated.

A large number of methods for achieving experimental mutagenesis have been developed. Initially, the kind of mutations artificially induced in the laboratory were entirely random; methods allowing for more specific site-directed mutagenesis were introduced later. Since 2013, development of the CRISPR/Cas9 technology, based on a prokaryotic viral defense system, has allowed for the editing or mutagenesis of a genome in vivo.[1]

Random mutagenesis

Early approaches to mutagenesis relied on methods which produced entirely random mutations. In such methods, cells or organisms are exposed to mutagens such as UV radiation or mutagenic chemicals, and mutants with desired characteristics are then selected. Hermann Muller discovered in 1927 that X-rays can cause genetic mutations in fruit flies,[2] and went on to use the mutants he created for his studies in genetics.[3] For Escherichia coli, mutants may be selected first by exposure to UV radiation, then plated onto an agar medium. The colonies formed are then replica-plated, one in a rich medium, another in a minimal medium, and mutants that have specific nutritional requirements can then be identified by their inability to grow in the minimal medium. Similar procedures may be repeated with other types of cells and with different media for selection.

A number of methods for generating random mutations in specific proteins were later developed to screen for mutants with interesting or improved properties. These methods may involve the use of doped nucleotides in oligonucleotide synthesis, or conducting a PCR reaction in conditions that enhance misincorporation of nucleotides (error-prone PCR), for example by reducing the fidelity of replication or using nucleotide analogues.[4] A variation of this method for integrating non-biased mutations in a gene is sequence saturation mutagenesis.[5] PCR products which contain mutation(s) are then cloned into an expression vector and the mutant proteins produced can then be characterised.

In animal studies, alkylating agents such as N-ethyl-N-nitrosourea (ENU) have been used to generate mutant mice.[6][7] Ethyl methanesulfonate (EMS) is also often used to generate animal and plant mutants.[8][9]

In a European Union law (as 2001/18 directive), this kind of mutagenesis may be used to produce GMOs but the products are exempted from regulation: no labeling, no evaluation.[10]

Site-directed mutagenesis

Many researchers seek to introduce selected changes to DNA in a precise, site-specific manner. Analogs of nucleotides and other chemicals were first used to generate localized point mutations.[11] Such chemicals include aminopurine, which induces an AT to GC transition,[12] while nitrosoguanidine,[13] bisulfite,[14] and N4-hydroxycytidine may induce a GC to AT transition.[15][16] These techniques allow specific mutations to be engineered into a protein; however, they are not flexible with respect to the kinds of mutants generated, nor are they as specific as later methods of site-directed mutagenesis and therefore have some degree of randomness.

Current techniques for site-specific mutation commonly involve using pre-fabricated mutagenic oligonucleotides in a primer extension reaction with DNA polymerase. This methods allows for point mutation or deletion or insertion of small stretches of DNA at specific sites. Advances in methodology have made such mutagenesis now a relatively simple and efficient process.[17]

The site-directed approach may be done systematically in such techniques as alanine scanning mutagenesis, whereby residues are systematically mutated to alanine in order to identify residues important to the structure or function of a protein.

Combinatorial mutagenesis

Combinatorial mutagenesis is a technique whereby large number of mutants may be screened for a particular characteristic. In this technique, a few selected positions or a short stretch of DNA may be exhaustively modified to obtain a comprehensive library of mutant proteins. One approach of this technique is to excise a portion of DNA and replaced with a library of sequences containing all possible combinations at the desired mutation sites. The segment may be at an enzyme active site, or sequences that have structural significance or immunogenic property. A segment however may also be inserted randomly into the gene in order to assess the structural or functional significance of particular part of protein.

Insertional mutagenesis

In cancer research engineered mutations also provide mechanistic insights into the development of the disease. Insertional mutagenesis using transposons, retrovirus such as mouse mammary tumor virus and murine leukemia virus may be used to identify genes involved in carcinogenesis and to understand the biological pathways of specific cancer. Various insertional mutagenesis techniques may also be used to study the function of particular gene.

Homologous recombination

Homologous recombination can be used to produce specific mutation in an organism. Vector containing DNA sequence similar to the gene to be modified is introduced to the cell, and by a process of recombination replaces the target gene in the chromosome. This method can be used to introduce a mutation or knock out a gene, for example as used in the production of knockout mice.[18]

Gene synthesis

As the cost of DNA oligonucleotide synthesis falls, artificial synthesis of a complete gene is now a viable method for introducing mutations into a gene. This method allows for extensive mutation at multiple sites, including the complete redesign of the codon usage of a gene to optimise it for a particular organism.[19]

See also

References

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  4. G. Michael Blackburn, ed. (2006). Nucleic Acids in Chemistry and Biology (3rd ed.). Royal Society of Chemistry. pp. 191–192. ISBN 978-0854046546.
  5. Wong, T.S.; Tee, K.L.; Hauer, B.; Schwaneberg, U. (2004). "Sequence Saturation Mutagenesis (SeSaM): a novel method for directed protein evolution". Nucleic Acids Res. 32 (3): e26. doi:10.1093/nar/gnh028. PMC 373423. PMID 14872057.
  6. Justice, MJ; Noveroske, JK; Weber, JS; Zheng, B; Bradley, A (1999). "Mouse ENU Mutagenesis" (PDF). Human Molecular Genetics. 8 (10): 1955–63. doi:10.1093/hmg/8.10.1955. PMID 10469849.
  7. Hrabé de Angelis M, Balling R (1998). "Large scale ENU screens in the mouse: genetics meets genomics". Mutation Research. 400 (1–2): 25–32. doi:10.1016/s0027-5107(98)00061-x. PMID 9685575.
  8. Flibotte S, Edgley ML, Chaudhry I, Taylor J, Neil SE, Rogula A, Zapf R, Hirst M, Butterfield Y, Jones SJ, Marra MA, Barstead RJ, Moerman DG (2010). "Whole-genome profiling of mutagenesis in Caenorhabditis elegans". Genetics. 185 (2): 431–41. doi:10.1534/genetics.110.116616. PMC 2881127. PMID 20439774.
  9. Bökel C (2008). "EMS screens : from mutagenesis to screening and mapping". Methods in Molecular Biology. 420: 119–38. doi:10.1007/978-1-59745-583-1_7. PMID 18641944.
  10. Krinke, C., « GMO directive : the origins of the mutagenesis exemption », Inf'OGM, march 2018, https://www.infogm.org/6509
  11. Shortle, D.; Dimaio, D.; Nathans, D. (1981). "Directed Mutagenesis". Annual Review of Genetics. 15: 265–294. doi:10.1146/annurev.ge.15.120181.001405. PMID 6279018.
  12. Caras, I. W.; MacInnes, M. A.; Persing, D. H.; Coffino, P.; Martin Jr, D. W. (1982). "Mechanism of 2-aminopurine mutagenesis in mouse T-lymphosarcoma cells". Molecular and Cellular Biology. 2 (9): 1096–1103. doi:10.1128/mcb.2.9.1096. PMC 369902. PMID 6983647.
  13. McHugh, G. L.; Miller, C. G. (1974). "Isolation and Characterization of Proline Peptidase Mutants of Salmonella typhimurium". Journal of Bacteriology. 120 (1): 364–371. PMC 245771. PMID 4607625.
  14. D Shortle & D Nathans (1978). "Local mutagenesis: a method for generating viral mutants with base substitutions in preselected regions of the viral genome". Proceedings of the National Academy of Sciences. 75 (5): 2170–2174. Bibcode:1978PNAS...75.2170S. doi:10.1073/pnas.75.5.2170. PMC 392513. PMID 209457.
  15. R A Flavell; D L Sabo; E F Bandle & C Weissmann (1975). "Site-directed mutagenesis: effect of an extracistronic mutation on the in vitro propagation of bacteriophage Qbeta RNA". Proceedings of the National Academy of Sciences. 72 (1): 367–371. doi:10.1073/pnas.72.1.367. PMC 432306. PMID 47176.
  16. Willi Müller; Hans Weber; François Meyer; Charles Weissmann (1978). "Site-directed mutagenesis in DNA: Generation of point mutations in cloned β globin complementary DNA at the positions corresponding to amino acids 121 to 123". Journal of Molecular Biology. 124 (2): 343–358. doi:10.1016/0022-2836(78)90303-0. PMID 712841.
  17. Papworth, C., Bauer, J. C., Braman, J. and Wright, D. A. (1996). "Site-directed mutagenesis in one day with >80% efficiency". Strategies. 9 (3): 3–4.CS1 maint: multiple names: authors list (link)
  18. "Homologous Recombination Method (and Knockout Mouse)". Davidson College.
  19. Yury E. Khudyakov, Howard A. Fields, ed. (25 September 2002). Artificial DNA: Methods and Applications. CRC Press. p. 13. ISBN 9781420040166.
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