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Fabrication and practical applications of molybdenum disulfide nanopores

Nature Protocols volume 14, pages 1130–1168 (2019)Cite this article

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Abstract

Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin membranes have the advantage of providing relatively high ionic currents at very small pore sizes. This increases the signal generated during translocation of biomolecules and improves the nanopores’ efficiency when used for desalination or reverse electrodialysis applications. The atomic thickness of MoS2 nanopores approaches the inter-base distance of DNA, creating a potential candidate for DNA sequencing. In terms of geometry, MoS2 nanopores have a well-defined vertical profile due to their atomic thickness, which eliminates any unwanted effects associated with uneven pore profiles observed in other materials. This protocol details all the necessary procedures for the fabrication of solid-state devices. We discuss different methods for transfer of monolayer MoS2, different approaches for the creation of nanopores, their applicability in detecting DNA translocations and the analysis of translocation data through open-source programming packages. We present anticipated results through the application of our nanopores in DNA translocations and osmotic power generation. The procedure comprises four parts: fabrication of devices (2–3 d), transfer of MoS2 and cleaning procedure (24 h), the creation of nanopores within MoS2 (30 min) and performing DNA translocations (2–3 h). We anticipate that our protocol will enable large-scale manufacturing of single-molecule-analysis devices as well as next-generation DNA sequencing.

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Fig. 1: Overview of the fabrication process.
Fig. 2: Nanopore-sensing principle.
Fig. 3: Osmotic power conversion.
Fig. 4: Power spectral density.
Fig. 5: Gold-plating the test chips.
Fig. 6: Leakage tests.
Fig. 7: Troubleshooting MoS2 transfer.
Fig. 8: Overview of PDMS-assisted selective transfer of MoS2.
Fig. 9: Beam damage.
Fig. 10: TEM characterization.
Fig. 11: Diameter and thickness of the aperture.
Fig. 12: Flow cell design.
Fig. 13: Overview of the substrate fabrication (Steps 1–30).
Fig. 14: Insufficient etching of the aperture (Step 19).
Fig. 15: Anticipated results: substrate fabrication.
Fig. 16: Anticipated results of the finished device when used for translocations.
Fig. 17: Anticipated results: osmotic power generation.

Code availability

All the code used to produce the figures, as well as the analysis of the raw data used in this protocol, is available publicly on Zenodo: https://doi.org/10.5281/zenodo.1463768.

Data availability

All the raw data used in this protocol are available publicly on Zenodo: https://doi.org/10.5281/zenodo.1463768.

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Acknowledgements

This work was financially supported by a Swiss National Science Foundation (SNSF) Consolidator grant (BIONIC BSCGI0_157802), by a CCMX project (‘Large Area Growth of 2D Materials for device integration’) and also by a sponsored research agreement from Hoffmann-LaRoche. We thank M. Macha (EPFL), D. Dumcenco (EPFL), H. Cun (EPFL), Y. Zhao (EPFL) and M. Fadlelmula (EPFL) for providing MoS2 material. We thank A. Kis (EPFL) for discussions on improving transfer methods. Device fabrication was partially carried out at the Center for Micro/Nanotechnology (CMi) at EPFL and at the National Institute of Standards and Technology (NIST) Center of Nanoscale Science and Technology (CNST). We thank the Centre Interdisciplinaire de Microscopie Electronique (CIME) at EPFL for access to electron microscopes. V.G. acknowledges support under the Cooperative Research Agreement between the University of Maryland and the National Institute of Standards and Technology Center for Nanoscale Science and Technology, award 70NANB14H209, through the University of Maryland. This article identifies certain commercial equipment, instruments and materials to specify the experimental procedure. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the equipment, instruments and materials identified are necessarily the best available for the purpose. The authors thank J. Gundlach (University of Washington) for constructive comments on the manuscript.

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  1. These authors contributed equally: Michael Graf, Martina Lihter, Mukeshchand Thakur.

Authors and Affiliations

  1. Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland

    Michael Graf, Martina Lihter, Mukeshchand Thakur, Ke Liu & Aleksandra Radenovic

  2. Roche Sequencing Solutions, Pleasanton, CA, USA

    Vasileia Georgiou, Juraj Topolancik & Yann Astier

  3. Institute for Research in Electronics and Applied Physics and Maryland NanoCenter, University of Maryland, College Park, MD, USA

    Vasileia Georgiou

  4. Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD, USA

    Juraj Topolancik & B. Robert Ilic

  5. Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou, China

    Jiandong Feng

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Contributions

K.L. and J.F. performed the initial work on device fabrication, MoS2 transfer and pore characterization. M.G., J.T., V.G. and B.R.I. developed the substrate fabrication process; V.G. fabricated the substrates. Y.A. supervised the substrate fabrication process. J.F., K.L. and A.R. developed the electrochemical reaction pore-drilling method; M.G. built the transfer microscope setup; M.G. and M.L. developed the PMMA transfer method and optimized the MoS2 cleaning procedure; M.T. developed the PDMS transfer method; M.L. and M.G. performed TEM characterization; M.L. and K.L. optimized the TEM pore-drilling method; and M.G. developed the translocation data acquisition and analysis software. M.G., M.L. and M.T. fabricated the devices and performed the experiments. M.G., M.L., M.T., J.T. and A.R. wrote the manuscript. All authors provided constructive comments on the manuscript. The work was performed under the supervision of A.R.

Corresponding author

Correspondence to Aleksandra Radenovic.

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Related links

Key references using this protocol

Liu, K., Feng, J., Kis, A. & Radenovic, A. ACS Nano 8, 2504–2511 (2014): https://doi.org/10.1021/nn406102h

Feng, J. et al. Nano Lett. 15, 3431–3438 (2015): https://doi.org/10.1021/acs.nanolett.5b00768

Feng, J. et al. Nat. Nanotechnol. 10, 1070–1076 (2015): https://doi.org/10.1038/nnano.2015.219

Feng, J. et al. Nature 536, 197–200 (2016): https://doi.org/10.1038/nature18593

Supplementary information

Reporting Summary

Supplementary Video 1

PMMA-assisted selective transfer of MoS2 to a SiNx membrane.

Supplementary Video 2

PDMS-assisted selective transfer of MoS2 to a SiNx membrane.

Supplementary Video 3

Preparation of an elastomer mix and precision painting of a SiNx membrane.

Supplementary Video 4

Procedure for chip mounting, and wetting and handling of the flow cell.

Supplementary Data 1

3D file for TEM holder.

Supplementary Data 2

3D file for flow cell.

Supplementary Data 3

CAD file for photolithography and e-beam lithography.

Supplementary Data 4

3D file for chip holder.

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Graf, M., Lihter, M., Thakur, M. et al. Fabrication and practical applications of molybdenum disulfide nanopores. Nat Protoc 14, 1130–1168 (2019). https://doi.org/10.1038/s41596-019-0131-0

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