Restriction Enzymes

Mala Mani, Dana Farber Cancer Institute, Boston, Massachusetts, USA
Karthikeyan Kandavelou, Johns Hopkins University, Baltimore, Maryland, USA
Srinivasan Chandrasegaran, Johns Hopkins University, Baltimore, Maryland, USA

Published online: December 2007

DOI: 10.1002/9780470015902.a0000973.pub3

Type II restriction enzymes are the molecular scissors that catalyse the double-strand cleavage of deoxyribonucleic acid (DNA) at specific base sequences. They are essential tools for manipulating DNA including but not limited to cloning, analysis and sequencing. Recent advances have made it possible to design and engineer chimaeric nucleases to target specific DNA sites within a genome thus making them useful tools to carry out gene therapy.

Keywords: restriction enzymes; endonucleases; methylases; restriction–modification; recombinant DNA; chimaeric nucleases

Figure 1. Representation of multimodular enzymes. (a) FokI (a type IIs restriction enzyme); (b) I-TevI (a homing endonuclease). R, recognition domain; EN, endonuclease domain.
Figure 2. Representation of various chimaeric nucleases. ZF-EN, Ubx-EN and Gal4-EN were made by fusing the isolated nuclease domain (EN) of FokI to the zinc-finger motif, helix–turn–helix motif and Gal4, respectively. R, recognition domain; EN, endonuclease domain.
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 References
    book Mani M, Kandavelou K, Wu J and Chandrasegaran S (2003) "Restriction enzymes". In: Cooper DN (ed.) Nature Encyclopedia of the Human Genome, vol. 5, pp. 31–35. London: Nature Publishing Group.
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    Urnov FD, Miller JC, Lee YL et al. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435: 646–651.
 Further Reading
    Aggarwal AK and Wah DA (1998) Novel site-specific DNA endonuclease. Current Opinion in Structural Biology 8(1): 19–25.
    Berg JM (1995) Zinc finger domains: from prediction to design. Accounts of Chemical Research 28: 14–19.
    Bibikova M, Beumer K, Trautman JK and Carroll D (2003) Enhancing gene targeting with designed zinc finger nucleases. Science 300: 764.
    Bibikova M, Carroll D, Segal DJ et al. (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Molecular and Cellular Biology 21: 289–297.
    Bibikova M, Golic M, Golic KG and Carroll D (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc finger nucleases. Genetics 161: 1169–1175.
    Carroll D (1996) Homologous genetic recombination in Xenopus: mechanisms and implications for gene manipulation. Progress in Nucleic Acid Research and Molecular Biology 54: 101–125.
    Choo Y and Klug A (1997) Physical basis of a protein–DNA recognition code. Current Opinion in Structural Biology 7: 117–125.
    Durai S, Mani M, Kandavelou K et al. (2005) Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Research 33: 5978–5990.
    other Gormley NA, Watson MA and Halford SE (2005) Bacterial restriction–modification systems, doi.wiley.com/10.1038/npg.els.0003897.
    book Kandavelou K, Mani M, Durai S and Chandrasegaran S (2004) "Engineering and applications of chimeric nucleases". In: Pingoud AM (ed.) Nucleic Acids and Molecular Biology, vol. 14, pp. 413–434. Berlin: Springer-Verlag.
    Kandavelou K, Mani M, Durai S and Chandrasegaran S (2005) “Magic” scissors for genome surgery. Nature Biotechnology 23: 686–687.
    other Kandavelou K, Mani M, Reddy SPM and Chandrasegaran S (2005) Ligation: theory and practice, doi.wiley.com/10.1038/npg.els.0003838.
    Kim J-S and Pabo CO (1998) Getting a handhold on DNA: design of poly zinc finger proteins with femtomolar dissociation constants. Proceedings of the National Academy of Sciences of the USA 95: 2812–2817.
    Kim Y-G, Cha J and Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusion to FokI cleavage domain. Proceedings of the National Academy of Sciences of the USA 93: 1156–1160.
    Li L, Wu LP and Chandrasegaran S (1992) Functional domains in FokI restriction endonuclease. Proceedings of the National Academy of Sciences of the USA 89: 4275–4279.
    book New England Biolabs (2000–2001) New England Biolabs Catalog and Technical Reference. Beverly, MA: New England Biolabs.
    Porteus MH and Baltimore D (2003) Chimeric nucleases stimulate gene targeting in human cells. Science 300: 763.
    Roberts RJ and Cheng X (1998) Base flipping. Annual Review of Biochemistry 67: 181–198.
    book Roberts RJ and Halford SE (1993) "Type II restriction endonuclease". In: Linn SM, Lloyd RS and Roberts RJ (eds) Nuclease, pp. 35–38. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
    Roberts RJ, Vincze T, Posfai J and Macelis D (2003) REBASE: restriction enzymes and methyltransferase. Nucleic Acids Research 31: 418–421 (http://rebase.neb.com/rebase/rebase.html).
    Samuelson JC, Morgan RD, Benner JS et al. (2006) Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants. Nucleic Acids Research 34: 796–805.
    Sistla S and Rao DN (2004) S-Adenosyl-l-methionine-dependent restriction enzymes. Critical Reviews in Biochemistry and Molecular Biology 39: 1–19.
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Related Sub-Topics:

Techniques and Tools in Clinical Genetics | Gene Therapy | DNA Structure and Function | Techniques and Tools in Molecular Biology | DNA Damage and Repair | Enzymes: Structure and Action Mechanism | Nucleic Acids: Structure, Function, Metabolism
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Article Title: Restriction Enzymes
 
How to Cite close
Mani, Mala, Kandavelou, Karthikeyan, and Chandrasegaran, Srinivasan(Dec 2007) Restriction Enzymes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000973.pub3]