Bright building blocks for chemical biology

Abstract

Small-molecule fluorophores manifest the ability of chemistry to solve problems in biology. As we noted in a previous review (Lavis, L. D.; Raines, R. T. ACS Chem. Biol. 2008, 3, 142-155), the extant collection of fluorescent probes is built on a modest set of "core" scaffolds that evolved during a century of academic and industrial research. Here, we survey traditional and modern synthetic routes to small-molecule fluorophores and highlight recent biological insights attained with customized fluorescent probes. Our intent is to inspire the design and creation of new high-precision tools that empower chemical biologists.

Figure 1

Photochemical concepts and examples of small-molecule fluorophores (A) Jabłoński diagram showing (i) absorption of a photon to give an excited state, (ii) internal conversion to S₁, (iii) fluorescence, (iv) nonradiative decay, (v) Förster resonance energy transfer (FRET), (vi) intersystem crossing to T₁, (vi) phosphorescence, and (viii) nonradiative decay. (B) Absorption and emission spectra of the dianionic form of the prototypical fluorophore, fluorescein (1). (C) Fluorescein derivatives (2–7) with biological utility.

Figure 2

Useful synthetic routes to key small-molecule fluorophores: (A) coumarins, (B) BODIPY dyes, (C) fluoresceins, (D) rhodamines, (E) phenoxazines, and (F) cyanines. The classical route to each fluorophore is boxed. The color of a fluorophore structure indicates its wavelength of maximum emission (λ_em).