Reaction-Based Genetically Encoded Fluorescent Hydrogen Sulfide Sensors

Responsive β-Diketonate-europium(III) Complex-Based Probe for Time-Gated Luminescence Detection and Imaging of Hydrogen Sulfide In Vitro and In Vivo

As a crucial biological gasotransmitter, hydrogen sulfide (H2S) plays important roles in many pathological and physiological processes. Highly selective and sensitive detection of H2S is significant for the precise diagnosis and evaluation of diverse diseases. Nevertheless, challenges remain in view of the interference of autofluorescence in organisms and the stronger reactivity of H2S itself. Herein, we report the design and synthesis of a novel H2S-responsive β-diketonate-europium(III) complex-based probe, [Eu(DNB-Npketo)3(terpy)], for background-free time-gated luminescence (TGL) detection and imaging of H2S in autofluorescence-rich biological samples. The probe, consisting of a 2,4-dinitrobenzenesulfonyl (DNB) group coupled to a β-diketonate-europium(III) complex, shows almost no luminescence owing to the existence of intramolecular photoinduced electron transfer. The cleavage of the DNB group by a H2S-triggered reaction results in the recovery of the long-lived luminescence of the Eu3+ complex, allowing the detection of H2S in complicated biological samples to be performed in TGL mode. The probe showed a fast response, high specificity, and high sensitivity toward H2S, which enabled it to be successfully used for the quantitative TGL detection of H2S in tissue homogenates of mouse organs. Additionally, the low cytotoxicity of the probe allowed it to be further used for the TGL imaging of H2S in living cells and mice under different stimuli. All of the results suggested the potential of the probe for the investigation and diagnosis of H2S-related diseases.

Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy

The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.

Activity-Based Fluorescent Probes for Hydrogen Sulfide and Related Reactive Sulfur Species

Hydrogen sulfide (H2S) is not only a well-established toxic gas but also an important small molecule bioregulator in all kingdoms of life. In contemporary biology, H2S is often classified as a "gasotransmitter," meaning that it is an endogenously produced membrane permeable gas that carries out essential cellular processes. Fluorescent probes for H2S and related reactive sulfur species (RSS) detection provide an important cornerstone for investigating the multifaceted roles of these important small molecules in complex biological systems. A now common approach to develop such tools is to develop "activity-based probes" that couple a specific H2S-mediated chemical reaction to a fluorescent output. This Review covers the different types of such probes and also highlights the chemical mechanisms by which each probe type is activated by specific RSS. Common examples include reduction of oxidized nitrogen motifs, disulfide exchange, electrophilic reactions, metal precipitation, and metal coordination. In addition, we also outline complementary activity-based probes for imaging reductant-labile and sulfane sulfur species, including persulfides and polysulfides. For probes highlighted in this Review, we focus on small molecule systems with demonstrated compatibility in cellular systems or related applications. Building from breadth of reported activity-based strategies and application, we also highlight key unmet challenges and future opportunities for advancing activity-based probes for H2S and related RSS.

NIR Light-Activated Mitochondrial RNA Cross-Linking Strategy for H2S Monitoring and Prolonged Colorectal Tumor Imaging

Molecular diffusion and leakage impede the long-term retention of probes/drugs and may cause potential adverse effects in theranostic fields. Spatiotemporally manipulating the organelle-immobilization behavior of probes/drugs for prolonged tumor retention is indispensable to achieving effective cancer diagnosis and therapy. Herein, we propose a rational strategy that could realize near-infrared light-activated ribonucleic acids (RNAs) cross-linking for prolonged tumor retention and simultaneously endogenous hydrogen sulfide (H2S) monitoring in colorectal tumors. Profiting from efficient singlet oxygen (1O2) generation from Cy796 under 808 nm light irradiation, the 1O2-animated furan moiety in Cy796 could covalently cross-link with cytoplasmic RNAs via a cycloaddition reaction and realize organelle immobilization. Subsequently, specific thiolysis of Cy796 assisted with H2S resulted in homologous product Cy644 with reduced 1O2 generation yields and enhanced absolute fluorescence quantum yields (from 7.42 to 27.70%) with blue-shifted absorption and emission, which avoided the molecular oxidation fluorescence quenching effect mediated by 1O2 and validated fluorescence imaging. Furthermore, studies have demonstrated that our proposed strategy possessed adequate capacity for fluorescence imaging and endogenous H2S detection in HCT116 cells, particularly accumulated at the tumor sites, and retained long-term imaging with excellent biocompatibility. The turn-on fluorescence mode and turn-off 1O2 generation efficiency in our strategy successfully realized a diminished fluorescence cross-talk and oxidation quenching effect. It is adequately envisioned that our proposed strategy for monitoring biomarkers and prolonged tumor retention will contribute tremendous dedication in the clinical, diagnostic, and therapeutic fields.

Targeting Ultrafast Spectroscopic Insights into Red Fluorescent Proteins

Red fluorescent proteins (RFPs) represent an increasingly popular class of genetically encodable bioprobes and biomarkers that can advance next-generation breakthroughs across the imaging and life sciences. Since the rational design of RFPs with improved functions or enhanced versatility requires a mechanistic understanding of their working mechanisms, while fluorescence is intrinsically an ultrafast event, a suitable toolset involving steady-state and time-resolved spectroscopic techniques has become powerful in delineating key structural features and dynamic steps which govern irreversible photoconverting or reversible photoswitching RFPs, and large Stokes shift (LSS)RFPs. The pertinent cis-trans isomerization and protonation state change of RFP chromophores in their local environments, involving key residues in protein matrices, lead to rich and complicated spectral features across multiple timescales. In particular, ultrafast excited-state proton transfer in various LSSRFPs showcases the resolving power of wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in mapping a photocycle with crucial knowledge about the red-emitting species. Moreover, recent progress in noncanonical RFPs with a site-specifically modified chromophore provides an appealing route for efficient engineering of redder and brighter RFPs, highly desirable for bioimaging. Such an effective feedback loop involving physical chemists, protein engineers, and biomedical microscopists will enable future successes to expand fundamental knowledge and improve human health.

Genetically Encoded Boronolectin as a Specific Red Fluorescent UDP-GlcNAc Biosensor

There is great interest in developing boronolectins that are synthetic lectin mimics containing a boronic acid functional group for reversible recognition of diol-containing molecules, such as glycans and ribonucleotides. However, it remains a significant challenge to gain specificity. Here, we present a genetically encoded boronolectin which is a hybrid protein consisting of a noncanonical amino acid (ncAA) p-boronophenylalanine (pBoF), natural-lectin-derived peptide sequences, and a circularly permuted red fluorescent protein (cpRFP). The genetic encodability permitted a straightforward protein engineering process to derive a red fluorescent biosensor that can specifically bind uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), an important nucleotide sugar involved in metabolic sensing and cell signaling. We further characterized the resultant boronic acid- and peptide-assisted UDP-GlcNAc sensor (bapaUGAc) both in vitro and in live mammalian cells. Because UDP-GlcNAc in the endoplasmic reticulum (ER) and Golgi apparatus plays essential roles in glycosylating biomolecules in the secretory pathway, we genetically expressed bapaUGAc in the ER and Golgi and validated the sensor for its responses to metabolic disruption and pharmacological inhibition. In addition, we combined bapaUGAc with UGAcS, a recently reported green fluorescent UDP-GlcNAc sensor based on an alternative sensing mechanism, to monitor UDP-GlcNAc level changes in the ER and cytosol simultaneously. We expect our work to facilitate the future development of specific boronolectins for carbohydrates. In addition, this newly developed genetically encoded bapaUGAc sensor will be a valuable tool for studying UDP-GlcNAc and glycobiology.

In Vivo Detection of Low Molecular Weight Platform Chemicals and Environmental Contaminants by Genetically Encoded Biosensors

Genetically encoded biosensor systems operating in living cells are versatile, cheap, and transferable tools for the detection and quantification of a broad range of small molecules. This review presents state-of-the-art biosensor designs and assemblies, featuring transcription factor-, riboswitch-, and enzyme-coupled devices, highly engineered fluorescent probes, and emerging two-component systems. Importantly, (bioinformatic-assisted) strategies to resolve contextual issues, which cause biosensors to miss performance criteria in vivo, are highlighted. The optimized biosensing circuits can be used to monitor chemicals of low molecular mass (<200 g mol^-1) and physicochemical properties that challenge conventional chromatographical methods with high sensitivity. Examples herein include but are not limited to formaldehyde, formate, and pyruvate as immediate products from (synthetic) pathways for the fixation of carbon dioxide (CO₂), industrially important derivatives like small- and medium-chain fatty acids and biofuels, as well as environmental toxins such as heavy metals or reactive oxygen and nitrogen species. Lastly, this review showcases biosensors capable of assessing the biosynthesis of platform chemicals from renewable resources, the enzymatic degradation of plastic waste, or the bioadsorption of highly toxic chemicals from the environment. These applications offer new biosensor-based manufacturing, recycling, and remediation strategies to tackle current and future environmental and socioeconomic challenges including the wastage of fossil fuels, the emission of greenhouse gases like CO₂, and the pollution imposed on ecosystems and human health.

Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor

Boronic acid-containing fluorescent molecules have been widely used to sense hydrogen peroxide and peroxynitrite, which are important reactive oxygen and nitrogen species in biological systems. However, it has been challenging to gain specificity. Our previous studies developed genetically encoded, green fluorescent peroxynitrite biosensors by genetically incorporating a boronic acid-containing noncanonical amino acid (ncAA), p-boronophenylalanine (pBoF), into the chromophore of circularly permuted green fluorescent proteins (cpGFPs). In this work, we introduced pBoF to amino acid residues spatially close to the chromophore of an enhanced circularly permuted red fluorescent protein (ecpApple). Our effort has resulted in two responsive ecpApple mutants: one bestows reactivity toward both peroxynitrite and hydrogen peroxide, while the other, namely, pnRFP, is a selective red fluorescent peroxynitrite biosensor. We characterized pnRFP in vitro and in live mammalian cells. We further studied the structure and sensing mechanism of pnRFP using X-ray crystallography, 11B-NMR, and computational methods. The boron atom in pnRFP adopts an sp2-hybridization geometry in a hydrophobic pocket, and the reaction of pnRFP with peroxynitrite generates a product with a twisted chromophore, corroborating the observed "turn-off" fluorescence response. Thus, this study extends the color palette of genetically encoded peroxynitrite biosensors, provides insight into the response mechanism of the new biosensor, and demonstrates the versatility of using protein scaffolds to modulate chemoreactivity.

Review of Chemical Sensors for Hydrogen Sulfide Detection in Organisms and Living Cells

As the third gasotransmitter, hydrogen sulfide (H₂S) is involved in a variety of physiological and pathological processes wherein abnormal levels of H₂S indicate various diseases. Therefore, an efficient and reliable monitoring of H₂S concentration in organisms and living cells is of great significance. Of diverse detection technologies, electrochemical sensors possess the unique advantages of miniaturization, fast detection, and high sensitivity, while the fluorescent and colorimetric ones exhibit exclusive visualization. All these chemical sensors are expected to be leveraged for H₂S detection in organisms and living cells, thus offering promising options for wearable devices. In this paper, the chemical sensors used to detect H₂S in the last 10 years are reviewed based on the different properties (metal affinity, reducibility, and nucleophilicity) of H₂S, simultaneously summarizing the detection materials, methods, linear range, detection limits, selectivity, etc. Meanwhile, the existing problems of such sensors and possible solutions are put forward. This review indicates that these types of chemical sensors competently serve as specific, accurate, highly selective, and sensitive sensor platforms for H₂S detection in organisms and living cells.

Hydrogen sulfide signaling in plants

SIGNIFICANCE

Hydrogen sulfide (H2S) is a multitasking potent regulator that facilitates plant growth, development, and responses to environmental stimuli.

RECENT ADVANCES

The important beneficial effects of H2S in various aspects of plant physiology aroused the interest of this chemical for agriculture. Protein cysteine persulfidation has been recognized as the main redox regulatory mechanism of H2S signaling. An increasing number of studies, including large-scale proteomic analyses and function characterizations, have revealed that H2S-mediated persulfidations directly regulate protein functions, altering downstream signaling in plants. To date, the importance of H2S-mediated persufidation in several abscisic acid signaling-controlling key proteins has been assessed as well as their role in stomatal movements, largely contributing to the understanding of the plant H2S-regulatory mechanism.

CRITICAL ISSUES

The molecular mechanisms of the H2S sensing and transduction in plants remain elusive. The correlation between H2S-mediated persulfidation with other oxidative posttranslational modifications of cysteines are still to be explored.

FUTURE DIRECTIONS

Implementation of advanced detection approaches for the spatiotemporal monitoring of H2S levels in cells and the current proteomic profiling strategies for the identification and quantification of the cysteine site-specific persulfidation will provide insight into the H2S signaling in plants.

Gold Nanocluster-Based Ratiometric Probe with Surface Structure Regulation-Triggered Sensing of Hydrogen Sulfide in Living Organisms

The development of reliable probes for in vivo detection of hydrogen sulfide (H₂S) with high sensitivity and selectivity is of great significance due to its key roles in many pathological and physiological processes. Herein, it was found that H₂S could finely regulate surface structure of gold nanoclusters (AuNCs) through reduction of surface Au(I)-ligand motifs and further quench their fluorescence by a two-stage kinetic reaction process. Stage I showed the H₂S-assisted surface Au(I)-ligand reduction and Au(0) core growth with a rapid fluorescence decrease; stage II showed the surface structure optimization and reconstruction with a relatively slow fluorescence quenching. By virtue of the excellent fluorescence response of AuNCs to H₂S, a novel ratiometric fluorescence probe (RBDA) for sensing H₂S was designed through electrostatic attraction-induced fluorescence resonance energy transfer (FRET) between AuNCs and rhodamine B. The probe was facilely prepared, showing a straightforward, rapid ratiometric fluorescence response to H₂S with built-in self-calibration. It presented the high detection sensitivity with a detection limit (LOD) of 56 nM and an excellent sensing selectivity for H₂S over various other biological species. The probe was demonstrated to possess high biostability, low cytotoxicity, good cell and issue penetrability, and favorable biocompatibility. It realizes successful monitoring of both exogenous and endogenous H₂S levels in living cells and zebrafish.

Genetically Encoded Boronolectin as a Specific Red Fluorescent UDP-GlcNAc Biosensor

There is great interest in developing boronolectins, which are synthetic lectin mimics containing a boronic acid functional group for reversible recognition of diol-containing molecules, such as glycans and ribonucleotides. However, it remains a significant challenge to gain specificity. Here, we present a genetically encoded boronolectin, which is a hybrid protein consisting of a noncanonical amino acid (ncAA) p-boronophenylalanine (pBoF), natural-lectin-derived peptide sequences, and a circularly permuted red fluorescent protein (cpRFP). The genetic encodability permitted a straightforward protein engineering process to derive a red fluorescent biosensor that can specifically bind uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), an important nucleotide sugar involved in metabolic sensing and cell signaling. We further characterized the resultant boronic acid-and peptide-assisted UDP-GlcNAc sensor (bapaUGAc) both in vitro and in live mammalian cells. Because UDP-GlcNAc in the endoplasmic reticulum (ER) and Golgi apparatus plays essential roles in glycosylating biomolecules in the secretory pathway, we genetically expressed bapaUGAc in the ER and Golgi and validated the sensor for its responses to metabolic disruption and pharmacological inhibition. In addition, we combined bapaUGAc with UGAcS, a recently reported green fluorescent UDP-GlcNAc sensor based on an alternative sensing mechanism, to monitor UDP-GlcNAc level changes in the ER and cytosol simultaneously. We expect our work to facilitate the future development of specific boronolectins for carbohydrates. In addition, this newly developed genetically encoded bapaUGAc sensor will be a valuable tool for studying UDP-GlcNAc and glycobiology.

Potentiometric nanosensor for real-time measurement of hydrogen sulfide in single cell

One potentiometric nanosensor for monitoring intracellular hydrogen sulfide (H₂S) with fast potential response, high selectivity and excellent antifouling properties was developed. This study constructs a powerful tool to real-time track the changes of intracellular H₂S in situ, promoting the future studies of physiologically relevant processes.

Genetic encoding of ε-N-L-lactyllysine for detecting delactylase activity in living cells

Lysine ε-N-L-lactylation is a newly discovered post-translational modification. Herein we present the genetic encoding of ε-N-L-lactyllysine in bacterial and mammalian cells, allowing the preparation of site-specifically ε-N-L-lactylated recombinant proteins and the construction of fluorescent and luminescent probes for detecting delactylases in living cells. Using these probes, we demonstrate sirtuin 1 as a potential delactylase for non-histone proteins.

Naphthalimide derivatives as fluorescent probes for imaging endogenous gasotransmitters

Gasotransmitters have gained significant recognition attributed to their evident biological impacts, and is accepted as a promising and less-explored area with immense research scope. The three-member family comprising of nitric oxide, carbon monoxide and hydrogen sulphide as endogenous gaseous signaling molecules have been found to elicit a plethora of crucial biological functions, spawning a new research area. The sensing of these small molecules is vital to gain deeper insights into their functions, as they can act both as a friend or a foe in mammalian systems. The initial sections of the review present the physiological and pathophysiological roles of these endogenous gas transmitters and their synergistic interactions. Further, various detection approaches, especially the usage of fascinating features of 1,8-naphthalimide as fluorescent probe in the detection and monitoring of these small signaling molecules are highlighted. The current limitations and the future scope of improving the sensing of the three gasotransmitters are also discussed.

Precursor Engineering for the Synthesis of Mixed Anionic Metal (Cu, Mn) Chalcogenide Nanomaterials via Solvent-Less Synthesis

Metal-organic ligands with mixed chalcogenides are potential compounds for the preparation of mixed anionic metal chalcogenide alloys. However, only a few of such ligands are known, and their complexes are not well explored. We have prepared homo- and hetero-dichalcogenoimidodiphosphinate [(EE'PⁱPr₂NH)] (E, E' = Se, Se; S, S; S, Se) complexes of manganese and copper through metathetical reactions. The X-ray single crystal structure of [Mn{(SePⁱPr₂)₂N}₂] 1 revealed a triclinic crystal system, with a MnSe₄ core unit, whereas the crystal structure determination of [Mn{(SPⁱPr₂)(SePⁱPr₂)N}₂] 2 indicated a triclinic crystal system with a Mn(S/Se)₂ unit. Both metal centers are tetrahedral, with two deprotonated bidentate ligands forming the coordination sphere. The free ligand was found to exhibit a gauche configuration in the solid state. The energies of the various rotamers of dithio-analogue were studied by DFT calculations. The decomposition behavior of complexes with homo- and heterochalcogenides was investigated, and the complexes were employed as single-source precursors to generate manganese and copper chalcogenides through solvent-less melt reactions between 500 and 550 °C. The deposited powders were characterized by powder X-ray diffraction (p-XRD), scanning electron microscopy (SEM), energy dispersive analysis of X-ray (EDAX), transmission electron microscopy (TEM), and elemental mapping. MnS, MnSe₂, and MnSSe phases were obtained from the decomposition of respective manganese complexes. In contrast, the decomposition of copper-based complexes yielded Cu_2-xSe and the sulfur-doped Cu₃Se₂ phase from seleno- and mixed thio/seleno-complexes of Cu, respectively. The morphology ranged from random sheet-like structures to agglomerated platelets, while the selected area electron diffraction (SAED) revealed the crystalline nature of the materials. Depending on the nature of the complex and the temperature, different amounts of phosphorus were present as an impurity in the synthesized products.

An ESIPT-based fluorescent probe with fast-response for detection of hydrogen sulfide in mitochondria

Excited-state intramolecular proton transfer (ESIPT) has recently received considerable attention due to its dual fluorescent changes and large Stokes shift. Hydrogen sulfide (H₂S) is a gas signal molecule that plays important roles in modulating the functions of different systems. Herein, by modifying 2-(2́-hydroxyphenyl) benzothiazole (HBT) scaffold, a novel near-infrared mitochondria-targeted fluorescent probe HBTP-H₂S has been rationally designed based on excited-state intramolecular proton transfer (ESIPT) effect. The nucleophilic addition reaction of the H₂S with probe HBTP-H₂S caused the break of the conjugated skeleton, resulting the shifting of maximum emission peak from 658 nm to 470 nm. HBTP-H₂S showed fast-response response time, good selectivity and a large Stokes shift (188 nm) toward H₂S. Most importantly, inspired by the inherent advantages of the probe, HBTP-H₂S was successfully employed to monitor mitochondrial H₂S in HepG2 cells.

A phenothiazine-based turn-on fluorescent probe for the selective detection of hydrogen sulfide in food, live cells and animals

In this work, a phenothiazine-based fluorescent probe (PR) has been developed for the selective detection of hydrogen sulfide (H₂S) in biosystems and monitoring H₂S produced in the food spoilage process. The nucleophilic attack of H₂S on the CC double bond of PRvia a Michael addition interdicted the ICT process to trigger 34-fold enhancement of the fluorescence emission. PR featured high selectivity and sensitivity (1.8 μM), low cytotoxicity and reliability at physiological pH. "Naked-eye" monitoring of H₂S produced in the food spoilage process using PR was successfully accomplished. The preliminary fluorescence imaging studies showed that PR is suitable for the visualization of exogenous and endogenous H₂S in living cells and live animals. Moreover, PR has been successfully applied to the visualization of H₂S generation in an inflammation model. The results indicated that PR is an effective tool to monitor H₂S production in the fields of biomedicine and food safety.

Beyond protein tagging: Rewiring the genetic code of fluorescent proteins - A review

Fluorescent proteins (FP) are an integral part of modern biology due to its diverse biochemical and photophysical properties. The boundaries of FP have been extended through conventional mutagenesis and directed evolution approaches. Engineering of FP based on the standard genetic code consisting of 20 amino acids with limited functional groups restrict its diversification. Degeneracy of genetic code has helped in covering this substantial gap through genetic code engineering, wherein introduction of unnatural amino acid (UAA) analogues resulted in a collection of FP with varying properties. This review features the work carried till date in the area of FP incorporated with UAAs and explores strategies employed for incorporation, impact of UAAs in chromophore and surrounding residues and changes in inherent properties of FP. The long-standing association of FP as a tool for high throughput screening of orthogonal aaRS/tRNA pairs used in site specific incorporation of UAAs is expounded. Insertion of UAAs in FP has enabled their use in contemporary fields such as biophotovoltaics, bioremediation, biosensors, biomaterials and imaging of acidic vesicles. Thus, expansion of genetic code of FP is envisaged to rejig the existing spectra of colors and future research initiative in this direction is expected to glow brighter and brighter.

Adding New Chemistries to the Central Dogma of Molecular Biology

The maturation of chemical synthesis during the 20th century has elevated the discipline from a largely empirical into a rational science. This ability to purposefully craft matter at the molecular level has put chemists in a privileged position to contribute to progress in neighboring natural sciences. Recently, we have witnessed another major advance in the field in which chemists use chemical and biological "synthetic" methods together to alter the structures and properties of biological macromolecules in ways heretofore unimagined. This interdisciplinary approach to synthesis has even allowed us to expand upon the defining characteristics of living organisms at the molecular level. In this perspective, we present a case study for the successful addition of new chemistries to the fundamental processes of the central dogma of molecular biology, exemplified by the expansion of the genetic code.

Ultrafast and nanomolar level detection of H2S in aqueous medium using a functionalized UiO-66 metal-organic framework based fluorescent chemosensor

Here, we present a 4-nitrophenyl functionalized Zr-UiO-66 MOF (MOF = metal-organic framework) and its applications towards the selective, sensitive and rapid detection of H₂S both in the aqueous medium and vapour phase. The MOF material was synthesized using the 2-(nitrophenoxy)terepththalic acid (H₂BDC-O-Ph-NO₂) linker and ZrCl₄ salt in the presence of a benzoic acid modulator. It was carefully characterized by thermogravimetric analysis (TGA), elemental analysis, powder X-ray diffraction (PXRD), FT-IR spectroscopy and surface area analysis. Noticeable thermal stability up to a temperature of 390 °C under air and the considerable chemical stability in different liquid media (H₂O, 1 M HCl, glacial acetic acid, NaOH in the pH = 8 to 10 range) confirmed the robustness of the MOF. The BET surface area (1040 m² g^-1) indicated the porous nature of the MOF. Remarkable selectivity of the MOF towards H₂S over other potential congeners of H₂S was observed in the aqueous medium. A very high fluorescence increment (∼77 fold) was observed after adding an aqueous Na₂S solution to the MOF suspension. The MOF probe displayed the lowest limit of detection (12.58 nM) among the existing MOF-based chemosensors of H₂S. Furthermore, it exhibited a very quick (60 s) response towards H₂S detection. The MOF compound could also detect H₂S in the vapour phase as well as in real water samples. Furthermore, we developed inexpensive MOF-coated paper strips for the naked-eye sensing of H₂S. A thorough investigation was carried out in order to elucidate the fluorescence turn-on sensing mechanism.

Genetically Encoded Fluorescent Redox Indicators for Unveiling Redox Signaling and Oxidative Toxicity

Redox-active molecules play essential roles in cell homeostasis, signaling, and other biological processes. Dysregulation of redox signaling can lead to toxic effects and subsequently cause diseases. Therefore, real-time tracking of specific redox-signaling molecules in live cells would be critical for deciphering their functional roles in pathophysiology. Fluorescent protein (FP)-based genetically encoded redox indicators (GERIs) have emerged as valuable tools for monitoring the redox states of various redox-active molecules from subcellular compartments to live organisms. In the first section of this review, we overview the background, focusing on the sensing mechanisms of various GERIs. Next, we review a list of selected GERIs according to their analytical targets and discuss their key biophysical and biochemical properties. In the third section, we provide several examples which applied GERIs to understanding redox signaling and oxidative toxicology in pathophysiological processes. Lastly, a summary and outlook section is included.

A color turn-on fluorescent probe for real-time detection of hydrogen sulfide and identification of food spoilage

A color and fluorescence turn-on H2S probe is synthesized, achieving real-time detection of H2S in pure water solution with high selectivity. Importantly, the probe is able to sense H2S gas in air via the probe-deposited test paper, which has been successfully used for food spoilage identification.

A self-immolated fluorogenic agent triggered by H2S exhibiting potential anti-glioblastoma activity

Glioblastoma is the most common and aggressive type of malignant brain tumor with poor survival and limited therapeutic options. Theranostic anticancer agents with dual functions of diagnosis and therapy are highly attractive. Self-immolation reaction is a promising approach for theranostic prodrugs triggered by the tumor microenvironment. Overexpression of hydrogen sulfide (H₂S) in glioma cells becomes a potential stimulus for activating prodrugs. Herein, a novel H₂S responsive agent (SNF) containing amonafide (ANF), a self-immolative linker and a trigger group has been developed for imaging and chemotherapy in living cells. SNF exhibited high selectivity and sensitivity towards H₂S and also showed excellent lysosome-targeted capability. The activated SNF could translocate to the nucleus, causing DNA damage and blocking the cell cycle. More mechanistic studies indicated that SNF altered the mitochondrial membrane potential and induced autophagy in human glioblastoma-astrocytoma (U87MG). In addition, 3D multicellular U87MG tumor spheroids were used to further confirm the active drug release and high anti-proliferative activity of SNF. This approach may provide a general strategy for developing H₂S-triggered prodrugs for synergic cancer therapy.

A fast, high-affinity fluorescent serotonin biosensor engineered from a tick lipocalin

Serotonin (5-HT) is an important signaling monoamine and neurotransmitter. We report structure-guided engineering of a green fluorescent, genetically encoded serotonin sensor (G-GESS) from a 5-HT-binding lipocalin in the soft tick Argas monolakensis. G-GESS shows fast response kinetics and high affinity, specificity, brightness and photostability. We used G-GESS to image 5-HT dynamics in cultured cells, brain slices and behaving mice.

A three-channel fluorescent probe to image mitochondrial stress

Dual-recognition probes based on one reacting site inevitably encounter competition problems. Here, NPClA, a two-photon fluorescent probe based on a dual-site response for SO2/HOCl, was developed and applied in imaging mitochondrial stress.

A high-performance genetically encoded fluorescent biosensor for imaging physiological peroxynitrite

Peroxynitrite is a reactive nitrogen species (RNS) that plays critical roles in signal transduction, stress response, and numerous human diseases. Advanced molecular tools that permit the selective, sensitive, and noninvasive detection of peroxynitrite are essential for understanding its pathophysiological functions. Here, we present pnGFP-Ultra, a high-performance, reaction-based, genetically encodable biosensor for imaging peroxynitrite in live cells. pnGFP-Ultra features a p-boronophenylalanine-modified chromophore as the sensing moiety and exhibits a remarkable ~110-fold fluorescence turn-on response toward peroxynitrite while displaying virtually no cross-reaction with other reactive oxygen/nitrogen species. To facilitate the expression of pnGFP-Ultra in mammalian cells, we engineered an efficient noncanonical amino acid (ncAA) expression system that is broadly applicable to the mammalian expression of ncAA-containing proteins. pnGFP-Ultra robustly detected peroxynitrite production in activated macrophages and primary glial cells. pnGFP-Ultra fills an important technical gap and represents a valuable addition to the molecular toolbox for probing RNS biology.

The effects of dithiothreitol (DTT) on fluorescent qPCR dyes

DNA extractions of semen samples commonly utilize dithiothreitol (DTT) to reduce and disrupt disulfide bonds. Although traditional extraction techniques remove DTT before downstream analyses, the forensic DNA community has recently explored Y-screening, direct amplification, and direct cell lysis assays that omit purification but employ reducing agents to lyse spermatozoa. This study examined the impact of residual DTT on downstream processes involving fluorescent dyes. Quantification using Investigator^® Quantiplex HYres revealed a significant increase in the male DNA yield (p = 0.00056) and a >150,000,000-fold increase in the male:human DNA ratio when DTT remained in extracts versus when it was filtered out using a traditional purification method. When DTT was present with Quantifiler™ Trio, the true mean DNA yield for the large autosomal target significantly increased (p = 0.038) and the average reported DNA yields increased 1.1-fold, >9.5-fold, and 1.3-fold for the small autosomal, large autosomal, and male targets, respectively. DTT-spiked DNA standards from both kits were impacted similarly to samples with residual DTT, demonstrating that observed effects were related to DTT and not the extraction method. This study corroborates other reports that DTT adversely affects multiple dyes (e.g., Cy5, Quasar 670, SYBR Green I, TMR, and Mustang Purple^® ). Overall, DTT causes inaccurate quantities and, consequently, inaccurate calculated male:female ratios when used in conjunction with these kits. Thus, implementation of newer direct-to-PCR assays incorporating DTT should either be avoided or used only with carefully evaluated, compatible dyes.

A general strategy to red-shift green fluorescent protein-based biosensors

Compared with green fluorescent protein-based biosensors, red fluorescent protein (RFP)-based biosensors are inherently advantageous because of reduced phototoxicity, decreased autofluorescence and enhanced tissue penetration. However, existing RFP-based biosensors often suffer from small dynamic ranges, mislocalization and undesired photoconversion. In addition, the choice of available RFP-based biosensors is limited, and development of each biosensor requires substantial effort. Herein, we describe a general and convenient method, which introduces a genetically encoded noncanonical amino acid, 3-aminotyrosine, to the chromophores of green fluorescent protein-like proteins and biosensors for spontaneous and efficient green-to-red conversion. We demonstrated that this method could be used to quickly expand the repertoire of RFP-based biosensors. With little optimization, the 3-aminotyrosine-modified biosensors preserved the molecular brightness, dynamic range and responsiveness of their green fluorescent predecessors. We further applied spectrally resolved biosensors for multiplexed imaging of metabolic dynamics in pancreatic β-cells.

In Vivo Imaging with Genetically Encoded Redox Biosensors

Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.

A new strategy for the fluorescence discrimination of Cys/Hcy and GSH/H2S simultaneously colorimetric detection for H2S

The development of fluorescent probes enabling distinguishable detection Cys, Hcy, GSH and H₂S is still a considerable challenge owing to their similar functional group with comparable reactivity. In this work, a novel fluorescent probe FHC-O-NBD has been synthesized, and a practicable strategy for the fluorescence discrimination of Cys/Hcy and GSH/H₂S, especially the colorimetric detection for H₂S have been presented. FHC-O-NBD reacted with Cys/Hcy to produce two fluorescent emissions at 486 nm and 550 nm, while for GSH/H₂S, only one fluorescent signal at 486 nm appeared. And, only upon addition of H₂S, the color of the system changed from colorless to pink. So it can serve as a colorimetric probe for H₂S by "naked eye". Furthermore, FHC-O-NBD can selectively distinguish Cys/Hcy and GSH/H₂S in living cells, meaning it has great potential in biological applications.

Near-infrared fluorescent chemodosimeter for real-time in vivo evaluation of H2S-release efficiency of prodrug

A promising platform for evaluating H₂S-release in pharmaceutical development, and enabling a great method for monitoring H₂S in future clinical medicine.

FRET-based fluorescent ratiometric probes for the rapid detection of endogenous hydrogen sulphide in living cells

FRET strategy was adopted for designing ratiometric fluorescent H₂S sensors using Coumarin-derived merocyanine fluorophore.

Functionalized Metal-Organic Framework UiO-66-NH-BQB for Selective Detection of Hydrogen Sulfide and Cysteine

Hydrogen sulfide (H₂S) is an important signaling molecule related to many diseases. Thus, H₂S has a great impact on the pathological and physiological processes in biological systems. Cysteine (l-Cys) is a building block for proteins and important metabolites. To understand their roles in the physiological metabolic procedures, the measurement of the H₂S level and identifying cysteine in the biological system is significant. In this study, through the functionalization of UiO-66-NH₂ by 4-(2,2-dicyanoethenyl)benzoic acid (BQB), a novel UiO-66-NH-BQB is successfully synthesized and used as a fluorescence probe to recognize and detect H₂S and l-Cys. The fluorescence signals of the probe are enhanced great when it is exposed to H₂S or cysteine molecules; thus, it is able to determine quantificationally the H₂S concentration in an aqueous solution. The detection limitation of the UiO-66-NH-BQB to H₂S concentration is found to be as low as 1.74 μM. The developed fluorescent probe based on UiO-66-NH-BQB displays a high selectivity and excellent biocompatibility, which is very promising for recognition and sensing of biothiols in organisms.

Hydrogen Sulfide From Cysteine Desulfurase, Not 3-Mercaptopyruvate Sulfurtransferase, Contributes to Sustaining Cell Growth and Bioenergetics in E. coli Under Anaerobic Conditions

Endogenous hydrogen sulfide (H₂S), which is primarily generated by 3-mercaptopyruvate sulfurtransferase (3-MST) in Escherichia coli (E. coli) under aerobic conditions, renders bacteria highly resistant to oxidative stress. However, the biosynthetic pathway and physiological role of this gas under anaerobic conditions remains largely unknown. In the present study, we demonstrate that cysteine desulfurase (IscS), not 3-MST, is the primary source of endogenous H₂S in E. coli under anaerobic conditions. A significant decrease in H₂S production under anaerobic conditions was observed in E. coli upon deletion of IscS, but not in 3-MST-deficient bacteria (ΔmstA). Furthermore, the H₂S-producing activity of recombinant IscS using L-cysteine as a substrate exhibited an approximately 2.6-fold increase in the presence of dithiothreitol (DTT), indicating that H₂S production catalyzed by IscS was greatly increased under reducing conditions. The activity of IscS was regulated under the different redox conditions and the midpoint redox potential was determined to be −329 ± 1.6 mV. Moreover, in E. coli cells H₂S production from IscS is regulated under oxidative and reductive stress. A mutant E. coli (ΔiscS) strain lacking a chromosomal copy of the IscS-encoding gene iscS showed significant growth defects and low levels of ATP under both aerobic and anaerobic conditions. The growth defects could be fully restored after addition of 500 μM Na₂S (an H₂S donor) under anaerobic conditions, but not by the addition of cysteine, sodium sulfite or sodium sulfate. We also showed that the addition of 500 μM Na₂S to culture medium stimulates ATP synthesis in the mutant E. coli (ΔiscS) strain in the logarithmic growth phase but suppresses ATP synthesis in wild-type E. coli. Our results reveal a new H₂S-producing pathway in E. coli under anaerobic conditions and show that hydrogen sulfide from IscS contributes to sustaining cell growth and bioenergetics under oxygen-deficient conditions.

Formation or Cleavage of Rings via Sulfide-Mediated Reduction Offers Background-Free Detection of Sulfide

A set of three highly selective probes for sulfide detection has been developed. Two novel mechanistic strategies for the detection, including (a) transformation of a pro-fluorophore into an active fluorophore and (b) destruction of a fused ring to activate a fluorophore, have been explored. The structural features of the probes including azido groups ("active" and "latent") and leaving groups (with or without being attached to the fluorophore) have been investigated. During the course of the mechanistic studies, the single-crystal structures of all the probes and the products were obtained. One of the probes proved to be superior in terms of its ability to detect sulfide in pure water via an in situ formation of a fluorophore from a nonfluorescent precursor. These cheap and easy-to-prepare probes offer practical applications of sulfide recognition in environmental water samples and in the ovaries of fruit flies. A detection and quantification method using one of these probes and analysis with a smartphone enabled nonspecialists to detect sulfide reliably.

Circularly Permuted Fluorescent Protein-Based Indicators: History, Principles, and Classification

Genetically encoded biosensors based on fluorescent proteins (FPs) are a reliable tool for studying the various biological processes in living systems. The circular permutation of single FPs led to the development of an extensive class of biosensors that allow the monitoring of many intracellular events. In circularly permuted FPs (cpFPs), the original N- and C-termini are fused using a peptide linker, while new termini are formed near the chromophore. Such a structure imparts greater mobility to the FP than that of the native variant, allowing greater lability of the spectral characteristics. One of the common principles of creating genetically encoded biosensors is based on the integration of a cpFP into a flexible region of a sensory domain or between two interacting domains, which are selected according to certain characteristics. Conformational rearrangements of the sensory domain associated with ligand interaction or changes in the cellular parameter are transferred to the cpFP, changing the chromophore environment. In this review, we highlight the basic principles of such sensors, the history of their creation, and a complete classification of the available biosensors.

Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells

Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.

A Genetically Encoded, Ratiometric Fluorescent Biosensor for Hydrogen Sulfide

As an important gasotransmitter, hydrogen sulfide (H₂S) plays crucial roles in cell signaling. Incorporation of p-azidophenylalanine ( pAzF) into fluorescent proteins (FPs) via genetic code expansion has been a successful strategy in developing intensity-based, genetically encoded fluorescent biosensors for H₂S. To extend this strategy for ratiometric measurement which eliminates many detection uncertainties via self-calibration at two wavelengths, we modified the chromophore of a circularly permutated, superfolder green fluorescent protein (cpsGFP) with pAzF to derive cpsGFP- pAzF, which subsequently served as a Förster resonance energy transfer (FRET) acceptor to EBFP2, an enhanced blue fluorescent protein. The resultant construct, namely, hsFRET, is the first ratiometric, genetically encoded fluorescent biosensor for H₂S. Both in vitro and in mammalian cells, H₂S reduces the azido functional group of hsFRET to amine, leading to an increase of FRET from EBFP2 to cpsGFP. Our results collectively demonstrated that hsFRET could be used to selectively and ratiometrically monitor H₂S.