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Carbon-Based Fluorogenics

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Carbon-Based Fluorogenics

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High-contrast fluorogenic derivatives of carbofluorescein and carborhodamine

The use of fluorescence technologies for biochemi-cal and biological research has exploded in recent years. Chemical fluorophores can enable super-resolution microscopy, high-throughput screening, and functional imaging in living tissue. Despite this utility, the current collection of chemical fluoro-phores remains insufficient for advanced biological imaging experiments and other assays.

To increase the usefulness of small molecule fluorophores, researchers continue to explore new chemical scaffolds with distinct and advantageous properties. Researchers at the Howard Hughes Medical Institute’s Janelia Research Campus have synthesized carbon-containing analogs of the eminently useful xanthene-based fluorescein and rhodamine dyes that exhibit red-shifted fluores-cence properties. These green-excited “carbo-fluorescein” and “carborhodamine” dyes display excellent fluorescence brightness and their proper-ties can be tuned through structural modification. In particular, these dyes can be “masked” by attachment of different blocking groups that squelch fluorescence. Removal or modification of these groups activates fluorescence.

These fluorogenic compounds based on carbo-fluorescein and carborhodamine exhibit extremely high on/off contrast ratios, yet upon activation are extremely bright and photostable. These probes will be useful for a variety of applications, from standard biochemical assays to super-resolution microscopy.


  • Fluorogenic derivatives display probes have a high on/off contrast ratio, and excellent brightness
  • Similarity to xanthene dyes allows use of established masking technologies
  • Researchers have developed a strategy that allows for efficient synthesis of these probes


  • Live cell imaging and super-resolution microscopy
  • Red-shifted fluorogenic enzyme substrates for ELISA experiments
  • Scaffolds for reaction based indicators


Free for Non-Profit Research and available for Commercial License

For inquiries, please reference:

Janelia 2013-018

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Enabling superior brightness, versatile
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Michael Perham
Director, Innovations and External Relations
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