fluorophore

A fluorophore is a fluorescent chemical compound that absorbs light at one wavelength and emits light at a longer wavelength. When attached to biomolecules or used as a dye, it provides a detectable optical signal.

Important properties include excitation and emission spectra, Stokes shift, quantum yield (the fraction of absorbed photons re-emitted as fluorescence), molar extinction coefficient, brightness (product of extinction coefficient and quantum yield), and photostability. The environment surrounding a fluorophore can affect its spectra and brightness.

Common classes are organic dyes such as fluorescein, rhodamine, and cyanine dyes; fluorescent proteins such as GFP and mCherry; and inorganic fluorophores such as quantum dots. Each class differs in brightness, photostability, size, and spectral compatibility. Fluorophores are often covalently linked to antibodies, nucleic acids, or small molecules to target specific biomolecules.

Applications include fluorescence microscopy, flow cytometry, fluorescence in situ hybridization, and in vivo imaging. Fluorescence resonance energy transfer (FRET) uses paired fluorophores to measure molecular interactions or distances. Multicolor labeling enables simultaneous detection of multiple targets.

Limitations include photobleaching, spectral overlap and bleed‑through, sample autofluorescence, and environmental sensitivity to pH or polarity. Careful experimental design, appropriate filter sets, controls, and data analysis are used to mitigate these issues.