Tuning the pK(a) of fluorescein to optimize binding assays

Evaluation of the Cytosolic Uptake of HaloTag Using a pH-Sensitive Dye

The efficient cytosolic delivery of proteins is critical for advancing novel therapeutic strategies. Current delivery methods are severely limited by endosomal entrapment, and detection methods lack sophistication in tracking the fate of delivered protein cargo. HaloTag, a commonly used protein in chemical biology and a challenging delivery target, is an exceptional model system for understanding and exploiting cellular delivery. Here, we employed a combinatorial strategy to direct HaloTag to the cytosol. We established the use of Virginia Orange, a pH-sensitive fluorophore, and Janelia Fluor 585, a similar but pH-agnostic fluorophore, in a fluorogenic assay to ascertain protein localization within human cells. Using this assay, we investigated HaloTag delivery upon modification with cell-penetrating peptides, carboxyl group esterification, and cotreatment with an endosomolytic agent. We found efficacious cytosolic entry with two distinct delivery methods. This study expands the toolkit for detecting the cytosolic access of proteins and highlights that multiple intracellular delivery strategies can be used synergistically to effect cytosolic access. Moreover, HaloTag is poised to serve as a platform for the delivery of varied cargo into human cells.

A Potentially Versatile Enzyme Sensor Platform: Enzyme-Loaded, Tagged, Porous Polymeric Nanocapsules

Enzymes are essential to life and indispensable in a wide range of industries (food, pharmaceutical, medical, biosensing, etc.); however, a significant shortcoming of these fragile biological catalysts is their poor stability. To address this challenge, a variety of immobilization methods have been described to enhance the enzyme's stability. These immobilization methods generally are specific to an individual enzyme or optimal for a particular application. The aim of this study is to explore the utility of porous, indicator moiety-tagged, polymeric nanocapsules (NCs) for the encapsulation of enzymes and measurement of the enzyme's substrate. As a model enzyme, glucose oxidase (GOx) is used. The GOx enzyme-loaded, fluorophore-tagged NCs were synthesized by using self-assembled surfactant vesicle templates. To show that the biological activity of GOx is preserved during entrapment, the rate of the GOx enzyme catalyzed reaction was measured. To evaluate the protective features of the porous NCs, the encapsulated GOx enzyme activity was followed in the presence of hydrolytic enzymes. During the encapsulation of GOx and the purification of the GOx-loaded NCs, the GOx activity decayed less than 10%, and up to 30% of the encapsulated GOx activity could be retained for 3-5 days in the presence of hydrolytic enzymes. In support of the potentially unique advantages of the enzyme-loaded NCs, as a proof-of-concept example, the fluorophore-tagged, GOx-loaded NCs were used for the determination of glucose in the concentration range between 18 and 162 mg/dL and for imaging the distribution of glucose concentration in imaging experiments.

Ratiometric, pH-Sensitive Probe for Monitoring siRNA Delivery

Many RNA delivery strategies require efficient endosomal uptake and release. To monitor this process, we developed a 2'-OMe RNA-based ratiometric pH probe with a pH-invariant 3'-Cy5 and 5'-FAM whose pH sensitivity is enhanced by proximal guanines. The probe, in duplex with a DNA complement, exhibits a 48.9-fold FAM fluorescence enhancement going from pH 4.5 to pH 8.0 and reports on both endosomal entrapment and release when delivered to HeLa cells. In complex with an antisense RNA complement, the probe constitutes an siRNA mimic capable of protein knockdown in HEK293T cells. This illustrates a general approach for measuring the localization and pH microenvironment of any oligonucleotide.

Polyester Fabric with Fluorescent Properties Using Microwave Technology for Anti-Counterfeiting Applications

The article presented concerns the application of fluorescein as a fluorescent material for anti-counterfeiting technology which will allow the labeling and identification of legitimate articles in the textile field. Fluorescein has been applied to polyester fabrics by microwave irradiation technique in the presence of a UV absorber. Thus, its presence in the textile substrate is detectable following an excitation at a specific wavelength belonging to the Ultra-violet zone, which makes this material very effective for tracking and detecting counterfeit articles. Fluorescent samples are characterized morphologically by scanning electron microscopy (SEM) and quantitatively by optical spectroscopy such as reflectance and transmission measurements. The treated samples show under UV light a yellowish green emission with a slight yellow coloration of the polyester fiber. The UV absorber applied to the fluorescent solution improves the light resistance of the treated samples by 25%. Their addition to the bath can also ensure the production of a protective fabric against UV.

Antibody mix-and-read assays based on fluorescence intensity probes

Antibodies and Fc fusion proteins are a rapidly growing class of pharmaceuticals. Cell culture and purification process development and operation require frequent measurement of product concentrations, commonly by complex enzyme-linked immunosorbent assay and high-performance liquid chromatography methods. Here we report a fast (<30 s), and simple antibody Fc assay based on mix-and-read reporting by fluorescence emission. A soluble fluorescein-labeled Fc-affinity reporter produced by standard peptide synthesis is mixed with an Fc-containing sample to produce an immediate shift in both fluorescence polarization and intensity, compatible with on- and at-line measurements and microbioreactor monitoring. We observed significant shifts in fluorescence intensity in Chinese hamster ovary cell culture fluid spiked with IgG and detected an adalimumab biosimilar down to 100 ng/mL (10^-4 g/L), despite the interferents in the complex sample matrix. Neither the fluorescence polarization nor the fluorescence intensity assay is significantly affected by the addition of clarified lysate of 2 million CHO-k1 cells/mL, suggesting applicability even to cultures of low viability. Biochemical and molecular docking approaches suggest that the fluorescence intensity enhancement is caused by changes in the fluorophore's local microenvironment upon binding to IgG Fc, especially by interactions with Fc His433.Abbreviations: CCF: Cell Culture Fluid; CHO: Chinese Hamster Ovary cells; ELISA: Enzyme Linked Immunosorbent Assay; Fc: Fragment Crystallizable of antibody; HPLC: High-Performance Liquid Chromatography; HPβCD: hydroxypropyl-β-cyclodextrin; IgG: ImmunoglobulinG; mAb: Monoclonal Antibody; PBS: Phosphate-Buffered Saline; PDB: Protein Data Bank; SpA: Staphylococcal protein A; SpG: Staphylococcal protein G.

Ultrahigh-Throughput Detection of Enzymatic Alcohol Dehydrogenase Activity in Microfluidic Droplets with a Direct Fluorogenic Assay

The exploration of large DNA libraries of metagenomic or synthetic origin is greatly facilitated by ultrahigh‐throughput assays that use monodisperse water‐in‐oil emulsion droplets as sequestered reaction compartments. Millions of samples can be generated and analysed in microfluidic devices at kHz speeds, requiring only micrograms of reagents. The scope of this powerful platform for the discovery of new sequence space is, however, hampered by the limited availability of assay substrates, restricting the functions and reaction types that can be investigated. Here, we broaden the scope of detectable biochemical transformations in droplet microfluidics by introducing the first fluorogenic assay for alcohol dehydrogenases (ADHs) in this format. We have synthesized substrates that release a pyranine fluorophore (8‐hydroxy‐1,3,6‐pyrenetrisulfonic acid, HPTS) when enzymatic turnover occurs. Pyranine is well retained in droplets for >6 weeks (i. e. 14‐times longer than fluorescein), avoiding product leakage and ensuring excellent assay sensitivity. Product concentrations as low as 100 nM were successfully detected, corresponding to less than one turnover per enzyme molecule on average. The potential of our substrate design was demonstrated by efficient recovery of a bona fide ADH with an >800‐fold enrichment. The repertoire of droplet screening is enlarged by this sensitive and direct fluorogenic assay to identify dehydrogenases for biocatalytic applications.

Fluorophore spectroscopy in aqueous glycerol solution: the interactions of glycerol with the fluorophore

A common perception exists that glycerol provides an inert-like environment modifying viscosity and index of refraction by its various concentrations in aqueous solution. Said perception is herein challenged by investigating the effects of the glycerol environment on the spectroscopic properties of fluorescein, as a representative fluorophore, using steady-state and time-resolved techniques and computational chemistry. Results strongly suggest that the fluorescence quantum yield, measured fluorescence lifetime (FLT), natural lifetime and calculated fluorescence lifetime are all highly sensitive to the presence of glycerol. Glycerol was found to impact both the ground and first excited states of fluorescein, quenching and modifying both absorption and emission spectra, affecting the fundamental electrical dipoles of the ground and first excited singlet states, and lowering FLT and quantum yield. Furthermore, the Stern-Volmer, Lippert-Mataga, Perrin and Strickler-Berg relations indicate that glycerol acts upon fluorescein in aqueous solution as a quencher and alters the fluorescein geometry. Predictions made by computational chemistry impressively correspond to experimental results, both indicating changes in the properties of fluorescein at around 35% v/v aqueous glycerol, a clear indication that glycerol is not an innocent medium. This study proposes the Strickler-Berg relation as a means of detecting non-negligible effects of a hosting medium on its host fluorophore. These new insights on the molecular structures, the interactions between glycerol and its host fluorophore, and the effects of one on the other may be essential for understanding fundamental phenomena in chemistry and related fields.

Subcellular Targeted Nanohoop for One- and Two-Photon Live Cell Imaging

Fluorophores are powerful tools for interrogating biological systems. Carbon nanotubes (CNTs) have long been attractive materials for biological imaging due to their near-infrared excitation and bright, tunable optical properties. The difficulty in synthesizing and functionalizing these materials with precision, however, has hampered progress in this area. Carbon nanohoops, which are macrocyclic CNT substructures, are carbon nanostructures that possess ideal photophysical characteristics of nanomaterials, while maintaining the precise synthesis of small molecules. However, much work remains to advance the nanohoop class of fluorophores as biological imaging agents. Herein, we report an intracellular targeted nanohoop. This fluorescent nanostructure is noncytotoxic at concentrations up to 50 μM, and cellular uptake investigations indicate internalization through endocytic pathways. Additionally, we employ this nanohoop for two-photon fluorescence imaging, demonstrating a high two-photon absorption cross-section (65 GM) and photostability comparable to a commercial probe. This work further motivates continued investigations into carbon nanohoop photophysics and their biological imaging applications.

Monitoring phagocytic uptake of amyloid β into glial cell lysosomes in real time

Phagocytosis by glial cells is essential to regulate brain function during health and disease. Therapies for Alzheimer's disease (AD) have primarily focused on targeting antibodies to amyloid β (Aβ) or inhibitng enzymes that make it, and while removal of Aβ by phagocytosis is protective early in AD it remains poorly understood. Impaired phagocytic function of glial cells during later stages of AD likely contributes to worsened disease outcome, but the underlying mechanisms of how this occurs remain unknown. We have developed a human Aβ1-42 analogue (AβpH) that exhibits green fluorescence upon internalization into the acidic organelles of cells but is non-fluorescent at physiological pH. This allowed us to image, for the first time, glial uptake of AβpH in real time in live animals. We find that microglia phagocytose more AβpH than astrocytes in culture, in brain slices and in vivo. AβpH can be used to investigate the phagocytic mechanisms responsible for removing Aβ from the extracellular space, and thus could become a useful tool to study Aβ clearance at different stages of AD.

Characterization of a fast response fiber-optic pH sensor and illustration in a biological application

Optical, and especially fiber-optic techniques for the sensing of pH have become very attractive and considerable research progress in this field has been made over recent years. The determination of the value of pH across a broad range of applications today, important for areas of study such as life sciences, environmental monitoring, manufacturing industry and widely in biological research is now accessible from such optical sensors. The need for such technology arises because familiar, commercial sensors are often limited in terms of their response time and the presence of drift, all of which emphasize the value of newer and rapidly developing technologies such as fiber-optic sensors, to address these wider applications. As a result, a new compact sensor design has been developed, designed around a specially-formed fiber-optic tip, coated with a pH-sensitive dye, and importantly covalently linked to a hydrogel matrix to provide high stability. The sensor developed was designed to have a very fast response time (to 90% of saturation, Δt₉₀) of <5 s and a sensing uncertainty of ∼±0.04 pH units. Given the covalently bonded nature of the dye, the problem of leaching of the indicator dye is reduced, creating a probe which has been shown to be very stable over many days of use. Illustrating this through extended continuous use, over ∼12 h at pH 7, this stability was confirmed showing a drift of <0.05 pH h^-1. In order to give an illustration of the value of the probe in an important biological application, the monitoring of pH levels between pH 7 to pH 8 in an AMES' medium, a substance which is important to maintain the metabolism of retinal cells is shown and the results as well as temperature stability of the probe discussed.

Live and Let Dye

The measurement of ion concentrations and fluxes inside living cells is key to understanding cellular physiology. Fluorescent indicators that can infiltrate and provide intel on the cellular environment are critical tools for biological research. Developing these molecular informants began with the seminal work of Racker and colleagues ( Biochemistry (1979) 18, 2210), who demonstrated the passive loading of fluorescein in living cells to measure changes in intracellular pH. This work continues, employing a mix of old and new tradecraft to create innovative agents for monitoring ions inside living systems.

Development and application of a high throughput assay system for the detection of Rieske dioxygenase activity

Herein we report the development of a new periodate-based reactive assay system for the fluorescent detection of the cis-diol metabolites produced by Rieske dioxygenases. This sensitive and diastereoselective assay system successfully evaluates the substrate scope of Rieske dioxygenases and determines the relative activity of a rationally designed Rieske dioxygenase variant library. The high throughput capacity of the assay system enables rapid and efficient substrate scope investigations and screening of large dioxygenase variant libraries.

Mechanistic Study of the Peroxyoxalate System in Completely Aqueous Carbonate Buffer

The peroxyoxalate reaction is one of the most efficient chemiluminescence transformations, with emission quantum yields of up to 50%; additionally, it is widely utilized in analytical and bioanalytical assays. Although the real reason for its extremely high efficiency is still not yet understood, the mechanism of this transformation has been well elucidated in anhydrous medium. Contrarily, only few mechanistic studies have been performed in aqueous media, which would be of great importance for its application in biological systems. We report here our experimental results of the peroxyoxalate reaction in completely aqueous carbonate buffer, using fluorescein as chemiluminescence activator. The kinetics are very fast in the used basic conditions (pH > 9); despite this, reproducible kinetic results were obtained. The reaction proceeds by specific base catalysis, with rate-limiting attack of hydrogen peroxide anion to the oxalic ester, in competition with ester hydrolysis by hydroxide ion. Emission quantum yields increase with the hydrogen peroxide concentration up to an optimal concentration of 10 mmol L^-1 . The infinite singlet quantum yield of (5.8 ± 0.2) × 10^-7 is much lower than in anhydrous medium; however, it is similar to quantum yields measured before in partially aqueous media.

Oxygen- and pH-Dependent Photophysics of Fluorinated Fluorescein Derivatives: Non-Symmetrical vs. Symmetrical Fluorination

Fluorescein, and derivatives of fluorescein, are often used as fluorescent probes and sensors. In systems where pH is a variable, protonation/deprotonation of the molecule can influence the pertinent photophysics. Fluorination of the xanthene moiety can alter the molecule’s pK_a such as to render a probe whose photophysics remains invariant over a wide pH range. Di-fluorination is often sufficient to accomplish this goal, as has been demonstrated with compounds such as Oregon Green in which the xanthene moiety is symmetrically difluorinated. In this work, we synthesized a non-symmetrical difluorinated analog of Oregon Green which we call Athens Green. We ascertained that the photophysics and photochemistry of Athens Green, including the oxygen-dependent photophysics that results in the sensitized production of singlet oxygen, O₂(a¹Δ_g), can differ appreciably from the photophysics of Oregon Green. Our data indicate that Athens Green will be a more benign fluorescent probe in systems that involve the production and removal of O₂(a¹Δ_g). These results expand the available options in the toolbox of fluorescein-based fluorophores.

Rhodium (II)-Catalyzed Synthesis of Tetracyclic 3,4-Fused Indoles and Dihydroindoles

An efficient synthetic method of tetracyclic 3,4-fused indoles and dihydroindoles via rhodium-catalyzed (3+2) cycloaddition of N-tosyl-4-(2-phenoxyphenyl)-1,2,3-triazole was described. The aromatized xanthene derivatives can be achieved in a one-pot synthesis starting from 1-ethynyl-2-phenoxybenzene. The xanthene-based fused heterocycles were considered as the valuable fluorophore.

Aminofluoresceins Versus Fluorescein: Ascertained New Unusual Features of Tautomerism and Dissociation of Hydroxyxanthene Dyes in Solution

Within the course of this spectroscopic research, we revealed novel features of the protolytic behavior, which extend the knowledge of the chemistry of xanthene dyes and rationalize the utilization of these compounds. In addition to the well-known tautomerism of the molecular form, H₂R, of fluorescein dyes, new aspects of tautomeric transformation of anions are disclosed. First, for the dyes bearing the substituents in the phthalic acid residue, 4'- and 5'-aminofluoresceins and 4'-fluorescein isothiocyanate, the monoanion HR^- exists in non-hydrogen-bond donor solvents not only as a tautomer with the ionized carboxylic and nonionized OH group but also as a "phenolate" ion with a nonionized COOH group. Such state of HR^- ions is typical for dyes bearing halogen atoms or NO₂ groups in the xanthene moiety but was not observed until now in the case of substitution in the phthalic residue. Second, the possibility of the existence of the HR^- species in DMSO in the form of colorless lactone is deduced for the 5'-aminofluorescein using the visible and infrared spectra. This results in a dramatic difference in medium effects. For instance, whereas for fluorescein in DMSO, the inversion of the stepwise ionization constants takes place and the K_a1/K_a2 value equals 0.08, the same ratio for 5'-aminofluorescein is as high as ∼800. In addition, the pK_a values of sulfonefluorescein, erythrosin, methyl ether of fluorescein, and phenol red were obtained to verify the acidity scale in DMSO and to support the detailed scheme of protolytic equilibria of fluorescein dyes.

Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging

Rhodamine dyes exist in equilibrium between a fluorescent zwitterion and a nonfluorescent lactone. Tuning this equilibrium toward the nonfluorescent lactone form can improve cell-permeability and allow creation of "fluorogenic" compounds-ligands that shift to the fluorescent zwitterion upon binding a biomolecular target. An archetype fluorogenic dye is the far-red tetramethyl-Si-rhodamine (SiR), which has been used to create exceptionally useful labels for advanced microscopy. Here, we develop a quantitative framework for the development of new fluorogenic dyes, determining that the lactone-zwitterion equilibrium constant (K _L-Z) is sufficient to predict fluorogenicity. This rubric emerged from our analysis of known fluorophores and yielded new fluorescent and fluorogenic labels with improved performance in cellular imaging experiments. We then designed a novel fluorophore-Janelia Fluor 526 (JF₅₂₆)-with SiR-like properties but shorter fluorescence excitation and emission wavelengths. JF₅₂₆ is a versatile scaffold for fluorogenic probes including ligands for self-labeling tags, stains for endogenous structures, and spontaneously blinking labels for super-resolution immunofluorescence. JF₅₂₆ constitutes a new label for advanced microscopy experiments, and our quantitative framework will enable the rational design of other fluorogenic probes for bioimaging.

Fluorescein-Stabilized i-Motif DNA and Its Unfolding Leading to a Stronger Adsorption Affinity

Several previous studies have indicated that polydeoxycytidine (poly-C) DNA has an anomalously high affinity for different types of surfaces. It was hypothesized that the formation of an i-motif structure could be a factor responsible for this enhanced affinity, but this is against the notion that a folded molecule should have fewer interactions with a surface. Herein, the properties of poly-C DNA were examined in detail, focusing on the presence or absence of a FAM (carboxyfluorescein) label and its subsequent adsorption on graphene oxide. Fluorescence and CD spectroscopy studies indicated that FAM can stabilize an i-motif structure in C15 DNA. In particular, the fluorescence of FAM is drastically quenched when the DNA is folded. This structure is irreversibly unfolded upon heating. Furthermore, the unfolded structure has an even higher affinity for graphene oxide than the folded structure. Finally, a large portion of the folded C15 unfolds upon desorption from graphene oxide, and unfolding could happen upon adsorption or desorption of the DNA. This study provides a method to further enhance the adsorption stability of poly-C DNA and calls for care when investigating the potential effects of dye labels on DNA.

Tuning the pKa of Carboxyfluorescein with Arginine-Rich Cell-Penetrating Peptides for Intracellular pH Imaging

5-Carboxylfluorescein (FAM) is a conventional pH-responsive fluorophore widely used in fluorescence labeling and imaging. Because of its nonfluorescent structure under acidic conditions, FAM has long been limited to pH determination in a neutral-basic environment. Here, we modified the optical properties of FAM with cationic arginine-rich cell-penetrating peptides (CPPs), tuning the pK_a value of FAM to adapt well to pH measurement under diverse pH conditions. With increasing length of polyarginine, the pK_a value of FAM was tuned from 6.20 ± 0.06 to 5.17 ± 0.05. The key mechanism for pK_a variations was attributed to intramolecular electrostatic attraction and the positive charge of cationic CPPs tend to stabilize the fluorescent dianionic form of FAM. Apart from tunable pK_a, arginine-rich CPPs also improved the water solubility, membrane permeability, and organelle-specific localization of FAM. Two conjugated probes FAM-R₁₂ and FAM-(F_xr)₃ were selected to monitor intracellular pH fluctuations. Compared to FAM-(F_xr)₃, highly positively charged FAM-R₁₂ was more effective in lower pH condition and realized targeted visualization of lysosomal pH changes. The arginine-rich CPP-based strategy offers a promising approach to obtain optimized fluorescent pH probes with adjustable pK_a values for organelle-specific pH measurement.

Identifying the factors for improving quality of oral fluorescein angiography

AIM

To evaluate the quality of oral fluorescein angiography (FA) in relation to food intake.

METHODS

This is an observational, case-crossover study. We collected information from patients undergoing routine oral FA for retinal disease at the Shiley Eye Institute. Eighty patients (160 eyes) were analysed. Fasting and non-fasting images of the same patient were recorded, compared and analysed for different image quality parameters and clinical relevance by experienced retina specialists.

RESULTS

When analysing the images, intergrader agreement was moderate to good with a Kappa averaging 0.60 (0.5-0.85). When patients were fasting pre-imaging, better angiography quality scores were achieved when compared with images taken when patients were non-fasting (mean 0.84 vs 0.72, p<0.001). Multivariate analysis showed that non-fasting patients with higher body mass index had the worst scores. Other clinical parameters, such as staining of drusen, staining of disciform scars or central and peripapillary atrophy, were also significantly better during the pre-fasting exam (p<0.001). Oral FA was approximately 22% faster (time to fluorescein dye appearance) under fasting conditions than non-fasting (mean±SD, minutes, 18.7±6.9 vs 25.14±8.1, p<0.001).

CONCLUSION

Fasting oral FA provided significantly better quality images as well as faster optimal imaging times when compared with non-fasting oral FA. By improving its overall quality, oral FA could be a useful adjunctive examination to optical coherence tomography (OCT) and OCT angiography in patients who require FA studies but who have difficult access or refuse an invasive procedure.

A fluorescent aminosugar to rapidly screen and study RNA binders

RNA targeted high-throughput assays that allow for rapid detection of high affinity binding ligands are important in RNA recognition studies. A number for fluorescent dyes have been reported that can assist in rapidly identifying nucleic acid (RNA) binding elements without the need for immobilization of RNA or the ligand. A number of these dyes are planar aromatic molecules that bind non-specifically to nucleic acids and often distort their parent nucleic acid structures leading to ambiguity in the interpretation of results. In this light, we report here, the use of an aminoglycoside (neomycin) based fluorescent probe (F-Neo) which can reversibly bind to different RNA motifs and help identify ligands with needed affinity and selectivity, without any immobilization of the probe or the target. In this chapter, we provide the details of the assay development, experimental considerations and data analysis to use the probe and identify novel ligands. We then provide a brief introduction to calorimetry (ITC) and circular dichroism (CD) spectroscopy based methods in validating the binding of such identified compounds.

A fluorescence anisotropy assay to discover and characterize ligands targeting the maytansine site of tubulin

Microtubule-targeting agents (MTAs) like taxol and vinblastine are among the most successful chemotherapeutic drugs against cancer. Here, we describe a fluorescence anisotropy-based assay that specifically probes for ligands targeting the recently discovered maytansine site of tubulin. Using this assay, we have determined the dissociation constants of known maytansine site ligands, including the pharmacologically active degradation product of the clinical antibody-drug conjugate trastuzumab emtansine. In addition, we discovered that the two natural products spongistatin-1 and disorazole Z with established cellular potency bind to the maytansine site on β-tubulin. The high-resolution crystal structures of spongistatin-1 and disorazole Z in complex with tubulin allowed the definition of an additional sub-site adjacent to the pocket shared by all maytansine-site ligands, which could be exploitable as a distinct, separate target site for small molecules. Our study provides a basis for the discovery and development of next-generation MTAs for the treatment of cancer.

What Has Been Seen Cannot Be Unseen-Detecting Auxin In Vivo

Auxins mediate various processes that are involved in plant growth and development in response to specific environmental conditions. Its proper spatio-temporal distribution that is driven by polar auxin transport machinery plays a crucial role in the wide range of auxins physiological effects. Numbers of approaches have been developed to either directly or indirectly monitor auxin distribution in vivo in order to elucidate the basis of its precise regulation. Herein, we provide an updated list of valuable techniques used for monitoring auxins in plants, with their utilities and limitations. Because the spatial and temporal resolutions of the presented approaches are different, their combination may provide a comprehensive outcome of auxin distribution in diverse developmental processes.

Semisynthetic fluorescent pH sensors for imaging exocytosis and endocytosis

The GFP-based superecliptic pHluorin (SEP) enables detection of exocytosis and endocytosis, but its performance has not been duplicated in red fluorescent protein scaffolds. Here we describe "semisynthetic" pH-sensitive protein conjugates with organic fluorophores, carbofluorescein, and Virginia Orange that match the properties of SEP. Conjugation to genetically encoded self-labeling tags or antibodies allows visualization of both exocytosis and endocytosis, constituting new bright sensors for these key steps of synaptic transmission.

Pickering Emulsions Stabilized by pH-Responsive Microgels and Their Scalable Transformation to Robust Submicrometer Colloidoisomes with Selective Permeability

Colloidosomes are micrometer-sized hollow particles that have shells consisting of coagulated or fused colloid particles. While many large colloidosomes with sizes well above 1.0 μm have been prepared, there are fewer examples of submicrometer colloidosomes. Here, we establish a simple emulsion templating-based method for the preparation of robust submicrometer pH-responsive microgel colloidosomes. The colloidosomes are constructed from microgel particles based on ethyl acrylate and methacrylic acid with peripheral vinyl groups. The pH-responsive microgels acted as both a Pickering emulsion stabilizer and macro-cross-linker. The emulsion formation studies showed that the minimum droplet diameter was reached when the microgel particles were partially swollen. Microgel colloidosomes were prepared by covalently interlinking the microgels adsorbed at the oil-water interface using thermal free-radical coupling. The colloidosomes were prepared using a standard high-shear mixer with two different rotor sizes that corresponded to high shear (HS) and very high shear (VHS) mixing conditions. The latter enabled the construction of submicrometer pH-responsive microgel-colloidosomes on the gram scale. The colloidosomes swelled strongly when the pH increased to above 6.0. The colloidosomes were robust and showed no evidence of colloidosome breakup at high pH. The effect of solute size on shell permeation was studied using a range of FITC-dextran polymers, and size-selective permeation occurred. The average pore size of the VHS microgel-colloidosomes was estimated to be between 6.6 and 9.0 nm at pH 6.2. The microgel-colloidosome properties suggest that they have the potential for future applications in cosmetics, photonics, and delivery.

Imaging the Neutrophil Phagosome and Cytoplasm Using a Ratiometric pH Indicator

Neutrophils are crucial to host innate defense and, consequently, constitute an important area of medical research. The phagosome, the intracellular compartment where the killing and digestion of engulfed particles take place, is the main arena for neutrophil pathogen killing that requires tight regulation. Phagosomal pH is one aspect that is carefully controlled, in turn regulating antimicrobial protease activity. Many fluorescent pH-sensitive dyes have been used to visualize the phagosomal environment. S-1 has several advantages over other pH-sensitive dyes, including its dual emission spectra, its resistance to photo-bleaching, and its high pKa. Using this method, we have demonstrated that the neutrophil phagosome is unusually alkaline in comparison to other phagocytes. By using different biochemical conjugations of the dye, the phagosome can be delineated from the cytoplasm so that changes in the size and shape of the phagosome can be assessed. This allows for further monitoring of ionic movement.

Molecular basis for the autonomous promotion of cell proliferation by angiogenin

Canonical growth factors act indirectly via receptor-mediated signal transduction pathways. Here, we report on an autonomous pathway in which a growth factor is internalized, has its localization regulated by phosphorylation, and ultimately uses intrinsic catalytic activity to effect epigenetic change. Angiogenin (ANG), a secreted vertebrate ribonuclease, is known to promote cell proliferation, leading to neovascularization as well as neuroprotection in mammals. Upon entering cells, ANG encounters the cytosolic ribonuclease inhibitor protein, which binds with femtomolar affinity. We find that protein kinase C and cyclin-dependent kinase phosphorylate ANG, enabling ANG to evade its inhibitor and enter the nucleus. After migrating to the nucleolus, ANG cleaves promoter-associated RNA, which prevents the recruitment of the nucleolar remodeling complex to the ribosomal DNA promoter. The ensuing derepression of rDNA transcription promotes cell proliferation. The biochemical basis for this unprecedented mechanism of signal transduction suggests new modalities for the treatment of cancers and neurological disorders.

A Thioacetal Photocage Designed for Dual Release: Application in the Quantitation of Therapeutic Release by Synchronous Reporter Decaging

Despite the immense potential of existing photocaging technology, its application is limited by the paucity of advanced caging tools. Here, we report on the design of a novel thioacetal ortho-nitrobenzaldehyde (TNB) dual arm photocage that enabled control of the simultaneous release of two payloads linked to a single TNB unit. By using this cage, which was prepared in a single step from commercial 6-nitroverataldehyde, three drug-fluorophore conjugates were synthesized: Taxol-TNB-fluorescein, Taxol-TNB-coumarin, and doxorubicin-TNB-coumarin, and long-wavelength UVA light-triggered release experiments demonstrated that dual payload release occurred with rapid decay kinetics for each conjugate. In cell-based assays performed in vitro, dual release could also be controlled by UV exposure, resulting in increased cellular fluorescence and cytotoxicity with potency equal to that of unmodified drug towards the KB carcinoma cell line. The extent of such dual release was quantifiable by reporter fluorescence measured in situ and was found to correlate with the extent of cytotoxicity. Thus, this novel dual arm cage strategy provides a valuable tool that enables both active control and real-time monitoring of drug activation at the delivery site.

Shaping Small Bioactive Molecules to Untangle Their Biological Function: A Focus on Fluorescent Plant Hormones

Modern biology overlaps with chemistry in explaining the structure and function of all cellular processes at the molecular level. Plant hormone research is perfectly located at the interface between these two disciplines, taking advantage of synthetic and computational chemistry as a tool to decipher the complex biological mechanisms regulating the action of plant hormones. These small signaling molecules regulate a wide range of developmental processes, adapting plant growth to ever changing environmental conditions. The synthesis of small bioactive molecules mimicking the activity of endogenous hormones allows us to unveil many molecular features of their functioning, giving rise to a new field, plant chemical biology. In this framework, fluorescence labeling of plant hormones is emerging as a successful strategy to track the fate of these challenging molecules inside living organisms. Thanks to the increasing availability of new fluorescent probes as well as advanced and innovative imaging technologies, we are now in a position to investigate many of the dynamic mechanisms through which plant hormones exert their action. Such a deep and detailed comprehension is mandatory for the development of new green technologies for practical applications. In this review, we summarize the results obtained so far concerning the fluorescent labeling of plant hormones, highlighting the basic steps leading to the design and synthesis of these compelling molecular tools and their applications.

Rapid biocompatible macrocyclization of peptides with decafluoro-diphenylsulfone

In this manuscript, we describe modification of Cys-residues in peptides and proteins in aqueous solvents via aromatic nucleophilic substitution (S_NAr) with perfluoroarenes (fAr).

In this manuscript, we describe modification of Cys-residues in peptides and proteins in aqueous solvents via aromatic nucleophilic substitution (S_NAr) with perfluoroarenes (fAr). Biocompatibility of this reaction makes it attractive for derivatization of proteins and peptide libraries comprised of 20 natural amino acids. Measurement of the reaction rates for fAr derivatives by ¹⁹F NMR with a model thiol donor (β-mercaptoethanol) in aqueous buffers identified decafluoro-diphenylsulfone (DFS) as the most reactive S_NAr electrophile. Reaction of DFS with thiol nucleophiles is >100 000 faster than analogous reaction of perfluorobenzene; this increase in reactivity enables application of DFS at low concentrations in aqueous solutions compatible with biomolecules and protein complexes irreversibly degraded by organic solvents (e.g., bacteriophages). DFS forms macrocycles when reacted with peptides of the general structure X_n–Cys–X_m–Cys–X_l, where X is any amino acid and m = 1–15. It formed cyclic peptides with 6 peptide hormones—oxytocin, urotensin II, salmon calcitonin, melanin-concentrating hormone, somatostatin-14, and atrial natriuretic factor (1–28) as well as peptides displayed on M13 phage. Rates up to 180 M^–1 s^–1 make this reaction one of the fastest Cys-modifications to-date. Long-term stability of macrocycles derived from DFS and their stability toward oxidation further supports DFS as a promising method for modification of peptide-based ligands, cyclization of genetically-encoded peptide libraries, and discovery of bioactive macrocyclic peptides.

Synthetic Fluorophores for Visualizing Biomolecules in Living Systems

The last decade has witnessed significant advance in the imaging of living systems using fluorescent markers. This progress has been primarily associated with the discovery of different spectral variants of fluorescent proteins. However, the fluorescent protein technology has its own limitations and, in some cases, the use of low-molecular-weight fluorophores is preferable. In this review, we describe the arsenal of synthetic fluorescent tools that are currently in researchers' hands and span virtually the entire spectrum, from the UV to visible and, further, to the near-infrared region. An overview of recent advances in site-directed introduction of synthetic fluorophores into target cellular objects is provided. Application of these fluorescent probes to the solution of a wide range of biological problems, in particular, to the determination of local ion concentrations and pH in living systems, is discussed.

A pH Sensitive High-Throughput Assay for miRNA Binding of a Peptide-Aminoglycoside (PA) Library

MicroRNAs (miRNA) are small RNAs that have a regulatory role in gene expression. Because of this regulatory role, miRNAs have become a new target for therapeutic compounds. Here, we outline an approach to target specific miRNAs using a high throughput capable assay and a 215 compound peptidic-aminosugar (PA) library. Aminosugars have been shown in a number of recent reports as important lead compounds that bind miRNA. In order to screen for compounds that bind miRNA, we have developed a high throughput displacement assay using a fluorescein-neomycin conjugated molecule (F-neo) as a probe for competitive miRNA binding compounds. We have applied the F-neo assay to four different miRNA constructs and the assay is applicable to most miRNAs, at various stages of processing. The results of the screen were validated by the determination of the IC₅₀ for a select group of compounds from the library. For example, we identified eight compounds that bind to hsa-miR 504 with higher affinity than the parent neomycin. From the F-neo displacement assay we found that the number of binding sites differs for each miRNA, and the binding sites appear to differ both physically and chemically, with different affinity of the compounds resulting from the size of the molecule as well as the chemical structure. Additionally, the affinity of the compounds was dependent on the identity and position of the amino acid position of conjugation and the affinity of the compounds relative to other compounds in the library was miRNA dependent with the introduction of a second amino acid.

On-demand in situ generation of oxygen in a nanofluidic embedded planar microband electrochemical reactor

In situ generation of reagents and their subsequent use downstream presents new opportunities to amplify the utility of nanofluidic devices by exploiting the confined geometry to address mass transport limitations on reaction kinetics and efficiency. Oxygen, an inherently valuable reactant, can be produced from electrolysis of water, a process that can be conveniently integrated within a nanofluidic system. Here, we construct and characterize a nanofluidic device consisting of a planar microband electrode embedded within a nanochannel for in situ electrochemical generation and optical monitoring of O₂. Fluorescein, a dye with a pH-sensitive emission intensity, was used to monitor the spatiotemporal characteristics of the oxidation of H₂O, using the co-produced H⁺. Application of anodic potentials at the nanochannel-embedded electrode results in a decrease in fluorescence intensity, which reflects the decreasing solution pH. A combination of fluorescence intensity and chronoamperometric response was used to quantitatively determine proton generation, and the H⁺/O₂ stoichiometry was then used to determine the concentration of the O₂ in the channel. Comparison of the experimental results to finite element simulations validates the use of fluorescein emission intensity to spectroscopically determine the local oxygen concentration in the nanochannel. By varying the applied potential, spatially averaged O₂ concentrations ranging from 0.13 to 0.41 mM were generated. The results demonstrate a convenient route to in situ modulation of the dissolved O₂ level in a nanofluidic device and the use of an optical probe to monitor its spatial and temporal distribution under flow conditions.

Probing the target-specific inhibition of sensitized protein tyrosine phosphatases with biarsenical probes

Selective control of enzyme activity is critical for elucidating the roles of specific proteins in signaling pathways. One potential means for developing truly target-specific inhibitors involves the use of protein engineering to sensitize a target enzyme to inhibition by a small molecule that does not inhibit homologous wild-type enzymes. Previously, it has been shown that protein tyrosine phosphatases (PTPs) can be sensitized to inhibition by a biarsenical probe, FlAsH-EDT2, which inhibits PTP activity by specifically binding to cysteine residues that have been introduced into catalytically important regions. In the present study, we developed an array of biarsenical probes, some newly synthesized and some previously reported, to investigate for the first time the structure-activity relationships for PTP inhibition by biarsenicals. Our data show that biarsenical probes which contain substitutions at the 2' and 7' positions are more effective than FlAsH-EDT2 at inhibiting sensitized PTPs. The increased potency of 2',7'-substituted probes was observed when PTPs were assayed with both para-nitrophenylphosphate and phosphopeptide PTP substrates and at multiple probe concentrations. The data further indicate that the enhanced inhibitory properties are the result of increased binding affinity between the 2',7'-substituted biarsenical probes and sensitized PTPs. In addition we provide previously unknown physicochemical and stability data for various biarsenical probes.

Analysis of chemical equilibrium of silicon-substituted fluorescein and its application to develop a scaffold for red fluorescent probes

Fluorescein is a representative green fluorophore that has been widely used as a scaffold of practically useful green fluorescent probes. Here, we report synthesis and characterization of a silicon-substituted fluorescein, i.e., 2-COOH TokyoMagenta (2-COOH TM), which is a fluorescein analogue in which the O atom at the 10' position of the xanthene moiety of fluorescein is replaced with a Si atom. This fluorescein analogue forms a spirolactone ring via intramolecular nucleophilic attack of the carboxylic group in a pH-dependent manner. Consequently, 2-COOH TM exhibits characteristic large pH-dependent absorption and fluorescence spectral changes: (1) 2-COOH TM is colorless at acidic pH, whereas fluorescein retains observable absorption and fluorescence even at acidic pH, and the absorption maximum is also shifted; (2) the absorption spectral change occurs above pH 7.0 for 2-COOH TM and below pH 7.0 for fluorescein; (3) 2-COOH TM shows a much sharper pH response than fluorescein because of its pKa inversion, i.e., pKa1 > pKa2. These features are also different from those of a compound without the carboxylic group, 2-Me TokyoMagenta (2-Me TM). Analysis of the chemical equilibrium between pH 3.0 and 11.0 disclosed that 2-COOH TM favors the colorless and nonfluorescent lactone form, compared with fluorescein. Substitution of Cl atoms at the 4' and 5' positions of the xanthene moiety of 2-COOH TM to obtain 2-COOH DCTM shifted the equilibrium so that the new derivative exists predominantly in the strongly fluorescent open form at physiological pH (pH 7.4). To demonstrate the practical utility of 2-COOH DCTM as a novel scaffold for red fluorescent probes, we employed it to develop a probe for β-galactosidase.

Fluorogenic Assay for Inhibitors of HIV-1 Protease with Sub-picomolar Affinity

A fluorogenic substrate for HIV-1 protease was designed and used as the basis for a hypersensitive assay. The substrate exhibits a k_cat of 7.4 s⁻¹, K_M of 15 μM, and an increase in fluorescence intensity of 104-fold upon cleavage, thus providing sensitivity that is unmatched in a continuous assay of HIV-1 protease. These properties enabled the enzyme concentration in an activity assay to be reduced to 25 pM, which is close to the K_d value of the protease dimer. By fitting inhibition data to Morrison’s equation, K_i values of amprenavir, darunavir, and tipranavir were determined to be 135, 10, and 82 pM, respectively. This assay, which is capable of measuring K_i values as low as 0.25 pM, is well-suited for characterizing the next generation of HIV-1 protease inhibitors.

Light-Triggered Disruption of PAG-Based Amphiphilic Random Copolymer Micelles

The amphiphilic random copolymer of P(NVP-co-NHPSS) with photocleavable N-O sulfonate side groups has been prepared to investigate the light-triggered disruption of copolymer micelles. Methods of absorption and emission spectra, solution transmittance, dynamic light scattering (DLS), and transmission electron microscopy (TEM) were applied. It was found that P(NVP-co-NHPSS) could form polymeric nanoaggregates in aqueous solution. And the photocleavage of the N-O bond within copolymer micelles upon 365 nm UV light could be conveniently controlled by changing the irradiation intensity, leading to the disruption of copolymer micelles and the photocontrolled release of Nile red encapsulation. And by encapsulating NaLuF4:Gd/Yb/Tm UCNPs inside copolymer micelles, the response of the photocleavable N-O bond to the 980 nm laser was much weaker than the response to 365 nm light; however, the photocontrolled release of Nile red could still be effectively triggered by the NIR light of the 980 nm laser.

A New Strategy for Fluorogenic Esterase Probes Displaying Low Levels of Non-specific Hydrolysis

A new design for fluorescence probes of esterase activity that features a carboxylate-side pro-fluorophore is demonstrated with boron dipyrromethene (BODIPY)-based probes 1 a and 1 b. Because the design relies on the enzyme-catalyzed hydrolysis of an ester group that is not electronically activated, these probes exhibit a stability to background hydrolysis that is far superior to classical alcohol-side profluorophore-based probes, large signal-to-noise ratios, reduced sensitivity to pH variations, and high enzymatic reactivity. The utility of probe 1 a was established with a real-time fluorescence imaging experiment of endogenous esterase activity that does not require washing of the extracellular medium.