The N-B Interaction through a Water Bridge: Understanding the Chemoselectivity of a Fluorescent Protein Based Probe for Peroxynitrite

A fluorescent NBD "turn-on" probe for the rapid and on-site analysis of fructose in food

High fructose intake is an important cause of metabolic disease. Due to the increasing prevalence of metabolic diseases worldwide, the development of an accurate and efficient tool for monitoring fructose in food is urgently needed to control the intake of fructose. Herein, a new fluorescent probe NBD-PQ-B with 7-nitrobenz-2-oxa-1, 3-diazole (NBD) as the fluorophore, piperazine (PQ) as the bridging group and phenylboronic acid (B) as the recognition receptor, was synthesized to detect fructose. The fluorescence of NBD-PQ-B increased linearly at 550 nm at an excitation wavelength of 497 nm with increasing fructose concentration from 0.1 to 20 mM. The limit of detection (LOD) of fructose was 40 μM. The pKa values of NBD-PQ-B and its fructose complexes were 4.1 and 10.0, respectively. In addition, NBD-PQ-B bound to fructose in a few seconds. The present technique was applied to determine the fructose content in beverages, honey, and watermelon with satisfactory results. Finally, the system could not only be applied in an aqueous solution with a spectrophotometer, but also be fabricated as a NBD-PQ-B/polyvinyl oxide (PEO) film by electrospinning for on-site food analysis simply with the assistance of a smartphone.

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.

A Small-Molecule Fluorescent Probe for the Detection of Mitochondrial Peroxynitrite

Reactive oxygen species (ROS) are pivotal signaling molecules that control a variety of physiological functions. As a member of the ROS family, peroxynitrite (ONOO-) possesses strong oxidation and nitrification abilities. Abnormally elevated levels of ONOO- can lead to cellular oxidative stress, which may cause several diseases. In this work, based on the rhodamine fluorophore, we designed and synthesized a novel small-molecule fluorescent probe (DH-1) for ONOO-. Upon reaction with ONOO-, DH-1 exhibited a significant fluorescence signal enhancement (approximately 34-fold). Moreover, DH-1 showed an excellent mitochondria-targeting capability. Confocal fluorescence imaging validated its ability to detect ONOO- changes in HeLa and RAW264.7 cells. Notably, we observed the ONOO- generation during the ferroptosis process by taking advantage of the probe. DH-1 displayed good biocompatibility, facile synthesis, and high selectivity, and may have potential applications in the study of ONOO--associated diseases in biosystems.

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.

Disulfide-Bridged Dendritic Organosilicas-Based Biodegradable Molecularly Imprinted Polymers for Multiple Targeting and pH/Redox-Responsive Drug Release toward Chemical/Photodynamic Synergistic Tumor Therapy

In this study, a sialic acid (SA) and transferrin (TF) imprinted biodegradable disulfide bridging organosilicas-based drug delivery system (SS-DMONS/DOX-Ce6@MIPs) for targeted cancer therapy is constructed, for the first time. Disulfide bridged dendritic mesoporous organosilicas nanoparticles (SS-DMONs) not only enhance drug loading as the drug repository, but also provide enough specific surface area for the molecular imprinting shell to expose more degradation and imprinted sites on the surface. In addition, SS can be disturbed in a highly reducing tumor microenvironment to achieve degradation. The biodegradable imprinting film, prepared with customized 2-amino-N-(3,4-dihydroxyphenethyl)-3-mercaptopropanamide and 4-mercaptophenylboronic acid as functional monomers, endows SS-DMONs with active targeting capacity, and responsive drug release through degradation under acidic and highly reductive tumor microenvironment. SS-DMONS/DOX-Ce6@MIPs after binding of TF can target tumor cells actively through multiple interactions, including the affinity between antigen and antibody, and the specific recognition between molecularly imprinted polymers and template molecules. Under laser irradiation the loaded chlorin e6 (Ce6) that can produce toxic reactive oxygen, combined with the doxorubicin (DOX), achieves chemical/photodynamic synergistic anticancer effects. SS-DMONS/DOX-Ce6@MIPs present excellent tumor targeting and dual-responsive drug release, which provides an effective strategy for chemical/photodynamic antitumor therapy.

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.

A Phenylboronic Acid-Based Transition State Analogue Yields Nanomolar Inhibition of Mandelate Racemase

Mandelate racemase (MR) catalyzes the Mg²⁺-dependent interconversion of (R)- and (S)-mandelate by stabilizing the altered substrate in the transition state (TS) by ∼26 kcal/mol. The enzyme has been employed as a model to explore the limits to which the free energy of TS stabilization may be captured by TS analogues to effect strong binding. Herein, we determined the thermodynamic parameters accompanying binding of a series of bromo-, chloro-, and fluoro-substituted phenylboronic acids (PBAs) by MR and found that binding was predominately driven by favorable entropy changes. 3,4-Dichloro-PBA was discovered to be the most potent inhibitor yet identified for MR, binding with a K_d^app value of 11 ± 2 nM and exceeding the binding of the substrate by ∼72,000-fold. The ΔC_p value accompanying binding (-488 ± 18 cal·mol^-1 K^-1) suggested that dispersion forces contribute significantly to the binding. The pH-dependence of the inhibition revealed that MR preferentially binds the anionic, tetrahedral form of 3,4-dichloro-PBA with a pH-independent K_i value of 5.7 ± 0.5 nM, which was consistent with the observed upfield shift of the ¹¹B NMR signal. The linear free energy relationship between log(k_cat/K_m) and log(1/K_i) for wild-type and 11 MR variants binding 3,4-dichloro-PBA had a slope of 0.8 ± 0.2, indicating that MR recognizes the inhibitor as an analogue of the TS. Hence, halogen substitution may be utilized to capture additional free energy of TS stabilization arising from dispersion forces to enhance the binding of boronic acid inhibitors by MR.

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.

Diazaborines oxidize slowly with H2O2 but rapidly with peroxynitrite in aqueous buffer

Reactive oxygen species (ROS) such as hydrogen peroxide (H₂O₂) and peroxynitrite (ONOO^-) oxidize arylboronic acids to their corresponding phenols. When used in molecular imaging probes and in ROS-responsive molecules, however, simple arylboronic acids struggle to discriminate between H₂O₂ and ONOO^- because of their fast rate of reaction with both ROS. Here, we show that diazaborines (DABs) react slowly with H₂O₂ but rapidly with peroxynitrite in an aqueous buffer. In addition to their slow reaction with H₂O₂, the immediate product of DAB oxidation with H₂O₂ and ONOO^- can yield a kinetically trapped CN Z-isomer that slowly equilibrates with its E-isomer. Taken together, our work shows that diazaborines exhibit enhanced kinetic discrimination between H₂O₂ and ONOO^- compared to arylboronic acids, opening up new opportunities for diazaborine-based tools in chemical biology.

Recent research progress in galactose-based fluorescent probes for detection of biomarkers of liver diseases

This highlight illustrates the challenges and latest progress in galactose-based fluorescent probes for early diagnosis of liver diseases.

A resorufin-based red-emitting fluorescent probe with high selectivity for tracking endogenous peroxynitrite in living cells and inflammatory mice

Peroxynitrite (ONOO^-) plays essential roles on various physiological and pathological processes of living systems as a short-lived and highly reactive nitrogen (RNS) specie. The construction of novel long-wavelength fluorescent probes with high specificity towards ONOO^- for imaging in vivo is still demand urgently. About this work, a novel resorufin-based red-emitting fluorescent probe for tracking ONOO^- has been constructed. The probe RFP exhibited high selectivity towards ONOO^- anion over other analytes. Utilizing the probe, ONOO^- could be directly observed by the naked eye. Furthermore, RFP was successfully applied for imaging endogenous ONOO^- in RAW264.7 cells and inflammatory mice. This work offers a convenient method for monitoring the intercellur ONOO^- that be expected to be applied for explaining the bio-functional roles of ONOO^- in living system.

The mechanisms of a bifunctional fluorescent probe for detecting fluoride and sulfite based on excited-state intramolecular proton transfer and intramolecular charge transfer

The mechanisms of 2-(Benzo[d]thiazol-2-yl)phenol-based bifunctional probe (HBT-FS) for detecting fluoride (F^-) and sulfite (SO₃ ^2-) based on excited-state intramolecular proton transfer (ESIPT) and intramolecular charge transfer (ICT) have been theoretically studied. Laplacian bond order of HBT-FS indicates that the F^- ion cleaves the Si-O bond and then forms Compound 2 possessing a six-membered ring with a hydrogen bond. Potential energy curves and dynamic simulations confirm that ESIPT in Compound 2 occurs along with this hydrogen bond and forms a keto structure with an emission at 623 nm, which agrees with the observed experimental value (634 nm) after adding F^-. Therefore, the fluorescence red-shift (from 498  to 634 nm) of HBT-FS observed in experiment after adding F^- is caused by ESIPT. The SO₃ ^2- ion is added to the C₅ site of HBT-FS, which is confirmed by orbital-weighted dual descriptor, and then forms Compound 3 with fluorescence located at 404 nm. The experimentally measured fluorescence at 371 nm after adding SO₃ ^2- is assigned to Compound 3. Charge transfer analyses indicate that the ICT extent of Compound 3 is relatively weak compared with that of HBT-FS because of the destruction of the conjugated structure by the addition reaction of SO₃ ^2-, which induces the blue-shift of the fluorescence of HBT-FS from 498 to 371 nm. The different fluorescence responses make HBT-FS a fluorescent probe to discriminatorily detect F^- and SO₃ ^2-.

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.

An inherently kidney-targeting near-infrared fluorophore based probe for early detection of acute kidney injury

Acute kidney injury (AKI) is common in hospital patients. Delayed diagnosis and treatment of AKI due to the lack of efficient early diagnosis is an important cause of its high mortality. While fluorescence imaging seems promising to non-intrusively interrogate AKI-related biomarkers, the low kidney contrast of many fluorophores conferred by their relatively low abundance of distribution in the kidney limits their application for AKI detection. Herein, we discovered a near-infrared fluorophore with inherent kidney-targeting ability. Based on this fluorophore, a fluorogenic probe (KNP-1) was developed by targeting peroxynitrite (ONOO^-), which is upregulated at the early onset of AKI. KNP-1 exhibits desirable kidney distribution after intravenous administration and is fluorescent only after activation by ONOO^-. These properties lead to excellent kidney contrast imaging results. KNP-1 is capable of detecting both nephrotoxin-induced and ischemia-reperfusion injury-induced AKI in live mice. Temporally resolved imaging of AKI-disease model mice with KNP-1 suggests a gradual increase in renal ONOO^- levels with disease progression. Notably, the upregulation of ONOO^- can be observed at least 24 h earlier than the clinically popular sCr and BUN methods. Blocking ONOO^- generation also proves beneficial. These results highlight the applicability of this inherently tissue targeting-based strategy for designing probes with desirable imaging contrast; potentiate ONOO^- as a biomarker and target for AKI early diagnosis and medical intervention; and imply the clinical relevance of KNP-1 for AKI early detection.

Potent Inhibition of Mandelate Racemase by Boronic Acids: Boron as a Mimic of a Carbon Acid Center

Boronic acids have been successfully employed as inhibitors of hydrolytic enzymes. Typically, an enzymatic nucleophile catalyzing hydrolysis adds to the electrophilic boron atom forming a tetrahedral species that mimics the intermediate(s)/transition state(s) for the hydrolysis reaction. We show that para-substituted phenylboronic acids (PBAs) are potent competitive inhibitors of mandelate racemase (MR), an enzyme that catalyzes a 1,1-proton transfer rather than a hydrolysis reaction. The K_i value for PBA was 1.8 ± 0.1 μM, and p-Cl-PBA exhibited the most potent inhibition (K_i = 81 ± 4 nM), exceeding the binding affinity of the substrate by ∼4 orders of magnitude. Isothermal titration calorimetric studies with the wild-type, K166M, and H297N MR variants indicated that, of the two Brønsted acid-base catalysts Lys 166 and His 297, the former made the greater contribution to inhibitor binding. The X-ray crystal structure of the MR·PBA complex revealed the presence of multiple H-bonds between the boronic acid hydroxyl groups and the side chains of active site residues, as well as formation of a His 297 N^ε2-B dative bond. The dramatic upfield change in chemical shift of 27.2 ppm in the solution-phase ¹¹B nuclear magnetic resonance spectrum accompanying binding of PBA by MR was consistent with an sp³-hybridized boron, which was also supported by density-functional theory calculations. These unprecedented findings suggest that, beyond substituting boron at carbon centers participating in hydrolysis reactions, substitution of boron at the acidic carbon center of a substrate furnishes a new approach for generating inhibitors of enzymes catalyzing the deprotonation of carbon acid substrates.

Luminescent Polymorphic Co-crystals: A Promising Way to the Diversity of Molecular Assembly, Fluorescence Polarization, and Optical Waveguide

The design of molecular optoelectronic materials based on fabricating polymorphs and/or co-crystals has received much recent attention in the fields of luminescence, sensors, nonlinear optics, and so on. If the advantages of the two crystal engineering strategies above were combined, the diversity of self-assembly fashions and the tuning of photofunctional performances would be largely extended. However, such multicomponent examples have still been very limited to date. Herein, we report the construction of luminescent polymorphic co-crystals by assembly of tris(pentafluorophenyl)borane (TPFB) with 9,10-dicyanoanthracene (DCA) and acridine (AC) as paradigms. Different stacking modes and arrangement styles based on identical building block units in polymorphic co-crystals result in adjustable crystalline morphologies and variant photophysical properties (such as fluorescence wavelength, lifetimes, and up-conversion luminescence). The optimized photoluminescence quantum yield (63.1%) and lifetime (57.1 ns) are much higher than those of the pristine assembled units. In addition, two polymorphic co-crystals (DCA@TPFB-1 and AC@TPFB-2) present prominent fluorescence polarization and optical waveguide behaviors due to the highly regulated molecular orientation. Their high one-dimensional luminescence anisotropy (0.652) and low optical waveguide loss (0.0079 dB/μm) outperform most state-of-the-art low-dimensional molecular systems and thus endow them with great opportunities for photonic materials and devices. Therefore, this work not only confirms that constructing polymorphic co-crystals can be an effective way to design new photofunctional materials for luminescence and photonic applications but also discloses a deep understanding on the relationship between variant self-assembled fashions and tunable photofunctional properties of new TPFB-based molecular materials.

Near-Infrared Dual-Emission Ratiometric Fluorescence Imaging Nanoprobe for Real-Time Tracing the Generation of Endogenous Peroxynitrite in Single Living Cells and In Vivo

Peroxynitrite (ONOO^-) is a highly reactive nitrogen species with potent oxidant and nitrating properties. Its excessive generation can cause DNA and protein damage, thereby contributing to cell injury, and it is closely related to the development of many diseases. Thus, there is an urgent need for a reliable method to determine changes in the steady-state levels of ONOO^- in vivo. Ratiometric imaging, due to its built-in self-calibration system, can reduce artifacts and enable reliable in vivo imaging. In this study, we designed and prepared near-infrared (NIR) biomass quantum dots (NI-BQDs) and covalently coupled them with the NIR dye Cyanine7 (Cy7) to construct an NIR dual-emission nanoprobe (NI-BQD-Cy7) for real-time tracing the generation of endogenous ONOO^- in single living cells and in vivo by ratiometric fluorescence imaging. NI-BQD-Cy7 exhibited high detection sensitivity and selectivity for ONOO^- in the mitochondria. Additionally, it can produce dual NIR fluorescence emission, thus allowing in situ ratiometric fluorescence imaging to real-time trace the generation and concentration changes of ONOO^- in vivo. The application of the proposed NIR dual-emission nanoprobe can provide accurate information for the study of the biological function of ONOO^- in single living cells and in vivo, and it is very useful to explain the mechanism of cell damage caused by ONOO^-.

Sensing mechanism of a fluorescent probe for thiophenols: Invalidity of excited-state intramolecular proton transfer mechanism

Simple and effective detection of thiophenols has attracted great attention. A fluorescent probe 1 with high selectivity and sensitivity is designed and synthesized based on the excited-state intramolecular proton transfer (ESIPT) in experiment. However, we conclude that the ESIPT process fails to happen actually based on the calculation results. In the present work, the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods are employed to investigate the real sensing mechanism. The calculated absorption and emission spectra agree well with the experimental results. By comparing the energy of enol and keto configurations and the constructed potential energy surfaces (PESs) in the ground (S₀) and excited (S₁) states of 3-(benzo[d]thiazol-2-yl)-10-butyl-10H-phenothiazin-2-ol (dye 2), the ESIPT process is confirmed impossible because of the relatively high keto form energy and potential energy barrier. Besides, the transition state of dye 2 is optimized to offer the accurate potential energy barrier. The results of calculated frontier molecular orbitals (FMOs) and spectra indicate that it is the photoinduced electron transfer (PET) process that results in the fluorescence quenching of probe 1. After adding thiophenols, the thiolysis of 2,4-dinitrophenyl ether bond is triggered and dye 2, which emits strong fluorescence because of the absence of PET process, is obtained. Consequently, our study has demonstrated that probe 1 can act as a fluorescent probe to detect thiophenols through the off-on fluorescence variation based on the PET mechanism but not the ESIPT process.

Sensing mechanism of a ratiometric near-infrared fluorescent chemosensor for cysteine hydropersulfide: Intramolecular charge transfer

Previous studies have shown that the cysteine hydropersulfide (Cys-SSH) as the sulfur donor is crucial to sulfur-containing cofactors synthesis. Recently, a selective and sensitive near-infrared ratiometric fluorescent chemosensor Cy-DiSe has been designed and synthesized to detect Cys-SSH spontaneously. Herein, by means of the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) approaches, the sensing mechanism has been thoroughly explored. According to our calculations, the experimental data have been reproduced. The results indicate the intramolecular charge transfer (ICT) is the reason for changes in fluorescence wavelengths. Compared with the chemosensor Cy-DiSe, the larger energy gap of Cy induced by ICT mechanism leads to the blue-shift of the absorption and emission spectra, which guarantees that Cy-DiSe can become a ratiometric fluorescent chemosensor to detect Cys-SSH.

Detection and quantification of nitric oxide-derived oxidants in biological systems

The free radical nitric oxide (NO^•) exerts biological effects through the direct and reversible interaction with specific targets (e.g. soluble guanylate cyclase) or through the generation of secondary species, many of which can oxidize, nitrosate or nitrate biomolecules. The NO^•-derived reactive species are typically short-lived, and their preferential fates depend on kinetic and compartmentalization aspects. Their detection and quantification are technically challenging. In general, the strategies employed are based either on the detection of relatively stable end products or on the use of synthetic probes, and they are not always selective for a particular species. In this study, we describe the biologically relevant characteristics of the reactive species formed downstream from NO^•, and we discuss the approaches currently available for the analysis of NO^•, nitrogen dioxide (NO₂ ^•), dinitrogen trioxide (N₂O₃), nitroxyl (HNO), and peroxynitrite (ONOO^-/ONOOH), as well as peroxynitrite-derived hydroxyl (HO^•) and carbonate anion (CO₃ ^•-) radicals. We also discuss the biological origins of and analytical tools for detecting nitrite (NO₂ ^-), nitrate (NO₃ ^-), nitrosyl-metal complexes, S-nitrosothiols, and 3-nitrotyrosine. Moreover, we highlight state-of-the-art methods, alert readers to caveats of widely used techniques, and encourage retirement of approaches that have been supplanted by more reliable and selective tools for detecting and measuring NO^•-derived oxidants. We emphasize that the use of appropriate analytical methods needs to be strongly grounded in a chemical and biochemical understanding of the species and mechanistic pathways involved.

Boronic acids as building blocks for the construction of therapeutically useful bioconjugates

This review summarizes boronic acid's contribution to the development of bioconjugates with a particular focus on the molecular mechanisms underlying its role in the construction and function of the bioconjugate, namely as a bioconjugation warhead, as a payload and as part of a bioconjugate linker.

Fluorescence and chemiluminescence approaches for peroxynitrite detection

In the last two decades, there has been a significant advance in understanding the biochemistry of peroxynitrite, an endogenously-produced oxidant and nucleophile. Its relevance as a mediator in several pathologic states and the aging process together with its transient character and low steady-state concentration, motivated the development of a variety of techniques for its unambiguous detection and estimation. Among these, fluorescence and chemiluminescence approaches have represented important tools with enhanced sensitivity but usual limited specificity. In this review, we analyze selected examples of molecular probes that permit the detection of peroxynitrite by fluorescence and chemiluminescence, disclosing their mechanism of reaction with either peroxynitrite or peroxynitrite-derived radicals. Indeed, probes have been divided into 1) redox probes that yield products by a free radical mechanism, and 2) electrophilic probes that evolve to products secondary to the nucleophilic attack by peroxynitrite. Overall, boronate-based compounds are emerging as preferred probes for the sensitive and specific detection and quantitation. Moreover, novel strategies involving genetically-modified fluorescent proteins with the incorporation of unnatural amino acids have been recently described as peroxynitrite sensors. This review analyzes the most commonly used fluorescence and chemiluminescence approaches for peroxynitrite detection and provides some guidelines for appropriate experimental design and data interpretation, including how to estimate peroxynitrite formation rates in cells.

Reduction-Responsive DNA Duplex Containing O 6-Nitrobenzyl-Guanine

Stimuli-controlled structural transitions of nucleic acids have received growing attentions owing to their potential applications in the fields of chemical and synthetic biology. Here, we describe the development of reduction-responsive deoxyribonucleic acid (DNA) duplexes, in which guanine rings bearing a reduction-responsive cleavable nitrobenzyl (NB) group at the O ⁶ position (G^NB) are introduced at defined positions. We demonstrate that the artificial NB group can be removed in response to reduction stimulus without the dissociation of the intermolecular duplex structure, which comprises a G-quadruplex forming nucleic acid strand with one G^NB and its complementary sequence with one mismatch pair. Meanwhile, another duplex that comprised a G-quadruplex forming nucleic acid strand with two G^NB and its complementary sequence with three mismatch pairs exhibited reduction-responsive structural transitions from intermolecular duplex to intramolecular quadruplex. These findings might be useful for the development of DNA architectures endowed with reduction-responsive functions.

Resurrecting the Bacterial Tyrosyl-tRNA Synthetase/tRNA Pair for Expanding the Genetic Code of Both E. coli and Eukaryotes

The bacteria-derived tyrosyl-tRNA synthetase (TyrRS)/tRNA pair was first used for unnatural amino acid (Uaa) mutagenesis in eukaryotic cells over 15 years ago. It provides an ideal platform to genetically encode numerous useful Uaas in eukaryotes. However, this pair has been engineered to charge only a small collection of Uaas to date. Development of Uaa-selective variants of this pair has been limited by technical challenges associated with a yeast-based directed evolution platform, which is currently required to alter its substrate specificity. Here we overcome this limitation by enabling its directed evolution in an engineered strain of E. coli (ATMY), where the endogenous TyrRS/tRNA pair has been functionally replaced with an archaeal counterpart. The facile E. coli-based selection system enabled rapid engineering of this pair to develop variants that selectively incorporate various Uaas, including p-boronophenylalanine, into proteins expressed in mammalian cells as well as in the ATMY strain of E. coli.

Playing with the Molecules of Life

Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.

Peroxynitrite-biosignal-responsive polymer micelles as intracellular hypersensitive nanoprobes

Copolymerization of a trifluoromethyl ketone-bearing monomer and a rhodamine monomer has led to the formation of peroxynitrite (ONOO⁻) signaling molecule-responsive polymer fluorescent micelles.

Fluorescent Protein-Based Turn-On Probe through a General Protection-Deprotection Design Strategy

We demonstrated a general protection-deprotection strategy for the design of fluorescent protein biosensors through the construction of a turn-on Hg²⁺ sensor. A combination of fluorescent protein engineering and unnatural amino acid mutagenesis was used. Unlike previously reported fluorescent protein-based Hg²⁺ sensors that relied on the binding of Hg²⁺ to the sulfhydryl group of cysteine residues, a well-established chemical reaction, oxymercuration, was transformed into biological format and incorporated into our sensor design. This novel Hg²⁺ sensor displayed good sensitivity and selectivity both in vitro and in live bacterial cells. Over 60-fold change in fluorescence signal output was observed in the presence of 10 μM Hg²⁺, while such a change was undetectable when nine other metal ions were tested. This new design strategy could expand the repertoire of fluorescent protein-based biosensors for the detection of small-molecule analytes.

Recent advances in boronic acid-based optical chemosensors

This minireview highlights the developments in optical chemosensors from 2014 to 2016 that utilise the boronic acid interaction with polyols or Lewis bases.

Sensitive detection and estimation of cell-derived peroxynitrite fluxes using fluorescein-boronate

The specific and sensitive detection of peroxynitrite (ONOO^-/ONOOH) in biological systems is a great challenge due to its high reactivity towards several biomolecules. Herein, we validated the advantages of using fluorescein-boronate (Fl-B) as a highly sensitive fluorescent probe for the direct detection of peroxynitrite under biologically-relevant conditions in two different cell models. The synthesis of Fl-B was achieved by a very simply two-step conversion synthetic route with high purity (>99%) and overall yield (∼42%). Reactivity analysis of Fl-B with relevant biological oxidants including hydrogen peroxide (H₂O₂), hypochlorous acid (HOCl) and peroxynitrite were performed. The rate constant for the reaction of peroxynitrite with Fl-B was 1.7×10⁶M^-1s^-1, a million times faster than the rate constant measured for H₂O₂ (k=1.7M^-1s^-1) and 2,700 faster than HOCl (6.2×10²M^-1s^-1) at 37°C and pH 7.4. The reaction of Fl-B with peroxynitrite was significant even in the presence of physiological concentrations of CO₂, a well-known peroxynitrite reactant. Experimental and simulated kinetic analyses confirm that the main oxidation process of Fl-B takes place with peroxynitrite itself via a direct bimolecular reaction and not with peroxynitrite-derived radicals. Fl-B was successfully applied for the detection of endogenously-generated peroxynitrite by endothelial cells and in macrophage-phagocyted parasites. Moreover, the generated data allowed estimating the actual intracellular flux of peroxynitrite. For instance, ionomycin-stimulated endothelial cells generated peroxynitrite at a rate of ∼ 0.1μMs^-1, while immunostimulated macrophages do so in the order of ∼1μMs^-1 inside T. cruzi-infected phagosomes. Fl-B revealed not to be toxic in concentrations up to 1mM for 24h. Cellular peroxynitrite detection was achieved by conventional laboratory fluorescence-based methods including flow cytometry and epi-fluorescence microscopy. Fl-B was shown to be more sensitive than the coumarin boronate due to a higher molar absorption coefficient and quantum yield. Overall, our results show that Fl-B is a kinetically selective and highly sensitive probe for the direct detection of cell-derived peroxynitrite.

Peroxynitrite (ONOO-) Redox Signaling Molecule-Responsive Polymersomes

Designing specific-responsive polymer nanocapsules toward a definite cell signaling molecule for targeted therapy faces a great challenge. Here we demonstrate that new block copolymer appended trifluoromethyl ketone side groups can chemoselectively respond to an endogenous redox biosignal, peroxynitrite (ONOO^-), but shield the interference of other biogenic reactive oxygen, nitrogen, and sulfur species (ROS/RNS/RSS). The ONOO^- signaling molecule is capable of triggering cascade oxidation-elimination reactions to cleave the side functionalities from the polymer chain, which induces a large alteration of the polymer amphiphilicity and further leads to controllable disassembly of their self-assembled vesicular structure. Modulating the ONOO^- stimulus concentrations could readily control the vesicle dissociation rates for desirable drug delivery. We envisage that this polymer model would provide a new scenario to construct bioresponsive macromolecular systems for future biomedical nanotechnologies.

“Click-fluors”: triazole-linked saccharide sensors

A series of boronic acid-containing saccharide receptors was synthesised via copper catalysed azide–alkyne cycloaddition (CuAAC) reactions.