Unlocking the Potential of Nanopores
A Curated Resource for Researchers Diving into Solid-State Nanopore Technology
Staying on top of the literature in your own subfield is challenging. Bridging your expertise into a new field, even more so. As part of our mission to make solid-state nanopores accessible to anyone, we believe that bringing diverse expertise from other disciplines into the nanopore research community is essential in realizing the full potential of this technology. To facilitate this transition, the collection of literature on this page is intended to provide an overview of the solid-state nanopore field to a researcher who is not currently working in nanopores. This is by no means a comprehensive list of papers on the subject, nor a comprehensive list of the labs that are active in the field. Rather, this is a living document relating to areas of research challenge for which an interdisciplinary approach will be needed, in the hopes of motivating participation by researchers in adjacent fields.
The content here relates primarily to the challenges discussed in Northern Nanopore’s webinar “Beyond the Lab: Research Challenges Facing Solid-state Nanopores”, and if you are new to nanopore research, we suggest reviewing that presentation as it will provide a clear challenge statement for each of the sections below and ground your perusal of the library. On the other hand, if you are a nanopore researcher and you know of papers that should be added to the library, please contact us, and we will update the library. Note that some papers appear in more than one section.
The quantity of information here can be daunting, but it is not necessary to cover all of it in order to be productive in nanopore research. If you’re interested in exploring any of the challenges discussed in the presentation with Northern Nanopore, please reach out, and we will be happy to assist in getting you up to speed with a more focused list relating to your target research.
Solid-state Nanopore Fabrication
Nanopore Fabrication by Controlled Breakdown
Nanopore fabrication inside a cavity
Localization of nanopores on membranes by local thinning
Localization of nanopores on membranes by fluidic contact
Fabrication in 2D material
Fabrication on metalized membranes
Localization by laser (either local thinning, enhanced conduction, or plasmonic effects)
Membrane from 2D Materials
Thin Dielectric Membranes
Low-noise Substrates
Nanopore Membrane Surface Coatings
Anti-stick coatings
Functional Coatings
Molecular Control (except surface coating methods)
Review
Control by Nanoconfinement
Control by Buffer Composition
Control by Pore Size
Control by Two Pores
Control by Plasmonics
Nucleic Acids
Proteins
Metabolites
Nanopore Readout
Synthetic polymer synthesis
Review Articles
These review articles (and book chapters) provide an overview of the different research areas and recent progress in the nanopore field.
L. Xue, H. Yamazaki, R. Ren, M. Wanunu, A. P. Ivanov, and J. B. Edel, ‘Solid-state nanopore sensors’, Nat Rev Mater, vol. 5, no. 12, pp. 931–951, 2020, https://doi.org/10.1038/s41578-020-0229-6.
S. Lindsay, ‘The promises and challenges of solid-state sequencing’, Nat Nanotechnol, vol. 11, no. 2, pp. 109–111, 2016, https://doi.org/10.1038/nnano.2016.9.
Y.-L. Ying et al., ‘Nanopore-based technologies beyond DNA sequencing’, Nat Nanotechnol, vol. 17, no. 11, pp. 1136–1146, 2022, https://doi.org/10.1038/s41565-022-01193-2.
J. P. Fried et al., ‘In situ solid-state nanopore fabrication’, Chem Soc Rev, vol. 50, no. 8, pp. 4974–4992, 2021, https://doi.org/10.1039/d0cs00924e.
Solid-state Nanopore Fabrication
Nanopore Fabrication by Controlled Breakdown
Physics
J. P. Fried et al., ‘In situ solid-state nanopore fabrication’, Chem Soc Rev, vol. 50, no. 8, pp. 4974–4992, 2021, https://doi.org/10.1039/d0cs00924e.
C. Leung, K. Briggs, M.-P. Laberge, S. Peng, M. Waugh, and V. Tabard-Cossa, ‘Mechanisms of solid-state nanopore enlargement under electrical stress’, Nanotechnology, vol. 31, no. 44, 2020, https://doi.org/10.1088/1361-6528/aba86e.
I. Yanagi, R. Akahori, and K. ichi Takeda, ‘Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules’, Sci Rep, vol. 9, no. 1, pp. 1–15, 2019, https://doi.org/10.1038/s41598-019-49622-y.
K. Briggs et al., ‘Kinetics of nanopore fabrication during controlled breakdown of dielectric membranes in solution’, Nanotechnology, vol. 26, no. 8, p. 084004, 2015, https://doi.org/10.1088/0957-4484/26/8/084004.
K. Briggs, H. Kwok, and V. Tabard-Cossa, ‘Automated Fabrication of 2-nm Solid-State Nanopores for Nucleic Acid Analysis’, Small, vol. 10, no. 10, pp. 2077–2086, 2014, https://doi.org/10.1002/smll.201303602.
H. Kwok, K. Briggs, and V. Tabard-Cossa, ‘Nanopore fabrication by controlled dielectric breakdown’, PLoS One, vol. 9, no. 3, p. e92880, Jan. 2014, https://doi.org/10.1371/journal.pone.0092880.
Implementation
M. Waugh et al., ‘Solid-state nanopore fabrication by automated controlled breakdown’, Nat Protoc, vol. 15, no. 1, pp. 122–143, 2020, https://doi.org/10.1038/s41596-019-0255-2.
Nanopore fabrication inside a cavity
G. R. Madejski et al., ‘Monolithic Fabrication of NPN/SiN<inf>x</inf> Dual Membrane Cavity for Nanopore-Based DNA Sensing’, Adv Mater Interfaces, vol. 6, no. 14, 2019, https://doi.org/10.1002/admi.201900684.
Localization of nanopores on membranes by local thinning
A. T. Carlsen, K. Briggs, A. R. Hall, and V. Tabard-Cossa, ‘Solid-state nanopore localization by controlled breakdown of selectively thinned membranes’, Nanotechnology, vol. 28, no. 8, p. 085304, 2017, https://doi.org/10.1088/1361-6528/aa564d.
Localization of nanopores on membranes by fluidic contact
R. Tahvildari et al., ‘Manipulating Electrical and Fluidic Access in Integrated Nanopore-Microfluidic Arrays Using Microvalves’, Small, vol. 13, no. 10, 2017, https://doi.org/10.1002/smll.201602601
R. Tahvildari, E. Beamish, V. Tabard-Cossa, and M. Godin, ‘Integrating nanopore sensors within microfluidic channel arrays using controlled breakdown’, Lab Chip, vol. 15, no. 6, pp. 1407–1411, 2015, https://doi.org/10.1039/C4LC01366B.
C. E. Arcadia, C. C. Reyes, and J. K. Rosenstein, ‘In Situ Nanopore Fabrication and Single-Molecule Sensing with Microscale Liquid Contacts’, ACS Nano, vol. 11, no. 5, pp. 4907–4915, 2017, https://doi.org/10.1021/acsnano.7b01519.
Fabrication in 2D material
A. T. Kuan, B. Lu, P. Xie, T. Szalay, and J. A. Golovchenko, ‘Electrical pulse fabrication of graphene nanopores in electrolyte solution’, Appl Phys Lett, vol. 106, no. May, p. 203109, 2015, https://doi.org/10.1063/1.4921620.
J. Feng et al., ‘Electrochemical reaction in single layer MoS2: Nanopores opened atom by atom’, Nano Lett, vol. 15, no. 5, pp. 3431–3438, 2015, https://doi.org/10.1021/acs.nanolett.5b00768.
Fabrication on metalized membranes
H. Kwok, M. Waugh, J. Bustamante, K. Briggs, and V. Tabard-Cossa, ‘Long passage times of short ssDNA molecules through metallized nanopores fabricated by controlled breakdown’, Adv Funct Mater, vol. 24, no. 48, pp. 7745–7753, 2014, https://doi.org/10.1002/adfm.201402468.
J. P. Fried et al., ‘Localised Solid-State Nanopore Fabrication via Controlled Breakdown using On-Chip Electrodes’, ArXiv e-prints, pp. 1–9, 2021, . Available: http://arxiv.org/abs/2111.02730
Localization by laser (either local thinning, enhanced conduction, or plasmonic effects)
Z. Tang, M. Dong, X. He, and W. Guan, ‘On Stochastic Reduction in Laser-Assisted Dielectric Breakdown for Programmable Nanopore Fabrication’, ACS Appl Mater Interfaces, vol. 13, no. 11, pp. 13383–13391, Mar. 2021, https://doi.org/10.1021/acsami.0c23106.
T. Gilboa, E. Zvuloni, A. Zrehen, A. H. Squires, and A. Meller, ‘Automated, Ultra-Fast Laser-Drilling of Nanometer Scale Pores and Nanopore Arrays in Aqueous Solutions’, Adv Funct Mater, vol. 30, no. 18, p. 1900642, May 2020, https://doi.org/https://doi.org/10.1002/adfm.201900642.
C. Ying et al., ‘Formation of Single Nanopores with Diameters of 20–50 nm in Silicon Nitride Membranes Using Laser-Assisted Controlled Breakdown’, ACS Nano, vol. 12, pp. 11458–11470, 2018, https://doi.org/10.1021/acsnano.8b06489.
T. Gilboa, A. Zrehen, A. Girsault, and A. Meller, ‘Optically-Monitored Nanopore Fabrication Using a Focused Laser Beam’, Sci Rep, vol. 8, no. 1, p. 9765, 2018, https://doi.org/10.1038/s41598-018-28136-z.
H. Yamazaki, R. Hu, Q. Zhao, and M. Wanunu, ‘Photothermally Assisted Thinning of Silicon Nitride Membranes for Ultrathin Asymmetric Nanopores’, ACS Nano, vol. 12, no. 12, pp. 12472–12481, Dec. 2018, https://doi.org/10.1021/acsnano.8b06805.
A. Zrehen, T. Gilboa, and A. Meller, ‘Real-Time Visualization and Sub-Diffraction Limit Localization of Nanometer-Scale Pore Formation by Dielectric Breakdown’, Nanoscale, 2017, https://doi.org/10.1039/C7NR02629C.
S. Pud, D. Verschueren, N. Vukovic, C. Plesa, M. P. Jonsson, and C. Dekker, ‘Self-Aligned Plasmonic Nanopores by Optically Controlled Dielectric Breakdown’, Nano Lett, vol. 15, no. 10, pp. 7112–7117, 2015, https://doi.org/10.1021/acs.nanolett.5b03239.
Fundamental Challenges
Membrane Design
Membrane from 2D Materials
R. Balasubramanian et al., ‘DNA Translocation through Vertically Stacked 2D Layers of Graphene and Hexagonal Boron Nitride Heterostructure Nanopore’, ACS Appl Bio Mater, vol. 4, no. 1, pp. 451–461, Jan. 2021, https://doi.org/10.1021/acsabm.0c00929.
M. Thakur et al., ‘Wafer-Scale Fabrication of Nanopore Devices for Single-Molecule DNA Biosensing using MoS2’, Small Methods, vol. 4, no. 11, p. 2000072, 2020, https://doi.org/https://doi.org/10.1002/smtd.202000072.
S. M. Gilbert et al., ‘Fabrication of Subnanometer-Precision Nanopores in Hexagonal Boron Nitride’, Sci Rep, vol. 7, no. 1, p. 15096, 2017, https://doi.org/10.1038/s41598-017-12684-x.
A. T. Kuan, B. Lu, P. Xie, T. Szalay, and J. A. Golovchenko, ‘Electrical pulse fabrication of graphene nanopores in electrolyte solution’, Appl Phys Lett, vol. 106, no. May, p. 203109, 2015, https://doi.org/10.1063/1.4921620
J. Feng et al., ‘Electrochemical reaction in single layer MoS2: Nanopores opened atom by atom’, Nano Lett, vol. 15, no. 5, pp. 3431–3438, 2015, https://doi.org/10.1021/acs.nanolett.5b00768.
M. Drndić, ‘Sequencing with graphene pores’, Nat Nanotechnol, vol. 9, no. 10, p. 743, 2014, https://doi.org/10.1038/nnano.2014.232.
Thin Dielectric Membranes
S. Dutt, B. I. Karawdeniya, Y. M. N. D. Y. Bandara, N. Afrin, and P. Kluth, ‘Ultrathin, High-Lifetime Silicon Nitride Membranes for Nanopore Sensing’, Anal Chem, Mar. 2023, https://doi.org/10.1021/acs.analchem.3c00023.
H. Yamazaki, R. Hu, Q. Zhao, and M. Wanunu, ‘Photothermally Assisted Thinning of Silicon Nitride Membranes for Ultrathin Asymmetric Nanopores’, ACS Nano, vol. 12, no. 12, pp. 12472–12481, Dec. 2018, https://doi.org/10.1021/acsnano.8b06805.
A. T. Carlsen, K. Briggs, A. R. Hall, and V. Tabard-Cossa, ‘Solid-state nanopore localization by controlled breakdown of selectively thinned membranes’, Nanotechnology, vol. 28, no. 8, p. 085304, 2017, https://doi.org/10.1088/1361-6528/aa564d.
J. Larkin, R. Henley, D. C. Bell, T. Cohen-Karni, J. K. Rosenstein, and M. Wanunu, ‘Slow DNA transport through nanopores in hafnium oxide membranes.’, ACS Nano, vol. 7, no. 11, pp. 10121–8, Nov. 2013, https://doi.org/10.1021/nn404326f.
M. Wanunu, T. Dadosh, V. Ray, J. Jin, L. McReynolds, and M. Drndić, ‘Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors’, Nat Nanotechnol, vol. 5, no. 11, pp. 807–814, 2010, https://doi.org/10.1038/nnano.2010.202.
Y. C. Chou, P. Masih Das, D. S. Monos, and M. Drndić, ‘Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements’, ACS Nano, vol. 14, no. 6, pp. 6715–6728, 2020, https://doi.org/10.1021/acsnano.9b09964.
J. A. Rodriguez-Manzo et al., ‘DNA Translocation in Nanometer Thick Silicon Nanopores’, ACS Nano, vol. 9, no. 6, pp. 6555–6564, 2015, https://doi.org/10.1021/acsnano.5b02531.
Low-noise Substrates
P. Xia, M. A. Rahman Laskar, and C. Wang, ‘Wafer-Scale Fabrication of Uniform, Micrometer-Sized, Triangular Membranes on Sapphire for High-Speed Protein Sensing in a Nanopore’, ACS Appl Mater Interfaces, vol. 15, no. 2, pp. 2656–2664, Jan. 2023, https://doi.org/10.1021/acsami.2c18983.
P. Xia et al., ‘Sapphire-supported nanopores for low-noise DNA sensing’, Biosens Bioelectron, vol. 174, p. 112829, 2021, https://doi.org/https://doi.org/10.1016/j.bios.2020.112829.
L. J. de Vreede et al., ‘Wafer-scale fabrication of fused silica chips for low-noise recording of resistive pulses through nanopores’, Nanotechnology, vol. 30, no. 26, p. 265301, 2019, https://doi.org/10.1088/1361-6528/ab0e2a.
C. C. Chien, S. Shekar, D. J. Niedzwiecki, K. L. Shepard, and M. Drndić, ‘Single-Stranded DNA Translocation Recordings through Solid-State Nanopores on Glass Chips at 10 MHz Measurement Bandwidth’, ACS Nano, vol. 13, no. 9, pp. 10545–10554, 2019, https://doi.org/10.1021/acsnano.9b04626.
A. Balan et al., ‘Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths’, Nano Lett, vol. 14, no. 12, pp. 7215–7220, 2014, https://doi.org/10.1021/nl504345y.
M. H. Lee et al., ‘A low-noise solid-state nanopore platform based on a highly insulating substrate’, Sci Rep, vol. 4, pp. 1–7, 2014, https://doi.org/10.1038/srep07448.
Nanopore Membrane Surface Coatings
Anti-stick coatings
J. Andersson et al., ‘Polymer Brushes on Silica Nanostructures Prepared by Aminopropylsilatrane Click Chemistry: Superior Antifouling and Biofunctionality’, ACS Appl Mater Interfaces, vol. 15, no. 7, pp. 10228–10239, Feb. 2023, https://doi.org/10.1021/acsami.2c21168.
I. Abrao-Nemeir et al., ‘Investigation of α-Synuclein and Amyloid-β(42)-E22Δ Oligomers Using SiN Nanopore Functionalized with L-Dopa’, Chem Asian J, no. 42, 2022, https://doi.org/10.1002/asia.202200726.
S. Schmid, P. Stömmer, H. Dietz, and C. Dekker, ‘Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations’, bioRxiv, vol. 18, pp. 2–9, 2021, https://doi.org/10.1101/2021.03.09.434634.
S. Awasthi et al., ‘Polymer Coatings to Minimize Protein Adsorption in Solid-State Nanopores’, Small Methods, vol. 4, no. 11, p. 2000177, Nov. 2020, https://doi.org/https://doi.org/10.1002/smtd.202000177.
O. M. Eggenberger et al., ‘Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-inspired lipid monolayers’, Nanotechnology, vol. 30, no. 32, p. 325504, 2019, https://doi.org/10.1088/1361-6528/ab19e6.
Functional Coatings
L. Yang, J. Hu, M.-C. Li, M. Xu, and Z.-Y. Gu, ‘Solid-state Nanopores: Chemical Modifications, Interactions, and Functionalities’, Chem Asian J, vol. 17, no. 22, p. e202200775, 2022, https://doi.org/https://doi.org/10.1002/asia.202200775.
G. Wei et al., ‘Oligonucleotide Discrimination Enabled by Tannic Acid-Coordinated Film-Coated Solid-State Nanopores’, Langmuir, vol. 38, no. 20, pp. 6443–6453, May 2022, https://doi.org/10.1021/acs.langmuir.2c00638.
J. T. Hagan et al., ‘Chemically tailoring nanopores for single-molecule sensing and glycomics’, Anal Bioanal Chem, vol. 412, no. 25, pp. 6639–6654, 2020, https://doi.org/10.1007/s00216-020-02717-2.
O. M. Eggenberger, C. Ying, and M. Mayer, ‘Surface coatings for solid-state nanopores’, Nanoscale, vol. 11, no. 42, pp. 19636–19657, 2019, https://doi.org/10.1039/c9nr05367k.
B. I. Karawdeniya, Y. M. N. D. Y. Bandara, J. W. Nichols, R. B. Chevalier, and J. R. Dwyer, ‘Surveying silicon nitride nanopores for glycomics and heparin quality assurance’, Nat Commun, vol. 9, no. 1, pp. 1–8, 2018, https://doi.org/10.1038/s41467-018-05751-y.
E. C. Yusko et al., ‘Real-time shape approximation and fingerprinting of single proteins using a nanopore’, Nat Nanotechnol, vol. 12, no. 4, pp. 360–367, 2017, https://doi.org/10.1038/nnano.2016.267.
E. C. Yusko et al., ‘Controlling protein translocation through nanopores with bio-inspired fluid walls.’, Nat Nanotechnol, vol. 6, no. 4, pp. 253–60, Apr. 2011, https://doi.org/10.1038/nnano.2011.12.
Molecular Control (except surface coating methods)
Review
Z. Yuan, Y. Liu, M. Dai, X. Yi, and C. Wang, ‘Controlling DNA Translocation Through Solid-state Nanopores’, Nanoscale Res Lett, vol. 15, no. 1, p. 80, 2020, https://doi.org/10.1186/s11671-020-03308-x.
Control by Nanoconfinement
M. H. Lam et al., ‘Entropic Trapping of DNA with a Nanofiltered Nanopore’, ACS Appl Nano Mater, vol. 2, no. 8, 2019, https://doi.org/10.1021/acsanm.9b00606.
K. Briggs et al., ‘DNA Translocations Through Nanopores Under Nanoscale Pre-Confinement’, Nano Lett, vol. 18, no. 2, pp. 660–668, 2017, https://doi.org/10.1021/acs.nanolett.7b03987.
Control by Buffer Composition
S. W. Kowalczyk, D. B. Wells, A. Aksimentiev, and C. Dekker, ‘Slowing down DNA translocation through a nanopore in lithium chloride.’, Nano Lett, vol. 12, no. 2, pp. 1038–44, Feb. 2012, https://doi.org/10.1021/nl204273h.
D. Fologea, J. Uplinger, B. Thomas, D. S. McNabb, and J. Li, ‘Slowing DNA Translocation in a Solid-State Nanopore’, Nano Lett, vol. 5, no. 9, pp. 1734–1737, Sep. 2005, https://doi.org/10.1021/nl051063o.
Control by Pore Size
S. Carson, J. Wilson, A. Aksimentiev, and M. Wanunu, ‘Smooth DNA Transport through a Narrowed Pore Geometry’, Biophys J, vol. 107, no. 10, pp. 2381–2393, 2014, https://doi.org/10.1016/j.bpj.2014.10.017.
Control by Two Pores
A. Rand et al., ‘Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control’, ACS Nano, vol. 16, no. 4, pp. 5258–5273, Apr. 2022, https://doi.org/10.1021/acsnano.1c09575.
S. Seth, A. Rand, W. Reisner, W. B. Dunbar, R. Sladek, and A. Bhattacharya, ‘Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device’, Sci Rep, vol. 12, no. 1, p. 11305, 2022, https://doi.org/10.1038/s41598-022-14609-9.
X. Liu, Y. Zhang, R. Nagel, W. Reisner, and W. B. Dunbar, ‘Controlling DNA Tug-of-War in a Dual Nanopore Device’, ArXiv, no. 1811.11105v1, pp. 1–33, 2018, [Online]. Available: http://arxiv.org/abs/1811.11105
Control by Plasmonics
D. Garoli, H. Yamazaki, N. Maccaferri, and M. Wanunu, ‘Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications’, Nano Lett, vol. 19, no. 11, pp. 7553–7562, Nov. 2019, https://doi.org/10.1021/acs.nanolett.9b02759.
M. Belkin, S. H. Chao, M. P. Jonsson, C. Dekker, and A. Aksimentiev, ‘Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA’, ACS Nano, vol. 9, no. 11, pp. 10598–10611, 2015, https://doi.org/10.1021/acsnano.5b04173.
Application Challenges
Target Biomolecular Detection
Nucleic Acids
S. King, K. Briggs, R. Slinger, and V. Tabard-Cossa, ‘Screening for Group A Streptococcal Disease via Solid-State Nanopore Detection of PCR Amplicons’, ACS Sens, vol. 7, no. 1, pp. 207–214, Jan. 2022, https://doi.org/10.1021/acssensors.1c01972.
N. E. Weckman et al., ‘Multiplexed DNA Identification Using Site Specific dCas9 Barcodes and Nanopore Sensing’, ACS Sens, vol. 4, no. 8, pp. 2065–2072, 2019, https://doi.org/10.1021/acssensors.9b00686.
E. Beamish, V. Tabard-Cossa, and M. Godin, ‘Digital counting of nucleic acid targets using solid-state nanopores’, Nanoscale, 2020, https://doi.org/10.1039/d0nr03878d.
E. Beamish, V. Tabard-Cossa, and M. Godin, ‘Programmable DNA Nanoswitch Sensing with Solid-State Nanopores’, ACS Sens, 2019, https://doi.org/10.1021/acssensors.9b01053.
J. Kong, J. Zhu, and U. F. Keyser, ‘Single molecule based SNP detection using designed DNA carriers and solid-state nanopores’, Chemical Communications, vol. 53, no. 2, pp. 436–439, 2017, https://doi.org/10.1039/c6cc08621g.
T. J. Morin et al., ‘Nanopore-Based Target Sequence Detection.’, PLoS One, vol. 11, no. 5, p. e0154426, 2016, https://doi.org/10.1371/journal.pone.0154426.
O. K. Zahid, B. S. Zhao, C. He, and A. R. Hall, ‘Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores’, Sci Rep, vol. 6, no. June, pp. 1–6, 2016, https://doi.org/10.1038/srep29565.
O. K. Zahid, F. Wang, J. A. Ruzicka, E. W. Taylor, and A. R. Hall, ‘Sequence-Specific Recognition of MicroRNAs and Other Short Nucleic Acids with Solid-State Nanopores’, Nano Lett, vol. 16, no. 3, pp. 2033–2039, 2016, https://doi.org/10.1021/acs.nanolett.6b00001.
Proteins
Shilo Ohayon, Arik Girsault, Maisa Nasser, Shai Shen-Orr, Amit Meller. Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PLoS Comput. Biol. 2019. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007067
Joseph Bush, William Maulbetsch; Mathilde Lepoitevin, Benjamin Wiener, Mirna Mihovilovic Skanata, Wooyoung Moon, Cole Pruitt, and Derek Stein. The nanopore mass spectrometer Rev. Sci. Inst. 88 133307 2017. https://doi.org/10.1063/1.4986043
William Maulbetsch, Benjamin Wiener, William Poole, Joseph Bush, and Derek Stein. Preserving the Sequence of a Biopolymer’s Monomers as They Enter an Electrospray Mass Spectrometer Phys. Rev. Applied 6 054006 2016. https://doi.org/10.1103/PhysRevApplied.6.054006
I. Abrao-Nemeir et al., ‘Investigation of α-Synuclein and Amyloid-β(42)-E22Δ Oligomers Using SiN Nanopore Functionalized with L-Dopa’, Chem Asian J, no. 42, 2022, https://doi.org/10.1002/asia.202200726
Liqun He et al., ‘Digital Immunoassay for Biomarker Concentration Quantification using Solid-State Nanopores’, Nat Commun, vol. 12, no. 1, p. 5348, 2021, https://doi.org/10.1038/s41467-021-25566-8.
S. Schmid and C. Dekker, ‘The NEOtrap – en route with a new single-molecule technique’, iScience, p. 103007, 2021, https://doi.org/10.1016/j.isci.2021.103007.
S. Schmid, P. Stömmer, H. Dietz, and C. Dekker, ‘Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations’, bioRxiv, vol. 18, pp. 2–9, 2021, https://doi.org/10.1101/2021.03.09.434634.
J. Kong, J. Zhu, K. Chen, and U. F. Keyser, ‘Specific Biosensing Using DNA Aptamers and Nanopores’, Adv Funct Mater, vol. 29, no. 3, p. 1807555, Jan. 2019, https://doi.org/https://doi.org/10.1002/adfm.201807555.
L. Restrepo-Pérez, C. Joo, and C. Dekker, ‘Paving the way to single-molecule protein sequencing’, Nat Nanotechnol, vol. 13, no. 9, pp. 786–796, 2018, https://doi.org/10.1038/s41565-018-0236-6.
E. C. Yusko et al., ‘Real-time shape approximation and fingerprinting of single proteins using a nanopore’, Nat Nanotechnol, vol. 12, no. 4, pp. 360–367, 2017, https://doi.org/10.1038/nnano.2016.267.
Metabolites
F. Rivas, P. L. DeAngelis, E. Rahbar, and A. R. Hall, ‘Optimizing the sensitivity and resolution of hyaluronan analysis with solid-state nanopores’, Sci Rep, vol. 12, no. 1, p. 4469, 2022, https://doi.org/10.1038/s41598-022-08533-1.
K. Xia, J. T. Hagan, L. Fu, B. S. Sheetz, S. Bhattacharya, and F. Zhang, ‘Synthetic heparan sulfate standards and machine learning facilitate the development of solid-state nanopore analysis’, PNAS, vol. 118, no. 11, pp. 1–7, 2021, https://doi.org/10.1073/pnas.2022806118.
Y. M. N. D. Y. Bandara et al., ‘Chemically Functionalizing Controlled Dielectric Breakdown Silicon Nitride Nanopores by Direct Photohydrosilylation’, ACS Appl Mater Interfaces, vol. 11, no. 33, pp. 30411–30420, Aug. 2019, https://doi.org/10.1021/acsami.9b08004.
F. Rivas et al., ‘Label-free analysis of physiological hyaluronan size distribution with a solid-state nanopore sensor’, Nat Commun, vol. 9, no. 1, p. 1037, 2018, https://doi.org/10.1038/s41467-018-03439-x.
B. I. Karawdeniya, Y. M. N. D. Y. Bandara, J. W. Nichols, R. B. Chevalier, and J. R. Dwyer, ‘Surveying silicon nitride nanopores for glycomics and heparin quality assurance’, Nat Commun, vol. 9, no. 1, pp. 1–8, 2018, https://doi.org/10.1038/s41467-018-05751-y.
E. Beamish, V. Tabard-Cossa, and M. Godin, ‘Identifying Structure in Short DNA Scaffolds Using Solid-State Nanopores’, ACS Sens, vol. 2, no. 12, pp. 1814–1820, 2017, https://doi.org/10.1021/acssensors.7b00628
Molecular Information Storage
Nanopore Readout
J. Zhu, N. Ermann, K. Chen, and U. F. Keyser, ‘Image Encoding Using Multi-Level DNA Barcodes with Nanopore Readout’, Small, vol. 17, no. 28, p. 2100711, Jul. 2021, https://doi.org/https://doi.org/10.1002/smll.202100711.
K. Chen, J. Zhu, F. Bošković, and U. F. Keyser, ‘Nanopore-Based DNA Hard Drives for Rewritable and Secure Data Storage’, Nano Lett, vol. 20, no. 5, pp. 3754–3760, May 2020, https://doi.org/10.1021/acs.nanolett.0c00755.
K. Chen, J. Kong, J. Zhu, N. Ermann, P. Predki, and U. F. Keyser, ‘Digital Data Storage Using DNA Nanostructures and Solid-State Nanopores’, Nano Lett, vol. 19, pp. 1210–1215, 2019, https://doi.org/10.1021/acs.nanolett.8b04715.
Synthetic polymer synthesis
L. Charles and J.-F. Lutz, ‘Design of Abiological Digital Poly(phosphodiester)s’, Acc Chem Res, vol. 54, no. 7, pp. 1791–1800, Apr. 2021, https://doi.org/10.1021/acs.accounts.1c00038.
J. De Neve, J. J. Haven, L. Maes, and T. Junkers, ‘Sequence-definition from controlled polymerization: The next generation of materials’, Polym Chem, vol. 9, no. 38, pp. 4692–4705, 2018, https://doi.org/10.1039/c8py01190g.
R. K. Roy, A. Meszynska, C. Laure, L. Charles, C. Verchin, and J.-F. Lutz, ‘Design and synthesis of digitally encoded polymers that can be decoded and erased’, Nat Commun, vol. 6, no. 1, p. 7237, 2015, https://doi.org/10.1038/ncomms8237.
A. Al Ouahabi, L. Charles, and J.-F. Lutz, ‘Synthesis of Non-Natural Sequence-Encoded Polymers Using Phosphoramidite Chemistry’, J Am Chem Soc, vol. 137, no. 16, pp. 5629–5635, Apr. 2015, https://doi.org/10.1021/jacs.5b02639.
H. Mutlu and J.-F. Lutz, ‘Reading Polymers: Sequencing of Natural and Synthetic Macromolecules’, Angewandte Chemie International Edition, vol. 53, no. 48, pp. 13010–13019, Nov. 2014, https://doi.org/https://doi.org/10.1002/anie.201406766.
J. F. Lutz, ‘Sequence-controlled polymerizations: The next Holy Grail in polymer science?’, Polym Chem, vol. 1, no. 1, pp. 55–62, 2010, https://doi.org/10.1039/b9py00329k.
Potential Impact
Proteomics
Ostermann, M. et al. Recommendations on Acute Kidney Injury Biomarkers From the Acute Disease Quality Initiative Consensus Conference: A Consensus Statement. JAMA Network 2020. https://www.doi.org/10.1001/jamanetworkopen.2020.19209
Silver, S. A., Long, J., Zheng, Y. & Chertow, G. M. Cost of acute kidney injury in hospitalized patients. J Hosp Med 12, 70–76 2017. https://doi.org/10.12788/jhm.2683
Abebe, A., Kumela, K., Belay, M., Kebede, B. & Wobie, Y. Mortality and predictors of acute kidney injury in adults: a hospital-based prospective observational study. Sci Rep 11, 1–8 2021. https://doi.org/10.1038/s41598-021-94946-3
Nordbank, E. Using Protein Biomarkers Increases the Chances of Success in Clinical Trials. Technology Networks, Proteomics and Metabolomics 2020. https://www.technologynetworks.com/proteomics/blog/using-protein-biomarkers-increases-the-chances-of-success-in-clinical-trials-329018
Sertkaya, A., Wong, H. H., Jessup, A. & Beleche, T. Key cost drivers of pharmaceutical clinical trials in the United States. Clinical Trials 13, 117–126 2016. https://doi.org/10.1177/1740774515625964
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