Advertisement

Restriction enzymes and their use in molecular biology: An overview

  • Francesca Di Felice
  • Gioacchino Micheli
  • Giorgio CamilloniEmail author
Review
  • 4 Downloads

Abstract

Restriction enzymes have been identified in the early 1950s of the past century and have quickly become key players in the molecular biology of DNA. Forty years ago, the scientists whose pioneering work had explored the activity and sequence specificity of these enzymes, contributing to the definition of their enormous potential as tools for DNA characterization, mapping and manipulation, were awarded the Nobel Prize. In this short review, we celebrate the history of these enzymes in the light of their many different uses, as these proteins have accompanied the history of DNA for over 50 years representing active witnesses of major steps in the field.

Keywords

Cloning DNA manipulation history restriction enzymes 

Notes

References

  1. Arber W 1965 Host-controlled modification of bacteriophage. Annu. Rev. Microbiol. 19 365–378CrossRefGoogle Scholar
  2. Balazs I 1992 Forensic applications. Curr. Opin. Biotechnol. 3 18–23CrossRefGoogle Scholar
  3. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA and Horvath P 2007 CRISPR provides acquired resistance against viruses in prokaryotes. Science 315 1709–1712CrossRefGoogle Scholar
  4. Bertani G and Weigle JJ 1953 Host controlled variation in bacterial viruses. J. Bacteriol. 65 113–121PubMedPubMedCentralGoogle Scholar
  5. Bird AP and Southern EM 1978 Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. J. Mol. Biol. 118 27–47CrossRefGoogle Scholar
  6. Botstein D, White RL, Skolnick M and Davis RW 1980 Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32 314–331PubMedPubMedCentralGoogle Scholar
  7. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ and Voytas DF 2010 Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186 757–761CrossRefGoogle Scholar
  8. Cohen SN 2013 DNA cloning: a personal view after 40 years. PNAS 110 15521–15529CrossRefGoogle Scholar
  9. Cohen SN, Maitra U and Hurwitz J 1967 Role of DNA in RNA synthesis: XI. Selective transcription of λ DNA segments in vitro by RNA polymerase of Escherichia coli. J. Mol. Biol. 26 19–38CrossRefGoogle Scholar
  10. Cohen SN, Chang ACY and Hsu L 1972 Nonchromosomal antibiotic resistance in bacteria: Genetic transformation of Escherichia coli by R-factor DNA*. Proc. Natl. Acad. Sci. USA 69 2110–2114CrossRefGoogle Scholar
  11. Cozzarelli NR, Melechen NE, Jovin TM and Kornberg A 1967 Polynucleotide cellulose as a substrate for a polynucleotide ligase induced by phage T4. Biochem. Biophys. Res. Commun. 28 578–586CrossRefGoogle Scholar
  12. Danna K and Nathans D 1971 Specific cleavage of Simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc. Natl. Acad. Sci. USA 5 75–81Google Scholar
  13. Durmaz AA, Karaca E, Demkow U, Toruner G, Schoumans J and Cogulu O 2015 Evolution of genetic techniques: Past, present, and beyond [WWW document]. BioMed Res. Int.  https://doi.org/10.1155/2015/461524 CrossRefGoogle Scholar
  14. Gaj T, Gersbach CA and Barbas CF 2013 ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 31 397–405CrossRefGoogle Scholar
  15. Gefter ML, Becker A and Hurwitz J 1967 The enzymatic repair of DNA. I. Formation of circular lambda-DNA. Proc. Natl. Acad. Sci. USA 58 240–247CrossRefGoogle Scholar
  16. Gellert M 1967 Formation of covalent circles of lambda DNA by E. coli extracts. Proc. Natl. Acad. Sci. USA 57 148–155CrossRefGoogle Scholar
  17. Goeddel DV, Kleid DG, Bolivar F, Heyneker HL, Yansura DG, Crea R, Hirose T, Kraszewski A, Itakura K and Riggs AD 1979 Expression in Escherichia coli of chemically synthesized genes for human insulin. Proc. Natl. Acad. Sci. USA 76 106–110CrossRefGoogle Scholar
  18. Grummt I and Gross HJ 1980 Structural organization of mouse rDNA: comparison of transcribed and non-transcribed regions. Mol. Gen. Genet. 177 223–229CrossRefGoogle Scholar
  19. Gupta R, Capalash N and Sharma P 2012 Restriction endonucleases: natural and directed evolution. Appl. Microbiol. Biotechnol. 94 583–599CrossRefGoogle Scholar
  20. Heather JM and Chain B 2016 The sequence of sequencers: The history of sequencing DNA. Genomics 107 1–8CrossRefGoogle Scholar
  21. Hershey AD, Burgi E and Ingraham L 1963 Cohesion of DNA molecules isolated from phage lambda. Proc. Natl. Acad. Sci. USA 49 748–755CrossRefGoogle Scholar
  22. Hewish DR and Burgoyne LA 1973 Chromatin sub-structure. The digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease. Biochem. Biophys. Res. Commun. 52 504–510CrossRefGoogle Scholar
  23. Hickson FT, Roth TF and Helinski DR 1967 Circular DNA forms of a bacterial sex factor. Proc. Natl. Acad. Sci. USA 58 1731–1738CrossRefGoogle Scholar
  24. Holsinger KE and Jansen RK 1993 Phylogenetic analysis of restriction site data; in: Methods in enzymology, molecular evolution: Producing the biochemical data (eds) Zimmer EA, White TJ, Cann RL, Wilson AC (Cambridge, USA: Academic Press) pp 439–455CrossRefGoogle Scholar
  25. Hörz W, Igo-Kemenes T, Pfeiffer W and Zachau HG 1976 Specific cleavage of chromatin by restriction nucleases. Nucleic Acids Res. 3 3213–3226CrossRefGoogle Scholar
  26. Jackson DA, Symons RH and Berg P 1972 Biochemical method for inserting New genetic information into DNA of Simian virus 40: Circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc. Natl. Acad. Sci. USA 69 2904–2909CrossRefGoogle Scholar
  27. Jensen RH, Wodzinski RJ and Rogoff MH 1971 Enzymatic addition of cohesive ends to T7 DNA. Biochem. Biophys. Res. Commun. 43 384–392CrossRefGoogle Scholar
  28. Jiang F and Doudna JA 2017 CRISPR–cas9 structures and mechanisms. Annu. Rev. Biophys. 46 505–529CrossRefGoogle Scholar
  29. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA and Charpentier E 2012 A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337 816–821CrossRefGoogle Scholar
  30. Kelly TJ and Smith HO 1970 A restriction enzyme from Hemophilus influenzae. II. J. Mol. Biol. 51 393–409CrossRefGoogle Scholar
  31. Khan S, Ullah MW, Siddique R, Nabi G, Manan S, Yousaf M and Hou H 2016 Role of recombinant DNA technology to improve life. Int. J. Genomics 2016 1–14Google Scholar
  32. Kim H and Kim J-S 2014 A guide to genome engineering with programmable nucleases. Nat. Rev. Genet. 15 321–334CrossRefGoogle Scholar
  33. Knizewski L, Kinch LN, Grishin NV, Rychlewski L and Ginalski K 2007 Realm of PD–(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. BMC Struct. Biol. 7 40CrossRefGoogle Scholar
  34. Kornberg RD 1974 Chromatin structure: a repeating unit of histones and DNA. Science 184 868–871CrossRefGoogle Scholar
  35. Lederberg J 1952 Cell genetics and hereditary symbiosis. Physiol. Rev. 32 403–430CrossRefGoogle Scholar
  36. Lin I-H 2018 Whole genome DNA methylation analysis using next-generation sequencing (BS-seq). Methods Mol. Biol. 1667 223–287CrossRefGoogle Scholar
  37. Lipchitz L and Axel R 1976 Restriction endonuclease cleavage of satellite DNA in intact bovine nuclei. Cell 9 355–364CrossRefGoogle Scholar
  38. Liu Q, Segal DJ, Ghiara JB and Barbas CF 1997 Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. PNAS 94 5525–5530CrossRefGoogle Scholar
  39. Lobban PE and Kaiser AD 1973 Enzymatic end-to-end joining of DNA molecules. J. Mol. Biol. 78 453–471CrossRefGoogle Scholar
  40. Luria SE and Human ML 1952 A nonhereditary, host-induced variation of bacterial viruses. J. Bacteriol. 64 557–569PubMedPubMedCentralGoogle Scholar
  41. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD and Rebar EJ 2011 A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 29 143–148CrossRefGoogle Scholar
  42. Morrow JF, Cohen SN, Chang ACY, Boyer HW, Goodman HM and Helling RB 1974 Replication and transcription of eukaryotic DNA in Esherichia coli. Proc. Natl. Acad. Sci. USA 71 1743–1747CrossRefGoogle Scholar
  43. Noll M 1974 Subunit structure of chromatin. Nature 251 249–251CrossRefGoogle Scholar
  44. Olivera BM and Lehman IR 1967 Linkage of polynucleotides through phosphodiester bonds by an enzyme from Escherichia coli. Proc. Natl. Acad. Sci. USA 57 1426–1433CrossRefGoogle Scholar
  45. Pfeiffer W, Horz W, Igo-Kemenes T and Zachau HG 1975 Restriction nucleases as probes of chromatin structure. Nature 258 450–452CrossRefGoogle Scholar
  46. Pingoud A, Fuxreiter M, Pingoud V and Wende W 2005 Type II restriction endonucleases: Structure and mechanism. Cell. Mol. Life Sci. 62 685–707CrossRefGoogle Scholar
  47. Rill R and Van Holde KE 1973 Properties of nuclease-resistant fragments of calf thymus chromatin. J. Biol. Chem. 248 1080–1083PubMedGoogle Scholar
  48. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal, RM, Degtyarev SK, et al. 2003 A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 31 1805–1812CrossRefGoogle Scholar
  49. Sajantila A and Budowle B 1991 Identification of individuals with DNA testing. Ann. Med. 23 637–642CrossRefGoogle Scholar
  50. Smith HO and Wilcox KW 1970 A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. J. Mol. Biol. 51 379–391CrossRefGoogle Scholar
  51. Southern EM 1975 Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98 503–517CrossRefGoogle Scholar
  52. Weatherall DJ, Old JM, Thein SL, Wainscoat JS and Clegg JB 1985 Prenatal diagnosis of the common haemoglobin disorders. J. Med. Genet. 22 422–430CrossRefGoogle Scholar
  53. Weiss B and Richardson CC 1967 Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. Proc. Natl. Acad. Sci. USA 57 1021–1028CrossRefGoogle Scholar
  54. Williams RJ 2003 Restriction endonucleases: Classification, properties, and applications. Mol. Biotechnol. 23 225–243CrossRefGoogle Scholar
  55. Wilson GG and Murray NE 1991 Restriction and modification systems. Annu. Rev. Genet. 25 585–627CrossRefGoogle Scholar
  56. Yoshimori R, Roulland-Dussoix D and Boyer HW 1972 R factor-controlled restriction and modification of deoxyribonucleic acid: Restriction mutants. J. Bacteriol. 112 1275–1279PubMedPubMedCentralGoogle Scholar

Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  1. 1.Dipartimento di Biologia e BiotecnologieSapienza, Università di RomaRomaItaly
  2. 2.Istituto di Biologia e Patologia Molecolari, CNR, RomaRomaItaly

Personalised recommendations