Skip to main content

Achilles’ Cleavage: Conferring the Specificities of DNA-Binding Molecules on Restriction Endonucleases

  • Chapter
Nucleic Acids and Molecular Biology

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 8))

  • 737 Accesses

Abstract

Achilles’ cleavage (AC) is a general method for combining the cleavage specificity of a restriction endonuclease with the binding specificity of other DNA-binding molecules. Restriction enzymes, which typically have recognition sequences of from 4 to 8 base pairs (bp) in length, cleave unmodified DNA from complex genomes at thousands or even millions of sites. By limiting the activity of these enzymes to a specific subset of these sites, the AC process makes it possible to cleave even the human genome at only a single site. The AC process can be used both as a means of obtaining basic information about the DNA-binding characteristics of the binding molecule employed and as a practical tool for creating unique cleavage specificities to analyze and manipulate DNA.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight 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

  • Arndt K, Fink GR (1986) GCN4 protein, a positive transcription factor in yeast, binds general control promoters at all 5′TGACTC3′ sequences. Proc Natl Acad Sci USA 83:8516–8520

    Article  PubMed  CAS  Google Scholar 

  • Cook PR (1984) A general method for preparing intact nuclear DNA. EMBO J 3:1837–1842

    PubMed  CAS  Google Scholar 

  • Demidov V, Frank-Kamenetskii MD, Egholm M, Buchardt O, Nielsen PE (1993) Sequence selective double-strand DNA cleavage by peptide nucleic acid (PNA) targeting using nuclease S1. Nucleic Acids Res 21:2103–2107

    Article  PubMed  CAS  Google Scholar 

  • Ferrin LJ, Camerini-Otero RD (1991) Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage. Science 254:1494–1497

    Article  PubMed  CAS  Google Scholar 

  • Garrison PN, Koob M, Barnes DL (1992) Physical mapping of the Saccharomyces cerevisea Ap4A Phosphorylase I-encoding gene by the Achilles’ cleavage method. Gene 111:131–134

    Article  PubMed  CAS  Google Scholar 

  • Gnirke A, Huxley C, Peterson K, Olson MV (1993) Microinjection of intact 200- to 500-kb fragments of YAC DNA into mammalian cells. Genomics 15:659–667

    Article  PubMed  CAS  Google Scholar 

  • Grimes E, Koob M, Szybalski W (1990) Achilles’ heel cleavage: creation of rare restriction sites in λ phage genomes and evaluation of additional operators, repressors and restriction/modification systems. Gene 90:1–7

    Article  PubMed  CAS  Google Scholar 

  • Hanvey JC, Shimizu M, Wells RD (1989) Site-specific inhibition of EcoRI restriction/modification by a DNA triple helix. Nucleic Acids Res 18:157–161

    Article  Google Scholar 

  • Koob M (1992) Conferring new cleavage specificities on restriction endonucleases. Methods Enzymol 216:321–329

    Article  PubMed  CAS  Google Scholar 

  • Koob M, Szybalski W (1990) Cleaving yeast and Escherichia coli genomes at a single site. Science 250:271–273

    Article  PubMed  CAS  Google Scholar 

  • Koob M, Szybalski W (1992) Preparing and using agarose microbeads. Methods Enzymol 216:13–20

    Article  PubMed  CAS  Google Scholar 

  • Koob M, Grimes E, Szybalski W (1988a) Conferring operator specificity on restriction endonucleases. Science 241:1084–1086

    Article  PubMed  CAS  Google Scholar 

  • Koob M, Grimes E, Szybalski W (1988b) Conferring new specificities upon restriction endonucleases by combining repressor-operator interaction and methylation. Gene 74:165–167

    Article  PubMed  CAS  Google Scholar 

  • Koob M, Burkiewicz A, Kur J, Szybalski W (1992) RecA-AC: single-site cleavage of plasmids and chromosomes at any predetermined restriction site. Nucleic Acids Res 20:5831–5836

    Article  PubMed  CAS  Google Scholar 

  • Kur J, Koob M, Burkiewicz A, Szybalski W (1992) A novel method for converting common restriction enzymes into rare cutters: integration host factor-mediated Achilles’ cleavage (IHF-AC). Gene 110:1–7

    Article  PubMed  CAS  Google Scholar 

  • Maher LJ, Wold B, Dervan PB (1989) Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. Science 245:725–730

    Article  PubMed  CAS  Google Scholar 

  • Nielsen PE, Egholm M, Berg RH, Buchardt O (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254:1497–1500

    Article  PubMed  CAS  Google Scholar 

  • Rigas B, Welcher AA, Ward DC, Weissman SM (1986) Rapid plasmid library screening using RecA-coated biotinylated probes. Proc Natl Acad Sci USA 90:9591–9595

    Article  Google Scholar 

  • Roca AI, Cox MM (1990) The RecA protein: structure and function. Crit Rev Biochem Mol Biol 25:415–456

    Article  PubMed  CAS  Google Scholar 

  • Smith CL, Cantor CR (1987) Purification, specific fragmentation, and separation of large DNA molecules. Methods Enzymol 155:449–467

    Article  PubMed  CAS  Google Scholar 

  • Strobel SA, Dervan PB (1991) Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation. Nature 350:172–174

    Article  PubMed  CAS  Google Scholar 

  • Strobel SA, Dervan PB (1992) Triple helix-mediated single-site enzymatic cleavage of megabase genomic DNA. Methods Enzymol 216:309–321

    Article  PubMed  CAS  Google Scholar 

  • Strobel SA, Doucette-Stamm LA, Riba L, Housman DE, Dervan PB (1991) Site-specific cleavage of human chromosome 4 mediated by triple-helix formation. Science 254:1639–1642

    Article  PubMed  CAS  Google Scholar 

  • Szybalski W (1991) Sequencing of prokaryotic and eukaryotic genomes without conventional cloning. In: Official Program and Abstracts. Human Genome III, San Diego, CA, p8

    Google Scholar 

  • Xu SY, Schildkraut I (1993) Protecting recognition sequences on DNA by a cleavage-deficient restriction endonuclease. BioTechniques 15:310–315

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1994 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Koob, M., Szybalski, W. (1994). Achilles’ Cleavage: Conferring the Specificities of DNA-Binding Molecules on Restriction Endonucleases. In: Eckstein, F., Lilley, D.M.J. (eds) Nucleic Acids and Molecular Biology. Nucleic Acids and Molecular Biology, vol 8. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-78666-2_16

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-78666-2_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-78668-6

  • Online ISBN: 978-3-642-78666-2

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics