Skip to main content

Southern Blot Analysis of Large DNA Fragments

  • Protocol

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 125))

Abstract

Pulsed-field gel electrophoresis (PFGE) has been used successfully to generate physical maps of a large region from many genomes. In addition, PFGE is useful for determining the order of genes or markers more precisely than is possible with genetic linkage analysis. Since a book in the Methods in Molecular Biology series (1) has already been devoted to this subject, the aim of this chapter is to give protocols that were successfully used in our laboratory for the human mucin genes. Whenever possible, we refer to the relevant chapters of this book or other references in which strat-egies or techniques are discussed in detail.

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

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   199.99
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

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Burmeister M. (1992) Strategies for mapping large regions of mammalian genomes, in Pulsed-Field Gel Electrophoresis: Protocols, Methods and Theories, Methods in Molecular Biology, vol. 12 (Burmeister M., and Vlanovsky L., eds.), Humana, Totowa, NJ pp. 259–284.

    Chapter  Google Scholar 

  2. Chu G., Vollrath D., and Davis R. W. (1986) Separation of large DNA molecules by coutour clamped homogeneous electric fields. Science 234, 1582–1585.

    Article  PubMed  CAS  Google Scholar 

  3. Vollrath D. (1992) Resolving multimegabase DNA molecules using contour-clamped homogeneous electric fields (CHEF), in Pulsed-Field Gel Electrophoresis, Methods in Molecular Biology, vol. 12 (Burmeister M., and Vlanovsky L., eds.), Humana, Totowa, NJ, pp. 19–30.

    Chapter  Google Scholar 

  4. Galiègue-Zouitina S., Collyn-d’Hooghe M., Denis C., Mainardi À., Hildebrand M. P., Tilly H., Bastard C., and Kerckaert J. P. (1994) Molecular cloning of at(11;14)(q13;q32) translocation breakpoint centromeric to the BCL1-MTC. Genes, Chromosomes Cancer 11, 246–255.

    Article  PubMed  Google Scholar 

  5. Pigny P., Guyonnet-Dupérat V., Hill A. S., Pratt W. S., Galiègue-Zouitina S., Collynd’Hooghe M., Laine A., Van Seuningen I., Degand P., Gum J. R., Kim Y. S., Swallow D. M., Aubert J. P., and Porchet N. (1996) Human mucin genes assigned to 11p15.5: identification and organization of a cluster of genes. Genomics 38, 340–352.

    Article  PubMed  CAS  Google Scholar 

  6. Antequera F., Boyes J., and Byrd A. (1990)High levels of de novo methylation and altered chromatin structure at CpG islands. Cell 62, 503–514.

    Article  PubMed  CAS  Google Scholar 

  7. Barlow D. P. (1992)Preparation, restriction and hybridization analysis of mammalian genomic DNA for pulsed-field gel electrophoresis, in Pulsed-Field Gel Electrophoresis, Methods in Molecular Biology, vol. 12 (Burmeister M. and Vlanovsky L., eds.), Humana, Totowa, NJ, pp. 107–128.

    Chapter  Google Scholar 

  8. Overhauser J. (1992) Encapsulation of cells in agarose beads, in Pulsed-Field Gel Electrophoresis, Methods in Molecular Biology, vol. 12: (Burmeister M. and Vlanovsky L., eds.), Humana, Totowa, NJ, pp. 129–134.

    Chapter  Google Scholar 

  9. Boultwood J. (1994) Physical mapping of the human genome by pulsed field gel electrophoresis, in Protocols for Gene Analysis, Methods in Molecular Biology, vol. 31: (Harwood A. J., ed.), Humana, Totowa, NJ, pp. 121–134.

    Chapter  Google Scholar 

  10. Birren B. and Lai E. (1993) Pulsed Field Gel Electrophoresis. A Practical Guide. Academic, San Diego, CA.

    Google Scholar 

  11. Gendler S. J., Lancaster C. A., Taylor-Papadimitriou J., Duhig T., Peat N., Burchell J. emberton L., Lalani E., and Wilson D. (1990) Molecular cloning and expression of a human tumor-associated polymorphic epithelial mucin. J. Biol. Chem. 265, 15,286–15,293.

    PubMed  CAS  Google Scholar 

  12. Gum J. R., Byrd J. C., Hicks J. W., Toribara N. W., Lamport D. T. A., and Kim Y. S. (1989) Molecular cloning of human intestinal mucin cDNA. Sequence analysis and evi-dence for genetic polymorphism. J. Biol. Chem. 264, 6480–6487.

    PubMed  CAS  Google Scholar 

  13. Gum J. R., Hicks J. W., Swallow D. M., Lagace R. L., Byrd J. C., Lamport D. T. A., Siddiki B. and Kim Y. S. (1990) Molecular cloning of cDNA derived from a novel human intestinal mucin gene. Biochem. Biophys. Res. Commun. 171, 407–415.

    Article  PubMed  CAS  Google Scholar 

  14. Porchet N., Nguyen V.C., Dufossé J., Audié J. P., Guyonnet-Dupérat V., Gross M. S., Denis C., Degand P., Beinheim A., and Aubert J. P. (1991) Molecular cloning and chromosomal localization of a novel human tracheo-bronchial mucin cDNA containing tandemlyrepeated sequences of 48 base pairs. Biochem. Biophys. Res. Commun. 175, 414–422.

    Article  PubMed  CAS  Google Scholar 

  15. Guyonnet-Dupérat V. Audié J. P. Debailleul, V., Laine A., Buisine M. P., GaliègueZouitina S., Pigny P. Degand P., Aubert J. P., and Porchet N. (1995) Characterization of the human mucin gene MUC5AC: a consensus cysteine-rich domain for 11p15 mucin genes? Biochem. J. 305, 211–219.

    PubMed  Google Scholar 

  16. Dufosé J., Porchet N., Audié J. P., Guyonnet-Dupérat V., Laine A., Van Seuningen I., Marrakchi S., Degand P., and Aubert J. P. (1993) Degenerate 87 base pair tandem repeats create hydrophilic/hydrophobic alternating domains in human mucin peptides mapped to 11p15. Biochem. J. 293, 329–337.

    Google Scholar 

  17. Toribara N. W., Robertson A. M., Ho S. B., Kuo W. L., Gum E., Hicks J. W., Gum J. R., Byrd J. C., Siddiki B., and Kim Y. S. (1993) Human gastric mucin. Identification of a unique species by expression cloning. J. Biol. Chem. 268, 5879–5885.

    PubMed  CAS  Google Scholar 

  18. Burmeister M. (1992) Strategies for mapping large regions of mammalian genomes, in Pulsed-Field Gel Electrophoresis, Methods in Molecular Biology, vol. 12 (Burmeister M. and Vlanovsky L., eds.), Humana, Totowa, NJ, pp. 259–284.

    Chapter  Google Scholar 

  19. Bickmore W. A. and Byrd A. P. (1992) Use of restriction endonucleases to detect and isolate genes from mammalian cells, in Recombinant DNA, part G, Methods in Enzymology, vol. 216 (Wu R., ed.), Academic, San Diego, CA.

    Google Scholar 

  20. Guyonnet-Dupérat V. (1993) Etude des gènes de mucines humaines localisées en 11p15: mégacartographie et approche de l’organisation génomique de MUC5B et MUC5AC. Thèse de Doctorat d’Université en Sciences de la Vie et de la Santé, Lille, France.

    Google Scholar 

  21. Pigny P. (1997) Les gènes de mucines humaines localisées en 11p15-Polymorphisme, cartographie physique et approches de régulation. Thèse de Doctorat d’Université des Sciences de la Vie et de la Santé.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2000 Humana Press Inc.

About this protocol

Cite this protocol

Porchet, N., Aubert, JP. (2000). Southern Blot Analysis of Large DNA Fragments. In: Corfield, A.P. (eds) Glycoprotein Methods and Protocols. Methods in Molecular Biology™, vol 125. Humana Press. https://doi.org/10.1385/1-59259-048-9:313

Download citation

  • DOI: https://doi.org/10.1385/1-59259-048-9:313

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-720-5

  • Online ISBN: 978-1-59259-048-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics