Skip to main content

Preparation of Cytolysin A (ClyA) Nanopores

  • Protocol
  • First Online:
Nanopore Technology

Abstract

The ionic currents passing through nanopores can be used to sequence DNA and identify molecules at the single-molecule level. Recently, researchers have started using nanopores for the detection and analysis of proteins, providing a new platform for single-molecule enzymology studies and more efficient biomolecular sensing applications. For this approach, the homo-oligomeric Cytolysin A (ClyA) nanopore has been demonstrated as a powerful tool. Here, we describe a simple protocol allowing the production of ClyA nanopores. Monomers of ClyA are expressed in Escherichia coli and oligomerized in the presence of detergent. Subsequently, different oligomer variants are electrophoretically resolved and stored in a gel matrix for long-term use.

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 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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. Bezrukov SM, Vodyanoy I, Parsegian VA (1994) Counting polymers moving through a single ion channel. Nature 370:279–281

    Article  CAS  Google Scholar 

  2. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A 93:13770–13773

    Article  CAS  Google Scholar 

  3. Wanunu M, Morrison W, Rabin Y, Grosberg AY, Meller A (2009) Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient. Nat Nanotechnol 5:160–165

    Article  Google Scholar 

  4. Meller A, Nivon L, Brandin E, Golovchenko J, Branton D (2000) Rapid nanopore discrimination between single polynucleotide molecules. Proc Natl Acad Sci U S A 97:1079–1084

    Article  CAS  Google Scholar 

  5. Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW (1999) Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys J 77:3227–3233

    Article  CAS  Google Scholar 

  6. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265–270

    Article  CAS  Google Scholar 

  7. Luchian T, Shin SH, Bayley H (2003) Single-molecule covalent chemistry with spatially separated reactants. Angew Chem Int Ed Engl 42:3766–3771

    Article  CAS  Google Scholar 

  8. Movileanu L, Howorka S, Braha O, Bayley H (2000) Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore. Nat Biotechnol 18:1091–1095

    Article  CAS  Google Scholar 

  9. Soskine M, Biesemans A, Maglia G (2015) Single-molecule analyte recognition with ClyA nanopores equipped with internal protein adaptors. J Am Chem Soc 137:5793–5797

    Article  CAS  Google Scholar 

  10. Maglia G, Heron AJ, Stoddart D, Japrung D, Bayley H (2010) Analysis of single nucleic acid molecules with protein nanopores. Methods Enzymol 475:591–623

    Article  CAS  Google Scholar 

  11. Lin Y, Ying YL, Gao R, Long YT (2018) Single-molecule sensing with nanopore confinement: from chemical reactions to biological interactions. Chemistry 24:13064–13071

    Article  CAS  Google Scholar 

  12. Ramsay WJ, Bell NAW, Qing Y, Bayley H (2018) Single-molecule observation of the intermediates in a catalytic cycle. J Am Chem Soc 140:17538–17546

    Article  CAS  Google Scholar 

  13. Soskine M, Biesemans A, Moeyaert B, Cheley S, Bayley H, Maglia G (2012) An engineered ClyA nanopore detects folded target proteins by selective external association and pore entry. Nano Lett 12:4895–4900

    Article  CAS  Google Scholar 

  14. Mueller M, Grauschopf U, Maier T, Glockshuber R, Ban N (2009) The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459:726–730

    Article  CAS  Google Scholar 

  15. Franceschini L, Brouns T, Willems K, Carlon E, Maglia G (2016) DNA translocation through nanopores at physiological ionic strengths requires precise nanoscale engineering. ACS Nano 10:8394–8402

    Article  CAS  Google Scholar 

  16. Soskine M, Biesemans A, De Maeyer M, Maglia G (2013) Tuning the size and properties of ClyA nanopores assisted by directed evolution. J Am Chem Soc 135:13456–13463

    Article  CAS  Google Scholar 

  17. Van Meervelt V, Soskine M, Singh S, Schuurman-Wolters GK, Wijma HJ, Poolman B, Maglia G (2017) Real-time conformational changes and controlled orientation of native proteins inside a protein nanoreactor. J Am Chem Soc 139:18640–18646

    Article  Google Scholar 

  18. Galenkamp NS, Soskine M, Hermans J, Wloka C, Maglia G (2018) Direct electrical quantification of glucose and asparagine from bodily fluids using nanopores. Nat Commun 9:4085

    Article  Google Scholar 

  19. Wloka C, Van Meervelt V, van Gelder D, Danda N, Jager N, Williams CP, Maglia G (2017) Label-free and real-time detection of protein ubiquitination with a biological nanopore. ACS Nano 11:4387–4394

    Article  CAS  Google Scholar 

  20. Van Meervelt V, Soskine M, Maglia G (2014) Detection of two isomeric binding configurations in a protein-aptamer complex with a biological nanopore. ACS Nano 8:12826–12835

    Article  Google Scholar 

  21. Willems K, Van Meervelt V, Wloka C, Maglia G (2017) Single-molecule nanopore enzymology. Philos Trans R Soc Lond B Biol Sci 372:1726

    Article  Google Scholar 

  22. Miles G, Cheley S, Braha O, Bayley H (2001) The staphylococcal leukocidin bicomponent toxin forms large ionic channels. Biochemistry 40:8514–8522

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Giovanni Maglia .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Galenkamp, N.S., Van Meervelt, V., Mutter, N.L., van der Heide, N.J., Wloka, C., Maglia, G. (2021). Preparation of Cytolysin A (ClyA) Nanopores. In: Fahie, M.A. (eds) Nanopore Technology. Methods in Molecular Biology, vol 2186. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0806-7_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0806-7_2

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0805-0

  • Online ISBN: 978-1-0716-0806-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics