Bright ideas forchemical biology

Abstract Click to copy section link Section link copied! Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular “core” dyes. The elaboration of these dyes with diverse chemical moieties is enabling the precise interrogation of biochemical and biological systems. The importance of fluorescence-based technologies in chemical biology elicits a necessity to understand the major classes of small-molecule fluorophores. Here, we examine the chemical and photophysical properties of oft-used fluorophores and highlight classic and contemporary examples in which utility has been built upon these scaffolds. ACS Publications Copyright © 2008 American Chemical Society Subjects what are subjects Article subjects are automatically applied from the ACS Subject Taxonomy and describe the scientific concepts and themes of the article. Dyes and pigments Fluorescence Fluorophores Molecules Peptides and proteins Keywords what are keywords Article keywords are supplied by the authors and highlight key terms and topics

of the paper. Fluorescence: A process involving (1) photon absorption by a fluorophore giving an excited state and (2) relaxation of the excited-state by emission of another photon Fluorophore: A fluorescent moiety that can consist of disparate chemical structures, including small molecules, proteins, and semiconductor beads Extinction coefficient (ϵ): The absorptivity of a molecule at a given wavelength as defined by the Beer−Lambert−Bouguer law Quantum yield (Φ): The ratio of photons fluoresced to photons absorbed Stokes shift: The difference (in nm) between the absorption or excitation maximum (λ max ) and the emission maximum (λ em ) Keywords what are keywords Article keywords are supplied by the authors and highlight key terms and topics

of the paper. Quenching: Nonradiative relaxation of the fluorophore excited state due to molecular collision, energy transfer, intersystem crossing, or other processes Förster resonance energy transfer (FRET): Distance-dependent, nonradiative energy transfer from the excited state of donor fluorophore to an acceptor dye Fluorescent ion indicator: A fluorophore exhibiting fluorescence that is sensitive to ion concentration Fluorogenic enzyme substrate: A compound in which enzymatic catalysis elicits a fluorescence increase