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

Show Author's information 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

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.

Keywords:

nanopore, DNA sequencing, MXenes, first-principles, quantum transport
Received: 21 December 2021 Revised: 07 May 2022 Accepted: 01 June 2022 Published: 30 June 2022 Issue date: October 2022
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Publication history

Received: 21 December 2021
Revised: 07 May 2022
Accepted: 01 June 2022
Published: 30 June 2022
Issue date: October 2022

Copyright

© The Author(s) 2022

Acknowledgements

Acknowledgements

J. P. acknowledges support from the Thailand Research Fund (MRG6280150). S. J. is supported by Suranaree University of Technology (SUT), Thailand Science Research and Innovation (TSRI), and National Science, Research and Innovation Fund (NSRF grant No. B05F640051). R. G. A. thanks for financial support from CNPq (Nos. 437182/2018-5 and 313076/2020-0) and also FAPERJ (Nos. E-26/010.101126/2018 and 26/202.699/2019). R. H. S. acknowledges the Swedish Research Council (VR grant 2017-04627).

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