A DNA nanodevice for mapping sodium at single-organelle resolution

Junyi Zou; Koushambi Mitra; Palapuravan Anees; Daphne Oettinger; Joseph R Ramirez; Aneesh Tazhe Veetil; Priyanka Dutta Gupta; Rajini Rao; Jayson J Smith; Paschalis Kratsios; Yamuna Krishnan

doi:10.1038/s41587-023-01950-1

A DNA nanodevice for mapping sodium at single-organelle resolution

Nat Biotechnol. 2023 Sep 21:10.1038/s41587-023-01950-1. doi: 10.1038/s41587-023-01950-1. Online ahead of print.

Authors

Junyi Zou^{1

2}, Koushambi Mitra^{1

2

3}, Palapuravan Anees^{1

2

3}, Daphne Oettinger^{1

2}, Joseph R Ramirez^{1

2}, Aneesh Tazhe Veetil^{1

2}, Priyanka Dutta Gupta^{1

2}, Rajini Rao⁴, Jayson J Smith^{2

5}, Paschalis Kratsios^{2

5}, Yamuna Krishnan^{6

7

8}

Affiliations

¹ Department of Chemistry, The University of Chicago, Chicago, IL, USA.
² Neuroscience Institute, The University of Chicago, Chicago, IL, USA.
³ Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
⁴ Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
⁵ Department of Neurobiology, The University of Chicago, Chicago, IL, USA.
⁶ Department of Chemistry, The University of Chicago, Chicago, IL, USA. yamuna@uchicago.edu.
⁷ Neuroscience Institute, The University of Chicago, Chicago, IL, USA. yamuna@uchicago.edu.
⁸ Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. yamuna@uchicago.edu.

PMID: 37735265
PMCID: PMC11004682 (available on 2025-03-21)
DOI: 10.1038/s41587-023-01950-1

Abstract

Cellular sodium ion (Na⁺) homeostasis is integral to organism physiology. Our current understanding of Na⁺ homeostasis is largely limited to Na⁺ transport at the plasma membrane. Organelles may also contribute to Na⁺ homeostasis; however, the direction of Na⁺ flow across organelle membranes is unknown because organellar Na⁺ cannot be imaged. Here we report a pH-independent, organelle-targetable, ratiometric probe that reports lumenal Na⁺. It is a DNA nanodevice containing a Na⁺-sensitive fluorophore, a reference dye and an organelle-targeting domain. By measuring Na⁺ at single endosome resolution in mammalian cells and Caenorhabditis elegans, we discovered that lumenal Na⁺ levels in each stage of the endolysosomal pathway exceed cytosolic levels and decrease as endosomes mature. Further, we find that lysosomal Na⁺ levels in nematodes are modulated by the Na⁺/H⁺ exchanger NHX-5 in response to salt stress. The ability to image subcellular Na⁺ will unveil mechanisms of Na⁺ homeostasis at an increased level of cellular detail.

Abstract

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