Fast Fabrication of Solid-State Nanopores for DNA Molecule Analysis
Abstract
:1. Introduction
2. Materials and Methods
3. Results and Discussion
4. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
- Miles, B.N.; Ivanov, A.P.; Wilson, K.A.; Dogan, F.; Japrung, D.; Edel, J.B. Single molecule sensing with solid-state nanopores: Novel materials, methods, and applications. Chem. Soc. Rev. 2013, 42, 15–28. [Google Scholar] [CrossRef]
- Muthukumar, M.; Plesa, C.; Dekker, C. Single-molecule sensing with nanopores. Phys. Today 2015, 68, 40–46. [Google Scholar] [CrossRef] [Green Version]
- Deamer, D.; Akeson, M.; Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 2016, 34, 518–524. [Google Scholar] [CrossRef] [PubMed]
- Shi, W.; Friedman, A.K.; Baker, L.A. Nanopore Sensing. Anal. Chem. 2017, 89, 157–188. [Google Scholar] [CrossRef] [Green Version]
- Charalampous, T.; Kay, G.L.; Richardson, H.; Aydin, A.; Baldan, R.; Jeanes, C.; Rae, D.; Grundy, S.; Turner, D.J.; Wain, J.; et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat. Biotechnol. 2019, 37, 783–792. [Google Scholar] [CrossRef] [PubMed]
- Roozbahani, G.M.; Chen, X.; Zhang, Y.; Wang, L.; Guan, X. Nanopore Detection of Metal Ions: Current Status and Future Directions. Small Methods 2020, 4, 2000266. [Google Scholar] [CrossRef] [PubMed]
- Gu, W.; Deng, X.; Lee, M.; Sucu, Y.D.; Arevalo, S.; Stryke, D.; Federman, S.; Gopez, A.; Reyes, K.; Zorn, K.; et al. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat. Med. 2020, 27, 115–124. [Google Scholar] [CrossRef] [PubMed]
- Manrao, E.A.; Derrington, I.M.; Laszlo, A.H.; Langford, K.W.; Hopper, M.K.; Gillgren, N.; Pavlenok, M.; Niederweis, M.; Gundlach, J.H. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 2012, 30, 349–353. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rusk, N. MinION takes center stage. Nat. Methods 2015, 12, 12. [Google Scholar] [CrossRef] [PubMed]
- Xue, L.; Yamazaki, H.; Ren, R.; Wanunu, M.; Ivanov, A.P.; Edel, J.B. Solid-state nanopore sensors. Nat. Rev. Mater. 2020, 5, 931–951. [Google Scholar] [CrossRef]
- Yuan, Z.; Wang, C.; Yi, X.; Ni, Z.; Chen, Y.; Li, T. Solid-State Nanopore. Nanoscale Res. Lett. 2018, 13, 56. [Google Scholar] [CrossRef]
- Rahman, M.; Sampad, M.J.N.; Hawkins, A.; Schmidt, H. Recent advances in integrated solid-state nanopore sensors. Lab Chip 2021, 21, 3030–3052. [Google Scholar] [CrossRef] [PubMed]
- Garoli, D.; Yamazaki, H.; Maccaferri, N.; Wanunu, M. Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications. Nano Lett. 2019, 19, 7553–7562. [Google Scholar] [CrossRef] [Green Version]
- Soni, G.V.; Singer, A.; Yu, Z.; Sun, Y.; McNally, B.; Meller, A. Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores. Rev. Sci. Instrum. 2010, 81, 014301. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Nelson, E.M.; Li, H.; Timp, G. Direct, Concurrent Measurements of the Forces and Currents Affecting DNA in a Nanopore with Comparable Topography. ACS Nano 2014, 8, 5484–5493. [Google Scholar] [CrossRef]
- Xie, P.; Xiong, Q.H.; Fang, Y.; Qing, Q.; Lieber, C.M. Local electrical potential detection of DNA by nanowire-nanopore sensors. Nat. Nanotechnol. 2012, 7, 119–125. [Google Scholar] [CrossRef] [Green Version]
- Traversi, F.; Raillon, C.; Benameur, S.M.; Liu, K.; Khlybov, S.; Tosun, M.; Krasnozhon, D.; Kis, A.; Radenovic, A. Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nat. Nanotechnol. 2013, 8, 939–945. [Google Scholar] [CrossRef] [PubMed]
- Parkin, W.M.; Drndić, M. Signal and Noise in FET-Nanopore Devices. ACS Sensors 2018, 3, 313–319. [Google Scholar] [CrossRef]
- Tsutsui, M.; Taniguchi, M.; Yokota, K.; Kawai, T. Identifying single nucleotides by tunnelling current. Nat. Nanotechnol. 2010, 5, 286–290. [Google Scholar] [CrossRef] [PubMed]
- Wanunu, M.; Dadosh, T.; Ray, V.; Jin, J.; McReynolds, L.; Drndic, M. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nat. Nanotechnol. 2010, 5, 807–814. [Google Scholar] [CrossRef]
- Skinner, G.M.; van den Hout, M.; Broekmans, O.; Dekker, C.; Dekker, N.H. Distinguishing Single- and Double-Stranded Nucleic Acid Molecules Using Solid-State Nanopores. Nano Lett. 2009, 9, 2953–2960. [Google Scholar] [CrossRef] [PubMed]
- Restrepo-Perez, L.; Joo, C.; Dekker, C. Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 2018, 13, 786–796. [Google Scholar] [CrossRef] [Green Version]
- Varongchayakul, N.; Song, J.; Meller, A.; Grinstaff, M.W. Single-molecule protein sensing in a nanopore: A tutorial. Chem. Soc. Rev. 2018, 47, 8512–8524. [Google Scholar] [CrossRef] [PubMed]
- Taniguchi, M.; Minami, S.; Ono, C.; Hamajima, R.; Morimura, A.; Hamaguchi, S.; Akeda, Y.; Kanai, Y.; Kobayashi, T.; Kamitani, W.; et al. Combining machine learning and nanopore construction creates an artificial intelligence nanopore for coronavirus detection. Nat. Commun. 2021, 12, 3726. [Google Scholar] [CrossRef]
- Ryuzaki, S.; Yasui, T.; Tsutsui, M.; Yokota, K.; Komoto, Y.; Paisrisarn, P.; Kaji, N.; Ito, D.; Tamada, K.; Ochiya, T.; et al. Rapid Discrimination of Extracellular Vesicles by Shape Distribution Analysis. Anal. Chem. 2021, 93, 7037–7044. [Google Scholar] [CrossRef]
- Im, J.; Lindsay, S.; Wang, X.; Zhang, P.M. Single Molecule Identification and Quantification of Glycosaminoglycans Using Solid-State Nanopores. ACS Nano. 2019, 13, 6308–6318. [Google Scholar] [CrossRef]
- Houghtaling, J.; List, J.; Mayer, M. Nanopore-Based, Rapid Characterization of Individual Amyloid Particles in Solution: Concepts, Challenges, and Prospects. Small 2018, 14, 1802412. [Google Scholar] [CrossRef] [PubMed]
- Liu, Z.; Wang, Y.; Deng, T.; Chen, Q. Solid-State Nanopore-Based DNA Sequencing Technology. J. Nanomater. 2016, 2016, 5284786. [Google Scholar] [CrossRef]
- Ryuzaki, S.; Tsutsui, M.; He, Y.; Yokota, K.; Arima, A.; Morikawa, T.; Taniguchi, M.; Kawai, T. Rapid structural analysis of nanomaterials in aqueous solutions. Nanotechnology 2017, 28, 155501. [Google Scholar] [CrossRef]
- Goyal, G.; Darvish, A.; Kim, M.J. Use of solid-state nanopores for sensing co-translocational deformation of nano-liposomes. Analyst 2015, 140, 4865–4873. [Google Scholar] [CrossRef] [PubMed]
- Li, J.; Stein, D.; McMullan, C.; Branton, D.; Aziz, M.J.; Golovchenko, J.A. Ion-beam sculpting at nanometre length scales. Nature 2001, 412, 166–169. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Storm, A.J.; Chen, J.H.; Ling, X.S.; Zandbergen, H.W.; Dekker, C. Fabrication of solid-state nanopores with single-nanometre precision. Nat. Mater. 2003, 2, 537–540. [Google Scholar] [CrossRef] [PubMed]
- Fried, J.P.; Swett, J.L.; Nadappuram, B.P.; Mol, J.A.; Edel, J.B.; Ivanov, A.P.; Yates, J.R. In situ solid-state nanopore fabrication. Chem. Soc. Rev. 2021, 50, 4974–4992. [Google Scholar] [CrossRef] [PubMed]
- Kwok, H.; Briggs, K.; Tabard-Cossa, V. Nanopore Fabrication by Controlled Dielectric Breakdown. PLoS ONE 2014, 9, e92880. [Google Scholar]
- Briggs, K.; Kwok, H.; Tabard-Cossa, V. Automated fabrication of 2-nm solid-state nanopores for nucleic acid analysis. Small 2014, 10, 2077–2086. [Google Scholar] [CrossRef]
- 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. 2014, 4, 5000. [Google Scholar] [CrossRef] [Green Version]
- Ying, C.; Zhang, Y.; Feng, Y.; Zhou, D.; Wang, D.; Xiang, Y.; Zhou, W.; Chen, Y.; Du, C.; Tian, J. 3D nanopore shape control by current-stimulus dielectric breakdown. Appl. Phys. Lett. 2016, 109, 063105. [Google Scholar] [CrossRef]
- Yanagi, I.; Fujisaki, K.; Hamamura, H.; Takeda, K. Thickness-dependent dielectric breakdown and nanopore creation on sub-10-nm-thick SiN membranes in solution. J. Appl. Phys. 2017, 121. [Google Scholar] [CrossRef]
- Wang, Y.F.; Chen, Q.; Deng, T.; Liu, Z.W. Self-Aligned Nanopore Formed on a SiO2 Pyramidal Membrane by a Multipulse Dielectric Breakdown Method. J. Phys. Chem. C 2018, 122, 11516–11523. [Google Scholar] [CrossRef]
- Wang, Y.; Chen, Q.; Deng, T.; Liu, Z. Nanopore fabricated in pyramidal HfO2 film by dielectric breakdown method. Appl. Phys. Lett. 2017, 111, 143103. [Google Scholar] [CrossRef]
- Carlsen, A.T.; Briggs, K.; Hall, A.R.; Tabard-Cossa, V. Solid-state nanopore localization by controlled breakdown of selectively thinned membranes. Nanotechnology 2017, 28, 085304. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ying, C.; Houghtaling, J.; Eggenberger, O.M.; Guha, A.; Nirmalraj, P.; Awasthi, S.; Tian, J.; Mayer, M. Formation of Single Nanopores with Diameters of 20–50 nm in Silicon Nitride Membranes Using Laser-Assisted Controlled Breakdown. ACS Nano 2018, 12, 11458–11470. [Google Scholar] [CrossRef] [PubMed]
- Dong, M.; Tang, Z.; He, X.; Guan, W. Direct Observation of Redox-Induced Bubble Generation and Nanopore Formation Dynamics in Controlled Dielectric Breakdown. ACS Appl. Electron. Mater. 2020, 2, 2954–2960. [Google Scholar] [CrossRef]
- Briggs, K.; Charron, M.; Kwok, H.; Le, T.; Chahal, S.; Bustamante, J.; Waugh, M.; Tabard-Cossa, V. Kinetics of nanopore fabrication during controlled breakdown of dielectric membranes in solution. Nanotechnology 2015, 26, 084004. [Google Scholar] [CrossRef] [PubMed]
- Kowalczyk, S.W.; Grosberg, A.Y.; Rabin, Y.; Dekker, C. Modeling the conductance and DNA blockade of solid-state nanopores. Nanotechnology 2011, 22, 315101. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Fried, J.P.; Swett, J.L.; Nadappuram, B.P.; Fedosyuk, A.; Sousa, P.M.; Briggs, D.P.; Ivanov, A.P.; Edel, J.B.; Mol, J.A.; Yates, J.R. Understanding Electrical Conduction and Nanopore Formation During Controlled Breakdown. Small 2021, 17, 2102543. [Google Scholar] [CrossRef] [PubMed]
- Yanagi, I.; Takeda, K.-i. Current–Voltage Characteristics of SiN Membranes in Solution. ACS Appl. Electron. Mater. 2020, 2, 2760–2771. [Google Scholar] [CrossRef]
- Kuyama, T.; Eriguchi, K. Optical and electrical characterization methods of plasma-induced damage in silicon nitride films. Jpn J. Appl. Phys. 2018, 57, 06JD03. [Google Scholar] [CrossRef]
- Luhmann, N.; Jachimowicz, A.; Schalko, J.; Sadeghi, P.; Sauer, M.; Foelske-Schmitz, A.; Schmid, S. Effect of oxygen plasma on nanomechanical silicon nitride resonators. Appl. Phys. Lett. 2017, 111, 063103. [Google Scholar] [CrossRef]
- Zrehen, A.; Gilboa, T.; Meller, A. Real-time visualization and sub-diffraction limit localization of nanometer-scale pore formation by dielectric breakdown. Nanoscale 2017, 9, 16437–16445. [Google Scholar] [CrossRef]
- Yanagi, I.; Hamamura, H.; Akahori, R.; Takeda, K.-I. Two-step breakdown of a SiN membrane for nanopore fabrication: Formation of thin portion and penetration. Sci. Rep. 2018, 8, 10129. [Google Scholar] [CrossRef]
- Wang, Y.; Ying, C.; Zhou, W.; de Vreede, L.; Liu, Z.; Tian, J. Fabrication of multiple nanopores in a SiNx membrane via controlled breakdown. Sci. Rep-Uk 2018, 8, 1234. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhan, L.; Zhang, Y.; Si, W.; Sha, J.; Chen, Y. Detection and Separation of Single-Stranded DNA Fragments Using Solid-State Nanopores. J. Phys. Chem. Lett. 2021, 12, 6469–6477. [Google Scholar] [CrossRef] [PubMed]
- Li, J.; Talaga, D.S. The distribution of DNA translocation times in solid-state nanopores. J. Phys. Condens. Matter 2010, 22, 454129. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ling, D.Y.; Ling, X.S. On the distribution of DNA translocation times in solid-state nanopores: An analysis using Schrodinger’s first-passage-time theory. J. Phys. Condens. Matter 2013, 25, 375102. [Google Scholar] [CrossRef] [Green Version]
- Szabo, A.; Schulten, K.; Schulten, Z. First passage time approach to diffusion controlled reactions. J. Chem. Phys. 1980, 72, 4350–4357. [Google Scholar] [CrossRef]
- Stellwagen, E.; Lu, Y.; Stellwagen, N.C. Unified Description of Electrophoresis and Diffusion for DNA and Other Polyions. Biochemistry 2003, 42, 11745–11750. [Google Scholar] [CrossRef]
- Edward, J.T. Molecular volumes and the Stokes-Einstein equation. J. Chem. Educ. 1970, 47, 261. [Google Scholar] [CrossRef]
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Zhang, Y.; Ma, D.; Gu, Z.; Zhan, L.; Sha, J. Fast Fabrication of Solid-State Nanopores for DNA Molecule Analysis. Nanomaterials 2021, 11, 2450. https://doi.org/10.3390/nano11092450
Zhang Y, Ma D, Gu Z, Zhan L, Sha J. Fast Fabrication of Solid-State Nanopores for DNA Molecule Analysis. Nanomaterials. 2021; 11(9):2450. https://doi.org/10.3390/nano11092450
Chicago/Turabian StyleZhang, Yin, Dexian Ma, Zengdao Gu, Lijian Zhan, and Jingjie Sha. 2021. "Fast Fabrication of Solid-State Nanopores for DNA Molecule Analysis" Nanomaterials 11, no. 9: 2450. https://doi.org/10.3390/nano11092450