Skip to main content

High Throughput Cloning with Restriction Enzymes

  • Protocol
Book cover Structural Proteomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 426))

The systematic structural analysis of many target proteins involves generating expression clones in high throughput. This requires robust laboratory procedures and benefits from laboratory automation and data management systems. This chapter gives an overview of the Protein Structure Factory, a structural genomics project focusing on human proteins, and presents the authors' method for cloning bacterial expression clones with the restriction enzymes BamHI and NotI and compatible enzymes. PCR amplification, product purification and digestion and vector ligation were adapted to the 96-well microtiter plate format.

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

Access this chapter

Protocol
USD 49.95
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 EPUB and 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

References

  1. Büssow, K., Scheich, C., Sievert, V., Harttig, U., Schultz, J., Simon, B., Bork, P., Lehrach, H., and Heinemann, U. (2005). Structural Genomics of human proteins—target selection and generation of a public catalog of expression clones. Microb. Cell Fact. 4, 21.

    Article  PubMed  Google Scholar 

  2. Heinemann, U., Büssow, K., Mueller, U., and Umbach, P. (2003). Facilities and methods for the high-throughput crystal structure analysis of human proteins. Acc. Chem. Res. 36, 157–163.

    Article  CAS  PubMed  Google Scholar 

  3. Voss, S., and Skerra, A. (1997). Mutagenesis of a flexible loop in streptavidin leads to higher affinity for the Strep-tag II peptide and improved performance in recom-binant protein purification. Protein Eng. 10, 975–982.

    Article  CAS  PubMed  Google Scholar 

  4. Scheich, C., Sievert, V., and Büssow, K. (2003). An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography. BMC Biotechnol. 3, 12.

    Article  PubMed  Google Scholar 

  5. Berrow, N. S., Büssow, K., Coutard, B., Diprose, J., Ekberg, M., Folkers, G. E., Levy, N., Lieu, V., Owens, R. J., Peleg, Y., Pinaglia, C., Quevillon-Cheruel, S., Salim, L., Scheich, C., Vincentelli, R., and Busso, D. (2006). Recombinant protein expression and solubility screening: a comparative study. Acta Cryst. Section D 62, 1218–1226.

    Article  Google Scholar 

  6. Büssow, K., Quedenau, C., Sievert, V., Tischer, J., Scheich, C., Seitz, H., Hieke, B., Niesen, F. H., Götz, F., Harttig, U., and Lehrach, H. (2004). A catalogue of human cDNA expression clones and its application to structural genomics. Genome Biol. 5, R71.

    Article  PubMed  Google Scholar 

  7. Mueller, U., Nyarsik, L., Horn, M., Rauth, H., Przewieslik, T., Saenger, W., Lehrach, H., and Eickhoff, H. (2001). Development of a technology for automation and miniaturization of protein crystallization. J. Biotechnol. 85, 7–14.

    Article  CAS  PubMed  Google Scholar 

  8. Aslanidis, C., and de Jong, P. J. (1990). Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 18, 6069–6074.

    Article  CAS  PubMed  Google Scholar 

  9. Hartley, J. L., Temple, G. F., and Brasch, M. A. (2000). DNA cloning using in vitro site-specific recombination. Genome Res. 10, 1788–1795.

    Article  CAS  PubMed  Google Scholar 

  10. Busso, D., Delagoutte-Busso, B., and Moras, D. (2005). Construction of a set Gateway-based destination vectors for high-throughput cloning and expression screening in Escherichia coli. Anal. Biochem. 343, 313–321.

    Article  CAS  PubMed  Google Scholar 

  11. Rual, J. F., Hirozane-Kishikawa, T., Hao, T., Bertin, N., Li, S., Dricot, A., Li, N., Rosenberg, J., Lamesch, P., Vidalain, P. O., Clingingsmith, T. R., Hartley, J. L., Esposito, D., Cheo, D., Moore, T., Simmons, B., Sequerra, R., Bosak, S., Doucette-Stamm, L., Le Peuch, C., Vandenhaute, J., Cusick, M. E., Albala, J. S., Hill, D. E., and Vidal, M. (2004). Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res. 14, 2128–2135.

    Article  CAS  PubMed  Google Scholar 

  12. Li, C., and Evans, R. M. (1997). Ligation independent cloning irrespective of restriction site compatibility. Nucleic Acids Res. 25, 4165–4166.

    Article  CAS  PubMed  Google Scholar 

  13. Novy, R., Drott, D., Yaeger, K., and Mierendorf, R. (2001). Overcoming the codon bias of E.coli for enhanced protein expression. inNovations 12, 1–3.

    Google Scholar 

  14. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual. 2 ed, Cold Spring Harbor Laboratory, Cold Spring Harbor, N Y.

    Google Scholar 

  15. Inoue, H., Nojima, H., and Okayama, H. (1990). High efficiency transformation of Escherichia coli with plasmids. Gene 96, 23–28.

    Article  CAS  PubMed  Google Scholar 

  16. Engelke, D. R., Krikos, A., Bruck, M. E., and Ginsburg, D. (1990). Purification of Thermus aquaticus DNA polymerase expressed in Escherichia coli. Anal. Biochem. 191, 396–400.

    Article  CAS  PubMed  Google Scholar 

  17. Ralser, M., Querfurth, R., Warnatz, H. J., Lehrach, H., Yaspo, M. L., and Krobitsch, S. (2006). An efficient and economic enhancer mix for PCR. Biochem. Biophys. Res. Commun. 347, 747–751.

    Article  CAS  PubMed  Google Scholar 

  18. Staden, R., Judge, D. P., and Bonfield, J. K. (2003). Analysing sequences using the Staden package and EMBOSS. Introduction to Bioinformatics. (Krawetz, S. A., and Womble, D. D., eds.), A Theoretical and Practical Approach, Humana Press, Inc., Totowa, NJ.

    Google Scholar 

  19. Scheich, C., Kümmel, D., Soumailakakis, D., Heinemann, U., and Büssow, K. (2007) Vectors for co-expression of an unrestricted number of proteins. Nucleic Acids Research 35, e43.

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

The authors thank Janett Tischer for excellent technical assistance and critical reading of the manuscript. This work was funded by the German Federal Ministry of Education and Research (BMBF) in the National Genome Network programme (NGFN FKZ 01GR0472) and the SFB 633 of the German Research Foundation.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Sievert, V., Ergin, A., Büssow, K. (2008). High Throughput Cloning with Restriction Enzymes. In: Kobe, B., Guss, M., Huber, T. (eds) Structural Proteomics. Methods in Molecular Biology™, vol 426. Humana Press. https://doi.org/10.1007/978-1-60327-058-8_9

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-058-8_9

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-809-6

  • Online ISBN: 978-1-60327-058-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics