Journal article
Bis(trifluoromethyl)carborhodamines: Highly Fluorogenic, Far-Red to Near-Infrared Dyes for Live Cell Fluorescence Microscopy, Activity-Based Sensing, and Single-Molecule Microscopy
Journal of the American Chemical Society, Vol.147(25), pp.21950-21960
06/25/2025
DOI: 10.1021/jacs.5c05473
PMCID: PMC12234253
PMID: 40501037
Abstract
Synthetic fluorophores built on a classic rhodamine scaffold are essential for modern microscopy. An attractive feature of synthetic fluorophores is their potential to access long-wavelength excitation and emission profiles (>650 nm) that are difficult to achieve through genetically encoded methods like fluorescent proteins. Here, we present a new strategy to achieve excitation and emission above 650 nm: bis(trifluoromethyl)carborhodamine dyes, or BF dyes. In BF dyes, the geminal methyl groups of carborhodamines are replaced with trifluoromethyl (CF
) groups. This accomplishes two things. First, CF
groups substantially red shift in the optical profile by over 90 nm compared to classic, oxygen-bridged rhodamine dyes, resulting in a dye framework with excitation and emission profiles >650 nm and high brightness (extinction coefficient >140,000 M
cm
and fluorescent quantum yield of 33%). Second, CF
groups render BF dyes fluorogenic, by shifting the position of the open-closed equilibrium of the colorless lactone and colored zwitterion form, resulting in up to a 30-fold improvement in fluorogenicity compared to silicon-bridged rhodamines. In this paper, we present the design and computational analysis of BF dyes; synthetic studies to access over a dozen new BF dyes through a unique, late-stage functionalization strategy; spectra characterization; and applications in advanced fluorescence microscopy including no-wash intracellular labeling, functional imaging with chemigenetic indicators, and single molecule tracking in living cells. Together, this report shows that bis(trifluoromethyl)carborhodamine dyes provide a complementary approach to achieving long-wavelength, fluorogenic dyes for live cell microscopy that do not rely on dimethyl silicon rhodamines.
Details
- Title: Subtitle
- Bis(trifluoromethyl)carborhodamines: Highly Fluorogenic, Far-Red to Near-Infrared Dyes for Live Cell Fluorescence Microscopy, Activity-Based Sensing, and Single-Molecule Microscopy
- Creators
- Nels C Gerstner - University of California, BerkeleyJack T McCann - University of California, BerkeleyJulia G Martin - University of California, BerkeleyKatharine M Henn - University of California, BerkeleyKathrin Riske - University of California, BerkeleySathvik Anantakrishnan - University of California, BerkeleyThomas G W Graham - Institute of Molecular and Cell BiologyXavier Darzacq - Institute of Molecular and Cell BiologyEvan W Miller - University of California, Berkeley
- Resource Type
- Journal article
- Publication Details
- Journal of the American Chemical Society, Vol.147(25), pp.21950-21960
- DOI
- 10.1021/jacs.5c05473
- PMID
- 40501037
- PMCID
- PMC12234253
- NLM abbreviation
- J Am Chem Soc
- ISSN
- 0002-7863
- eISSN
- 1520-5126
- Grant note
- R35 GM153237 / NIGMS NIH HHS T32 GM152983 / NIGMS NIH HHS
- Language
- English
- Date published
- 06/25/2025
- Academic Unit
- Chemistry
- Record Identifier
- 9984934817102771
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