Frontiers in Chemical Biology Seminar

Specific labeling of biomolecules with bright, photostable fluorophores is the keystone of fluorescence microscopy. An expanding method to label cellular components utilizes genetically encoded self‑labeling tags, which enable the attachment of chemical fluorophores to specific proteins inside living cells. This strategy combines the genetic specificity of fluorescent proteins with the favorable photophysics of synthetic dyes. However, intracellular labeling using these techniques requires small, cell-permeable fluorophores, thereby limiting utility to a small number of classic, unoptimized dyes. We discovered a simple structural modification to standard fluorophores that improves brightness and photostability while preserving other spectral properties and cell permeability. Inspired by computational experiments, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with a four-membered azetidine ring. This net addition of two carbon atoms doubles the quantum efficiency and improves the photon yield in living cells. The novel substitution is generalizable to fluorophores from different structural classes, yielding a palette of synthetically tractable chemical dyes with improved quantum efficiency and enabling multicolor single-molecule imaging experiments. These brighter versions of classic fluorophores can be further modified to fine-tune spectral and chemical properties for advanced imaging experiments in increasingly complex biological samples.