Abstract
Restriction endonucleases, which cleave DNA in a site-specific manner, are a fundamental tool of molecular biology. The discovery of endonucleases began in the 1960s and led to commercial availability in the early 1970s. The number of characterized enzymes continues to grow, as does the number of vendors and the size of their product lines. Although many similarities exist among endonucleases in terms of their structures, mechanisms, and uses, important differences remain. Now a staple of molecular biology, restriction endonucleases are an area of active research as models of site-specific DNA recognition, cleavage mechanism, in vivo function, and evolutionary origins. New enzymes continue to be discovered or developed by using protein engineering to modify the specificity of existing enzymes.
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References
Roberts, R. J. and Halford, S. E. (1993) Type II restriction endonucleases, in Nucleases, 2nd ed. (Linn, S. M., Lloyd, S. R., and Roberts, R. J., eds.), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 35–88.
Roberts, R. J. and Macelis, D. (1998) REBASE—restriction enzymes and methylases. Nucleic Acids Res. 26, 338–350.
Wilson, G. G. and Murray, N. E. (1991) Restriction and modification systems. Annu. Rev. Genet. 25, 585–627.
Stahl, F., Wende, W., Jeltsch, A., and Pingoud, A. (1998) The mechanism of DNA cleavage by the Type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis. Biol. Chem. 379, 467–473.
Smith, H. O., Annau, T. M., and Chandrasegaran, S. (1990) Finding sequence motifs in groups of functionally related proteins. Proc. Natl. Acad. Sci. USA. 87, 826–830.
Szomolanyi, E., Kiss, A., and Venetianer, P. (1980) Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. Gene. 10, 219–225.
Tao, T., Bourne, J. C., and Blumenthal, R. M. (1991) A family of regulatory genes associated with Type II restriction-modification systems. J. Bact. 173, 1367–1375.
Ives, C. L., Sohail, A., and Brooks, J. E. (1995) The regulatory C proteins from different restriction-modification systems can cross-complement. J. Bact. 177, 6313–6315.
Smith, H. O. and Nathans, D. (1973) A suggested nomenclature for bacterial host modification and restriction systems and their enzymes. J. Mol. Biol 81, 419–423.
Bickle, T. A. (1993) The ATP-dependent restriction enzymes, in Nucleases, 2nd ed. (Linn, S. M., Lloyd, S. R., and Roberts, R. J., eds.), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 35–88.
Pingoud, A. and Jeltsch, A. (1997) Recognition and cleavage of DNA by type-II restriction endonucleases. Eur. J. Biochem. 246, 1–22.
Kong, H. (1998) Analyzing the functional organization of a novel restriction modification system, the BcgI system. J. Mol. Biol. 279, 823–832.
Sears, L. E., Zhou, B., Aliotta, J. M., Morgan, R. D., and Kong, H. (1996) BaeI, another unusual BcgI-like restriction endonuclease. Nucleic Acids Res 24, 3590–3592.
Reuter, M., Kupper, D., Pein, C. D., Petrusyte, M., Siksnys, V., Frey, B., and Kruger, D. H. (1993) Use of specific oligonucleotide duplexes to stimulate cleavage of refractory DNA sites by restriction endonucleases. Anal. Biochem. 209, 232–237.
Oller, A. R., Broek, W. V., Conrad, M., and Topal, M. (1991) Ability of DNA and spermidine to affect the activity of restriction endonucleases from several bacterial species. Biochem. 30, 2543–2549.
Szybalski, W., Kim, S. C., Hasan, N., and Podhajska, A. J. (1991) Class-IIS restriction enzymes—a review. Gene 100, 13–26.
Janulaitis, A., Petrusyte, M., Maneliene, Z., Klimasauskas, S., and Butkus, V. (1992) Purification and properties of the Eco57I restriction endonuclease and methylase—prototypes of a new class (type IV). Nucleic Acids Res. 20, 6043–6049.
Belfort, M. and Roberts, R. J. (1997) Homing endonucleases: keeping the house in order. Nucleic Acids Res. 25, 3379–3388.
Meisel, A., Mackeldanz, P., Bickle, T. A., Kruger, D. H., and Schroeder, C. (1995) Type III restriction endonucleases translocate DNA in a reaction driven by recognition sitespecific ATP hydrolysis. EMBO J. 14, 2958–2966.
Kruger, D. H., Kupper, D., Meisel, A., Reuter, M., and Schroeder, C. (1995) The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes. FEMS Microbiol. Rev. 17, 177–184.
Mise, K. and Nakajima, K. (1985) Purification of a new restriction endonuclease, StyI, from Escherichia coli carrying the hsd+ minplasmid. Gene 33, 357–361.
Sam, M. D. and Perona, J. J. (1999) Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease. Biochem. 38, 6576–6586.
Wentzell, L. M., Nobbs, T. J., and Halford, S. E. (1995) The SfiI restriction endonuclease makes a 4-strand DNA break at two copies of its recognition sequence. J. Mol. Biol. 248, 581–595.
Sato, H., Suzuki, T., and Yamada, Y. (1990) Purification of restriction endonuclease from Acetobacter aceti IFO 3281 (AatII) and its properties. Agric. Biol. Chem. 54, 3319–3325.
Nobbs, T. J. and Halford, S. E. (1995) DNA cleavage at two recognition sites by the SfiI restriction endonuclease: salt dependence of cis and trans interactions between distand DNA sites. J. Mol. Biol. 252, 399–411.
Nobbs, T. J., Williams, S. A., Connolly, B. A., and Halford, S. E. (1998) Phosphorothioate substrates for the SfiI restriction endonuclease. Biol. Chem. 379, 599–604.
Kong, H. and Smith, C. L. (1998) Does BcgI, a uniquerestriction endonuclease, require two recognition sites for cleavage? Biol. Chem. 379, 605–609.
Kong, H. and Smith, C. L. (1997) Substrate DNA and cofactor regulate the activities of a multi-functional restriction-modification enzyme, Bcg I. Nucl. Acids Res. 25, 3687–3692.
Wah, D. A., Hirsch, J. A., Dorner, L. F., Schildkraut, I., and Aggarwal, A. K. (1997) Structure of the multimodular endonuclease FokI bound to DNA. Nature 388, 97–100.
Bitinaite, J., Wah, D. A., Aggarwal, A. K., and Schildkraut, I. (1998) FokI dimerization is required for DNA cleavage. Proc. Natl. Acad. Sci. 95, 10,570–10,575.
Reuter, M., Kupper, D., Meisel, A., Schroeder, C., and Kruger, D. H. (1998) Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J. Biol. Chem. 273, 8294–8300.
Pein, C. D., Reuter, M., Meisel, A., Cech, D., and Kruger, D. H. (1991) Activation of restriction endonuclease EcoRII does not depend on the cleavage of stimulator DNA. Nucleic Acids Res. 19, 5139–5142.
Conrad, M. and Topal, M. (1992) Modified DNA fragments activate NaeI cleavage of refractory DNA sites. Nucleic Acids Res. 20, 5127–5130.
Senesac, J. H. and Allen, J. R. (1995) Oligonucleaotide activation of the Type IIe restriction enzyme NaeI for digestion of refractory sites. BioTechniques 19, 990–993.
Jo, K. and Topal, M. D. (1995) DNA topoisomerase and recombinase activities in NaeI restriciton endonuclease. Science 267, 1817–1820.
Jo, K. and Topal, M. D. (1998) Step-wise DNA relaxation and decatenation by NaeI-43K. Nucleic Acids Res. 26, 2380–2384.
Yoo, O. J. and Agarwal, K. L. (1980) Cleavage of single strand oligonucleotides and bacteriophage phiX174 DNA by Msp I endonuclease. J. Biol. Chem. 255, 10,559–10,562.
Blakesley, R. W., Dodgson, J. B., Nes, I. F., and Wells, R. D. (1977) Duplex regions in “single-stranded” phiX174 DNA are cleaved by a restriction endonuclease from Haemophilus aegypius. J. Biol. Chem. 252, 7300–7306.
Shaw, P. C. and Mok, Y. K. (1993) XcmI as a universal restriction enzyme for singlestranded DNA. Gene 133, 85–89.
Robinson, C. R. and Sligar, S. G. (1998) Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease. Proc. Natl. Acad. Sci. USA 95, 2186–2191.
Lesser, D. R., Kurpiewski, M. R., and Jen-Jacobson, L. (1990) The energetic basis of specificity in the EcoRI endonuclease-DNA interaction. Science 250, 776–786.
Vermote, C. L. M. and Halford, S. E. (1992) EcoRV restriction endonuclease: communication between catalytic metal ions and DNA recognition. Biochemistry 31, 6082–6089.
Wenz, C., Selent, U., Wende, W., Jeltsch, A., Wolfes, H., and Pingoud, A. (1994) Protein engineering of the restriction endonuclease EcoRV: replacement of an amino acid residue in the DNA binding site leads to an altered selectivity towards unmodified and modified substrates. Biochim. Biophys. Acta. 1219, 73–80.
Lanio, T., Selent, U., Wnez, C., Wende, W., Schulz, A., Adiraj, M., Katti, S. B., and Pingoud, A. (1996) EcoRV-T94V: a mutant restriction endonuclease with an altered substrate specificity towards modified oligodeoxynucleotides. Protein Eng. 9, 1005–1010.
Schottler, S., Wenz, C., Lanio, A., Jeltsch, A., and Pingoud, A. (1998) Protein engineering of the restriction endonuclease EcoRV: structure-guided design of enzyme variants that recognize the base pairs flanking the recognition site. Eur. J. Biochem. 258, 184–191.
Lanio, T., Jeltsch, A., and Pingoud, A. (1998) Towards the design of rare cutting restriction endonucleases: using directed evolution to generate variants of EcoRV differing in their substrate specificity by two orders of magnitude. J. Mol. Biol. 283, 59–69.
Stahl, F., Wende, W., Jeltsch, A., and Pingoud, A. (1996) Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein. Proc. Natl. Acad. Sci. USA 93, 6175–6180.
Kim, Y. G. and Chandrasegaran, S. (1994) Chimeric restriction endonuclease. Proc. Natl. Acad. Sci USA 91, 883–887.
Kim, Y. G., Shi, Y., Berg, J. M., and Chandrasegaran, S. (1997) Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions. Gene 203, 43–49.
Kim, Y. G., Smith, J., Durgesha, M., and Chandrasegaran, S. (1998) Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain. Biol. Chem. 379, 489–495.
Dervan, P. B. (1992) Reagents for the site-specific cleavage of megabase DNA. Nature 359, 87,88.
Ebright, Y. W., Chen, Y., Pendergrast, P. S., and Ebright, R. H. (1992) Incorporation of an EDTA-metal complex at a rationally selected site within a protein: application to EDTA-iron DNA affinity cleaving with catabolite gene activator protein (CAP) and Cro. Biochem. 31, 10,664–10,670.
Pendergrast, P. S., Ebright, Y. W., and Ebright, R. H. (1994) High-specificity DNA cleavage agent: design and application to kilobase and megabase DNA substrates. Science 265, 959–962.
Shang, Z., Ebright, Y. W., Iler, N., Pendergrast, P. S., Echelard, Y., McMahon, A. P., Ebright, R. H., and Abate, C. (1994) DNA affinity cleaving analysis of homeodomain-DNA interaction: identification of homeodomain consensus sites in genomic DNA. Proc. Natl. Acad. Sci. USA 91, 118–122.
Koob, M., Burkiewicz, A., Kur, J., and Szybalski, W. (1992) RecA-AC: single-site cleavage of plasmids and chromosones at any predetermined restriction site. Nucleic Acids. Res. 20, 5831–5836.
Schoenfeld, T., Harper, T., and Slater, M. (1995) RecA cleavage and protection for genomic mapping and subcloning. Promega Notes 50, 9–14.
Strobel, S. A. and Dervan, P. B. (1991) Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation. Nature 350, 172–174.
Hung, L., Murray, E., Murray, W., Bandziulis, R., Lowery, R., Williams, R., and Noble, R. (1991) A blue/white cloning assay for quality control of DNA restriction and modifying enzymes. Promega Notes 33, 12,13.
Murray, E., Singer, K., Cash, K., and Williams, R. (1993) Cloning-qualified blunt end restriction enzymes: causes and cures for light blue colonies. Promega Notes 41, 1–5.
Turbett, G. R. and Sellner, L. N. (1996) Digestion of PCR and RT-PCR products with restriction endonucleases without prior purification or precipitation. Promega Notes 60, 23–27.
New England BioLabs 1998/99 Catalog (1998) New England BioLabs, 258,259.
Dallas-Yang, Q., Jiang, G., and Sladek, F. M., (1998) Digestion of terminal restriction endonuclease recognition sites on PCR products. BioTechniques 24, 582–584.
Moreira, R. F. and Noren, C. J. (1995) Minimum duplex requirements for restriction enzyme cleavage near the termini of linear DNA fragments. BioTechniques 19, 57–59.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Gel electrophoresis of DNA, in Molecular Cloning, A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, p. 65.
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Williams, R.J. (2001). Restriction Endonucleases and Their Uses. In: Schein, C.H. (eds) Nuclease Methods and Protocols. Methods in Molecular Biology™, vol 160. Humana Press. https://doi.org/10.1385/1-59259-233-3:409
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DOI: https://doi.org/10.1385/1-59259-233-3:409
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