skip to main content


Title: Rational design of small molecule fluorescent probes for biological applications
Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to “modulate” fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure–property relationships concerning the substituents are discussed in detail with examples for several dye families. We also present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena.  more » « less
Award ID(s):
1708759
NSF-PAR ID:
10278331
Author(s) / Creator(s):
; ;
Date Published:
Journal Name:
Organic & Biomolecular Chemistry
Volume:
18
Issue:
30
ISSN:
1477-0520
Page Range / eLocation ID:
5747 to 5763
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Small molecular NIR‐II dyes are highly desirable for various biomedical applications. However, NIR‐II probes are still limited due to the complex synthetic processes and inadequate availability of fluorescent core. Herein, the design and synthesis of three small molecular NIR‐II dyes are reported. These dyes can be excited at 850–915 nm and emitted at 1280–1290 nm with a large stokes shift (≈375 nm). Experimental and computational results indicate a 2:1 preferable host–guest assembly between the cucurbit[8]uril (CB) and dye molecules. Interestingly, the dyes when self‐assembled in presence of CB leads to the formation of nanocubes (≈200 nm) and exhibits marked enhancement in fluorescence emission intensity (Switch‐On). However, the addition of red carbon dots (rCDots, ≈10 nm) quenches the fluorescence of these host–guest complexes (Switch‐Off) providing flexibility in the user‐defined tuning of photoluminescence. The turn‐ON complex found to have comparable quantum yield to the commercially available near‐infrared fluorophore, IR‐26. The aqueous dispersibility, cellular and blood compatibility, and NIR‐II bioimaging capability of the inclusion complexes is also explored. Thus, a switchable fluorescence behavior, driven by host–guest complexation and supramolecular self‐assembly, is demonstrated here for three new NIR‐II dyes.

     
    more » « less
  2. Abstract

    Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as excitation and emission spectra, brightness) and require similar equipment for data acquisition. Selecting an ideal set of fluorophores for a particular measurement technology or vice versa is a multidimensional problem that is difficult to solve with ad hoc methods due to the enormous solution space of possible fluorophore panels. Choosing sub-optimal fluorophore panels can result in unreliable or erroneous measurements of biochemical properties in model systems. Here, we describe a set of algorithms, implemented in an open-source software tool, for solving these problems efficiently to arrive at fluorophore panels optimized for maximal signal and minimal bleed-through.

     
    more » « less
  3. Abstract

    Near‐infrared (NIR) fluorescent dyes with favorable photophysical properties are highly useful for bioimaging, but such dyes are still rare. The development of a unique class of NIR dyes via modifying the rhodol scaffold with fused tetrahydroquinoxaline rings is described. These new dyes showed large Stokes shifts (>110 nm). Among them, WR3, WR4, WR5, and WR6 displayed high fluorescence quantum yields and excellent photostability in aqueous solutions. Moreover, their fluorescence properties were tunable by easy modifications on the phenolic hydroxy group. Based on WR6, two NIR fluorescent turn‐on probes, WSP‐NIR and SeSP‐NIR, were devised for the detection of H2S. The probe SeSP‐NIR was applied in visualizing intracellular H2S. These dyes are expected to be useful fluorophore scaffolds in the development of new NIR probes for bioimaging.

     
    more » « less
  4. Abstract

    Near‐infrared (NIR) fluorescent dyes with favorable photophysical properties are highly useful for bioimaging, but such dyes are still rare. The development of a unique class of NIR dyes via modifying the rhodol scaffold with fused tetrahydroquinoxaline rings is described. These new dyes showed large Stokes shifts (>110 nm). Among them, WR3, WR4, WR5, and WR6 displayed high fluorescence quantum yields and excellent photostability in aqueous solutions. Moreover, their fluorescence properties were tunable by easy modifications on the phenolic hydroxy group. Based on WR6, two NIR fluorescent turn‐on probes, WSP‐NIR and SeSP‐NIR, were devised for the detection of H2S. The probe SeSP‐NIR was applied in visualizing intracellular H2S. These dyes are expected to be useful fluorophore scaffolds in the development of new NIR probes for bioimaging.

     
    more » « less
  5. Abstract

    A general synthetic method creates a new class of covalently connected, self‐threaded, fluorescent molecular probes with figure‐eight topology, an encapsulated deep‐red fluorophore, and two peripheral peptide loops. The globular molecular shape and rigidified peptide loops enhance imaging performance by promoting water solubility, eliminating probe self‐aggregation, and increasing probe stability. Moreover, the peptide loops determine the affinity and selectivity for targets within complex biological samples such as cell culture, tissue histology slices, or living subjects. For example, a probe with cell‐penetrating peptide loops targets the surface of cell plasma membranes, whereas, a probe with bone‐targeting peptide loops selectively stains the skeleton within a living mouse. The unique combination of bright deep‐red fluorescence, high stability, and predictable peptide‐based targeting is ideal for photon intense fluorescence microscopy and biological imaging.

     
    more » « less