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Research Article | Open Access

Single-molecule DNA sequencing using two-dimensional Ti2C(OH)2 MXene nanopores: A first-principles investigation

Jariyanee Prasongkit1( )Sirichok Jungthawan2,3,4Rodrigo G. Amorim5Ralph H. Scheicher6( )
Division of Physics, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
School of Physics, Institute of Science, Suranaree University of Technology, 111 University Ave, Nakhon Ratchasima 30000, Thailand
Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, 328 Si Ayutthaya Road, Bangkok 10400, Thailand
Departamento de Física, ICEx, Universidade Federal Fluminense-UFF, Volta Redonda/RJ 27213-145, Brazil
Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, Uppsala SE-751 20, Sweden
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Graphical Abstract

We have assessed the potential of Ti2C(OH)2 MXene nanopores proposed for a promising two-dimensional (2D) material for nanopore-based DNA sensing.

Abstract

Nanopore-based devices have provided exciting opportunities to develop affordable label-free DNA sequencing platforms. Over a decade ago, graphene has been proposed as a two-dimensional (2D) nanopore membrane in order to achieve single-base resolution. However, it was experimentally revealed that clogging of the graphene nanopore can occur due to the hydrophobic nature of graphene, thus hindering the translocation of DNA. To overcome this problem, the exploration of alternative 2D materials has gained considerable interest over the last decade. Here we show that a Ti2C-based MXene nanopore functionalized by hydroxyl groups (–OH) exhibits transverse conductance properties that allow for the distinction between all four naturally occurring DNA bases. We have used a combination of density functional theory and non-equilibrium Green’s function method to sample over multiple orientations of the nucleotides in the nanopore, as generated from molecular dynamics simulations. The conductance variation resulting from sweeping an applied gate voltage demonstrates that the Ti2C-based MXene nanopore possesses high potential to rapidly and reliably sequence DNA. Our findings open the door to further theoretical and experimental explorations of MXene nanopores as a promising 2D material for nanopore-based DNA sensing.

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References

[1]

Wheeler, D. A.; Srinivasan, M.; Egholm, M.; Shen, Y. F.; Chen, L.; McGuire, A.; He, W.; Chen, Y. J.; Makhijani, V.; Roth, G. T. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452, 872–876.

[2]

Hayden, E. C. Technology: The $1, 000 genome. Nature 2014, 507, 294–295.

[3]

Mardis, E. R. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008, 24, 133–141.

[4]

Ziegler, A.; Koch, A.; Krockenberger, K.; Großhennig, A. Personalized medicine using DNA biomarkers: A review. Hum. Genet. 2012, 131, 1627–1638.

[5]

Feng, Y. X.; Zhang, Y. C.; Ying, C. F.; Wang, D. Q.; Du, C. L. Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics 2015, 13, 4–16.

[6]

Venkatesan, B. M.; Bashir, R. Nanopore sensors for nucleic acid analysis. Nat. Nanotechnol. 2011, 6, 615–624.

[7]

Olasagasti, F.; Lieberman, K. R.; Benner, S.; Cherf, G. M.; Dahl, J. M.; Deamer, D. W.; Akeson, M. Replication of individual DNA molecules under electronic control using a protein nanopore. Nat. Nanotechnol. 2010, 5, 798–806.

[8]

Clarke, J.; Wu, H. C.; Jayasinghe, L.; Patel, A.; Reid, S.; Bayley, H. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 2009, 4, 265–270.

[9]

Stoloff, D. H.; Wanunu, M. Recent trends in nanopores for biotechnology. Curr. Opin. Biotechnol. 2013, 24, 699–704.

[10]

Dekker, C. Solid-state nanopores. Nat. Nanotechnol. 2007, 2, 209–215.

[11]

Fologea, D.; Uplinger, J.; Thomas, B.; McNabb, D. S.; Li, J. L. Slowing DNA translocation in a solid-state nanopore. Nano Lett. 2005, 5, 1734–1737.

[12]

Li, J. L.; Stein, D.; McMullan, C.; Branton, D.; Aziz, M. J.; Golovchenko, J. A. Ion-beam sculpting at nanometre length scales. Nature 2001, 412, 166–169.

[13]

Fologea, D.; Gershow, M.; Ledden, B.; McNabb, D. S.; Golovchenko, J. A.; Li, J. L. Detecting single stranded DNA with a solid state nanopore. Nano Lett. 2005, 5, 1905–1909.

[14]

Gierhart, B. C.; Howitt, D. G.; Chen, S. J.; Zhu, Z. N.; Kotecki, D. E.; Smith, R. L.; Collins, S. D. Nanopore with transverse nanoelectrodes for electrical characterization and sequencing of DNA. Sens. Actuators B:Chem. 2008, 132, 593–600.

[15]

Tsutsui, M.; He, Y. H.; Furuhashi, M.; Rahong, S.; Taniguchi, M.; Kawai, T. Transverse electric field dragging of DNA in a nanochannel. Sci. Rep. 2012, 2, 394.

[16]

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.

[17]

Wang, Z.; Lv, T. Y.; Shi, Z. B.; Yang, S. S.; Gu, Z. Y. Two-dimensional materials as solid-state nanopores for chemical sensing. Dalton Trans. 2021, 50, 13608–13619.

[18]

Choi, J.; Lee, C. C.; Park, S. Scalable fabrication of sub-10 nm polymer nanopores for DNA analysis. Microsyst. Nanoeng. 2019, 5, 12.

[19]

Yuan, Z. S.; Wang, C. Y.; Yi, X.; Ni, Z. H.; Chen, Y. F.; Li, T. Solid-state nanopore. Nanoscale Res. Lett. 2018, 13, 56.

[20]

Schneider, G. F.; Kowalczyk, S. W.; Calado, V. E.; Pandraud, G.; Zandbergen, H. W.; Vandersypen, L. M. K.; Dekker, C. DNA translocation through graphene nanopores. Nano Lett. 2010, 10, 3163–3167.

[21]

Merchant, C. A.; Healy, K.; Wanunu, M.; Ray, V.; Peterman, N.; Bartel, J.; Fischbein, M. D.; Venta, K.; Luo, Z. T.; Johnson, A. T. C. et al. DNA translocation through graphene nanopores. Nano Lett. 2010, 10, 2915–2921.

[22]

Garaj, S.; Hubbard, W.; Reina, A.; Kong, J.; Branton, D.; Golovchenko, J. A. Graphene as a subnanometre trans-electrode membrane. Nature 2010, 467, 190–193.

[23]

Van Den Hout, M.; Hall, A. R.; Wu, M. Y.; Zandbergen, H. W.; Dekker, C.; Dekker, N. H. Controlling nanopore size, shape and stability. Nanotechnology 2010, 21, 115304.

[24]

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

[25]

Balandin, A. A. Low-frequency 1/f noise in graphene devices. Nat. Nanotechnol. 2013, 8, 549–555.

[26]

Heerema, S. J.; Schneider, G. F.; Rozemuller, M.; Vicarelli, L.; Zandbergen, H. W.; Dekker, C. 1/f noise in graphene nanopores. Nanotechnology 2015, 26, 074001.

[27]

Waduge, P.; Larkin, J.; Upmanyu, M.; Kar, S.; Wanunu, M. Programmed synthesis of freestanding graphene nanomembrane arrays. Small 2015, 11, 597–603.

[28]

Rajan, A. C.; Rezapour, M. R.; Yun, J.; Cho, Y.; Cho, W. J.; Min, S. K.; Lee, G.; Kim, K. S. Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition. ACS Nano 2014, 8, 1827–1833.

[29]

Liu, S.; Lu, B.; Zhao, Q.; Li, J.; Gao, T.; Chen, Y. B.; Zhang, Y. F.; Liu, Z. F.; Fan, Z. C.; Yang, F. H. et al. Boron nitride nanopores: Highly sensitive DNA single-molecule detectors. Adv. Mater. 2013, 25, 4549–4554.

[30]

Liu, K.; Lihter, M.; Sarathy, A.; Caneva, S.; Qiu, H.; Deiana, D.; Tileli, V.; Alexander, D. T. L.; Hofmann, S.; Dumcenco, D. et al. Geometrical effect in 2D nanopores. Nano Lett. 2017, 17, 4223–4230.

[31]

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

[32]

Waduge, P.; Bilgin, I.; Larkin, J.; Henley, R. Y.; Goodfellow, K.; Graham, A. C.; Bell, D. C.; Vamivakas, N.; Kar, S.; Wanunu, M. Direct and scalable deposition of atomically thin low-noise MoS2 membranes on apertures. ACS Nano 2015, 9, 7352–7359.

[33]

Graf, M.; Lihter, M.; Altus, D.; Marion, S.; Radenovic, A. Transverse detection of DNA using a MoS2 nanopore. Nano Lett. 2019, 19, 9075–9083.

[34]

Danda, G.; Das, P. M.; Chou, Y. C.; Mlack, J. T.; Parkin, W. M.; Naylor, C. H.; Fujisawa, K.; Zhang, T. Y.; Fulton, L. B.; Terrones, M. et al. Monolayer WS2 nanopores for DNA translocation with light-adjustable sizes. ACS Nano 2017, 11, 1937–1945.

[35]

Naguib, M.; Kurtoglu, M.; Presser, V.; Lu, J.; Niu, J. J.; Heon, M.; Hultman, L.; Gogotsi, Y.; Barsoum, M. W. Two-dimensional nanocrystals produced by exfoliation of Ti3AlC2. Adv. Mater. 2011, 23, 4248–4253.

[36]

Naguib, M.; Mashtalir, O.; Carle, J.; Presser, V.; Lu, J.; Hultman, L.; Gogotsi, Y.; Barsoum, M. W. Two-dimensional transition metal carbides. ACS Nano 2012, 6, 1322–1331.

[37]

Anasori, B.; Lukatskaya, M. R.; Gogotsi, Y. 2D metal carbides and nitrides (MXenes) for energy storage. Nat. Rev. Mater. 2017, 2, 16098.

[38]

Mojtabavi, M.; VahidMohammadi, A.; Liang, W. T.; Beidaghi, M.; Wanunu, M. Single-molecule sensing using nanopores in two-dimensional transition metal carbide (MXene) membranes. ACS Nano 2019, 13, 3042–3053.

[39]

Yadav, P.; Cao, Z. L.; Farimani, A. B. DNA detection with single-layer Ti3C2 MXene nanopore. ACS Nano 2021, 15, 4861–4869.

[40]

Xue, Y. Q.; Datta, S.; Ratner, M. A. First-principles based matrix Green’s function approach to molecular electronic devices: General formalism. Chem. Phys. 2002, 281, 151–170.

[41]

Brandbyge, M.; Mozos, J. L.; Ordejón, P.; Taylor, J.; Stokbro, K. Density-functional method for nonequilibrium electron transport. Phys. Rev. B 2002, 65, 165401.

[42]

Hohenberg, P.; Kohn, W. Inhomogeneous electron gas. Phys. Rev. 1964, 136, B864–B871.

[43]

Kohn, W.; Sham, L. J. Self-consistent equations including exchange and correlation effects. Phys. Rev. 1965, 140, A1133–A1138.

[44]

Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 1996, 77, 3865–3868.

[45]

Smidstrup, S.; Markussen, T.; Vancraeyveld, P.; Wellendorff, J.; Schneider, J.; Gunst, T.; Verstichel, B.; Stradi, D.; Khomyakov, P. A.; Vej-Hansen, U. G. et al. QuantumATK: An integrated platform of electronic and atomic-scale modelling tools. J. Phys.: Condens. Matter 2019, 32, 015901.

[46]

Troullier, N.; Martins, J. L. Efficient pseudopotentials for plane-wave calculations. Phys. Rev. B 1991, 43, 1993–2006.

[47]
Zhang, Q. X. ; Wei, J. ; Liu, J. C. ; Wang, Z. C. ; Lei, M. ; Quhe, R. 2D/2D electrical contacts in the monolayer WSe2 transistors: A first-principles study. ACS Appl. Nano Mater. 2019, 2, 2796–2805.
[48]

Monkhorst, H. J.; Pack, J. D. Special points for Brillouin-zone integrations. Phys. Rev. B 1976, 13, 5188–5192.

[49]

Boys, S. F.; Bernardi, F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 1970, 19, 553–566.

[50]

Fisher, R. S.; Lee, P. A. Relation between conductivity and transmission matrix. Phys. Rev. B 1981, 23, 6851–6854.

[51]

Solomon, G. C.; Herrmann, C.; Hansen, T.; Mujica, V.; Ratner, M. A. Exploring local currents in molecular junctions. Nat. Chem. 2010, 2, 223–228.

[52]

Paulsson, M.; Brandbyge, M. Transmission eigenchannels from nonequilibrium Green’s functions. Phys. Rev. B 2007, 76, 115117.

[53]

Prasongkit, J.; Grigoriev, A.; Pathak, B.; Ahuja, R.; Scheicher, R. H. Transverse conductance of DNA nucleotides in a graphene nanogap from first principles. Nano Lett. 2011, 11, 1941–1945.

[54]

Prasongkit, J.; Feliciano, G. T.; Rocha, A. R.; He, Y. H.; Osotchan, T.; Ahuja, R.; Scheicher, R. H. Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene. Sci. Rep. 2015, 5, 17560.

[55]

Prasongkit, J.; De Freitas Martins, E.; De Souza, F. A. L.; Scopel, W. L.; Amorim, R. G.; Amornkitbamrung, V.; Rocha, A. R.; Scheicher, R. H. Topological line defects around graphene nanopores for DNA sequencing. J. Phys. Chem. C 2018, 122, 7094–7099.

[56]

Sadeghi, H.; Bailey, S.; Lambert, C. J. Silicene-based DNA nucleobase sensing. Appl. Phys. Lett. 2014, 104, 103104.

[57]

Amorim, R. G.; Scheicher, R. H. Silicene as a new potential DNA sequencing device. Nanotechnology 2015, 26, 154002.

[58]

Kumawat, R. L.; Garg, P.; Kumar, S.; Pathak, B. Electronic transport through DNA nucleotides in atomically thin phosphorene electrodes for rapid DNA sequencing. ACS Appl. Mater. Interfaces 2019, 11, 219–225.

[59]

Fragasso, A.; Schmid, S.; Dekker, C. Comparing current noise in biological and solid-state nanopores. ACS Nano 2020, 14, 1338–1349.

[60]

Carson, S.; Wilson, J.; Aksimentiev, A.; Wanunu, M. Smooth DNA transport through a narrowed pore geometry. Biophys. J. 2014, 107, 2381–2393.

[61]

Li, J. L.; Talaga, D. S. The distribution of DNA translocation times in solid-state nanopores. J. Phys.: Condens. Matter. 2010, 22, 454129.

[62]

Henry, M. B.; Tumbapo, M.; Tayo, B. O. Identification of DNA bases using nanopores created in finite-size nanoribbons from graphene, phosphorene, and silicene. AIP Adv. 2021, 11, 035324.

[63]

Chandiramouli, R.; Nagarajan, V. Silicene nanosheet device with nanopore to identify the nucleobases-a first-principles perspective. Chem. Phys. Lett. 2019, 730, 70–75.

[64]

Farimani, A. B.; Min, K.; Aluru, N. R. DNA base detection using a single-layer MoS2. ACS Nano 2014, 8, 7914–7922.

[65]

Gouveia, J. D.; Morales-García, Á.; Viñes, F.; Illas, F.; Gomes, J. R. B. MXenes as promising catalysts for water dissociation. Appl. Catal. B 2020, 260, 118191.

[66]

Akkuş, Ü. Ö.; Balcı, E.; Berber, S. Device characteristics of Ti2CT2 MXene-based field-effect transistor. Superlattices Microstruct. 2020, 140, 106433.

[67]

De Freitas Martins, E.; Amorim, R. G.; Feliciano, G. T.; Scheicher, R. H.; Rocha, A. R. The role of water on the electronic transport in graphene nanogap devices designed for DNA sequencing. Carbon 2020, 158, 314–319.

Nano Research
Pages 9843-9849
Cite this article:
Prasongkit J, Jungthawan S, Amorim RG, et al. Single-molecule DNA sequencing using two-dimensional Ti2C(OH)2 MXene nanopores: A first-principles investigation. Nano Research, 2022, 15(11): 9843-9849. https://doi.org/10.1007/s12274-022-4632-8
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Received: 21 December 2021
Revised: 07 May 2022
Accepted: 01 June 2022
Published: 30 June 2022
© The Author(s) 2022

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