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A DNA-based voltmeter for organelles

Nature Nanotechnology volume 16, pages 96–103 (2021)Cite this article

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Abstract

The role of membrane potential in most intracellular organelles remains unexplored because of the lack of suitable tools. Here, we describe Voltair, a fluorescent DNA nanodevice that reports the absolute membrane potential and can be targeted to organelles in live cells. Voltair consists of a voltage-sensitive fluorophore and a reference fluorophore for ratiometry, and acts as an endocytic tracer. Using Voltair, we could measure the membrane potential of different organelles in situ in live cells. Voltair can potentially guide the rational design of biocompatible electronics and enhance our understanding of how membrane potential regulates organelle biology.

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Fig. 1: Design and characterization of Voltair probes.
Fig. 2: Targeting VoltairIM to membranes of specific endocytic organelles.
Fig. 3: VoltairIM measures lysosomal membrane potential.
Fig. 4: Membrane potential of organelles along endocytic, recycling and retrograde trafficking pathway.

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Data availability

The data supporting the plots in this paper and other findings of this study are available from the corresponding author upon reasonable request.

Code availability

The MATLAB code for the voltage clamping experiments are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank J. Kuriyan, J. C. Clardy, J. W. Szostak, H. Xu and F. Bezanilla for critical comments; K. Chakraborty, X. Zhang, J. L. C. Souza, J. Delgado and Y. Jiang for discussions; and the integrated light microscopy and mass spectrometry facilities at the University of Chicago. This work was supported by the Women’s Board of the University of Chicago; FA9550-19-0003 from AFOSR, NIH grants R21NS114428, 1R01NS112139-01A1, Pilot and Feasibility award from an NIH-NIDDK Center grant P30DK42086 to the University of Chicago’s Digestive Diseases Research Center; and Chicago Biomedical Consortium with support from the Searle Funds at the Chicago Community Trust, C-084. M.S. was a Heisenberg fellow supported by the Deutsche Forschungsgemeinschaft.

Author information

Authors and Affiliations

  1. Department of Chemistry, The University of Chicago, Chicago, IL, USA

    Anand Saminathan, Aneesh Tazhe Veetil, Bhavyashree Suresh, Kavya Smitha Pillai & Yamuna Krishnan

  2. Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA

    Anand Saminathan, Aneesh Tazhe Veetil, Bhavyashree Suresh & Yamuna Krishnan

  3. Department of Physics, The University of Chicago, Chicago, IL, USA

    John Devany

  4. Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA

    Michael Schwake

  5. Biochemistry III/Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, Bielefeld, Germany

    Michael Schwake

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Contributions

A.S., A.T.V. and Y.K. designed the project. A.S., A.T.V. and K.S.P. synthesized the probe, A.S. and J.D. built the instrumentation, and A.S., J.D. and B.S. performed the experiments. M.S. provided a scavenger receptor plasmid. A.S. and Y.K. designed the experiments and analysed and interpreted the data. A.S. and Y.K. wrote the paper. All authors provided input on the manuscript.

Corresponding author

Correspondence to Yamuna Krishnan.

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The authors declare no competing interests.

Additional information

Peer review information Nature Nanotechnology thanks Yonggang Ke, Haoxing Xu and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Schematic of lysosomal Vmem measurement.

Imaging protocol of organelles labelled with VoltairIM. Resting organelles are imaged in the G and R channels, neutralized with valinomycin-monensin. The second set of images is acquired in the G and R channels. The resting membrane potential of the organelle is calculated by normalizing the G/R values from untreated lysosomes (xi) to neutralized lysosomes (yi).

Supplementary information

Supplementary Information

Supplementary Figs. 1–28, Notes 1–6, Tables 1,2.

Supplementary Video 1

Pseudo-coloured video showing the sensitivity of RVF. RVF-labelled HEK 293T cells were voltage clamped from −100 mV to +100 mV at increments of 10 mV in extracellular buffer. The clamped cell is shown by a white arrow; scale = 10 µm.

Supplementary Video 2

Pseudo-coloured video showing the sensitivity of VoltairPM. Labelled HEK 293T cells were voltage clamped from −100 mV to +100 mV at increments of 10 mV in extracellular buffer. The RVF channel shows the fluorescence change with respect to the membrane potential, whereas Atto647N fluorescence is insensitive to the applied voltage increments. The G/R ratio quantitatively shows the change in the membrane potential difference; scale = 10 µm.

Supplementary Video 3

Time-lapse imaging of lysosomal membrane potential in COS-7 cells labelled with VoltairIM. ML-SA1 (20 µM) or Vehicle (DMSO) is added to cells at 100 s. The pseudo-coloured images represent the computed intensity ratio of VoltairIM in the G (RVF) and R (Atto647N) channels. The cell of interest is represented by a white ROI (region of interest); scale = 10 µm.

Supplementary Video 4

Time-lapse imaging of endosomal membrane potential in COS-7 cells labelled with VoltairIM. ML-SA1 (20 µM) is added to cells at 100 s. The pseudo-coloured images represent the computed intensity ratio of VoltairIM in the G (RVF) and R (Atto647N) channels. The cell of interest is represented by a white ROI (region of interest); scale = 10 µm.

Supplementary Video 5

Time-lapse imaging of cytosolic calcium levels in ATP-treated COS-7 cells, labelled with Fluo-4 AM. 100 µM ATP is added to cells at 35 s. The pseudo-coloured images represent the intensity of Fluo-4 in a heat map; scale = 10 µm.

Supplementary Video 6

Time-lapse imaging of lysosomal membrane potential in ATP-treated COS-7 cells labelled with VoltairIM. 100 µM ATP or 1X PBS is added to cells at 35 s. The pseudo-coloured images represent the computed intensity ratio of VoltairIM in the G (RVF) and R (Atto647N) channels. The cell of interest is represented by a white ROI (region of interest). The white arrowheads indicate the lysosomes undergoing ATP-induced hyperpolarization. The decrease in G/R (observed in movie) represents the increase in positive membrane potential; scale = 10 µm.

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Saminathan, A., Devany, J., Veetil, A.T. et al. A DNA-based voltmeter for organelles. Nat. Nanotechnol. 16, 96–103 (2021). https://doi.org/10.1038/s41565-020-00784-1

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