Ex Tenebris Lux: Illuminating Reactive Oxygen and Nitrogen Species with Small Molecule Probes

Reactive oxygen and nitrogen species are small reactive molecules derived from elements in the air─oxygen and nitrogen. They are produced in biological systems to mediate fundamental aspects of cellular signaling but must be very tightly balanced to prevent indiscriminate damage to biological molecules. Small molecule probes can transmute the specific nature of each reactive oxygen and nitrogen species into an observable luminescent signal (or even an acoustic wave) to offer sensitive and selective imaging in living cells and whole animals. This review focuses specifically on small molecule probes for superoxide, hydrogen peroxide, hypochlorite, nitric oxide, and peroxynitrite that provide a luminescent or photoacoustic signal. Important background information on general photophysical phenomena, common probe designs, mechanisms, and imaging modalities will be provided, and then, probes for each analyte will be thoroughly evaluated. A discussion of the successes of the field will be presented, followed by recommendations for improvement and a future outlook of emerging trends. Our objectives are to provide an informative, useful, and thorough field guide to small molecule probes for reactive oxygen and nitrogen species as well as important context to compare the ecosystem of chemistries and molecular scaffolds that has manifested within the field.

What can reactive oxygen species (ROS) tell us about the action mechanism of herbicides and other phytotoxins?

Reactive oxygen species (ROS) are formed in plant cells continuously. When ROS production exceeds the antioxidant capacity of the cells, oxidative stress develops which causes damage of cell components and may even lead to the induction of programmed cell death (PCD). The levels of ROS production increase upon abiotic stress, but also during pathogen attack in response to elicitors, and upon application of toxic compounds such as synthetic herbicides or natural phytotoxins. The commercial value of many synthetic herbicides is based on weed death as result of oxidative stress, and for a number of them, the site and the mechanism of ROS production have been characterized. This review summarizes the current knowledge on ROS production in plants subjected to different groups of synthetic herbicides and natural phytotoxins. We suggest that the use of ROS-specific fluorescent probes and of ROS-specific marker genes can provide important information on the mechanism of action of these toxins. Furthermore, we propose that, apart from oxidative damage, elicitation of ROS-induced PCD is emerging as one of the important processes underlying the action of herbicides and phytotoxins.

A novel micronutrients and methyl jasmonate cocktail of elicitors via seed priming improves drought tolerance by mitigating oxidative stress in rice (Oryza sativa L.)

Drought is a major limiting factor for rice (Oryza sativa L.) production globally, and a cost-effective seed priming technique using bio-elicitors has been found to have stress mitigating effects. Till date, mostly phytohormones have been preferred as bio-elicitors, but the present study is a novel attempt to demonstrate the favorable role of micronutrients-phytohormone cocktail, i.e., iron (Fe), zinc (Zn), and methyl jasmonate (MJ) via seed priming method in mitigating the deleterious impacts of drought stress through physio-biochemical and molecular manifestations. The effect of cocktail/priming was studied on the relative water content, chlorophyll a/b and carotenoid contents, proline content, abscisic acid (ABA) content, and on the activities of ascorbate peroxidase (APX), superoxide dismutase (SOD), NADPH oxidase (Nox), and catalase (CAT). The expressions of drought-responsive genes OsZn-SOD, OsFe-SOD, and Nox1 were found to be modulated under drought stress in contrasting rice genotypes -N-22 (Nagina-22, drought-tolerant) and PS-5 (Pusa Sugandh-5, drought-sensitive). A progressive rise in carotenoids (10-19%), ABA (18-50%), proline (60-80%), activities of SOD (27-62%), APX (46-61%), CAT (50-80%), Nox (16-30%), and upregulated (0.9-1.6-fold) expressions of OsZn-SOD, OsFe-SOD, and Nox1 genes were found in the primed plants under drought condition. This cocktail would serve as a potential supplement in modern agricultural practices utilizing seed priming technique to mitigate drought stress-induced oxidative burst in food crops.

Magnetic Field Intervention Enhances Cellular Migration Rates in Biological Scaffolds

The impact of magnetic fields on cellular function is diverse but can be described at least in part by the radical pair mechanism (RPM), where magnetic field intervention alters reactive oxygen species (ROS) populations and downstream cellular signaling. Here, cellular migration within three-dimensional scaffolds was monitored in an applied oscillating 1.4 MHz radiofrequency (RF) magnetic field with an amplitude of 10 µT and a static 50 µT magnetic field. Given that cellular bioenergetics can be altered based on applied RF magnetic fields, this study focused on a magnetic field configuration that increased cellular respiration. Results suggest that RF accelerated cell clustering and elongation after 1 day, with increased levels of clustering and cellular linkage after 7 days. Cell distribution analysis within the scaffolds revealed that the clustering rate during the first day was increased nearly five times in the RF environment. Electron microscopy provided additional topological information and verified the development of fibrous networks, with a cell-derived matrix (CDM) visualized after 7 days in samples maintained in RF. This work demonstrates time-dependent cellular migration that may be influenced by quantum biology (QB) processes and downstream oxidative signaling, enhancing cellular migration behavior.

A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems

IMPORTANCE

The elucidation of the molecular basis of virus-host coevolutionary interactions is boosted with state-of-the-art sequencing technologies. However, the sequence-only information is often insufficient to output a conclusive argument without biochemical characterizations. We proposed a 1-day and one-pot approach to confirm the exact function of putative restriction-modification (R-M) genes that presumably mediate microbial coevolution. The experiments mainly focused on a series of putative R-M enzymes from a deep-sea virus and its host bacterium. The results quickly unveiled unambiguous substrate specificities, superior catalytic performance, and unique sequence preferences for two new restriction enzymes (capable of cleaving DNA) and two new methyltransferases (capable of modifying DNA with methyl groups). The reality of the functional R-M system reinforced a model of mutually beneficial interactions with the virus in the deep-sea microbial ecosystem. The cell culture-independent approach also holds great potential for exploring novel and biotechnologically significant R-M enzymes from microbial dark matter.

A review on solution- and vapor-responsive sensors for the detection of phthalates

Phthalic acid esters, largely referred to as phthalates, are today acknowledged as important pollutants used in the manufacture of polyvinyl chloride (PVC)-based plastics, whose use extends to almost every aspect of modern life. The risk of exposure to phthalates is particularly relevant as high concentrations are regularly found in drinking water, food-contact materials and medical devices, motivating an immense body of research devoted to methods for their detection in liquid samples. Conversely, phthalate vapors have only recently been acknowledged as potentially important atmospheric pollutants and as early fire indicators; additionally, deposition of these vapors can pose significant problems to the proper functioning of spacecraft and diverse on-board devices, leading to major space agencies recognizing the need of developing vapor-responsive phthalate sensors. In this manuscript we present a literature survey on solution- and vapor-responsive sensors and analytical assays for the detection of phthalates, providing a detailed analysis of a vast array of analytical data to offer a clear idea on the analytical performance (limits of detection and quantification, linear range) and advantages provided by each class of sensor covered in this review (electrochemical, optical and vapor-responsive) in the context of their potential real-life applications; the manuscript also gives detailed fundamental information on the various physicochemical responses exploited by these sensors and assays that could potentially be harnessed by new researchers entering the field.

Sodium nitroprusside alleviates nanoplastics-induced developmental toxicity by suppressing apoptosis, ferroptosis and inflammation

The health damage caused by nanoplastics (NPs) pollution has become one of the global scientific problems to be solved urgently. However, the toxicological mechanism of NPs is complex, and the research progress of anti-toxicity is limited. Thus, it has potential application value to explore or develop drugs that can effectively alleviate or remove NPs with biological toxicity. In this research, 8 μM sodium nitroprusside (SNP) solution was used to treat zebrafish larvae with 20 mg/L NPs for up to 12 days, and the results showed that SNP treatments were effective in alleviating NPs-caused developmental toxicity in zebrafish larvae. Further examination of its signaling pathway revealed that NPs-induced oxidative stress was mitigated by activating the NO-sGC-cGMP signaling pathway and reduced most of the reactive oxygen species (ROS). Subsequently, we detected the key substances and the key enzymes involved in apoptosis and ferroptosis, and found that oxidative stress-induced mitochondria-dependent apoptosis and lipid peroxidation-caused ferroptosis were alleviated. Finally, observed the accumulation of NPs and ROS in the liver of zebrafish larvae, which is the target organ of immunotoxicity, and we found that SNP could alleviate NPs-caused inflammation by analyzing the fluorescence intensity of neutrophils and macrophages in transgenic zebrafish and detecting the expression of key immune genes. In conclusion, this research has shown for the first time that SNP treatment can significantly inhibit NPs-induced developmental toxicity, resulting from oxidative stress-induced apoptosis, ferroptosis and inflammation in zebrafish larvae.

Factors Important in the Use of Fluorescent or Luminescent Probes and Other Chemical Reagents to Measure Oxidative and Radical Stress

Numerous chemical probes have been used to measure or image oxidative, nitrosative and related stress induced by free radicals in biology and biochemistry. In many instances, the chemical pathways involved are reasonably well understood. However, the rate constants for key reactions involved are often not yet characterized, and thus it is difficult to ensure the measurements reflect the flux of oxidant/radical species and are not influenced by competing factors. Key questions frequently unanswered are whether the reagents are used under 'saturating' conditions, how specific probes are for particular radicals or oxidants and the extent of the involvement of competing reactions (e.g., with thiols, ascorbate and other antioxidants). The commonest-used probe for 'reactive oxygen species' in biology actually generates superoxide radicals in producing the measured product in aerobic systems. This review emphasizes the need to understand reaction pathways and in particular to quantify the kinetic parameters of key reactions, as well as measure the intracellular levels and localization of probes, if such reagents are to be used with confidence.

Delivery of Lipid Nanoparticles with ROS Probes for Improved Visualization of Hepatocellular Carcinoma

Reactive oxygen species (ROS) are highly reactive products of the cell metabolism derived from oxygen molecules, and their abundant level is observed in many diseases, particularly tumors, such as hepatocellular carcinoma (HCC). In vivo imaging of ROS is a necessary tool in preclinical research to evaluate the efficacy of drugs with antioxidant activity and for diagnosis and monitoring of diseases. However, most known sensors cannot be used for in vivo experiments due to low stability in the blood and rapid elimination from the body. In this work, we focused on the development of an effective delivery system of fluorescent probes for intravital ROS visualization using the HCC model. We have synthesized various lipid nanoparticles (LNPs) loaded with ROS-inducible hydrocyanine pro-fluorescent dye or plasmid DNA (pDNA) with genetically encoded protein sensors of hydrogen peroxide (HyPer7). LNP with an average diameter of 110 ± 12 nm, characterized by increased stability and pDNA loading efficiency (64 ± 7%), demonstrated preferable accumulation in the liver compared to 170 nm LNPs. We evaluated cytotoxicity and demonstrated the efficacy of hydrocyanine-5 and HyPer7 formulated in LNP for ROS visualization in mouse hepatocytes (AML12 cells) and in the mouse xenograft model of HCC. Our results demonstrate that obtained LNP could be a valuable tool in preclinical research for visualization ROS in liver diseases.

Reactive oxygen species in biological media are they friend or foe? Major In vivo and In vitro sensing challenges

The role of Reactive Oxygen Species (ROS) on biological media has been shifting over the years, as the knowledge on the complex mechanism that lies in underneath their production and overall results has been growing. It has been known for some time that these species are associated with a number of health conditions. However, they also participate in the immunoactivation cascade process, and can have an active role in theranostics. Macrophages, for example, react to the presence of pathogens through ROS production, potentially allowing the development of new therapeutic strategies. However, their short lifetime and limited spatial distribution of ROS have been limiting factors to the development and understanding of this phenomenon. Even though, ROS have shown successful theranostic applications, e.g., photodynamic therapy, their wide applicability has been hampered by the lack of effective tools for monitoring these processes in real time. Thus the development of innovative sensing strategies for in vivo monitoring of the balance between ROS concentration and the resultant immune response is of the utmost relevance. Such knowledge could lead to major breakthroughs towards the development of more effective treatments for neurodegenerative diseases. Within this review we will present the current understanding on the interaction mechanisms of ROS with biological systems and their overall effect. Additionally, the most promising sensing tools developed so far, for both in vivo and in vitro tracking will be presented along with their main limitations and advantages. This review focuses on the four main ROS that have been studied these are: singlet oxygen species, hydrogen peroxide, hydroxyl radical and superoxide anion.

Defining the nuanced nature of redox biology in post-traumatic stress disorder

Post-traumatic stress disorder (PTSD) is a mental health disorder that arises after experiencing or witnessing a traumatic event. Despite affecting around 7% of the population, there are currently no definitive biological signatures or biomarkers used in the diagnosis of PTSD. Thus, the search for clinically relevant and reproducible biomarkers has been a major focus of the field. With significant advances of large-scale multi-omic studies that include genomic, proteomic, and metabolomic data, promising findings have been made, but the field still has fallen short. Amongst the possible biomarkers examined, one area is often overlooked, understudied, or inappropriately investigated: the field of redox biology. Redox molecules are free radical and/or reactive species that are generated as a consequence of the necessity of electron movement for life. These reactive molecules, too, are essential for life, but in excess are denoted as "oxidative stress" and often associated with many diseases. The few studies that have examined redox biology parameters have often utilized outdated and nonspecific methods, as well as have reported confounding results, which has made it difficult to conclude the role for redox in PTSD. Herein, we provide a foundation of how redox biology may underlie diseases like PTSD, critically examine redox studies of PTSD, and provide future directions the field can implement to enhance standardization, reproducibility, and accuracy of redox assessments for the use of diagnosis, prognosis, and therapy of this debilitating mental health disorder.

Expression of the H2O2 Biosensor roGFP-Tpx1.C160S in Fission and Budding Yeasts and Jurkat Cells to Compare Intracellular H2O2 Levels, Transmembrane Gradients, and Response to Metals

Intracellular hydrogen peroxide (H2O2) levels can oscillate from low, physiological concentrations, to intermediate, signaling ones, and can participate in toxic reactions when overcoming certain thresholds. Fluorescent protein-based reporters to measure intracellular H2O2 have been developed in recent decades. In particular, the redox-sensitive green fluorescent protein (roGFP)-based proteins fused to peroxiredoxins are among the most sensitive H2O2 biosensors. Using fission yeast as a model system, we recently demonstrated that the gradient of extracellular-to-intracellular peroxides through the plasma membrane is around 300:1, and that the concentration of physiological H2O2 is in the low nanomolar range. Here, we have expressed the very sensitive probe roGFP2-Tpx1.C169S in two other model systems, budding yeast and human Jurkat cells. As in fission yeast, the biosensor is ~40–50% oxidized in these cell types, suggesting similar peroxide steady-state levels. Furthermore, probe oxidation upon the addition of extracellular peroxides is also quantitatively similar, suggesting comparable plasma membrane H2O2 gradients. Finally, as a proof of concept, we have applied different concentrations of zinc to all three model systems and have detected probe oxidation, demonstrating that an excess of this metal can cause fluctuations of peroxides, which are moderate in yeasts and severe in mammalian cells. We conclude that the principles governing H2O2 fluxes are very similar in different model organisms.

The application of optical technology in the diagnosis and therapy of oxidative stress-mediated hepatic ischemia-reperfusion injury

Hepatic ischemia-reperfusion injury (HIRI) is defined as liver tissue damage and cell death caused by reperfusion during liver transplantation or hepatectomy. Oxidative stress is one of the important mechanisms of HIRI. Studies have shown that the incidence of HIRI is very high, however, the number of patients who can get timely and efficient treatment is small. The reason is not hard to explain that invasive ways of detection and lack of timely of diagnostic methods. Hence, a new detection method is urgently needed in clinic application. Reactive oxygen species (ROS), which are markers of oxidative stress in the liver, could be detected by optical imaging and offer timely and effective non-invasive diagnosis and monitoring. Optical imaging could become the most potential tool of diagnosis of HIRI in the future. In addition, optical technology can also be used in disease treatment. It found that optical therapy has the function of anti-oxidative stress. Consequently, it has possibility to treat HIRI caused by oxidative stress. In this review, we mainly summarized the application and prospect of optical techniques in oxidative stress-induced by HIRI.

Enzymatic Recording of Local Hydrogen Peroxide Generation Using Genetically Encodable Enzyme

Reactive oxygen species (ROS) are endogenously generated in live cells and essential for cell signaling. However, excess ROS generation can cause oxidative damage to biomolecules, which are implicated in various human diseases, including aging. Here, we developed an in vivo hydrogen peroxide monitoring method using a genetically encodable peroxidase (APEX2)-based system. We confirmed that APEX2 is activated by endogenous H₂O₂ and generates phenoxyl radicals to produce biotinylated signals (i.e., biotin-phenol) and fluorescent signals (i.e., AmplexRed), which can be detected using a fluorescence microscope. We observed that all subcellular targeted APEX2s were activated by local H₂O₂ generation by menadione treatment. Among them, the endoplasmic reticulum lumen and lysosome-targeted APEX2 showed the highest response upon addition of menadione which implies that local H₂O₂ levels in those spaces are highly increased by menadione treatment. Using APEX2, we also found that a minimum amount of menadione (>10 μM) is required to generate detectable levels of H₂O₂ in all subcellular compartments. We also checked the local H₂O₂-quenching effect of N-acetylcysteine using our system. As APEX2 can be genetically expressed in diverse live organisms (e.g., cancer cell lines, mice, fly, worm, and yeast), our method can be effectively used to detect local generation of endogenously produced H₂O₂ in diverse live models.

Observation of HOCl generation associated with diabetic cataract using a highly sensitive fluorescent probe

Diagnosis of diabetic cataract (DC) in the early stage is of great significance for drug intervention and surgery circumvention for DC patients. However, the lack of reliable imaging tools greatly limits the diagnosis of early DC. In this context, a fluorescent probe BBPy for hypochlorous acid (HOCl) is presented based on the oxidation of phenothiazine. The probe displays apparent emission enhancement at 562 nm toward HOCl with high selectivity, superb sensitivity (detection limit: 12.6 nM), and rapid response (within seconds). Using the probe, the HOCl generation in diabetic human lens epithelial cells was monitored, as well as the HOCl down-regulation during antioxidant treatment. Therefore, it is proposed that HOCl can be a promising biomarker for DC and fluorescence imaging technique can be regarded as a candidate tool for DC diagnosis.

HClO-Activated Near-Infrared Fluorogenic Aza-BODIPY-Bisferrocene Triad with High Turn-on Ratio for In Vivo Biosensing

Optically monitoring hypochlorous acid (HClO) in living body favors diagnosis and study of inflammatory diseases. However, this has been hampered by limited strategies to develop highly fluorogenic tools in the deep-penetration near-infrared spectrum. Herein, a near-infrared aza-BODIPY-bisferrocene triad Fc₂ -CBDP that unexpectedly achieves an exceptionally sensitive and selective fluorescence turn-on (>220-fold) response toward HClO through single-ferrocene oxidation and boron-alkynyl hydrolysis cascade is reported. Mechanism insight shows that Fc₂ -CBDP features "enhanced charge transfer"-caused quenching due to intramolecular bisferrocene electronic coupling, which is decoupled in the reaction with HClO. The utility of Fc₂ -CBDP for intracellular HClO imaging is evaluated and, more importantly, in vivo high-contrast deep-tissue imaging of lymphatic inflammation and colitis is realized. This work provides new insights into both HClO and ferrocene chemistry, and extends the reach of fluorogenic strategies in the near-infrared biosensing.

Recent development of small-molecule fluorescent probes based on phenothiazine and its derivates

Fluorescence probes, as analytical tools with the ability to perform rapid and sensitive detection of target analytes, have made outstanding contributions to environmental analysis and bioassays. Considering the expanding developments in these areas, fluorophores play a key role in the de-sign of fluorescence probes. Compared to classical fluorophores, phenothiazines with elec-tron-rich characteristics have been widely applied to construct electron donor-acceptor dyes, which exhibit outstanding performance in both fluorimetric and colorimetric analysis. In addition, these probes also exhibit the pronounced ability in both solution and solid-state, achieving portable detection for environmental analysis. In this review, we summarize recent advances in the performance of phenothiazine-based fluorescent probes for detecting various analytes, especially in cations, anions, ROS/RSS, enzyme and other small molecules. The general design rules, response mechanisms and practical applications of the probes are analyzed, followed by a discussion of exiting challenges and future research perspectives. It is hoped that this review will provide a few strategies for the development of phenothiazine-based fluorescent probes.

A ratiometric fluorescence probe for imaging endoplasmic reticulum (ER) hypochlorous acid in living cells undergoing excited state intramolecular proton transfer

Hypochlorous acid (HOCl), one of the most important ROS in living organisms, appears to serve an important role in the immune system in vivo. Endoplasmic reticulum (ER), the largest organelle in cells, manages many biological processes connected to vital activities. To better obtain insight into the relationship of ER stress and HOCl level, a ratiometric fluorescent probe RHE, based on rhodamine combined with HBT and ER-targeting group, was designed and synthesized for HOCl detection in the ER. Probe RHE shows a large stokes shift about 155 nm, which is derived to ESIPT principle. In addition, probe RHE exhibited excellent properties such as fast response (<80 s), high sensitivity with a low detection limit (40 nM), high selectivity and anti-interference. Moreover, probe RHE displayed an excellent ER-targeting ability and had been successfully applied for detection of exogenous and endogenous HOCl in HepG2 cells.

Nitrogen-doped carbon quantum dots as fluorescent nanosensor for selective determination and cellular imaging of ClO. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022;271:120941. [PMID: 35114635 DOI: 10.1016/j.saa.2022.120941]

The carbon nanomaterial based fluorescent probes have been widely applied in biological imaging. In the current research, we propose an interesting strategy for selective sensing of hypochlorite (ClO^-) by a water-soluble and highly fluorescent nanosensor based on the N-doped carbon quantum dots (CDs) which was fabricated by a facile and environmental friendly hydrothermal approach from polyvinyl pyrrolidone, L-arginine and tryptophan. The structural characteristics of the probe were measured by multitudinous methods which proved the nanometer spherical structure of the probe and the successfully N-doping. Fluorescent investigation demonstrated that the probe is not only highly stable under interferences of pH, ionic strength, and irradiation, but also significantly selective toward ClO^- amongst a variety of attractive bioactive species through the fluorescent quenching process which was correlative with the concentration of ClO^- and linearly in the range of 0.1-50 μmol·L^-1 with the sensitivity of 0.03 μmol·L^-1. The probe can also be further illustrated in a prospective application for determination of ClO^- in environmental water through both solution response and filer paper sensing. Moreover, the positive biocompatibility and ignorable cytotoxicity made the probe a promising effective agent for detection and visualizing ClO^- in living cells which can facilitate the understanding the oxidative stress from the overexpressing ClO^-.

Cell-Based Chemical Safety Assessment and Therapeutic Discovery Using Array-Based Sensors

Synthetic chemicals are widely used in food, agriculture, and medicine, making chemical safety assessments necessary for environmental exposure. In addition, the rapid determination of chemical drug efficacy and safety is a key step in therapeutic discoveries. Cell-based screening methods are non-invasive as compared with animal studies. Cellular phenotypic changes can also provide more sensitive indicators of chemical effects than conventional cell viability. Array-based cell sensors can be engineered to maximize sensitivity to changes in cell phenotypes, lowering the threshold for detecting cellular responses under external stimuli. Overall, array-based sensing can provide a robust strategy for both cell-based chemical risk assessments and therapeutics discovery.

In vitro assays for investigating the FLASH effect

FLASH radiotherapy is a novel technique that has been shown in numerous preclinical in vivo studies to have the potential to be the next important improvement in cancer treatment. However, the biological mechanisms responsible for the selective FLASH sparing effect of normal tissues are not yet known. An optimal translation of FLASH radiotherapy into the clinic would require a good understanding of the specific beam parameters that induces a FLASH effect, environmental conditions affecting the response, and the radiobiological mechanisms involved. Even though the FLASH effect has generally been considered as an in vivo effect, studies finding these answers would be difficult and ethically challenging to carry out solely in animals. Hence, suitable in vitro studies aimed towards finding these answers are needed. In this review, we describe and summarise several in vitro assays that have been used or could be used to finally elucidate the mechanisms behind the FLASH effect.

Phosphinate-benzoindocyanin fluorescent probe for endogenous mitochondrial peroxynitrite detection in living cells and gallbladder access in inflammatory zebrafish animal models

Potent oxidants such as peroxynitrite (ONOO^-) play important roles in the regulation of different physiopathological processes; their overproduction is thought to potentially cause several diseases in living organisms. Hence, the precise and selective monitoring of ONOO^- is imperative for elucidating its interplay and roles in pathological and physiological processes. Herein, we present a novel diphenyl phosphinate-masked benzoindocyanin "turn-on" fluorogenic probe to help detect mitochondrial ONOO^- in living cells and zebrafish models. A pale yellow color solution of BICBzDP turns rose-red upon the addition of ONOO^-_, selectively, contrary to that of other competitive bioactive molecules. BICBzDP displays an ultra-sensitivity detection limit (47.8 nM) with outstanding selectivity and sensitivity towards mitochondrial ONOO^- and possesses a notable 68-fold fluorescence enhancement involving a large redshift of 91 nm. Importantly, further biological experimental investigations with BICBzDP indicate specific sensitivity and reliability of the probe to track the ONOO^- level, not only in live cells, but also demonstrates dynamic fluctuations in the inflammatory zebrafish animal models. Thus, BICBzDP could be employed as a future potential biological tool for exploiting the role of ONOO^- in a variety of different physiological systems.

Caveat fluorophore: an insiders' guide to small-molecule fluorescent labels

The last three decades have brought a revolution in fluorescence microscopy. The development of new microscopes, fluorescent labels and analysis techniques has pushed the frontiers of biological imaging forward, moving from fixed to live cells, from diffraction-limited to super-resolution imaging and from simple cell culture systems to experiments in vivo. The large and ever-evolving collection of tools can be daunting for biologists, who must invest substantial time and effort in adopting new technologies to answer their specific questions. This is particularly relevant when working with small-molecule fluorescent labels, where users must navigate the jargon, idiosyncrasies and caveats of chemistry. Here, we present an overview of chemical dyes used in biology and provide frank advice from a chemist's perspective.

A pyrene-pyridyl nanooligomer as a methoxy-triggered reactive probe for highly specific fluorescence assaying of hypochlorite

A novel pyrene-pyridyl conjugated oligomer (OPP-OMe) was conveniently prepared by one-pot Sonogashira coupling. Intriguingly, it was found that introducing only one methoxy moiety at the 4-pyridyl position can be sufficient for creating an oligomer-based ultrafine reactive fluorescent nanoprobe, i.e., OPP-OMe NPs (ca. 2.5 nm in diameter). Spectral analyses and elucidation of the intermediate structure revealed that the methoxy triggered-oxidation, together with nanoaggregation of OPP-OMe NPs, results in rapid, specific and supersensitive sensing of hypochlorite (LOD, 0.3 nM, S/N = 3).

Low-invasive 5D visualization of mitotic progression by two-photon excitation spinning-disk confocal microscopy

Non-linear microscopy, such as multi-photon excitation microscopy, offers spatial localities of excitations, thereby achieving 3D cross-sectional imaging with low phototoxicity even in thick biological specimens. We had developed a multi-point scanning two-photon excitation microscopy system using a spinning-disk confocal scanning unit. However, its severe color cross-talk has precluded multi-color simultaneous imaging. Therefore, in this study, we introduced a mechanical switching system to select either of two NIR laser light pulses and an image-splitting detection system for 3- or 4-color imaging. As a proof of concept, we performed multi-color fluorescent imaging of actively dividing human HeLa cells and tobacco BY-2 cells. We found that the proposed microscopy system enabled time-lapse multi-color 3D imaging of cell divisions while avoiding photodamage. Moreover, the application of a linear unmixing method to the 5D dataset enabled the precise separation of individual intracellular components in multi-color images. We thus demonstrated the versatility of our new microscopy system in capturing the dynamic processes of cellular components that could have multitudes of application.

Self-Targeting Carbon Quantum Dots for Peroxynitrite Detection and Imaging in Live Cells

Peroxynitrite (ONOO^-), a highly reactive nitrogen species (RNS) generated mainly in mitochondria, has been identified to be associated with numerous pathophysiological processes, and thus accurate ONOO^- imaging with superior sensitivity and selectivity is highly desirable. Herein, we prepared a new type of carbon quantum dots (CQDs) with mitochondria-targeting function without the aid of any targeting molecules via a simple one-step hydrothermal route. The as-prepared CQDs not only displayed relatively uniform size distribution, few surface defects, high photostability, and excellent biocompatibility but also exhibited good selective fluorescence turn-off response toward ONOO^-, owing to the oxidation of amino groups on the surface of carbon dots. A great linear correlation between the quenching efficiency and ONOO^- concentration in the range from 0.15 to 1.0 μM with a detection limit of 38.9 nM is shown. Moreover, the as-prepared CQDs acting as a functional optical probe through a self-targeting mechanism were successfully applied for in situ visualization of endogenous ONOO^- generated in the mitochondria of live cells, providing great promise for elucidating the complex biological roles of ONOO^- in related pathological processes.

An ESIPT-Dependent AIE Fluorophore Based on HBT Derivative: Substituent Positional Impact on Aggregated Luminescence and its Application for Hydrogen Peroxide Detection

Aiming to develop the facile organic fluorophore possessing excited state intramolecular proton transfer (ESIPT) and aggregation-induced emission (AIE), we designed and synthesized two isomers with different linkage site between hydroxyl of 2-(2-hydroxyphenyl) benzothiazole (HBT) and a benzothiazole substituent (para position refers to p-BHBT and ortho position refers to o-BHBT). Fluorescence emission properties of p-BHBT and o-BHBT in THF/water mixtures with different water volume fractions indicated an opposite luminescence in aggregates, in which p-BHBT showed an ESIPT-dependent AIE properties while o-BHBT displayed ESIPT effect and aggregation-caused quenching (ACQ) qualities. A possible mechanism for molecular actions to illustrate the aggregating luminescence alteration of these two isomers had been proposed and verified by theoretical and experimental studies. More importantly, Probe-1, generated from dual ESIPT-AIE fluorophore p-BHBT, was successfully used as a ratiometric fluorescent chemosensor for highly selective (above 15-fold over other ROS) and sensitive (69-fold fluorescence enhancement with 0.22 μM of detection limit) detection of hydrogen peroxide in aqueous solution and living cells, respectively.

Nanotechnologies for Reactive Oxygen Species"Turn-On" Detection

Reactive oxygen species (ROS) encompasses a collection of complicated chemical entities characterized by individually specific biological reactivities and physicochemical properties. ROS detection is attracting tremendous attention. The reaction-based nanomaterials for ROS "turn-on" sensing represent novel and efficient tools for ROS detection. These nanomaterials have the advantages of high sensitivity, real-time sensing ability, and almost infinite contrast against background. This review focuses on appraising nanotechnologies with the ROS "turn-on" detection mechanism coupled with the ability for broad biological applications. In this review, we highlighted the weaknesses and advantages in prior sensor studies and raised some guidelines for the development of future nanoprobes.

Two-photon ESIPT-based fluorescent probe using 4-hydroxyisoindoline-1,3-dione for the detection of peroxynitrite

Excited-state intramolecular proton transfer (ESIPT)-based fluorophores with two-photon excitation fluorescence (TPEF) are rare. Our aim with this research was to develop ESIPT-based fluorophores exhibiting TPEF. Herein, we used 4-hydroxyisoindoline-1,3-dione as a scaffold to develop a two-photon fluorescent probe BHID-Bpin, for the detection of peroxynitrite (ONOO^-). BHID-Bpin exhibits excellent selectivity, sensitivity, and fast response towards ONOO^- in PBS buffer solution (10 mM, pH = 7.40). Additionally, BHID-Bpin displays high photo-stability under two-photon irradiation at 750 nm. Furthermore, the probe can image endogenous ONOO^- in HeLa cells and exogenous ONOO^- in rat hippocampal slices at a depth of 110 μm.

Synthesis and fluorescence properties of red-to-near-infrared-emitting push-pull dyes based on benzodioxazole scaffolds

Fluorescence imaging with high temporal and spatial resolution has emerged as one of the most promising techniques to monitor biomolecules and biological processes in living systems. Among many kinds of small molecular fluorescent dyes, 2,1,3-benzoxadiazole (BD) derivatives have been widely applied in many chemical and biological applications due to their excellent photophysical properties. However, only a limited number of BD dyes with long emission wavelengths were reported. Herein, we have reported a new class of red-to near-infrared-emitting small molecular dyes 2a-3a based on benzodioxazole scaffolds, which are named VBDfluors. To bathochromically shift both absorption and emission, the conjugation system was extended by introducing electron-withdrawing group-substituted vinyl groups at position 7 via a Knoevenagel condensation reaction. The basic photophysical properties of VBDfluors were detected and summarized. The VBDfluors display excellent photophysical properties, including emission in the red-to-NIR region, large Stokes shifts, good stability/photostability and cell permeability. The geometry of the molecules was optimized by density functional theory (DFT) and time-dependent DFT (TDDFT) methods. Bioimaging results indicated that 2a and 3a exhibited excellent cell permeability and could be utilized for visualization of lipid droplets in living cells.

Leucomethylene blue probe detects a broad spectrum of reactive oxygen and nitrogen species

Reactive oxygen and nitrogen species (ROS, RNS) are ubiquitous in biology with a variety of physiological and pathological functions. Here we describe a broad spectrum ROS/RNS detecting fluorogenic probe with red fluorescence emission and up to 100-fold gain. Hence these modified probes are useful for in vivo non-invasive quantification of ROS/RNS.

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.

Seeking Illumination: The Path to Chemiluminescent 1,2-Dioxetanes for Quantitative Measurements and In Vivo Imaging

Chemiluminescence is a fascinating phenomenon that evolved in nature and has been harnessed by chemists in diverse ways to improve life. This Account tells the story of our research group's efforts to formulate and manifest spiroadamantane 1,2-dioxetanes with triggerable chemiluminescence for imaging and monitoring important reactive analytes in living cells, animals, and human clinical samples. Analytes like reactive sulfur, oxygen and nitrogen species, as well as pH and hypoxia can be indicators of cellular function or dysfunction and are often implicated in the causes and effects of disease. We begin with a foundation in binding-based and activity-based fluorescence imaging that has provided transformative tools for understanding biological systems. The intense light sources required for fluorescence excitation, however, introduce autofluorescence and light scattering that reduces sensitivity and complicates in vivo imaging. Our work and the work of our collaborators were the first to demonstrate that spiroadamantane 1,2-dioxetanes had sufficient brightness and biological compatibility for in vivo imaging of enzyme activity and reactive analytes like hydrogen sulfide (H₂S) inside of living mice. This launched an era of renewed interest in 1,2-dioxetanes that has resulted in a plethora of new chemiluminescence imaging agents developed by groups around the world. Our own research group focused its efforts on reactive sulfur, oxygen, and nitrogen species, pH, and hypoxia, resulting in a large family of bright chemiluminescent 1,2-dioxetanes validated for cell monitoring and in vivo imaging. These chemiluminescent probes feature low background and high sensitivity that have been proven quite useful for studying signaling, for example, the generation of peroxynitrite (ONOO^-) in cellular models of immune function and phagocytosis. This high sensitivity has also enabled real-time quantitative reporting of oxygen-dependent enzyme activity and hypoxia in living cells and tumor xenograft models. We reported some of the first ratiometric chemiluminescent 1,2-dioxetane systems for imaging pH and have introduced a powerful kinetics-based approach for quantification of reactive species like azanone (nitroxyl, HNO) and enzyme activity in living cells. These tools have been applied to untangle complex signaling pathways of peroxynitrite production in radiation therapy and as substrates in a split esterase system to provide an enzyme/substrate pair to rival luciferase/luciferin. Furthermore, we have pushed chemiluminescence toward commercialization and clinical translation by demonstrating the ability to monitor airway hydrogen peroxide in the exhaled breath of asthma patients using transiently produced chemiluminescent 1,2-dioxetanedione intermediates. This body of work shows the powerful possibilities that can emerge when working at the interface of light and chemistry, and we hope that it will inspire future scientists to seek out ever brighter and more illuminating ideas.

Chemical Biology Tools To Investigate Malaria Parasites

Parasitic diseases like malaria tropica have been shaping human evolution and history since the beginning of mankind. After infection, the response of the human host ranges from asymptomatic to severe and may culminate in death. Therefore, proper examination of the parasite's biology is pivotal to deciphering unique molecular, biochemical and cell biological processes, which in turn ensure the identification of treatment strategies, such as potent drug targets and vaccine candidates. However, implementing molecular biology methods for genetic manipulation proves to be difficult for many parasite model organisms. The development of fast and straightforward applicable alternatives, for instance small-molecule probes from the field of chemical biology, is essential. In this review, we will recapitulate the highlights of previous molecular and chemical biology approaches that have already created insight and understanding of the malaria parasite Plasmodium falciparum. We discuss current developments from the field of chemical biology and explore how their application could advance research into this parasite in the future. We anticipate that the described approaches will help to close knowledge gaps in the biology of P. falciparum and we hope that researchers will be inspired to use these methods to gain knowledge - with the aim of ending this devastating disease.

Cyanine-Dyad Molecular Probe for the Simultaneous Profiling of the Evolution of Multiple Radical Species During Bacterial Infections

Real-time monitoring of the evolution of bacterial infection-associated multiple radical species is critical to accurately profile the pathogenesis and host-defense mechanisms. Here, we present a unique dual wavelength near-infrared (NIR) cyanine-dyad molecular probe (HCy5-Cy7) for simultaneous monitoring of reactive oxygen and nitrogen species (RONS) variations both in vitro and in vivo. HCy5-Cy7 specifically turns on its fluorescence at 660 nm via superoxide or hydroxyl radical (O₂ ^.- , ^. OH)-mediated oxidation of reduced HCy5 moiety to Cy5, while peroxynitrite or hypochlorous species (ONOO^- , ClO^- )-induced Cy7 structural degradation causes the emission turn-off at 800 nm. Such multispectral but reverse signal responses allow multiplex manifestation of in situ oxidative and nitrosative stress events during the pathogenic and defensive processes in both bacteria-infected macrophage cells and living mice. Most importantly, this study may also provide new perspectives for understanding the bacterial pathogenesis and advancing the precision medicine against infectious diseases.

Nanohoop Rotaxane Design to Enhance the Selectivity of Reaction-Based Probes: A Proof-of-Principle Study

Mechanical interlocking of a nanohoop fluorophore and a reactive thread couples the benefits of a reaction-based probe with a sterically congested active site for enhanced selectivity. Advantageously, the thread design uses dual function stoppers that act as both a quencher and a trigger for sensing. In progress toward expanding this approach to biologically relevant analytes, this system is used to demonstrate steric differentiation and provide a selective turn-on fluorescent response with size selectivity for HS^- rather than larger thiolates.

Structurally-thrifty and visible-absorbing fluorophores

Fluorophores with a minimal push-pull backbone are actively pursued due to their potentials in biological labelling. Herein a series of structurally-thrifty and visible-absorbing fluorophores (SDXs) were successfully constructed following the D'D-π-A design strategy, in which a secondary donor (D') was introduced in conjugation with the donor (D) to enhance its electron donating capability. For a very small scaffold, SDXs exhibit a surprisingly long-wavelength absorption band in the visible spectral range (λ_abs = 420 nm) and a strong green fluorescence emission (λ_em = 530 nm) with a fluorescence quantum yield up to 0.84. Notably, fluorescence of SDXs was quenched in hydrogen-bonding solvents, e.g. MeOH and H₂O. This phenomenon renders SDXs feasibility for imaging of cellular non-hydrogen-bonding microenvironment, as demonstrated with BEAS-2B cells. These results proved that the D'D-π-A is a powerful design strategy to construct novel structurally-thrifty fluorophores.

Fluorescent Probes for Selective Recognition of Hypobromous Acid: Achievements and Future Perspectives

Reactive oxygen species (ROS) have been implicated in numerous pathological processes and their homeostasis facilitates the dynamic balance of intracellular redox states. Among ROS, hypobromous acid (HOBr) has a high similarity to hypochlorous acid (HOCl) in both chemical and physical properties, whereas it has received relatively little attention. Meanwhile, selective recognition of endogenous HOBr suffers great challenges due to the fact that the concentration of this molecule is much lower than that of HOCl. Fluorescence-based detection systems have emerged as very important tools to monitor biomolecules in living cells and organisms owing to distinct advantages, particularly the temporal and spatial sampling for in vivo imaging applications. To date, the development of HOBr-specific fluorescent probes is still proceeding quite slowly, and the research related to this area has not been systematically summarized. In this review, we are the first to review the progress made so far in fluorescent probes for selective recognition and detection of HOBr. The molecular structures, sensing mechanisms, and their successful applications of these probes as bioimaging agents are discussed here in detail. Importantly, we hope this review will call for more attention to this rising field, and that this could stimulate new future achievements.

Different Approaches to Develop Nanosensors for Diagnosis of Diseases

The success of clinical treatments is highly dependent on early detection and much research has been conducted to develop fast, efficient, and precise methods for this reason. Conventional methods relying on nonspecific and targeting probes are being outpaced by so-called nanosensors. Over the last two decades a variety of activatable sensors have been engineered, with a great diversity concerning the operating principle. Therefore, this review delineates the achievements made in the development of nanosensors designed for diagnosis of diseases.

Fluorescent probes for in vitro and in vivo quantification of hydrogen peroxide

Hydrogen peroxide (H2O2) plays essential roles in redox signaling and oxidative stress, and its dynamic concentration is critical to human health and diseases. Here we report the design, syntheses, and biological applications of HKPerox-Red and HKPerox-Ratio for quantitative measurement of H2O2. Both probes were successfully applied to detect endogenous H2O2 fluxes in living cells or zebrafish, and biological effects of multiple stress inducers including rotenone, arsenic trioxide, and starvation were investigated. As H2O2 is a common by-product for oxidase oxidation, a general assay was developed for ultrasensitive detection of various metabolites (glucose, uric acid, and sarcosine). Moreover, cellular H2O2 measurements were achieved for the first time by combining flow cytometry with live cell calibration. This study provides a pair of unique molecular tools for advanced H2O2 bio-imaging and assay development.

Poly-d-lysine coated nanoparticles to identify pro-inflammatory macrophages

Identifying pro-inflammatory macrophages (M1) is of immense importance to diagnose, monitor, and treat various pathologies. In addition, adoptive cell therapies, where harvested cells are isolated, modified to express an M1-like phenotype, then re-implanted to the patient, are also becoming more prevalent to treat diseases such as cancer. In a step toward identifying, labeling, and monitoring macrophage phenotype for adoptive cell therapies, we developed a reactive oxygen species (ROS)-sensitive, gold nanoparticle (AuNP) that fluorescently labels M1 macrophages. AuNPs are electrostatically coated with a proteolysis resistant, fluorescein isothiocyanate-conjugated, poly-d-lysine (PDL-FITC) that is susceptible to backbone cleavage by ROS. When PDL-FITC is bound to AuNPs, fluorescence is quenched via a combination of nanoparticle surface (NSET) and Forster resonance (FRET) energy transfer mechanisms. Upon ROS-induced cleavage of PDL-FITC, up to a 7-fold change in fluorescence is demonstrated. PDL-FITC AuNPs were loaded into RAW 264.7 macrophages (RAWs) and primary bone marrow- derived macrophages (BMDMs) prior to in vitro polarization. For both cell types, detectable differences in intracellular fluorescence were observed between M1 polarized and non-stimulated (M0) control groups after 24 h using both confocal imaging and flow cytometry. PDL-FITC AuNPs can potentially be useful in identifying M1 macrophages within diverse cell populations and provide longitudinal macrophage response data to external cues.