A general method to improve fluorophores for live-cell and single-molecule microscopy

Jonathan B. Grimm, Brian P. English, Jiji Chen, Joel P. Slaughter, Zhengjian Zhang, Andrey Revyakin, Ronak Patel, John J. Macklin, Davide Normanno, Robert H. Singer, Timothée Lionnet, Luke D. Lavis

Research output: Contribution to journalArticlepeer-review

982 Scopus citations


Specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. Genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. Intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. Here we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. Inspired by molecular modeling, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. This addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. The novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the UV and visible range.

Original languageEnglish (US)
Pages (from-to)244-250
Number of pages7
JournalNature Methods
Issue number3
StatePublished - Feb 26 2015

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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