Localized detection of ions and biomolecules with a force-controlled scanning nanopore microscope


Proteins, nucleic acids and ions secreted from single cells are the key signalling factors that determine the interaction of cells with their environment and the neighbouring cells. It is possible to study individual ion channels by pipette clamping, but it is difficult to dynamically monitor the activity of ion channels and transporters across the cellular membrane. Here we show that a solid-state nanopore integrated in an atomic force microscope can be used for the stochastic sensing of secreted molecules and the activity of ion channels in arbitrary locations both inside and outside a cell. The translocation of biomolecules and ions through the nanopore is observed in real time in live cells. The versatile nature of this approach allows us to detect specific biomolecules under controlled mechanical confinement and to monitor the ion-channel activities of single cells. Moreover, the nanopore microscope was used to image the surface of the nuclear membrane via high-resolution scanning ion conductance measurements.

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Fig. 1: Nanopore fabrication on the AFM cantilevers.
Fig. 2: Localized detection of proteins near the surface under mechanical confinement with a nanopore AFM.
Fig. 3: Extracellular recording from single cells.
Fig. 4: Extracellular recording from MEFs with and without Fn expression.
Fig. 5: Current maps for the cells with a controlled number of ion channels and the ratio of class II to class I events.
Fig. 6: Intracellular recording with nanopore AFM.

Data availability

All the data needed to evaluate the conclusions in the paper are present in the paper. Additional data and other findings of this study are available from the corresponding authors upon reasonable request.


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This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Individual Fellowship (project reference 706930) and the Career Seed Grant from ETH Zürich (project reference 0-20440-18) to M.A. The work was partially funded by the EUROSTARS project grant E!11644. D.M. is supported by the Swiss National Science Foundation Ambizione grant PZ00P2_174217/1. I.S. is thankful to Empa for financial support and to the Swiss National Science Foundation for support in equipment procurement (R’Equip 206021_133823). This work was supported by the Human Frontiers Science Program RGY0065/2017 to E.K.

The authors acknowledge the valuable and insightful discussions with C. Frei, V. Gatterdam, O. Guillaume-Gentil and V. Vogel. We are grateful to members of our laboratories for assistance during the project. We appreciate the technical assistance from S. Wheeler. The PAcrAm-g-(PMOXA, NH2, Si) polymer was a kind donation of SuSoS AG, Switzerland. We are grateful to the Martinac lab and M. Vassalli for valuable discussions and the provided materials. The authors acknowledge support of the Scientific Center for Optical and Electron Microscopy ScopeM of the Swiss Federal Institute of Technology ETHZ.

Author information

M.A. and J.V. designed the experiments. M.A., C.F., L.D.-C., I.L., T.S., S.J.I., I.S. and V.H. performed the experiments. M.A., C.F. and S.J.I. performed the statistical analysis and coding with support from J.V. All the authors discussed the results and commented on the manuscript. M.A. wrote the manuscript with support from J.V.

Correspondence to Morteza Aramesh or János Vörös.

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