Solid-state nanopore fabrication by automated controlled breakdown.
Journal
Nature protocols
ISSN: 1750-2799
Titre abrégé: Nat Protoc
Pays: England
ID NLM: 101284307
Informations de publication
Date de publication:
01 2020
01 2020
Historique:
received:
06
02
2019
accepted:
10
10
2019
pubmed:
15
12
2019
medline:
18
4
2020
entrez:
15
12
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31836867
doi: 10.1038/s41596-019-0255-2
pii: 10.1038/s41596-019-0255-2
doi:
Substances chimiques
Membranes, Artificial
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
122-143Références
Yusko, E. C. et al. Real-time shape approximation and fingerprinting of single proteins using a nanopore. Nat. Nanotechnol. 12, 360–367 (2017).
pubmed: 27992411
Briggs, K., Kwok, H. & Tabard-Cossa, V. Automated fabrication of 2-nm solid-state nanopores for nucleic acid analysis. Small 10, 2077–2086 (2014).
pubmed: 24585682
Wanunu, M. Nanopores: a journey towards DNA sequencing. Phys. Life Rev. 9, 125–158 (2012).
pubmed: 22658507
pmcid: 3780799
Brown, C. G. & Clarke, J. Nanopore development at oxford nanopore. Nat. Biotechnol. 34, 810 (2016).
pubmed: 27504770
Morin, T. J. et al. A handheld platform for target protein detection and quantification using disposable nanopore strips. Sci. Rep. 8, 1–12 (2018).
Quick, J. et al. Real-time, portable genome sequencing for ebola surveillance. Nature 530, 228–232 (2016).
pubmed: 26840485
pmcid: 4817224
Derrington, I. M. et al. Nanopore DNA sequencing with MspA. Proc. Natl Acad. Sci. USA 107, 16060–5 (2010).
pubmed: 20798343
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).
pubmed: 26076426
Szalay, T. & Golovchenko, J. A. De novo sequencing and variant calling with nanopores using PoreSeq. Nat. Biotechnol. 33, 1087–1091 (2015).
pubmed: 26352647
pmcid: 4877053
Jain, M. et al. Improved data analysis for the MinION nanopore sequencer. Nat. Methods 12, 351–356 (2015).
pubmed: 25686389
pmcid: 4907500
Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146–1153 (2008).
pubmed: 18846088
pmcid: 2683588
Bayley, H. Nanopore sequencing: from imagination to reality. Clin. Chem. 61, 25–31 (2015).
pubmed: 25477535
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).
pubmed: 22446694
pmcid: 3757088
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).
pubmed: 22334048
pmcid: 3408072
Bayley, H. Getting to the bottom of the well. Nat. Nanotechnol. 12, 1116 (2017).
pubmed: 28945241
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).
Rodriguez-Larrea, D. & Bayley, H. Multistep protein unfolding during nanopore translocation. Nat. Nanotechnol. 8, 288–295 (2013).
pubmed: 23474543
pmcid: 4830145
Benner, S. et al. Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore. Nat. Nanotechnol. 2, 718–724 (2007).
pubmed: 18654412
pmcid: 2507869
Nivala, J., Marks, D. B. & Akeson, M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat. Biotechnol. 31, 247–250 (2013).
pubmed: 23376966
pmcid: 3772521
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).
pubmed: 25402970
Wallace, E. V. B. et al. Identification of epigenetic DNA modifications with a protein nanopore. Chem. Commun. 46, 8195–8197 (2010).
Howorka, S. & Siwy, Z. S. Nanopores as protein sensors. Nat. Biotechnol. 30, 506–507 (2012).
pubmed: 22678388
Briggs, K. et al. DNA translocations through nanopores under nanoscale preconfinement. Nano Lett. 18, 660–668 (2018).
pubmed: 29087723
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: 28855527
pmcid: 5577289
Morin, T. J. et al. Nanopore-based target sequence detection. PLoS ONE 11, e0154426 (2016).
pubmed: 27149679
pmcid: 4858282
Atas, E., Singer, A. & Meller, A. DNA sequencing and bar-coding using solid-state nanopores. Electrophoresis 33, 3437–3447 (2012).
pubmed: 23109189
pmcid: 3773941
Beamish, E., Tabard-cossa, V. & Godin, M. Identifying structure in short DNA scaffolds using solid-state nanopores. ACS Sens. 2, 1814–1820 (2017).
pubmed: 29182276
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).
pubmed: 27121643
pmcid: 4901370
Singer, A. et al. Nanopore based sequence specific detection of duplex DNA for genomic profiling. Nano Lett. 10, 738–742 (2010).
pubmed: 20088590
pmcid: 2834191
Tabard-cossa, V. et al. Single-molecule bonds characterized by solid-state nanopore force spectroscopy. ACS Nano 3, 3009–3014 (2009).
pubmed: 19751064
pmcid: 2800075
Karau, P. & Tabard-cossa, V. Capture and translocation characteristics of short branched DNA labels in solid-state nanopores. ACS Sens. 3, 1308–1315 (2018).
pubmed: 29874054
Alibakhshi, M. A. et al. Picomolar fingerprinting of nucleic acid nanoparticles using solid-state nanopores. ACS Nano 11, 9701–9710 (2017).
pubmed: 28841287
pmcid: 5959297
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).
Kowalczyk, S. W. et al. Single-molecule transport across an individual biomimetic nuclear pore complex. Nat. Nanotechnol. 6, 433–438 (2011).
pubmed: 21685911
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).
Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016).
pubmed: 27153285
pmcid: 6733523
Wu, M. Y., Krapf, D., Zandbergen, M., Zandbergen, H. & Batson, P. E. Formation of nanopores in a SiN/SiO
Kwok, H., Briggs, K. & Tabard-Cossa, V. Nanopore fabrication by controlled dielectric breakdown. PLoS ONE 9, e92880 (2014).
pubmed: 24658537
pmcid: 3962464
Briggs, K. et al. Kinetics of nanopore fabrication during controlled breakdown of dielectric membranes in solution. Nanotechnology 26, 084004 (2015).
pubmed: 25648336
Pud, S. et al. Self-aligned plasmonic nanopores by optically controlled dielectric breakdown. Nano Lett. 15, 7112–7117 (2015).
pubmed: 26333767
pmcid: 4859154
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).
pubmed: 25631885
Gilboa, T., Zrehen, A., Girsault, A. & Meller, A. Optically-monitored nanopore fabrication using a focused laser beam. Sci. Rep. 8, 9765 (2018).
pubmed: 29950607
pmcid: 6021433
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).
pubmed: 27499264
pmcid: 4976334
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).
Wang, Y., Chen, Q., Deng, T. & Liu, Z. Nanopore fabricated in pyramidal HfO
Feng, J. et al. Electrochemical reaction in single layer MoS
pubmed: 25928894
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: 26045626
pmcid: 4441703
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).
pubmed: 31459326
pmcid: 6649298
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).
pubmed: 30457833
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).
pubmed: 28485922
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).
Tahvildari, R. et al. Manipulating electrical and fluidic access in integrated nanopore-microfluidic arrays using microvalves. Small 13, 1–7 (2017).
Lam, M. H. et al. Entropic trapping of DNA with a nano filtered nanopore. ACS Appl. Nano Mater. 2, 4773–4781 (2019).
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).
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).
pubmed: 30335956
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: 28045003
pmcid: 5408306
Wang, Y. et al. Fabrication of multiple nanopores in a SiNx membrane via controlled breakdown. Sci. Rep. 8, 1–9 (2018).
Zhang, Y. et al. Nanopore formation via tip-controlled local breakdown using an atomic force microscope. Small Methods 3, 1900147 (2019).
Abe, K. et al. The T2K experiment. Nucl. Instrum. Meth. 659, 106–135 (2011).
Venkatesan, B. M. et al. Highly sensitive, mechanically stable nanopore sensors for DNA analysis. Adv. Mater. 21, 2771–2776 (2009).
pubmed: 20098720
pmcid: 2808638
Larkin, J. et al. Slow DNA transport through nanopores in hafnium oxide membranes. ACS Nano 7, 10121–8 (2013).
pubmed: 24083444
pmcid: 4729694
Russo, C. J. & Golovchenko, J. A. Atom-by-atom nucleation and growth of graphene nanopores. Proc. Natl Acad. Sci. USA 109, 5953–5957 (2012).
pubmed: 22492975
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).
pubmed: 24547924
Wu, M. et al. Control of shape and material composition of solid-state nanopores. Nano Lett. 9, 479–484 (2009).
pubmed: 19143508
Li, J. et al. Ion-beam sculpting at nanometre length scales. Nature 412, 166–169 (2001).
pubmed: 11449268
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: 27981944
Hemamouche, A. et al. FIB patterning of dielectric, metallized and graphene membranes: a comparative study. Microelectron. Eng. 121, 87–91 (2014).
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). https://doi.org/10.1007/978-3-319-41990-9_18
Yang, J. et al. Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection. Nanotechnology 22, 285310 (2011).
pubmed: 21659692
Emmrich, D. et al. Nanopore fabrication and characterization by helium ion microscopy. Appl. Phys. Lett. 108, 163103 (2016).
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).
pubmed: 24847795
pmcid: 4028839
Bustamante, J. Synchronous Optical and Electrical Measurements of Single DNA Molecules Translocating Through a Solid-State Nanopore. MSc thesis, Univ. Ottawa (2014).
Briggs, K. Solid-State Nanopores: Fabrication, Application, and Analysis. PhD thesis, Univ. Ottawa (2018).
Tabard-Cossa, V., Trivedi, D., Wiggin, M., Jetha, N. N. & Marziali, A. Noise analysis and reduction in solid-state nanopores. Nanotechnology 18, 305505 (2007).
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: 21730759
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: 22983670
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).
pubmed: 28974095
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).
pubmed: 24041089
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).
Fragasso, A., Pud, S. & Dekker, C. 1/f noise in solid-state nanopores is governed by access and surface regions. Nanotechnology 30, 395202 (2019).
pubmed: 31247592