Tuning the Color Palette of Fluorescent Copper Sensors through Systematic Heteroatom Substitution at Rhodol Cores

Small-Molecule Fluorescent Probes for Binding- and Activity-Based Sensing of Redox-Active Biological Metals

Although transition metals constitute less than 0.1% of the total mass within a human body, they have a substantial impact on fundamental biological processes across all kingdoms of life. Indeed, these nutrients play crucial roles in the physiological functions of enzymes, with the redox properties of many of these metals being essential to their activity. At the same time, imbalances in transition metal pools can be detrimental to health. Modern analytical techniques are helping to illuminate the workings of metal homeostasis at a molecular and atomic level, their spatial localization in real time, and the implications of metal dysregulation in disease pathogenesis. Fluorescence microscopy has proven to be one of the most promising non-invasive methods for studying metal pools in biological samples. The accuracy and sensitivity of bioimaging experiments are predominantly determined by the fluorescent metal-responsive sensor, highlighting the importance of rational probe design for such measurements. This review covers activity- and binding-based fluorescent metal sensors that have been applied to cellular studies. We focus on the essential redox-active metals: iron, copper, manganese, cobalt, chromium, and nickel. We aim to encourage further targeted efforts in developing innovative approaches to understanding the biological chemistry of redox-active metals.

Strategies to convert organic fluorophores into red/near-infrared emitting analogues and their utilization in bioimaging probes

Organic fluorophores aided by current microscopy imaging modalities are essential for studying biological systems. Recently, red/near-infrared emitting fluorophores have attracted great research efforts, as they enable bioimaging applications with reduced autofluorescence interference and light scattering, two significant obstacles for deep-tissue imaging, as well as reduced photodamage and photobleaching. Herein, we analyzed the current strategies to convert key organic fluorophores bearing xanthene, coumarin, and naphthalene cores into longer wavelength-emitting derivatives by focussing on their effectiveness and limitations. Together, we introduced typical examples of how such fluorophores can be used to develop molecular probes for biological analytes, along with key sensing features. Finally, we listed several critical issues to be considered in developing new fluorophores.

THQ-Xanthene: An Emerging Strategy to Create Next-Generation NIR-I/II Fluorophores

Near-infrared fluorescence imaging is vital for exploring the biological world. The short emissions (<650 nm) and small Stokes shifts (<30 nm) of current xanthene dyes obstruct their biological applications since a long time. Recently, a potent and universal THQ structural modification technique that shifts emission to the NIR-I/II range and enables a substantial Stokes shift (>100 nm) for THQ-modified xanthene dyes is established. Thus, a timely discussion of THQ-xanthene and its applications is extensive. Hence, the advent, working principles, development trajectory, and biological applications of THQ-xanthene dyes, especially in the fields of fluorescence probe-based sensing and imaging, cancer theranostics, and super-resolution imaging, are introduced. It is envisioned that the THQ modification tactic is a simple yet exceptional approach to upgrade the performance of conventional xanthene dyes. THQ-xanthene will advance the strides of xanthene-based potentials in early fluorescent diagnosis of diseases, cancer theranostics, and imaging-guided surgery.

Activity-Based Approach for Selective Molecular CO2 Sensing

Carbon dioxide (CO₂) impacts every aspect of life, and numerous sensing technologies have been established to detect and monitor this ubiquitous molecule. However, its selective sensing at the molecular level remains an unmet challenge, despite the tremendous potential of such an approach for understanding this molecule's role in complex environments. In this work, we introduce a unique class of selective fluorescent carbon dioxide molecular sensors (CarboSen) that addresses these existing challenges through an activity-based approach. Besides the design, synthesis, and evaluation of these small molecules as CO₂ sensors, we demonstrate their utility by tailoring their reactivity and optical properties, allowing their use in a broad spectrum of multidisciplinary applications, including atmospheric sensing, chemical reaction monitoring, enzymology, and live-cell imaging. Collectively, these results showcase the potential of CarboSen sensors as broadly applicable tools to monitor and visualize carbon dioxide across multiple disciplines.

Ratiometric Luminescence Detection of Copper(I) by a Resonant System Comprising Two Antenna/Lanthanide Pairs

Selective and sensitive detection of Cu(I) is an ongoing challenge due to its important role in biological systems, for example. Herein, we describe a photoluminescent molecular chemosensor integrating two lanthanide ions (Tb³⁺ and Eu³⁺) and respective tryptophan and naphthalene antennas onto a polypeptide backbone. The latter was structurally inspired from copper-regulating biomacromolecules in Gram-negative bacteria and was found to bind Cu⁺ effectively under pseudobiological conditions (log K_Cu⁺ = 9.7 ± 0.2). Ion regulated modulation of lanthanide luminescence in terms of intensity and long, millisecond lifetime offers perspectives in terms of ratiometric and time-gated detection of Cu⁺. The role of the bound ion in determining the photophysical properties is discussed with the aid of additional model compounds.

Bioinspired Luminescent Europium-Based Probe Capable of Discrimination between Ag+ and Cu. Inorg Chem 2021;60:10791-10798. [PMID: 34236828 DOI: 10.1021/acs.inorgchem.1c01486]

Due to their similar coordination properties, discrimination of Cu⁺ and Ag⁺ by water-soluble luminescent probes is challenging. We have synthesized LCC4^Eu, an 18 amino acid cyclic peptide bearing a europium complex, which is able to bind one Cu⁺ or Ag⁺ ion by the side chains of two methionines, a histidine and a 3-(1-naphthyl)-l-alanine. In this system, the naphthyl moiety establishes a cation-π interaction with these cations. It also acts as an antenna for the sensitization of Eu³⁺ luminescence. Interestingly, when excited at 280 nm, LCC4^Eu behaves as a turn-on probe for Ag⁺ (+150% Eu emission) and as a turn-off probe for Cu⁺ (-50% Eu³⁺ emission). Shifting the excitation wavelength to 305 nm makes the probe responsive to Ag⁺ (+380% Eu³⁺ emission) but not to Cu⁺ or other physiological cations. Thus, LCC4^Eu is uniquely capable of discriminating Ag⁺ from Cu⁺. A detailed spectroscopic characterization based on steady-state and time-resolved measurements clearly demonstrates that Eu³⁺ sensitization relies on electronic energy transfer from the naphthalene triplet state to the Eu³⁺ excited states and that the cation-π interaction lowers the energy of this triplet state by 700 and 2400 cm^-1 for Ag⁺ and Cu⁺, respectively. Spectroscopic data point to a modulation of the efficiency of the electronic energy transfer caused by the differential red shift of the naphthalene triplet, deciphering the differential luminescence response of LCC4^Eu toward Ag⁺ and Cu⁺.

Late-stage functionalisation of alkyne-modified phospha-xanthene dyes: lysosomal imaging using an off-on-off type of pH probe

Near-infrared (NIR) fluorescent molecules are of great importance for the visualisation of biological processes. Among the most promising dye scaffolds for this purpose are P[double bond, length as m-dash]O-substituted phospha-xanthene (POX) dyes, which show NIR emission with high photostability. Their practical utility for in vitro and in vivo imaging has recently been demonstrated. Although classical modification methods have been used to produce POX-based fluorescent probes, it is still a challenge to introduce additional functional groups to control the localisation of the probe in cells. Herein, we report on the development of POXs that bear a 4-ethynylphenyl group on the phosphorus atom. These dyes can subsequently be functionalised with azide-tagged biomolecules via a late-stage Cu-catalysed azide/alkyne cycloaddition (CuAAC) reaction, thus achieving target-selective labelling. To demonstrate the practical utility of the functionalised POXs, we designed a sophisticated NIR probe that exhibits a bell-shaped off-on-off pH-response and is able to assess the degree of endosomal maturation.

Kinetic spectroscopic quantification using two-step chromogenic and fluorogenic reactions: From theoretical modeling to experimental quantification of biomarkers in practical samples

Kinetic chromogenic (CG) and fluorogenic (FG) quantification deduces analyte concentration based on the reaction rate between the CG/FG probe and its targeted molecule. Little progress has been made in the past half century in either the theory or the applications of the kinetic spectroscopic quantification methods. Current kinetic CG/FG quantification is limited only to a subset of CG/FG reactions that can be approximated as the single-step process, and more problematically, to research samples with no matrix interferences. Reported herein is a kinetic quantification model established for multistep CG/FG reactions and a proof-of-concept demonstration of direct kinetic FG quantification of biomarkers in practical samples. The kinetic spectral intensity of the CG/FG reactions with two rate-limiting steps comprises three temporal regions: an accelerating period where rate of signal change is increasingly rapid, a linear region where the rate of signal change is approximately constant, and a deceleration region where the rate of signal increase becomes progressively small. Kinetic quantification is performed through simple linear-curve-fitting of the kinetic signal in its linear time-course region. The theoretical model is validated with the dual CG/FG 2-thiobarbituric acid (TBA) and malondialdehyde (MDA) reaction. Proof-of-concept kinetic spectroscopic quantification of analytes in practical samples is demonstrated with the FG quantification of MDA in canned chicken. The only sample preparation is bench-top centrifugation followed by two sequential syringe filtrations. The total kinetic FG assay time is less than 10 min, more than 10 times more efficient than the current equilibrium-based MDA assay. The theoretical model and the measurement design strategies offered by this work should help transform the current kinetic spectroscopic quantification from a niche research tool to an indispensable technique for time-sensitive applications.

Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes

The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.

Far-red imaging of β-galactosidase through a phospha-fluorescein

The introduction of phosphine oxide into a fluorescein scaffold has yielded phospha-fluorescein with bathochromically shifted spectra, reliable photostability and solubility. Moreover, ratiometric and turn-on fluorescence in the decaging process has ensured that the phospha-fluorescein is a unique scaffold for fluorescence bioimaging. Probe DiMe-PF-Gal without further structural decoration was designed for accurately monitoring β-galactosidase in vivo.

A bio-bar-code photothermal probe triggered multi-signal readout sensing system for nontoxic detection of mycotoxins

Herein, a photothermal triggered multi-signal readout (MSR) system was innovatively established with great convenience for low-cost and sensitive point-of-care testing (POCT). In this sensing system, an intelligent multi-signal readout interface (MSRI) with multidimensional response-ability to thermal stimulus was developed and utilized as a sensing element. A bio-bar-code photothermal probe peptides@H₂N-HCNTs acted as a target associated photothermal agent anchored on MSRI via competitive reaction. The multi-signal assay of target was realized under the driven of 808 nm laser, photo-to-thermal conversion effect of photothermal probe caused dramatically thermal energy increase on MSRI. As a result, the competitive recognition events were translated into several detectable signals on MSRI, including a local temperature elevation, a visual color change from blue to green as well as weight loss on MSRI, all of these signals were proportional to the target concentration. This assay has been successfully applied in field work for detecting zearalenone (ZEN), a common mycotoxin in grain food, with linear ranger from 10^-7 ng/mL to 10^-1 ng/mL and detection limits of 1.06 × 10^-7 ng/mL. Combination of the different signal principles was expected to result in more reliable and precise results. Accordingly, this creatively designed MSR-system not only provided a platform for sensitive monitor of mycotoxin but also offered new method for reliable and affordable personal assays in daily life and low-resource setting.

Activity-Based Sensing with a Metal-Directed Acyl Imidazole Strategy Reveals Cell Type-Dependent Pools of Labile Brain Copper

Copper is a required nutrient for life and particularly important to the brain and central nervous system. Indeed, copper redox activity is essential to maintaining normal physiological responses spanning neural signaling to metabolism, but at the same time copper misregulation is associated with inflammation and neurodegeneration. As such, chemical probes that can track dynamic changes in copper with spatial resolution, especially in loosely bound, labile forms, are valuable tools to identify and characterize its contributions to healthy and disease states. In this report, we present an activity-based sensing (ABS) strategy for copper detection in live cells that preserves spatial information by a copper-dependent bioconjugation reaction. Specifically, we designed copper-directed acyl imidazole dyes that operate through copper-mediated activation of acyl imidazole electrophiles for subsequent labeling of proximal proteins at sites of elevated labile copper to provide a permanent stain that resists washing and fixation. To showcase the utility of this new ABS platform, we sought to characterize labile copper pools in the three main cell types in the brain: neurons, astrocytes, and microglia. Exposure of each of these cell types to physiologically relevant stimuli shows distinct changes in labile copper pools. Neurons display translocation of labile copper from somatic cell bodies to peripheral processes upon activation, whereas astrocytes and microglia exhibit global decreases and increases in intracellular labile copper pools, respectively, after exposure to inflammatory stimuli. This work provides foundational information on cell type-dependent homeostasis of copper, an essential metal in the brain, as well as a starting point for the design of new activity-based probes for metals and other dynamic signaling and stress analytes in biology.

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.

Improving the quantum yields of fluorophores by inhibiting twisted intramolecular charge transfer using electron-withdrawing group-functionalized piperidine auxochromes

Herein, we present that the negative inductive effect exerted by electron-withdrawing groups, such as sulfone groups, can obviously improve the ionization potential of amino auxochromes, thereby effectively inhibiting twisted intramolecular charge transfer (TICT) and markedly improving the quantum yields of several families of fluorophores in aqueous solution.

DNAzyme-Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells

Genetically encoded fluorescent proteins (FPs) have been used for metal ion detection. However, their applications are restricted to a limited number of metal ions owing to the lack of available metal-binding proteins or peptides that can be fused to FPs and the difficulty in transforming the binding of metal ions into a change of fluorescent signal. We report herein the use of Mg²⁺ -specific 10-23 or Zn²⁺ -specific 8-17 RNA-cleaving DNAzymes to regulate the expression of FPs as a new class of ratiometric fluorescent sensors for metal ions. Specifically, we demonstrate the use of DNAzymes to suppress the expression of Clover2, a variant of the green FP (GFP), by cleaving the mRNA of Clover2, while the expression of Ruby2, a mutant of the red FP (RFP), is not affected. The Mg²⁺ or Zn²⁺ in HeLa cells can be detected using both confocal imaging and flow cytometry. Since a wide variety of metal-specific DNAzymes can be obtained, this method can likely be applied to imaging many other metal ions, expanding the range of the current genetically encoded fluorescent protein-based sensors.

Rhodols - synthesis, photophysical properties and applications as fluorescent probes

The formal replacement of one dialkylamino group in rhodamines with a hydroxyl group transforms them into rhodols. This apparently minor difference is not as small as one may think; rhodamines belong to the cyanine family whereas rhodols belong to merocyanines. Discovered in the late 19th century, rhodols have only very recently begun to gain momentum in the field of advanced fluorescence imaging. This is in part due to the increased understanding of their photophysical properties, and new methods of synthesis. Rationalization of how the nature and arrangement of polar substituents around the core affect the photophysical properties of rhodols is now possible. The emergence of so-called π-expanded and heteroatom-modified rhodols has also allowed their fluorescence to be bathochromically shifted into regions applicable for biological imaging. This review serves to outline applicable synthetic strategies for the synthesis of rhodols, and to highlight important structure-property relationships. In the first part of this Review, various synthetic methods leading to rhodols are presented, followed by structural considerations and an overview of photophysical properties. The second part of this review is entirely devoted to the applications of rhodols as fluorescent reporters in biological imaging.

SCOTfluors: Small, Conjugatable, Orthogonal, and Tunable Fluorophores for In Vivo Imaging of Cell Metabolism

The transport and trafficking of metabolites are critical for the correct functioning of live cells. However, in situ metabolic imaging studies are hampered by the lack of fluorescent chemical structures that allow direct monitoring of small metabolites under physiological conditions with high spatial and temporal resolution. Herein, we describe SCOTfluors as novel small-sized multi-colored fluorophores for real-time tracking of essential metabolites in live cells and in vivo and for the acquisition of metabolic profiles from human cancer cells of variable origin.

Synthesis and living cell imaging of a novel fluorescent sensor for selective cupric detection

Copper is an important element indispensable for human life and health. Many copper-determining probes have been created for exploring its functional behavior in various cell types but few of them contains both fluorescent and colorimetric characters. In the present study, we developed a set of copper probes by synthesizing several novel thiophene-based Schiff bases in order to make a suitable sensor for quantifying and imaging copper in living cells. We find that the ligand FS-1 has a splendid selectivity and affinity toward Cu²⁺ among the common divalent metal ions. Living cell imaging show that FS-1 has a robust and repetitive fluorescence response in the presence of Cu²⁺ only in the cytosolic space of Hepg2 cell and not in the other cells examined. These data suggest that we have developed a new copper probe that can be used as a Cu²⁺ fluorescent and colorimetric sensor for in vivo and in vitro copper studies.

Sulfonamides Are an Overlooked Class of Electron Donors in Luminogenic Luciferins and Fluorescent Dyes

Many fluorophores, and all bright light-emitting substrates for firefly luciferase, contain hydroxyl or amine electron donors. Sulfonamides were found to be capable of serving as replacements for these canonical groups. Unlike "caged" carboxamides, sulfonamide donors enable bioluminescence, and sulfonamidyl luciferins, coumarins, rhodols, and rhodamines are fluorescent in water.

Cu2+ selective chelators relieve copper-induced oxidative stress in vivo

Copper ions are essential for biological function yet are severely detrimental when present in excess. At the molecular level, copper ions catalyze the production of hydroxyl radicals that can irreversibly alter essential bio-molecules. Hence, selective copper chelators that can remove excess copper ions and alleviate oxidative stress will help assuage copper-overload diseases. However, most currently available chelators are non-specific leading to multiple undesirable side-effects. The challenge is to build chelators that can bind to copper ions with high affinity but leave the levels of essential metal ions unaltered. Here we report the design and development of redox-state selective Cu ion chelators that have 108 times higher conditional stability constants toward Cu2+ compared to both Cu+ and other biologically relevant metal ions. This unique selectivity allows the specific removal of Cu2+ ions that would be available only under pathophysiological metal overload and oxidative stress conditions and provides access to effective removal of the aberrant redox-cycling Cu ion pool without affecting the essential non-redox cycling Cu+ labile pool. We have shown that the chelators provide distinct protection against copper-induced oxidative stress in vitro and in live cells via selective Cu2+ ion chelation. Notably, the chelators afford significant reduction in Cu-induced oxidative damage in Atp7a-/- Menkes disease model cells that have endogenously high levels of Cu ions. Finally, in vivo testing of our chelators in a live zebrafish larval model demonstrate their protective properties against copper-induced oxidative stress.