Skip to main content
SpringerLink
Log in

Analysis of Type II Restriction Endonucleases that Interact with Two Recognition Sites

  • Chapter
Restriction Endonucleases

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 14))

Abstract

Many students of molecular biology know for certain that the Type II restriction endonucleases are dimeric proteins that recognise a palindromic DNA sequence, 4–8 bp (base pairs) long, and cut this single sequence with exquisite specificity. This idea is also propagated by many text-books and commonly-used laboratory manuals in molecular biology (viz. Sambrook and Russell 2001). Like most generalisations, it is in fact wrong. The Type II restriction enzymes encompass not only dimeric proteins but also monomers, tetramers and higher assemblies. Their recognition sequences are not always unique palindromes but can instead be degenerate, discontinuous or asymmetric sequences (Roberts et al. 2003b). The sites at which they cleave the DNA are not necessarily within the recognition sequence. Many cleave the DNA at fixed positions several bp away from their recognition sequence. Most excitingly, many of the Type II enzymes have to interact with two copies of their recognition sites before they can cleave DNA(Halford 2001).When these enzymes bind two sites in the same DNA molecule, the intervening DNA is sequestered in a loop. DNA-looping interactions play central roles in many genetic processes (Schleif 1992; Rippe et al. 1995), such as replication, recombination and transcription, but these processes are often difficult to study. In contrast, the reactions of restriction enzymes can be monitored by a variety of simple techniques, so these enzymes make good tools for analysing the nature of long-range interactions between distant DNA sites.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Adzuma K, Mizuuchi K (1989) Interaction of proteins located at a distance along DNA: mechanism of target immunity in the Mu DNA strand-transfer reaction. Cell 57:41–47

    Article  PubMed  CAS  Google Scholar 

  • Bath AJ, Milsom SE, Gormley NA, Halford SE (2002) Many Type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J Biol Chem 277:4024–4033

    Article  PubMed  CAS  Google Scholar 

  • Bilcock DT, Daniels LE, Bath AJ, Halford SE (1999) Reactions of Type II restriction endonucleases with 8-base pair recognition sites. J Biol Chem 274:36379–36386

    Article  PubMed  CAS  Google Scholar 

  • Bilcock DT, Halford SE (1999) DNA restriction dependent on two recognition sites: activities of the SfiI restriction-modification system in Escherichia coli. Mol Micro-biol 31:1243–1254

    Article  CAS  Google Scholar 

  • Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I (1998) FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci USA 95:10564–10569

    Article  PubMed  Google Scholar 

  • Daniels LE, Wood KE, Scott DJ, Halford SE (2003) Subunit assembly for DNA cleavage by restriction endonuclease SgrAI. J Mol Biol 327:579–591

    Article  PubMed  CAS  Google Scholar 

  • Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber R (2000) Structure of the tetra-meric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat Struct Biol 7:792–799

    Article  PubMed  CAS  Google Scholar 

  • Dunn TM, Hahn S, Ogden S, Schleif RF (1984). An operator at-280 base pairs that is required for repression of araBAD operon promotor: addition of helical turns between the operator and promoter cyclically hinders repression. Proc Natl Acad Sci USA 81:5017–5020

    Article  PubMed  CAS  Google Scholar 

  • Embleton ML, Williams SA, Watson MA, Halford, SE (1999) Specificity from the synapsis of DNA elements by the SfiI endonuclease. J Mol Biol 289:785–797

    Article  PubMed  CAS  Google Scholar 

  • Embleton ML, Siksnys V, Halford SE (2001) DNA cleavage reactions by Type II restriction enzymes that require two copies of their recognition sites. J Mol Biol 311:503–514

    Article  PubMed  CAS  Google Scholar 

  • Erskine SG, Baldwin GS, Halford SE (1997) Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease. Biochemistry 36:7567–7576

    Article  PubMed  CAS  Google Scholar 

  • Friedhoff P, Lurz R, Lueder G, Pingoud A (2001) Sau3AI, a monomeric Type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops. J Biol Chem 276:23581–588

    Article  PubMed  CAS  Google Scholar 

  • Gabbara S, Bhagwat AS (1992) Interaction of EcoRII endonuclease with DNA substrates containing single recognition sites. J Biol Chem 267:18623–630

    PubMed  CAS  Google Scholar 

  • Gormley NA, Hillberg AL, Halford SE (2002) The Type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence. J Biol Chem 277:4034–4041

    Article  PubMed  CAS  Google Scholar 

  • Gowers DM, Halford SE (2003) Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling. EMBO J 22:1410–1418

    Article  PubMed  CAS  Google Scholar 

  • Halford SE (2001) Hopping, jumping and looping by restriction enzymes. Biochem Soc Trans 29:363–373

    Article  PubMed  CAS  Google Scholar 

  • Halford SE, Johnson NP, Grinsted J (1980) The EcoRI restriction endonuclease with bacteriophage lambda DNA: kinetic studies. Biochem J 191:581–592

    PubMed  CAS  Google Scholar 

  • Huai Q, Colandene JD, Topal MD, Ke H (2001) Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nat Struct Biol 8:665–669

    Article  PubMed  CAS  Google Scholar 

  • Kong H (I998) Analyzing the functional organization of a novel restriction modification system, the BcgI system. J Mol Biol 279:823–832

    Article  Google Scholar 

  • Kong H, Smith CL (I998) Does BcgI,a unique restriction endonuclease, require two sites for cleavage? Biol Chem 379:605–609

    Google Scholar 

  • Krämer H, Niemöller M, Amouyal M, Revet B, von Wicklen-Bergmann B, Müller-Hill B (1987) lac repressor forms loops with linear DNA carrying two suitably spaced lac operators. EMBO J 6:1481–1491

    PubMed  Google Scholar 

  • Krüger DH, Barcak GJ, Reuter M, Smith HO (1988) EcoRII can be activated to cleave refractory DNA recognition sites. Nucleic Acids Res 11:3997–4008

    Article  Google Scholar 

  • Lagunavicius A, Sasnauskas G, Halford SE, Siksnys V (2003) The metal-independent Type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre. J Mol Biol 326:1051–1064

    Article  PubMed  CAS  Google Scholar 

  • Levene SD, Donahue C, Boles TC, Cozzarelli NR (1995) Analysis of the structure of dimeric DNA catenanes by electron microscopy. Biophys J 69:1036–1045

    Article  PubMed  CAS  Google Scholar 

  • Milsom SE, Halford SE, Embleton ML, Szczelkun MD (2001) Analysis of DNA looping interactions by Type II restriction enzymes that require two copies of their recognition sites. J Mol Biol 311:515–527

    Article  PubMed  CAS  Google Scholar 

  • Nobbs TJ, Halford SE (1995) DNA cleavage at two recognition sites by the SfiI restriction-endonuclease — salt dependence of cis and trans interactions between distant DNA sites. J Mol Biol 252:399–411

    Article  PubMed  CAS  Google Scholar 

  • Nobbs TJ, Szczelkun MD, Wentzell, Halford SE (1998) Excision by the SfiI restriction endonuclease. J Mol Biol 281:419–432

    Article  PubMed  CAS  Google Scholar 

  • Oller AR, Van den Broek W, Conrad M, Topal MD (1991) Ability of DNA and spermidine to affect the activity of restriction endonucleases from several bacterial species. Biochemistry 30:2543–2549

    Article  PubMed  CAS  Google Scholar 

  • Parker CN, Halford SE (1991) Dynamics of long-range interactions on DNA-the speed of synapsis during site-specific recombination by resolvase. Cell 66:781–791

    Article  PubMed  CAS  Google Scholar 

  • Pingoud A, Jeltsch A (2001) Structure and function of Type II restriction endonucleases. Nucleic Acids Res 29:3705–3727

    Article  PubMed  CAS  Google Scholar 

  • Reuter M, Kupper D, Pein CD, Petrusyte M, Siksnys V, Frey B, Kruger DH (1993) Use of specific oligonucleotide duplexes to stimulate cleavage of refractory DNA sites by restriction endonucleases. Anal Biochem 209:232–237

    Article  PubMed  CAS  Google Scholar 

  • Reuter M, Kupper D, Meisel A, Schroeder C, Kruger DH (1998) Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J Biol Chem 273:8294–8300

    Article  PubMed  CAS  Google Scholar 

  • Rippe, K (2001) Making contacts on a nucleic acid polymer. Trends Biochem Sci 26:733–740

    Article  PubMed  CAS  Google Scholar 

  • Rippe K, von Hippel PH, Langowski J (1995) Action at a distance: DNA-looping and initiation of transcription. Trends Biochem Sci 20:500–6

    Article  PubMed  CAS  Google Scholar 

  • Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SKh, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Ianulaitis A, Ieltsch A, Iosephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY(2003a) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31:1805–1812

    Article  PubMed  CAS  Google Scholar 

  • Roberts RJ, Vincze T, Posfai J, Macelis D (2003b) REBASE: restriction enzymes and methyltransferases. Nucleic Acids Res 31:418–420

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  • Sapranauskas R, Sasnauskas G, Lagunavicius A, Vilkaitis G, Lubys A, Siksnys V (2000) Novel subtype of Type IIs restriction enzymes BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium. J Biol Chem 275: 30878–885

    Article  PubMed  CAS  Google Scholar 

  • Schleif R (1992) DNA looping. Annu Rev Biochem 61:199–223

    Article  PubMed  CAS  Google Scholar 

  • Siksnys V, Skirgaila R, Sasnauskas G, Urbanke C, Cherny D, Grazulis S, Huber R (1999) The Cfr10I restriction enzyme is functional as a tetramer. J Mol Biol 291:1105–1118

    Article  PubMed  CAS  Google Scholar 

  • Soundararajan M, Chang Z, Morgan RD, Heslop P, Connolly BA(2002) DNA binding and recognition by the IIs restriction endonuclease MboII. J Biol Chem 277:887–895

    Article  PubMed  CAS  Google Scholar 

  • Stanford NP, Szczelkun MD, Marko JF, Halford SE (2000) One-and three-dimensional pathways for proteins to reach specific DNA sites. EMBO J 19:6546–6557

    Article  PubMed  CAS  Google Scholar 

  • Szczelkun MD, Halford SE (1996) Recombination by resolvase to analyze DNA communications by the SfiI restriction-endonuclease. EMBO J 15 1460–1469

    PubMed  CAS  Google Scholar 

  • Szczelkun MD, Dillingham MS, Janscak P, Firman K. Halford SE (1996) Repercussions of DNA tracking by the Type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates. EMBO J 15:6335–6347

    PubMed  CAS  Google Scholar 

  • Terry BJ, Jack WE, Modrich P (1987) Mechanism of specific site location and DNA cleavage by EcoRI endonuclease Gene Amplif Anal 5:103–118

    PubMed  CAS  Google Scholar 

  • Thomas M, Davis RW (1975) Studies on the cleavage of bacteriophage lambda DNA with EcoRI restriction endonuclease. J Mol Biol 91:315–328

    Article  PubMed  CAS  Google Scholar 

  • Topal MD, Thrsher RJ, Conrad M, Griffth J (1991) NaeI endonuclease binding to pBR 322 DNA induces looping. Biochemistry 30:2006–2010

    Article  PubMed  CAS  Google Scholar 

  • Vanamee ES, Santaga S, Aggarwal AK (2001) FokI requires two specific DNA sites for cleavage. J Mol Biol 309:69–78

    Article  PubMed  CAS  Google Scholar 

  • Vipond IB, Baldwin GS, Oram M, Erskine SG, Wentzell LM, Szczelkun MD, Nobbs TJ, Halford SE (1995) Ageneral assay for restriction endonucleases and other DNA-modifying enzymes with plasmid substrates. Mol Biotech 4:259–268

    Article  CAS  Google Scholar 

  • Vologodskii AV, Cozzarelli NR (1994) Conformational and thermodynamic properties of supercoiled DNA. Annu Rev Biophys Biomol Struct 23:609–643

    Article  PubMed  CAS  Google Scholar 

  • Vologodskii AV, Cozzarelli NR (1996) Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. DNA. Biophys J 70:2548–2556

    Article  CAS  Google Scholar 

  • Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK (1998) Structure of FokI has implications for DNAcleavage. Proc Natl Acad Sci USA 95:10570–10575

    Article  PubMed  Google Scholar 

  • Waters TR, Connolly BA (1992) Continuous spectrophotometric assay for restriction endonucleases using synthetic oligodeoxynucleotides and based on the hyperchromic effect. Anal Biochem 204:204–209

    Article  PubMed  CAS  Google Scholar 

  • Watson MA, Gowers DM, Halford SE (2000) Alternative geometries of DNA looping: an analysis using the SfiI endonuclease. J Mol Biol 298:461–475

    Article  PubMed  CAS  Google Scholar 

  • Wentzell LM, Halford SE (1998) DNA looping by the SfiI restriction endonuclease. J Mol Biol 281:433–444

    Article  PubMed  CAS  Google Scholar 

  • Wentzell LM, Nobbs TJ, Halford SE (1995) The SfiI restriction-endonuclease makes a 4strand DNA break at 2 copies of its recognition sequence. J Mol Biol 248:581–595

    Article  PubMed  CAS  Google Scholar 

  • Williams SA, Halford SE (2001) SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site. Nucleic Acids Res 29: 1476–1483

    Article  PubMed  CAS  Google Scholar 

  • Williams SA, Halford SE (2002) Communications between catalytic sites in the protein DNA synapse by the SfiI endonuclease. J Mol Biol 318:387–394

    Article  PubMed  CAS  Google Scholar 

  • Yang CC, Topal MD (1992) Nonidentical DNA-binding sites of endonuclease NaeI recognize different families of sequences flanking the recognition site Biochemistry 31:9657–9664

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, School of Medical Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK

    A. J. Welsh, S. E. Halford & D. J. Scott

Authors
  1. A. J. Welsh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. E. Halford
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. D. J. Scott
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institute for Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 58, 35392, Giessen, Germany

    Alfred M. Pingoud

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Welsh, A.J., Halford, S.E., Scott, D.J. (2004). Analysis of Type II Restriction Endonucleases that Interact with Two Recognition Sites. In: Pingoud, A.M. (eds) Restriction Endonucleases. Nucleic Acids and Molecular Biology, vol 14. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18851-0_11

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-18851-0_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-62324-0

  • Online ISBN: 978-3-642-18851-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation