Conventional bodipy conjugates for live-cell super-resolution microscopy and single-molecule tracking

Santosh Adhikari, Chiranjib Banerjee, Joe Moscatelli, Elias M. Puchner

Research output: Contribution to journalArticlepeer-review


Single molecule localization microscopy (SMLM) techniques overcome the optical diffraction limit of conventional fluorescence microscopy and can resolve intracellular structures and the dynamics of biomolecules with ~20 nm precision. A prerequisite for SMLM are fluorophores that transition from a dark to a fluorescent state in order to avoid spatio-temporal overlap of their point spread functions in each of the thousands of data acquisition frames. BODIPYs are well-established dyes with numerous conjugates used in conventional microscopy. The transient formation of red-shifted BODIPY ground-state dimers (DII) results in bright single molecule emission enabling single molecule localization microscopy (SMLM). Here we present a simple but versatile protocol for SMLM with conventional BODIPY conjugates in living yeast and mammalian cells. This procedure can be used to acquire super-resolution images and to track single BODIPY-DII states to extract spatio-temporal information of BODIPY conjugates. We apply this procedure to resolve lipid droplets (LDs), fatty acids, and lysosomes in living yeast and mammalian cells at the nanoscopic length scale. Furthermore, we demonstrate the multi-color imaging capability with BODIPY dyes when used in conjunction with other fluorescent probes. Our representative results show the differential spatial distribution and mobility of BODIPY-fatty acids and neutral lipids in yeast under fed and fasted conditions. This optimized protocol for SMLM can be used with hundreds of commercially available BODIPY conjugates and is a useful resource to study biological processes at the nanoscale far beyond the applications of this work.

Original languageEnglish (US)
Article numbere60950
Pages (from-to)1-9
Number of pages9
JournalJournal of Visualized Experiments
Issue number160
StatePublished - 2020

Bibliographical note

Funding Information:
The research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R21GM127965.


  • Biochemistry
  • Fluorescence microscopy
  • Ground-state dimers
  • Issue 160
  • Mammalian cells
  • Single-molecule localization microscopy
  • Single-molecule tracking
  • Super-resolution microscopy
  • Yeast

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Video-Audio Media

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