Simultaneous Zn2+ tracking in multiple organelles using super-resolution morphology-correlated organelle identification in living cells

Nat Commun. 2021 Jan 4;12(1):109. doi: 10.1038/s41467-020-20309-7.


Zn2+ plays important roles in metabolism and signaling regulation. Subcellular Zn2+ compartmentalization is essential for organelle functions and cell biology, but there is currently no method to determine Zn2+ signaling relationships among more than two different organelles with one probe. Here, we report simultaneous Zn2+ tracking in multiple organelles (Zn-STIMO), a method that uses structured illumination microscopy (SIM) and a single Zn2+ fluorescent probe, allowing super-resolution morphology-correlated organelle identification in living cells. To guarantee SIM imaging quality for organelle identification, we develop a new turn-on Zn2+ fluorescent probe, NapBu-BPEA, by regulating the lipophilicity of naphthalimide-derived Zn2+ probes to make it accumulate in multiple organelles except the nucleus. Zn-STIMO with this probe shows that CCCP-induced mitophagy in HeLa cells is associated with labile Zn2+ enhancement. Therefore, direct organelle identification supported by SIM imaging makes Zn-STIMO a reliable method to determine labile Zn2+ dynamics in various organelles with one probe. Finally, SIM imaging of pluripotent stem cell-derived organoids with NapBu-BPEA demonstrates the potential of super-resolution morphology-correlated organelle identification to track biospecies and events in specific organelles within organoids.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autophagosomes / metabolism
  • Autophagy
  • Carbonyl Cyanide m-Chlorophenyl Hydrazone / pharmacology
  • Cell Survival
  • Cell Tracking*
  • Endoplasmic Reticulum / metabolism
  • Fluorescent Dyes / metabolism
  • HeLa Cells
  • Humans
  • Induced Pluripotent Stem Cells / metabolism
  • Intracellular Space / metabolism
  • Lysosomes / metabolism
  • Molecular Probes / chemistry
  • Molecular Probes / metabolism
  • Naphthalimides / metabolism
  • Organelles / metabolism*
  • Organoids / metabolism
  • Spectrometry, Fluorescence
  • Zinc / metabolism*


  • Fluorescent Dyes
  • Molecular Probes
  • Naphthalimides
  • Carbonyl Cyanide m-Chlorophenyl Hydrazone
  • Zinc