Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Solid-state nanopore fabrication by automated controlled breakdown


Solid-state nanopores are now well established as single-biomolecule sensors that hold great promise as sensing elements in diagnostic and sequencing applications. However, until recently this promise has been limited by the expensive, labor-intensive, and low-yield methods used to fabricate low-noise and precisely sized pores. To address this problem, we pioneered a low-cost and scalable solid-state nanopore fabrication method, termed controlled breakdown (CBD), which is rapidly becoming the method of choice for fabricating solid-state nanopores. Since its initial development, nanopore research groups around the world have applied and adapted the CBD method in a variety of ways, with varying levels of success. In this work, we present our accumulated knowledge of nanopore fabrication by CBD, including a detailed description of the instrumentation, software, and procedures required to reliably fabricate low-noise and precisely sized solid-state nanopores with a yield of >85% in less than 1 h. The assembly instructions for the various custom instruments can be found in the Supplementary Manual, and take approximately a day to complete, depending on the unit that the user is building and their level of skill with mechanical and electrical assembly. Unlike traditional beam-based nanopore fabrication technologies, the methods presented here are accessible to non-experts, lowering the cost of, and technical barriers to, fabricating nanoscale pores in thin solid-state membranes.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Overview of the workflow for nanopore fabrication by CBD and beam-based methods.
Fig. 2: Overview of custom-built hardware.
Fig. 3: Overview of the disposable parts and hardware.
Fig. 4: Stage transition diagram for the nanopore automation algorithm.
Fig. 5: Overview of automated nanopore fabrication and conditioning processes.
Fig. 6: Overview of automated nanopore size and noise measurements.
Fig. 7: Typical pore fabrication and results.
Fig. 8: Results of noise, speed, and precision tests performed on several nanopores fabricated using the presented procedure.
Fig. 9: Results of a typical sensing experiment.

Data availability

Data for all graphs is available from the corresponding author upon reasonable request.

Code availability

An executable version of the custom software presented (CBD Soft) is freely available for non-commercial uses, as outlined in the End-User License Agreement in the installer.


  1. 1.

    Yusko, E. C. et al. Real-time shape approximation and fingerprinting of single proteins using a nanopore. Nat. Nanotechnol. 12, 360–367 (2017).

    CAS  PubMed  Google Scholar 

  2. 2.

    Briggs, K., Kwok, H. & Tabard-Cossa, V. Automated fabrication of 2-nm solid-state nanopores for nucleic acid analysis. Small 10, 2077–2086 (2014).

    CAS  PubMed  Google Scholar 

  3. 3.

    Wanunu, M. Nanopores: a journey towards DNA sequencing. Phys. Life Rev. 9, 125–158 (2012).

    PubMed  PubMed Central  Google Scholar 

  4. 4.

    Brown, C. G. & Clarke, J. Nanopore development at oxford nanopore. Nat. Biotechnol. 34, 810 (2016).

    CAS  PubMed  Google Scholar 

  5. 5.

    Morin, T. J. et al. A handheld platform for target protein detection and quantification using disposable nanopore strips. Sci. Rep. 8, 1–12 (2018).

    Google Scholar 

  6. 6.

    Quick, J. et al. Real-time, portable genome sequencing for ebola surveillance. Nature 530, 228–232 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Derrington, I. M. et al. Nanopore DNA sequencing with MspA. Proc. Natl Acad. Sci. USA 107, 16060–5 (2010).

    CAS  PubMed  Google Scholar 

  8. 8.

    Loman, N. J., Quick, J. & Simpson, J. T. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods 12, 733–735 (2015).

    CAS  PubMed  Google Scholar 

  9. 9.

    Szalay, T. & Golovchenko, J. A. De novo sequencing and variant calling with nanopores using PoreSeq. Nat. Biotechnol. 33, 1087–1091 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Jain, M. et al. Improved data analysis for the MinION nanopore sequencer. Nat. Methods 12, 351–356 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146–1153 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Bayley, H. Nanopore sequencing: from imagination to reality. Clin. Chem. 61, 25–31 (2015).

    CAS  PubMed  Google Scholar 

  13. 13.

    Manrao, E. A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349–53 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Cherf, G. M. et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat. Biotechnol. 30, 344–8 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Bayley, H. Getting to the bottom of the well. Nat. Nanotechnol. 12, 1116 (2017).

    CAS  PubMed  Google Scholar 

  16. 16.

    Galenkamp, N. S., Soskine, M., Hermans, J., Wloka, C. & Maglia, G. Direct electrical quantification of glucose and asparagine from bodily fluids using nanopores. Nat. Commun. 9, 1–8 (2018).

    CAS  Google Scholar 

  17. 17.

    Rodriguez-Larrea, D. & Bayley, H. Multistep protein unfolding during nanopore translocation. Nat. Nanotechnol. 8, 288–295 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Benner, S. et al. Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore. Nat. Nanotechnol. 2, 718–724 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Nivala, J., Marks, D. B. & Akeson, M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat. Biotechnol. 31, 247–250 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Nivala, J., Mulroney, L., Li, G., Schreiber, J. & Akeson, M. Discrimination among protein variants using an unfoldase-coupled nanopore. ACS Nano 8, 12365–12375 (2014).

    CAS  PubMed  Google Scholar 

  21. 21.

    Wallace, E. V. B. et al. Identification of epigenetic DNA modifications with a protein nanopore. Chem. Commun. 46, 8195–8197 (2010).

    CAS  Google Scholar 

  22. 22.

    Howorka, S. & Siwy, Z. S. Nanopores as protein sensors. Nat. Biotechnol. 30, 506–507 (2012).

    CAS  PubMed  Google Scholar 

  23. 23.

    Briggs, K. et al. DNA translocations through nanopores under nanoscale preconfinement. Nano Lett. 18, 660–668 (2018).

    CAS  PubMed  Google Scholar 

  24. 24.

    Bell, N. A. W., Chen, K., Ghosal, S., Ricci, M. & Keyser, U. F. Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore. Nat. Commun. 8, 380 (2017).

    PubMed  PubMed Central  Google Scholar 

  25. 25.

    Morin, T. J. et al. Nanopore-based target sequence detection. PLoS ONE 11, e0154426 (2016).

    PubMed  PubMed Central  Google Scholar 

  26. 26.

    Atas, E., Singer, A. & Meller, A. DNA sequencing and bar-coding using solid-state nanopores. Electrophoresis 33, 3437–3447 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Beamish, E., Tabard-cossa, V. & Godin, M. Identifying structure in short DNA scaffolds using solid-state nanopores. ACS Sens. 2, 1814–1820 (2017).

    CAS  PubMed  Google Scholar 

  28. 28.

    Kong, J., Bell, N. A. W. & Keyser, U. F. Quantifying nanomolar protein concentrations using designed DNA carriers and solid-state nanopores. Nano Lett. 16, 3557–3562 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. 29.

    Singer, A. et al. Nanopore based sequence specific detection of duplex DNA for genomic profiling. Nano Lett. 10, 738–742 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Tabard-cossa, V. et al. Single-molecule bonds characterized by solid-state nanopore force spectroscopy. ACS Nano 3, 3009–3014 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Karau, P. & Tabard-cossa, V. Capture and translocation characteristics of short branched DNA labels in solid-state nanopores. ACS Sens. 3, 1308–1315 (2018).

    CAS  PubMed  Google Scholar 

  32. 32.

    Alibakhshi, M. A. et al. Picomolar fingerprinting of nucleic acid nanoparticles using solid-state nanopores. ACS Nano 11, 9701–9710 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Bell, N. A. W. & Keyser, U. F. Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores. Nat. Nanotechnol. 11, 1–28 (2016).

    Google Scholar 

  34. 34.

    Kowalczyk, S. W. et al. Single-molecule transport across an individual biomimetic nuclear pore complex. Nat. Nanotechnol. 6, 433–438 (2011).

    CAS  PubMed  Google Scholar 

  35. 35.

    Karawdeniya, B. I., Bandara, Y. M. N. D. Y., Nichols, J. W., Chevalier, R. B. & Dwyer, J. R. Surveying silicon nitride nanopores for glycomics and heparin quality assurance. Nat. Commun. 9, 1–8 (2018).

    CAS  Google Scholar 

  36. 36.

    Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Wu, M. Y., Krapf, D., Zandbergen, M., Zandbergen, H. & Batson, P. E. Formation of nanopores in a SiN/SiO2 membrane with an electron beam. Appl. Phys. Lett. 87, 1–4 (2005).

    Google Scholar 

  38. 38.

    Kwok, H., Briggs, K. & Tabard-Cossa, V. Nanopore fabrication by controlled dielectric breakdown. PLoS ONE 9, e92880 (2014).

    PubMed  PubMed Central  Google Scholar 

  39. 39.

    Briggs, K. et al. Kinetics of nanopore fabrication during controlled breakdown of dielectric membranes in solution. Nanotechnology 26, 084004 (2015).

    CAS  PubMed  Google Scholar 

  40. 40.

    Pud, S. et al. Self-aligned plasmonic nanopores by optically controlled dielectric breakdown. Nano Lett. 15, 7112–7117 (2015).

    PubMed  PubMed Central  Google Scholar 

  41. 41.

    Tahvildari, R., Beamish, E., Tabard-Cossa, V. & Godin, M. Integrating nanopore sensors within microfluidic channel arrays using controlled breakdown. Lab Chip 15, 1407–1411 (2015).

    CAS  PubMed  Google Scholar 

  42. 42.

    Gilboa, T., Zrehen, A., Girsault, A. & Meller, A. Optically-monitored nanopore fabrication using a focused laser beam. Sci. Rep. 8, 9765 (2018).

    PubMed  PubMed Central  Google Scholar 

  43. 43.

    Goto, Y., Yanagi, I., Matsui, K., Yokoi, T. & Takeda, K. Integrated solid-state nanopore platform for nanopore fabrication via dielectric breakdown, DNA-speed deceleration and noise reduction. Sci. Rep. 6, 31324 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Yanagi, I., Fujisaki, K., Hamamura, H. & Takeda, K. I. Thickness-dependent dielectric breakdown and nanopore creation on sub-10-nm-thick SiN membranes in solution. J. Appl. Phys. 121, 045301 (2017).

    Google Scholar 

  45. 45.

    Wang, Y., Chen, Q., Deng, T. & Liu, Z. Nanopore fabricated in pyramidal HfO2 film by dielectric breakdown method. Appl. Phys. Lett. 111, 143103 (2017).

    Google Scholar 

  46. 46.

    Feng, J. et al. Electrochemical reaction in single layer MoS2: Nanopores opened atom by atom. Nano Lett. 15, 3431–3438 (2015).

    CAS  PubMed  Google Scholar 

  47. 47.

    Kuan, A. T., Lu, B., Xie, P., Szalay, T. & Golovchenko, J. A. Electrical pulse fabrication of graphene nanopores in electrolyte solution. Appl. Phys. Lett. 106, 203109 (2015).

    PubMed  PubMed Central  Google Scholar 

  48. 48.

    Bandara, Y. M. N. D. Y., Karawdeniya, B. I. & Dwyer, J. R. Push-button method to create nanopores using a tesla-coil lighter. ACS Omega 4, 226–230 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Yamazaki, H., Hu, R., Zhao, Q. & Wanunu, M. Photothermally assisted thinning of silicon nitride membranes for ultrathin asymmetric nanopores. ACS Nano 12, 12472–12481 (2018).

    CAS  PubMed  Google Scholar 

  50. 50.

    Arcadia, C. E., Reyes, C. C. & Rosenstein, J. K. In situ nanopore fabrication and single-molecule sensing with microscale liquid contacts. ACS Nano 11, 4907–4915 (2017).

    CAS  PubMed  Google Scholar 

  51. 51.

    Kwok, H., Waugh, M., Bustamante, J., Briggs, K. & Tabard-Cossa, V. Long passage times of short ssDNA molecules through metallized nanopores fabricated by controlled breakdown. Adv. Funct. Mater. 24, 7745–7753 (2014).

    CAS  Google Scholar 

  52. 52.

    Tahvildari, R. et al. Manipulating electrical and fluidic access in integrated nanopore-microfluidic arrays using microvalves. Small 13, 1–7 (2017).

    Google Scholar 

  53. 53.

    Lam, M. H. et al. Entropic trapping of DNA with a nano filtered nanopore. ACS Appl. Nano Mater. 2, 4773–4781 (2019).

    CAS  Google Scholar 

  54. 54.

    Madejski, G. R. et al. Monolithic fabrication of NPN / SiN x dual membrane cavity for nanopore-based DNA sensing. Adv. Mater. Interfaces 6, 1900684 (2019).

    Google Scholar 

  55. 55.

    Ying, C. et al. Formation of single nanopores with diameters of 20–50 nm in silicon nitride membranes using laser-assisted controlled breakdown. ACS Nano 12, 11458–11470 (2018).

    CAS  PubMed  Google Scholar 

  56. 56.

    Carlsen, A. T., Briggs, K., Hall, A. R. & Tabard-Cossa, V. Solid-state nanopore localization by controlled breakdown of selectively thinned membranes. Nanotechnology 28, 085304 (2017).

    PubMed  PubMed Central  Google Scholar 

  57. 57.

    Wang, Y. et al. Fabrication of multiple nanopores in a SiNx membrane via controlled breakdown. Sci. Rep. 8, 1–9 (2018).

    Google Scholar 

  58. 58.

    Zhang, Y. et al. Nanopore formation via tip-controlled local breakdown using an atomic force microscope. Small Methods 3, 1900147 (2019).

    Google Scholar 

  59. 59.

    Abe, K. et al. The T2K experiment. Nucl. Instrum. Meth. 659, 106–135 (2011).

    CAS  Google Scholar 

  60. 60.

    Venkatesan, B. M. et al. Highly sensitive, mechanically stable nanopore sensors for DNA analysis. Adv. Mater. 21, 2771–2776 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61.

    Larkin, J. et al. Slow DNA transport through nanopores in hafnium oxide membranes. ACS Nano 7, 10121–8 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Russo, C. J. & Golovchenko, J. A. Atom-by-atom nucleation and growth of graphene nanopores. Proc. Natl Acad. Sci. USA 109, 5953–5957 (2012).

    CAS  PubMed  Google Scholar 

  63. 63.

    Liu, K., Feng, J., Kis, A. & Radenovic, A. Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano 8, 2504–2511 (2014).

    CAS  PubMed  Google Scholar 

  64. 64.

    Wu, M. et al. Control of shape and material composition of solid-state nanopores. Nano Lett. 9, 479–484 (2009).

    CAS  PubMed  Google Scholar 

  65. 65.

    Li, J. et al. Ion-beam sculpting at nanometre length scales. Nature 412, 166–169 (2001).

    CAS  PubMed  Google Scholar 

  66. 66.

    Deng, Y. et al. Precise fabrication of a 5 nm graphene nanopore with a helium ion microscope for biomolecule detection. Nanotechnology 28, 045302 (2017).

    PubMed  Google Scholar 

  67. 67.

    Hemamouche, A. et al. FIB patterning of dielectric, metallized and graphene membranes: a comparative study. Microelectron. Eng. 121, 87–91 (2014).

    CAS  Google Scholar 

  68. 68.

    Zahid, O. K. & Hall, A. R. in Helium Ion Microscope Fabrication of Solid-State Nanopore Devices for Biomolecule Analysis. 447–470. Hlawacek G., Gölzhäuser A. (eds). Helium Ion Microscopy. NanoScience and Technology (Springer International Publishing, 2016).

    Google Scholar 

  69. 69.

    Yang, J. et al. Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection. Nanotechnology 22, 285310 (2011).

    PubMed  Google Scholar 

  70. 70.

    Emmrich, D. et al. Nanopore fabrication and characterization by helium ion microscopy. Appl. Phys. Lett. 108, 163103 (2016).

    Google Scholar 

  71. 71.

    Yanagi, I., Akahori, R., Hatano, T. & Takeda, K. Fabricating nanopores with diameters of sub-1 nm to 3 nm using multilevel pulse-voltage injection. Sci. Rep. 4, 5000 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. 72.

    Bustamante, J. Synchronous Optical and Electrical Measurements of Single DNA Molecules Translocating Through a Solid-State Nanopore. MSc thesis, Univ. Ottawa (2014).

  73. 73.

    Briggs, K. Solid-State Nanopores: Fabrication, Application, and Analysis. PhD thesis, Univ. Ottawa (2018).

  74. 74.

    Tabard-Cossa, V., Trivedi, D., Wiggin, M., Jetha, N. N. & Marziali, A. Noise analysis and reduction in solid-state nanopores. Nanotechnology 18, 305505 (2007).

    Google Scholar 

  75. 75.

    Kowalczyk, S. W., Grosberg, A. Y., Rabin, Y. & Dekker, C. Modeling the conductance and DNA blockade of solid-state nanopores. Nanotechnology 22, 315101 (2011).

    PubMed  Google Scholar 

  76. 76.

    Beamish, E., Kwok, H., Tabard-Cossa, V. & Godin, M. Precise control of the size and noise of solid-state nanopores using high electric fields. Nanotechnology 23, 405301 (2012).

    PubMed  Google Scholar 

  77. 77.

    Wen, C., Zhang, Z. & Zhang, S. L. Physical model for rapid and accurate determination of nanopore size via conductance measurement. ACS Sens. 2, 1523–1530 (2017).

    CAS  PubMed  Google Scholar 

  78. 78.

    Frament, C. M., Bandara, N. & Dwyer, J. R. Nanopore surface coating delivers nanopore size and shape through conductance-based sizing. ACS Appl. Mater. Interfaces 5, 9330–9337 (2013).

    CAS  PubMed  Google Scholar 

  79. 79.

    Frament, C. M. & Dwyer, J. R. Conductance-based determination of solid-state nanopore size and shape: an exploration of performance limits. J. Phys. Chem. C. 116, 23315–23321 (2012).

    CAS  Google Scholar 

  80. 80.

    Fragasso, A., Pud, S. & Dekker, C. 1/f noise in solid-state nanopores is governed by access and surface regions. Nanotechnology 30, 395202 (2019).

    CAS  PubMed  Google Scholar 

Download references


We would like to acknowledge financial support from the Natural Sciences and Engineering Research Council of Canada (NSERC) i2i and CRD, as well as Ontario Centres of Excellence (OCE) VIP II grant programs. K.B. acknowledges the support of the Vanier Canadian Graduate Scholarship program. The authors would like to thank all members of the Tabard-Cossa and Godin laboratories at the University of Ottawa for their help in testing and troubleshooting the hardware, software, and protocols presented in this work.

Author information




K.B. and V.T.-C. developed the CBD method. K.B. and M.W. designed the software protocols. M.G. wrote the LabView code of the software. D.G., M.W., S.K., Q.I., A.M.J., S.B., D.L., and L.A. designed and built the hardware. M.W. and K.B. developed the particular protocols provided. M.W., K.B., and V.T.-C. wrote the manuscript.

Corresponding author

Correspondence to Vincent Tabard-Cossa.

Ethics declarations

Competing interests

V.T.-C. and K.B. hold several patents related to CBD. All other authors have no competing interests.

Additional information

Peer review information Nature Protocols thanks Sébastien Balme and Ralph Scheicher for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Manual

Component lists, assembly instructions, circuit diagrams and enlarged screenshots of our custom software

Reporting Summary

Supplementary Note 1

Detailed CAD designs and technical drawings

Supplementary Note 2

The PCB layout, in NI Ultiboard file format

Supplementary Software

An executable version of the custom software presented (CBD Soft). Updated versions will be available on our lab’s website (

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Waugh, M., Briggs, K., Gunn, D. et al. Solid-state nanopore fabrication by automated controlled breakdown. Nat Protoc 15, 122–143 (2020).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing