The Chemistry of Small-Molecule Fluorogenic Probes - Progress in Molecular Biology and Translational Science - page 2

10. Cyanines 22

10.1 Overview 22

10.2 Enzyme substrates 23

10.3 Photoactivatable probes 23

10.4 Indicators 23

11. Other Fluorogenic Scaffolds 24

11.1 Overview 24

11.2 Fluorogenic enzyme substrates 25

11.3 Photoactivatable probes 26

11.4 Indicators 26

12. Conclusions and Future Directions 26

References 27

Abstract
Chemical fluorophores find wide use in biology to detect and visualize different phenom-
ena. A key advantage of small-molecule dyes is the ability to construct compounds where
fluorescence is activated by chemical or biochemical processes. Fluorogenic molecules, in
which fluorescence is activated by enzymatic activity, light, or environmental changes,
enable advanced bioassays and sophisticated imaging experiments. Here, we detail
the collection of fluorophores and highlight both general strategies and unique
approaches that are employed to control fluorescence using chemistry.

1. INTRODUCTION
Small-molecule fluorophores are indispensible tools formodern scientific
research. Such compounds find use as biomolecule labels, cellular stains, ion
indicators, and enzyme substrates, enabling a wide variety of biochemical
and biological experiments. 1-9 A benefit of small-molecule fluorophores is
their ability to use organic chemistry to fine-tune the structure of the dye. 5
The entire lexicon of organic synthesis can be leveraged to prepare molecules
with properties that are tailored for a specific application. Chemistry can also
be used to control the fluorescence of a dye. This ability to regulate the
fluorescence of small-molecule fluorophores forms the basis for a large
number of useful fluorogenic probes. In this chapter, we detail the collection
of different fluorophore structures and the chemistry of fluorogenicity. Many
of the strategies to modulate fluorescence behavior are generalizable, applying
across many classes of small-molecule fluorophores. However, each small-
molecule fluorophore scaffold displays unique properties that can be
exploited to give useful fluorogenic molecules. An understanding of the