Skip to main content
SpringerLink
Log in

Probing Amyloid-DNA Interaction with Nanofluidics

  • Protocol
  • First Online:
Bacterial Amyloids

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2538))

  • 440 Accesses

Abstract

Nanofluidics is an emerging methodology to investigate single biomacromolecules without functionalization and/or attachment of the molecules to a substrate. In conjunction with fluorescence microscopy, it can be used to investigate structural and dynamical aspects of amyloid-DNA interaction. Here, we summarize the methodology for fabricating lab-on-chip devices in relatively cheap polymer resins and featuring quasi one-dimensional nanochannels with a cross-sectional diameter of tens to a few hundred nanometers. Site-specific staining of amyloid-forming protein Hfq with a fluorescence dye is also described. The methodology is illustrated with two application studies. The first study involves assembling bacterial amyloid proteins such as Hfq on double-stranded DNA and monitoring the folding and compaction of DNA in a condensed state. The second study is about the concerted motion of Hfq on DNA and how this is related to DNA’s internal motion. Explicit details of procedures and workflows are given throughout.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
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

Institutional subscriptions

Similar content being viewed by others

References

  1. Abgrall P, Nguyen NT (2008) Nanofluidic devices and their applications. Anal Chem 80:2326–2341

    Article  CAS  Google Scholar 

  2. Reisner W, Pedersen JN, Austin RH (2012) DNA confinement in nanochannels: physics and biological applications. Rep Prog Phys 75:106601. https://doi.org/10.1088/0034-4885/75/10/106601

    Article  CAS  PubMed  Google Scholar 

  3. van der Maarel JRC, Zhang C, van Kan JA (2014) A nanochannel platform for single DNA studies: from crowding, protein DNA interaction, to sequencing of genomic information. Isr J Chem 54:1573–1588. https://doi.org/10.1002/ijch.201400091

    Article  CAS  Google Scholar 

  4. Frykholm K, Nyberg LK, Westerlund F (2017) Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools. Integr Biol 9:650–661. https://doi.org/10.1039/C7IB00085E

    Article  CAS  Google Scholar 

  5. Das SK, Austin MD, Akana MC, Deshpande P, Cao H, Xiao M (2010) Single molecule linear analysis of DNA in nanochannel labeled with sequence specific fluorescent probes. Nucleic Acids Res 38:e177–e177. https://doi.org/10.1093/nar/gkq673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lam E, Hastie A, Lin C, Ehrlich D, Das S, Austin M, Deshpande P, Cao H, Nagarajan N, Xiao M, Kwok P (2012) Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol 30:771–776

    Article  CAS  Google Scholar 

  7. Basak R, Liu F, Qureshi S, Gupta N, Zhang C, de Vries R, van Kan JA, Dheen ST, van der Maarel JRC (2019) Linearization and labeling of single-stranded DNA for optical sequence analysis. J Phys Chem Lett 10:316–321. https://doi.org/10.1021/acs.jpclett.8b03465

    Article  CAS  PubMed  Google Scholar 

  8. Guttula D, Liu F, van Kan JA, Arluison V, van der Maarel JRC (2018) Effect of HU protein on the conformation and compaction of DNA in a nanochannel. Soft Matter 14:2322–2328. https://doi.org/10.1039/C7SM02118F

    Article  CAS  PubMed  Google Scholar 

  9. Jiang K, Zhang C, Guttula D, Liu F, van Kan JA, Lavelle C, Kubiak K, Malabirade A, Lapp A, Arluison V, van der Maarel JRC (2015) Effects of Hfq on the conformation and compaction of DNA. Nucleic Acids Res 43:4332–4341. https://doi.org/10.1093/nar/gkv268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Malabirade A, Jiang K, Kubiak K, Diaz-Mendoza A, Liu F, van Kan JA, Berret J-F, Arluison V, van der Maarel JRC (2017) Compaction and condensation of DNA mediated by the C-terminal domain of Hfq. Nucleic Acids Res 45:7299–7308. https://doi.org/10.1093/nar/gkx431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Zhang C, Guttula D, Liu F, Malar PP, Ng SY, Dai L, Doyle PS, van Kan JA, van der Maarel JRC (2013) Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace. Soft Matter 9:9593. https://doi.org/10.1039/c3sm51214b

    Article  CAS  PubMed  Google Scholar 

  12. Yadav I, Rosencrans W, Basak R, van Kan JA, van der Maarel JRC (2020) Intramolecular dynamics of dsDNA confined to a quasi-one-dimensional nanochannel. Phys Rev Research 2:013294. https://doi.org/10.1103/PhysRevResearch.2.013294

    Article  CAS  Google Scholar 

  13. Yadav I, Basak R, Yan P, van Kan JA, Arluison V, van der Maarel JRC (2020) Role of internal DNA motion on the mobility of a nucleoid-associated protein. J Phys Chem Lett 11:8424–8429. https://doi.org/10.1021/acs.jpclett.0c02251

    Article  CAS  PubMed  Google Scholar 

  14. van Kan JA, Bettiol AA, Watt F (2006) Proton beam writing of three-dimensional nanostructures in hydrogen silsesquioxane. Nano Lett 6:579–582

    Article  Google Scholar 

  15. van Kan JA, Zhang C, Perumal Malar P, van der Maarel JRC (2012) High throughput fabrication of disposable nanofluidic lab-on-chip devices for single molecule studies. Biomicrofluidics 6:036502. https://doi.org/10.1063/1.4740231

    Article  CAS  PubMed Central  Google Scholar 

  16. van der Maarel JRC, Guttula D, Arluison V, Egelhaaf SU, Grillo I, Forsyth VT (2016) Structure of the H-NS–DNA nucleoprotein complex. Soft Matter 12:3636–3642. https://doi.org/10.1039/C5SM03076E

    Article  CAS  PubMed  Google Scholar 

  17. Wang YM, Austin RH, Cox EC (2006) Single molecule measurements of repressor protein 1D diffusion on DNA. Phys Rev Lett 97:048302. https://doi.org/10.1103/PhysRevLett.97.048302

    Article  CAS  PubMed  Google Scholar 

  18. Kabata H, Kurosawa O, Arai I, Washizu M, Margarson S, Glass R, Shimamoto N (1993) Visualization of single molecules of RNA polymerase sliding along DNA. Science 262:1561–1563. https://doi.org/10.1126/science.8248804

    Article  CAS  PubMed  Google Scholar 

  19. Blainey PC, van Oijen AM, Banerjee A, Verdine GL, Xie XS (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc Natl Acad Sci 103:5752–5757. https://doi.org/10.1073/pnas.0509723103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Graneli A, Yeykal CC, Robertson RB, Greene EC (2006) Long-distance lateral diffusion of human Rad51 on double-stranded DNA. Proc Natl Acad Sci 103:1221–1226. https://doi.org/10.1073/pnas.0508366103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kim JH, Larson RG (2007) Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules. Nucleic Acids Res 35:3848–3858. https://doi.org/10.1093/nar/gkm332

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Bonnet I, Biebricher A, Porté P-L, Loverdo C, Bénichou O, Voituriez R, Escudé C, Wende W, Pingoud A, Desbiolles P (2008) Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res 36:4118–4127. https://doi.org/10.1093/nar/gkn376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Davidson IF, Goetz D, Zaczek MP, Molodtsov MI, Huis in ‘t Veld PJ, Weissmann F, Litos G, Cisneros DA, Ocampo-Hafalla M, Ladurner R, Uhlmann F, Vaziri A, Peters J (2016) Rapid movement and transcriptional re-localization of human cohesin on DNA. EMBO J 35(2671–2685):10.15252/embj.201695402

    Google Scholar 

  24. Vestergaard CL, Blainey PC, Flyvbjerg H (2018) Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA. Nucleic Acids Res 46:2446–2458. https://doi.org/10.1093/nar/gky004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Hu T, Shklovskii BI (2007) How a protein searches for its specific site on DNA: the role of intersegment transfer. Phys Rev E 76:051909. https://doi.org/10.1103/PhysRevE.76.051909

    Article  CAS  Google Scholar 

  26. Gorman J, Greene EC (2008) Visualizing one-dimensional diffusion of proteins along DNA. Nat Struct Mol Biol 15:768–774. https://doi.org/10.1038/nsmb.1441

    Article  CAS  PubMed  Google Scholar 

  27. Mahmutovic A, Berg OG, Elf J (2015) What matters for lac repressor search in vivo—sliding, hopping, intersegment transfer, crowding on DNA or recognition? Nucleic Acids Res 43:3454–3464. https://doi.org/10.1093/nar/gkv207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Mondal A, Bhattacherjee A (2015) Searching target sites on DNA by proteins: role of DNA dynamics under confinement. Nucleic Acids Res 43:9176–9186. https://doi.org/10.1093/nar/gkv931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Tan C, Terakawa T, Takada S (2016) Dynamic coupling among protein binding, sliding, and DNA bending revealed by molecular dynamics. J Am Chem Soc 138:8512–8522. https://doi.org/10.1021/jacs.6b03729

    Article  CAS  PubMed  Google Scholar 

  30. Chow E, Skolnick J (2017) DNA internal motion likely accelerates protein target search in a packed nucleoid. Biophys J 112:2261–2270. https://doi.org/10.1016/j.bpj.2017.04.049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by Ministry of Education, Singapore (MOE) Academic Research Fund Grants (Tier 1 R-144-000-451-114 and Tier 2 MOE-T2EP50121-00030.

Author information

Authors and Affiliations

  1. Department of Physics, National University of Singapore, Singapore, Singapore

    Rajib Basak, Indresh Yadav, Jeroen A. van Kan & Johan R. C. van der Maarel

  2. Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris Saclay, CEA Saclay, Gif-sur-Yvette, France

    Véronique Arluison

  3. Université de Paris, Paris, France

    Véronique Arluison

Authors
  1. Rajib Basak
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Indresh Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Véronique Arluison
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jeroen A. van Kan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Johan R. C. van der Maarel
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. CEA Saclay, Lab Léon Brillouin UMR12 CEA/CNRS, Gif sur Yvette Cedex, France

    Véronique Arluison

  2. Synchrotron SOLEIL, Gif-sur-Yvette Cedex, France

    Frank Wien

  3. Departamento de Biología, University of Chile, Santiago, Chile

    Andrés Marcoleta

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Basak, R., Yadav, I., Arluison, V., van Kan, J.A., van der Maarel, J.R.C. (2022). Probing Amyloid-DNA Interaction with Nanofluidics. In: Arluison, V., Wien, F., Marcoleta, A. (eds) Bacterial Amyloids. Methods in Molecular Biology, vol 2538. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2529-3_20

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2529-3_20

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2528-6

  • Online ISBN: 978-1-0716-2529-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation