Real-time Monitoring of Newly Acidified Organelles During Autophagy Enabled by Reaction-Based BODIPY Dyes

Commun Biol. 2019 Nov 28;2:442. doi: 10.1038/s42003-019-0682-1. eCollection 2019.


Real-time monitoring of newly acidified organelles during autophagy in living cells is highly desirable for a better understanding of intracellular degradative processes. Herein, we describe a reaction-based boron dipyrromethene (BODIPY) dye containing strongly electron-withdrawing diethyl 2-cyanoacrylate groups at the α-positions. The probe exhibits intense red fluorescence in acidic organelles or the acidified cytosol while exhibiting negligible fluorescence in other regions of the cell. The underlying mechanism is a nucleophilic reaction at the central meso-carbon of the indacene core, resulting in the loss of π-conjugation entailed by dramatic spectroscopic changes of more than 200 nm between its colorless, non-fluorescent leuco-BODIPY form and its red and brightly emitting form. The reversible transformation between red fluorescent BODIPY and leuco-BODIPY along with negligible cytotoxicity qualifies such dyes for rapid and direct intracellular lysosome imaging and cytosolic acidosis detection simultaneously without any washing step, enabling the real-time monitoring of newly acidified organelles during autophagy.

Keywords: Autophagy; Cellular imaging; Chemical modification; Fluorescent dyes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autophagy*
  • Boron Compounds / chemistry
  • Boron Compounds / metabolism*
  • Fluorescent Dyes / chemistry
  • Fluorescent Dyes / metabolism*
  • Lysosomes / metabolism
  • Magnetic Resonance Spectroscopy
  • Molecular Imaging / methods*
  • Optical Imaging / methods*
  • Organelles / metabolism*
  • Oxidation-Reduction
  • Photochemical Processes
  • Spectrometry, Fluorescence


  • 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene
  • Boron Compounds
  • Fluorescent Dyes