Efficient Fluorescence Enhancement and Cooperative Binding of an Organic Dye in a Supra-biomolecular Host–Protein Assembly

Near-Infrared Photothermal Manipulates Cellular Excitability and Animal Behavior in Caenorhabditis elegans

Near-infrared (NIR) photothermal manipulation has emerged as a promising and noninvasive technology for neuroscience research and disease therapy for its deep tissue penetration. NIR stimulated techniques have been used to modulate neural activity. However, due to the lack of suitable in vivo control systems, most studies are limited to the cellular level. Here, a NIR photothermal technique is developed to modulate cellular excitability and animal behaviors in Caenorhabditis elegans in vivo via the thermosensitive transient receptor potential vanilloid 1 (TRPV1) channel with an FDA-approved photothermal agent indocyanine green (ICG). Upon NIR stimuli, exogenous expression of TRPV1 in AFD sensory neurons causes Ca2+ influx, leading to increased neural excitability and reversal behaviors, in the presence of ICG. The GABAergic D-class motor neurons can also be activated by NIR irradiation, resulting in slower thrashing behaviors. Moreover, the photothermal manipulation is successfully applied in different types of muscle cells (striated muscles and nonstriated muscles), enhancing muscular excitability, causing muscle contractions and behavior changes in vivo. Altogether, this study demonstrates a noninvasive method to precisely regulate the excitability of different types of cells and related behaviors in vivo by NIR photothermal manipulation, which may be applied in mammals and clinical therapy.

Spectroscopic features of a perylenediimide probe for sensing amyloid fibrils: in vivo imaging of Aβ-aggregates in a Drosophila model organism

Customised perylenediimide (PDI) chromophores find diverse applications not only as chemosensors, inorganic-organic semiconductors, photovoltaics, photocatalysts, etc., but also in protein surface engineering, bio-sensors and drug delivery systems. This study focuses on the interaction of a custom synthesized phenylalanine derivatized perylenediimide (L-Phe-PDI) dye with a model protein, insulin, and its structurally distinct fibrils to develop fluorescence sensors for fibrillar aggregates and in vivo imaging applications. Detailed photophysical studies revealed that L-Phe-PDI gets aggregated in the presence of insulin and causes emission quenching at pH 7.4, which in the absence of insulin occurs only at pH ∼2. During in vitro incubation of insulin to its fibrils, the fluorescence intensity of the L-Phe-PDI probe is enhanced to ∼150 fold in a two-stage manner, manifesting the pathways of structural transformation to β-sheet rich mature fibrils. The in vivo sensing has further been validated in living models of the Aβ-mutant Drosophila fly, which is known to develop progressive neurodegeneration comparable to that of human brains with Alzheimer's disease (AD). Bioimaging of the L-Phe-PDI treated Aβ-mutant Drosophila documented the blood-brain/blood-retina-barrier cross-over ability of L-Phe-PDI with no toxic effects. Comparison of the fibrillar images from the brain and eye region with the reference thioflavin T (ThT) probe established the uptake of L-Phe-PDI by the aggregate/fibrillar moieties. The samples from L-Phe-PDI-treated flies apparently displayed reduced fibrillar spots, a possible case of L-Phe-PDI-induced disintegration of fibrillar aggregates at large, an observation substantiated by the improved phenotype activities as compared to the untreated flies. The findings reported both in vitro and in vivo with the L-Phe-PDI material for the first time open up avenues to explore the therapeutic potential of custom-designed PDI derivatives for amyloid fibril sensors and bioimaging.

In house synthesized novel distyryl-BODIPY dye and polymer assembly as deep-red emitting probe for protamine detection

In this contribution, we designed and synthesized a deep-red emitting distyryl-BODIPY dye (dye 3) which is non-fluorescent in aqueous solution due to the formation of non-emissive aggregates. However, in presence of an amphiphilic polymer (polystyrene sulfonate, PSS), the aggregated dye molecules de-aggregate and form dye 3-PSS complex, which significantly modulates the optical features of the bound dye. Interestingly, the dye 3-PSS complex shows turn-on fluorescence response in deep-red region in presence of protamine (Pr) due to the formation of dye 3-PSS-Pr ternary complex. Such enhancement follows a linear trend in the dynamic range of 0-8.75 μM of Pr which has been utilized to determine Pr with limit of detection (LOD) of 15.04(±0.5) nM in phosphate buffer. Furthermore, excellent selectivity of the dye 3-PSS system towards Pr allows us to determine Pr even in complex biological matrix like 1% human serum. Thus, dye 3-PSS system can be applied as a very effective tool for the detection and quantification of Pr in deep-red region, overcoming several limitations encountered with the probes in the shorter wavelength region. This is the first report on BODIPY dye based supramolecular assembly for sensing and quantification of protamine.

Metal-Assisted Complexation of Fluorogenic Dyes by Cucurbit[7]uril and Cucurbit[8]uril: A DFT Evaluation of the Key Factors Governing the Host-Guest Recognition

With the emergence of host-guest systems, a novel branch of complexation chemistry has found wide application in industries such as food, pharmacy, medicine, environmental protection and cosmetics. Along with the extensively studied cyclodextrins and calixarenes, the innovative cucurbiturils (CB) have enjoyed increased popularity among the scientific community as they possess even better qualities as cavitands as compared to the former molecules. Moreover, their complexation abilities could further be enhanced with the assistance of metal cations, which can interestingly exert a dual effect on the complexation process: either by competitively binding to the host entity or cooperatively associating with the CB@guest structures. In our previous work, two metal species (Mg²⁺ and Ga³⁺) have been found to bind to CB molecules in the strongest fashion upon the formation of host-guest complexes. The current study focuses on their role in the complex formation with three dye molecules: thiazole orange, neutral red, and thioflavin T. Various key factors influencing the process have been recognized, such as pH and the dielectric constant of the medium, the cavity size of the host, Mⁿ⁺ charge, and the presence/absence of hydration shell around the metal cation. A well-calibrated DFT methodology, solidly based and validated and presented in the literature experimental data, is applied. The obtained results shed new light on several aspects of the cucurbituril complexation chemistry.

A supramolecular cucurbit[8]uril-based rotaxane chemosensor for the optical tryptophan detection in human serum and urine

Sensing small biomolecules in biofluids remains challenging for many optical chemosensors based on supramolecular host-guest interactions due to adverse interplays with salts, proteins, and other biofluid components. Instead of following the established strategy of developing alternative synthetic binders with improved affinities and selectivity, we report a molecular engineering approach that addresses this biofluid challenge. Here we introduce a cucurbit[8]uril-based rotaxane chemosensor feasible for sensing the health-relevant biomarker tryptophan at physiologically relevant concentrations, even in protein- and lipid-containing human blood serum and urine. Moreover, this chemosensor enables emission-based high-throughput screening in a microwell plate format and can be used for label-free enzymatic reaction monitoring and chirality sensing. Printed sensor chips with surface-immobilized rotaxane-microarrays are used for fluorescence microscopy imaging of tryptophan. Our system overcomes the limitations of current supramolecular host-guest chemosensors and will foster future applications of supramolecular sensors for molecular diagnostics.

General Method for Pesticide Recognition Using Albumin-Based Host-Guest Ensembles

The massive use of pesticides nowadays has led to serious consequences for the environment and public health. Fluorescence analytical methods for pesticides are particularly advantageous with respect to simplicity and portability; however, currently available fluorescence methods (enzyme-based assays and indicator displacement assays) with poor universality are only able to detect few specific pesticides (e.g., organophosphorus). Making use of the multiple flexible and asymmetrical binding sites in albumin, we herein report a set of multicolor albumin-based host-guest ensembles. These ensembles exhibit a universal but distinctive fluorescent response to most of the common pesticides and allow array-based identification of pesticides with high accuracy. Furthermore, the simplicity, portability, and visualization of this method enable on-site determination of pesticides in a practical setting. This albumin host strategy largely expands the toolbox of traditional indicator displacement assays (synthetic macrocycles as hosts), and we expect it to inspire a series of sensor designs for pesticide detection.

Cucurbituril-Based Supramolecular Assemblies: Prospective on Drug Delivery, Sensing, Separation, and Catalytic Applications

Precise control over the stimuli-responsive noncovalent interactions operative in a complex molecular system has emerged as a convenient way to realize applications in the detection and sensing of trace analytes, metal ion separation, uptake-release, in situ nanoparticle synthesis, and catalytic activity. This feature article focuses on the attributes and advantages of noncovalent host-guest interactions involving cucurbituril homologues (CBs) with a wide range of organic and inorganic guests, starting from organic dyes to drugs, proteins, surfactants, metal ions, and polyoxometalates. The unique structural features of CBs provide interaction sites for cations at the portals, polyanions at the periphery, and hydrophobic groups in its cavity. The facile complexation and consequent compositional and geometrical arrangements of guests such as naphthalenediimides, coumarins, porphyrins, and triphenylpyrylium ions with the host CBs led to remarkable changes in many molecular properties, especially aggregation, the proton binding and release affinity, and novel emissive dimers, and each of such spectroscopic signatures have been appropriately channeled to drug delivery and activation to improve the antibacterial efficacy and shelf life of drugs by increasing their photostability. Several technological advantages have also been extracted from the interaction of CBs with inorganic guests as well. The interaction of CB7 with the heptamolybdate anion resulted in the precipitation of a hybrid complex material which enabled a convenient separation methodology for the use of clinically pure radioactive ^99mTc in diagnostic applications. Certain cucurbituril-based hybrid materials have been developed for enhanced SO₂ adsorption at low pressures, high-efficiency hydrogen production, and reversible catalytic systems. Thus, this feature article provides a glimpse of the vast potential of cucurbituril homologues with organic and inorganic guests and calls for a dedicated effort to explore supramolecular strategies for better sensors, therapeutics, smart drug delivery modules, and facile devices.

Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids

Synthetic molecular probes, chemosensors, and nanosensors used in combination with innovative assay protocols hold great potential for the development of robust, low-cost, and fast-responding sensors that are applicable in biofluids (urine, blood, and saliva). Particularly, the development of sensors for metabolites, neurotransmitters, drugs, and inorganic ions is highly desirable due to a lack of suitable biosensors. In addition, the monitoring and analysis of metabolic and signaling networks in cells and organisms by optical probes and chemosensors is becoming increasingly important in molecular biology and medicine. Thus, new perspectives for personalized diagnostics, theranostics, and biochemical/medical research will be unlocked when standing limitations of artificial binders and receptors are overcome. In this review, we survey synthetic sensing systems that have promising (future) application potential for the detection of small molecules, cations, and anions in aqueous media and biofluids. Special attention was given to sensing systems that provide a readily measurable optical signal through dynamic covalent chemistry, supramolecular host-guest interactions, or nanoparticles featuring plasmonic effects. This review shall also enable the reader to evaluate the current performance of molecular probes, chemosensors, and nanosensors in terms of sensitivity and selectivity with respect to practical requirement, and thereby inspiring new ideas for the development of further advanced systems.

Achieving AIE from ACQ in positional isomeric triarylmethanes

This report demonstrate that the usual ‘aggregation caused quenching’ (ACQ) can be overcome by a change in the substitution position in naphthalene derivatives, leading to the much desired ‘aggregation induced emission’ (AIE).

Photophysical and NMR studies of encapsulation of 2-cyano-6-hydroxy benzothiazole in p-sulfonatocalix[6]arene and its biological applications

This work deals with the study of the interaction between 2-cyano-6-hydroxy benzothiazole (CHBT) and p-sulfonatocalix[6]arene (SCX6) at different pH values in aqueous medium by UV-visible absorption spectroscopy and steady-state fluorescence spectroscopy. The results demonstrate the strong influence of SCX6 on the fluorescence properties of CHBT. The steady-state emission of CHBT shows strong sensitivity to its environment. The mode of inclusion complexation of CHBT and SCX6 has also been investigated using HR-MS, FT-IR, NMR, 2D NMR, and FESEM analysis. With the increase in SCX6 concentration, absorbance decreased with an isosbestic point at 305 nm. The binding constant is calculated by a spectrofluorimetric method and stoichiometry by Job's method. The formation of an inclusion complex has been confirmed by 2D NMR NOESY, COSY, ROESY, HMBC, and HSQC spectroscopic methods. The complex is seen to be stabilized by electrostatic interactions between CHBT and the nanocavity of SCX6. Studies with cellular systems support that the CHBT-SCX6 complex is more effective in killing cancerous cells and hence, SCX6 may prove to be an effective carrier for drug molecules like CHBT.

Metal-Free Supramolecular Catalytic Hydrolysis of Ammonia Borane through Cucurbituril Nanocavitands

Ammonia borane (AB) is considered a potential "on-board" hydrogen storage material. However, its implementation as a hydrogen reservoir in fuel cells is lacking due to the extremely slow release of hydrogen at room-temperature hydrolysis. In this study, a metal-free supramolecular strategy is demonstrated at room temperature to increase the hydrolysis rate and yield of hydrogen along with significant reduction in ammonia release by using cucurbit[5/8]uril (CB5/CB8) nanocavitands as catalysts. The complex of AB with CB stabilizes the ammonium ion at the host portals, which reduces ammonia release and enhances hydrogen yield. The complexation brings down the activation energy of hydrolysis from 103.8 to ∼27.5 kJ mol^-1 (for CB5), a value close to the Pt/Pd nanoparticle-based catalysts reported so far. The high catalytic performance and reusability of CB catalysts at very low concentration make AB a promising supramolecular alternative for a sustainable "on-board" energy source.

Supramolecular and suprabiomolecular photochemistry: a perspective overview

In this perspective review article, we have attempted to bring out the important current trends of research in the areas of supramolecular and suprabiomolecular photochemistry. Since the spans of the subject areas are very vast, it is impossible to cover all the aspects within the limited space of this review article. Nevertheless, efforts have been made to assimilate the basic understanding of how supramolecular interactions can significantly change the photophysical and other related physiochemical properties of chromophoric dyes and drugs, which have enormous academic and practical implications. We have discussed with reference to relevant chemical systems where supramolecularly assisted modulations in the properties of chromophoric dyes and drugs can be used or have already been used in different areas like sensing, dye/drug stabilization, drug delivery, functional materials, and aqueous dye laser systems. In supramolecular assemblies, along with their conventional photophysical properties, the acid-base properties of prototropic dyes, as well as the excited state prototautomerization and related proton transfer behavior of proton donor/acceptor dye molecules, are also largely modulated due to supramolecular interactions, which are often reflected very explicitly through changes in their absorption and fluorescence characteristics, providing us many useful insights into these chemical systems and bringing out intriguing applications of such changes in different applied areas. Another interesting research area in supramolecular photochemistry is the excitation energy transfer from the donor to acceptor moieties in self-assembled systems which have immense importance in light harvesting applications, mimicking natural photosynthetic systems. In this review article, we have discussed varieties of these aspects, highlighting their academic and applied implications. We have tried to emphasize the progress made so far and thus to bring out future research perspectives in the subject areas concerned, which are anticipated to find many useful applications in areas like sensors, catalysis, electronic devices, pharmaceuticals, drug formulations, nanomedicine, light harvesting, and smart materials.

Visual and dual-fluorescence homogeneous sensor for the detection of pyrophosphatase in clinical hyperthyroidism samples based on selective recognition of CdTe QDs and coordination polymerization of Ce3+

A visual / dual fluorescent strategy based on selective recognition of QDs and coordination polymerization of Ce³⁺ was developed for pyrophosphatase detection.

Fluorescence Enhancement by Calixarene Supramolecular Aggregate

We herein constructed supramolecular assemblies from guanidinocalixarenes and sulfonatocalixarenes by exploiting multiple salt bridge interactions. They encapsulate six different kinds of fluorescent dyes (both cationic and anionic), leading to a fluorescence enhancement that could not be achieved by either single calixarene. As such, this study advances the research on high-performance fluorophores.

Universal quenching of common fluorescent probes by water and alcohols

Although biological imaging is mostly performed in aqueous media, it is hardly ever considered that water acts as a classic fluorescence quencher for organic fluorophores. By investigating the fluorescence properties of 42 common organic fluorophores recommended for biological labelling, we demonstrate that H2O reduces their fluorescence quantum yield and lifetime by up to threefold and uncover the underlying fluorescence quenching mechanism. We show that the quenching efficiency is significantly larger for red-emitting probes and follows an energy gap law. The fluorescence quenching finds its origin in high-energy vibrations of the solvent (OH groups), as methanol and other linear alcohols are also found to quench the emission, whereas it is restored in deuterated solvents. Our observations are consistent with a mechanism by which the electronic excitation of the fluorophore is resonantly transferred to overtones and combination transitions of high-frequency vibrational stretching modes of the solvent through space and not through hydrogen bonds. Insight into this solvent-assisted quenching mechanism opens the door to the rational design of brighter fluorescent probes by offering a justification for protecting organic fluorophores from the solvent via encapsulation.

Supramolecular Encapsulation of a Neurotransmitter Serotonin by Cucurbit[7]uril

pH-dependent host-guest complexation of a monoamine neurotransmitter, Serotonin, with cucurbit[7]uril has been thoroughly investigated. The binding phenomena were explored using steady-state and time-resolved fluorescence spectroscopy at different pH values. At lower pH, i.e., protonated Serotonin, the binding affinity with cucurbit[7]uril was significantly higher compared to higher pH. Furthermore, detailed NMR titration experiments depicted the solution structure of the host-guest complex through the complexation induced chemical shift values. A competitive binding assay with cesium ions at pD 2.8 was subsequently performed for the further manifestation of the binding. Finally, the molecular docking studies provided well-documented proof of the 1:1 inclusion complex and the geometry of the complex. We believe that understanding from such studies can be important for pH-controlled delivery of serotonin for biological applications.

Cucurbit[7]uril-driven modulation of ligand-DNA interactions by ternary assembly

The design of small organic molecules with a predictable and desirable DNA-binding mechanism is a topical research task for biomedicine application. Herein, we demonstrate an attractive supramolecular strategy for controlling the non-covalent ligand-DNA interaction by binding with cucurbituril as a synthetic receptor. With a combination of UV/vis, CD and NMR experiments, we demonstrate that the bis-styryl dye with two suitable binding sites can involve double stranded DNA and cucurbituril in the formation of the supramolecular triad. The ternary assembly is formed as a result of the interaction of macrocyclic cucurbituril with one pyridinium fragment of the bis-styryl dye, while the second pyridinium fragment of the dye is effectively associated with DNA backbones, which leads to a change in the ligand-DNA binding mode from aggregation to a minor groove. This exciting outcome was supported by molecular docking studies that help to understand the molecular orientation of the supramolecular triad and elucidate the destruction of dye aggregates caused by cucurbituril. These studies provide valuable information on the mechanisms of DNA binding to small molecules and recognition processes in bioorganic supramolecular assemblies constructed from multiple non-covalent interactions.

Electrochemical Quantitation of Supramolecular Excipient@Drug Complexation: A General Assay Strategy Based on Competitive Host Binding with Surface-Immobilized Redox Guest

The macrocyclic cucurbit[7]uril (CB[7]) host has exhibited great application potential as a pharmaceutical excipient due to its versatile abilities to modulate the chemical/physical properties of drug molecules (guests) and to control their in vivo delivery and release (upon complexation). The formation of stable CB[7]@drug complexes is the prerequisite for these promising applications; we report herein a general assay strategy to quantitate the complexation based on competitive binding with surface-immobilized redox guests in conjunction with conventional electrochemical techniques (e.g., cyclic voltammetry). Particularly, by incubating a mixture of CB[7] and a drug molecule with ferrocene (Fc)-terminated self-assembled monolayers (SAMs) on gold, the competitive host@guest binding between the CB[7]@drug complex formed in solution and the CB[7]@Fc complex formed on surface can be quantified with direct cyclic voltammetry measurements. On the basis of the known concentrations of CB[7]/drug and electrochemically determined surface densities of free/complexed Fc groups, the formation constant of CB[7]@drug complex can be determined. With several drug molecules as examples, we have demonstrated the capability of this method for quantitative studies of the formation of supramolecular excipient@drug complexes that are of interest in pharmaceutical and biomedical sciences. More importantly, this work promises a general assay strategy that allows electrochemical quantitation of a wide range of electro-inactive analytes based on the competitive supramolecular host@guest binding at redox-tagged molecular interfaces.

Light-induced metal-free transformations of unactivated pyridotriazoles

A highly efficient and practical method for incorporation of the arylmethylpyridyl moiety into diverse molecules has been developed. This method features the transition metal-free light-induced room temperature transformation of pyridotriazoles into pyridyl carbenes, which are capable of smooth arylation, X-H insertion, and cyclopropanation reactions. The synthetic usefulness of the developed method was illustrated in a facile synthesis of biologically active molecules.

Structure-Based Mutagenesis of Phycobiliprotein smURFP for Optoacoustic Imaging

Photo- or optoacoustics (OA) imaging is increasingly being used as a non-invasive imaging method that can simultaneously reveal structure and function in deep tissue. However, the most frequent transgenic OA labels are current fluorescent proteins that are not optimized for OA imaging. Thus, they lack OA signal strength, and their absorption maxima are positioned at short wavelengths, thus giving small penetration depths and strong background signals. Here, we apply insights from our recent determination of the structure of the fluorescent phycobiliprotein smURFP to mutate a range of residues to promote the nonradiative decay pathway that generates the OA signal. We identified hydrophobic and aromatic substitutions within the chromophore-binding pocket that substantially increase the intensity of the OA signal and red-shift the absorption. Our results demonstrate the feasibility of structure-based mutagenesis to repurpose fluorescent probes for OA imaging, and they may provide structure-function insights for de novo engineering of transgenic OA probes.

Applications of Cucurbiturils in Medicinal Chemistry and Chemical Biology

The supramolecular chemistry of cucurbit[n]urils (CBn) has been rapidly developing to encompass diverse medicinal applications, including drug formulation and delivery, controlled drug release, and sensing for bioanalytical purposes. This is made possible by their unique recognition properties and very low cytotoxicity. In this review, we summarize the host-guest complexation of biologically important molecules with CBn, and highlight their implementation in medicinal chemistry and chemical biology.

Inclusion Complexes of Melphalan with Gemini-Conjugated β-Cyclodextrin: Physicochemical Properties and Chemotherapeutic Efficacy in In-Vitro Tumor Models

β-cyclodextrin (βCD) has been widely explored as an excipient for pharmaceuticals and nutraceuticals as it forms stable host–guest inclusion complexes and enhances the solubility of poorly soluble active agents. To enhance intracellular drug delivery, βCD was chemically conjugated to an 18-carbon chain cationic gemini surfactant which undergoes self-assembly to form nanoscale complexes. The novel gemini surfactant-modified βCD carrier host (hereafter referred to as 18:1βCDg) was designed to combine the solubilization and encapsulation capacity of the βCD macrocycle and the cell-penetrating ability of the gemini surfactant conjugate. Melphalan (Mel), a chemotherapeutic agent for melanoma, was selected as a model for a poorly soluble drug. Characterization of the 18:1βCDg-Mel host–guest complex was carried out using 1D/2D ¹H NMR spectroscopy and dynamic light scattering (DLS). The 1D/2D NMR spectral results indicated the formation of stable and well-defined 18:1βCDg-Mel inclusion complexes at the 2:1 host–guest mole ratio; whereas, host–drug interaction was attenuated at greater 18:1βCDg mole ratio due to hydrophobic aggregation that accounts for the reduced Mel solubility. The in vitro evaluations were performed using monolayer, 3D spheroid, and Mel-resistant melanoma cell lines. The 18:1βCDg-Mel complex showed significant enhancement in the chemotherapeutic efficacy of Mel with 2–3-fold decrease in Mel half maximal inhibitory concentration (IC₅₀) values. The findings demonstrate the potential applicability of the 18:1βCDg delivery system as a safe and efficient carrier for a poorly soluble chemotherapeutic in melanoma therapy.

Modular supramolecular dimerization of optically tunable extended aryl viologens

Cucurbit[8]uril (CB[8]) mediated assembly of extended aryl viologens (EVs) into optically tunable dimers is reported for the first time.

Cucurbit[8]uril (CB[8]) mediated assembly of extended aryl viologens (EVs) into optically tunable dimers is reported for the first time. We show that the modular design and synthesis of a new class of π-conjugated viologen derivatives with rigid aromatic or heteroaromatic bridging units as well as electron donating molecular recognition motifs enable their self-assembly into 2 : 2 complexes with CB[8]. The quantitative dimerization process involving these two molecular components in an aqueous solution enables excimer-like interactions between closely packed charged guests giving rise to distinct spectroscopic behavior. The nature of these dimers (CB[8]₂·(EV[X]R)₂) in the ground and excited states was characterized by NMR, isothermal titration calorimetry, and steady-state spectroscopic measurements.

A duplex connection can further illuminate G-quadruplex/crystal violet complex

Duplex-connected G-quadruplex (dsG4) has a more evident promotion of the fluorescent emission of crystal violet than pure G-quadruplex (G4), which is firstly found and investigated systematically using fluorescence spectra, circular dichroism, and density functional theory. This new phenomenon also shows potential in application for target nucleic acid detection.

Solubilization of Pyridone-Based Fluorescent Tag by Complexation in Cucurbit[7]uril

Aimed at further exploring the hosting properties of cucurbit[7]uril (CB7), we have exploited the spectroscopic and photophysical properties of a known fluorescent label as the guest molecule, namely, 3-cyano-6-(2-thienyl)-4-trifluoromethyl pyridine (TFP), in neat solvents. The formation of an inclusion host-guest complex with CB7 was checked by UV-vis absorption spectroscopy, and the value of binding constant (9.7 × 10⁵ M^-1) was extracted from the spectrophotometric data. The modulation of keto-enol equilibrium in TFP by the local environment is governed by the interplay between dimerization through intermolecular hydrogen bonding between individual solute molecules, favoring the enol form, and intermolecular hydrogen bonding between TFP and the surrounding solvents, favoring the keto form. Time-resolved fluorescence results established that the macromolecular CB7 host stabilizes preferentially the neutral enol form over the keto form of TFP. Unprecedentedly, our results reveal a linear dependence of the amplitudes of the extracted decay-associated spectra from the time-resolved fluorescence spectra of TFP on the sum of polarity/polarizability and hydrogen bonding parameters of the local environment, confirming that TFP at micromolar concentration in the CB7 complexes is experiencing a methanol-like environment. The results rationalized the 42-fold enhancement in the solubility of TFP in water media by complexation in CB7.

A Supramolecular Approach for Enhanced Antibacterial Activity and Extended Shelf-life of Fluoroquinolone Drugs with Cucurbit[7]uril

The host-guest interactions of a third-generation fluoroquinone, danofloxacin (DOFL), with the macrocyclic host cucurbit[7]uril (CB7) have been investigated at different pH values (~3.5, 7.5, and 10). The photophysical properties have been positively affected, that is, the fluorescence yield and lifetime increased, as well as the photostability of DOFL improved in the presence of CB7. The antibacterial activity of DOFL is enhanced in the presence of CB7, as tested against four pathogenic bacteria; highest activity has been found towards B. cereus and E. coli, and lower activity towards S. aureus and S. typhi. The antibacterial activity of two additional second-generation fluoroquinones, i.e., norfloxacin and ofloxacin, has also been investigated in the absence as well as the presence of CB7 and compared with that of DOFL. In case of all drugs, the minimum inhibitory concentration (MIC) was reduced 3–5 fold in the presence of CB7. The extended shelf-life (antibacterial activity over time) of the fluoroquinone drugs in the presence of CB7, irrespective of four types of bacteria, can be attributed to the enhanced photostability of their CB7 complexes, which can act as better antibiotics with a longer expiry date than uncomplexed DOFL.

Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from Aβ

Soluble oligomers of the β-amyloid peptide, Aβ, are associated with the progression of Alzheimer's disease. Although many small molecules bind to these assemblies, the details of how these molecules interact with Aβ oligomers remain unknown. This paper reports that crystal violet, and other C3 symmetric triphenylmethane dyes, bind to C3 symmetric trimers derived from Aβ_17-36. Binding changes the color of the dyes from purple to blue, and causes them to fluoresce red when irradiated with green light. Job plot and analytical ultracentrifugation experiments reveal that two trimers complex with one dye molecule. Studies with several triphenylmethane dyes reveal that three N, N-dialkylamino substituents are required for complexation. Several mutant trimers, in which Phe₁₉, Phe₂₀, and Ile₃₁ were mutated to cyclohexylalanine, valine, and cyclohexylglycine, were prepared to probe the triphenylmethane dye binding site. Size exclusion chromatography, SDS-PAGE, and X-ray crystallographic studies demonstrate that these mutations do not impact the structure or assembly of the triangular trimer. Fluorescence spectroscopy and analytical ultracentrifugation experiments reveal that the dye packs against an aromatic surface formed by the Phe₂₀ side chains and is clasped by the Ile₃₁ side chains. Docking and molecular modeling provide a working model of the complex in which the triphenylmethane dye is sandwiched between two triangular trimers. Collectively, these findings demonstrate that the X-ray crystallographic structures of triangular trimers derived from Aβ can be used to guide the discovery of ligands that bind to soluble oligomers derived from Aβ.

Temperature responsive nanoparticles: poloxamers as a modulator of Förster resonance energy transfer (FRET)

An effective strategy to control the Förster resonance energy transfer (FRET) of a donor/acceptor emitter pair that were attached to a 60 nm poly(propargyl acrylate)(PA) nanoparticle using temperature variations was developed. The size dependent properties of a poly-(ethylene oxide)-poly-(propylene oxide)-poly-(ethylene oxide) (PEO-PPO-PEO) block copolymer (poloxamer) was exploited to vary the spatial separation of the emitters and vary the FRET efficiency. Specifically, a 2% change in FRET efficiency between the donor/acceptor pair was achieved per 1 °C change in temperature from 49 °C to 60 °C when using a poloxamer of 2950 g mol-1 molecular weight, with sections of PPO consisting of 32 repeat units, PEO sections consisting of 12 repeat units and a lower critical solution temperature (LCST) of 58 °C. The methodology presented in this effort is easily extended to other temperature regimes through a judicious choice in poloxamer and corresponding LCST.

A highly efficient nucleophilic substitution reaction between R2P(O)H and triarylmethanols to synthesize phosphorus-substituted triarylmethanes

A highly efficient nucleophilic substitution reaction between R₂P(O)H and triarylmethanols was reported, which provides phosphorus-substituted triarylmethanes in rich diversity with 40–96% yields.

Cucurbit[7]uril-Driven Host-Guest Chemistry for Reversible Intervention of 5-Formylcytosine-Targeted Biochemical Reactions

5-Formylcytosine (5fC) is identified as one of the key players in active DNA demethylation and also as an epigenetic mark in mammals, thus representing a novel attractive target to chemical intervention. The current study represents an attempt to develop a reversible 5fC-targeted intervention tool. A supramolecular aldehyde reactive probe was therefore introduced for selective conversion of the 5fC to 5fC-AD nucleotide. Using various methods, we demonstrate that cucurbit[7]uril (CB7) selectively targets the 5fC-AD nucleotide in DNA, however, the binding of CB7 to 5fC-AD does not affect the hydrogen bonding properties of natural nucleobases in duplex DNA. Importantly, CB7-driven host-guest chemistry has been applied for reversible intervention of a variety of 5fC-targeted biochemical reactions, including restriction endonuclease digestion, DNA polymerase elongation, and polymerase chain reaction. On the basis of the current study, the macrocyclic CB7 creates obstructions that, through steric hindrance, prevent the enzyme from binding to the substrate, whereas the CB7/5fC-AD host-guest interactions can be reversed by treatment with adamantanamine. Moreover, fragment- and site-specific identification of 5fC modification in DNA has been accomplished without sequence restrictions. These findings thus show promising potential of host-guest chemistry for DNA/RNA epigenetics.

Chameleonic Dye Adapts to Various Environments Shining on Macrocycles or Peptide and Polysaccharide Aggregates

This work describes latent fluorescence particles (LFPs) based on a new environmentally sensitive carbazole compound aggregated in water and their use as sensors for probing various cavitands and the different stages of aggregating systems. Cyclodextrins (CDs), cucurbit[n]urils (CB[n], n = 6, 7, 8), and a resorcinarene capsule were used to study the dynamic nature of the LFPs. The fluorescence was dramatically enhanced by a proposed disaggregation-induced emission enhancement (DIEE) mechanism with specific features for CB[n]. Then, the aggregated states of the dipeptides Leu-Leu, Phe-Phe, and Fmoc-Leu-Leu (vesicles, crystals, fibers) were studied by fluorescence spectroscopy and confocal fluorescence microscopy thanks to the adaptive and emissive behavior of the LFPs, allowing us to study an interesting polymorphism phenomenon. The LFPs have then been used in the sensing of the aggregation of the polysaccharide alginate, for which distinct fluorescence turn-on is detected upon stepwise biopolymer assembly, and for amylose detection. The carbazole particles not only adapt to various environments but also display multicolor fluorescent signals. They can be used for the fast probing of the aggregation propensity of newly prepared molecules or biologically relevant compounds or to accelerate the discovery of new macrocycles or of self-assembling peptides in water.

A high quantum yield molecule-protein complex fluorophore for near-infrared II imaging

Fluorescence imaging in the second near-infrared window (NIR-II) allows visualization of deep anatomical features with an unprecedented degree of clarity. NIR-II fluorophores draw from a broad spectrum of materials spanning semiconducting nanomaterials to organic molecular dyes, yet unfortunately all water-soluble organic molecules with >1,000 nm emission suffer from low quantum yields that have limited temporal resolution and penetration depth. Here, we report tailoring the supramolecular assemblies of protein complexes with a sulfonated NIR-II organic dye (CH-4T) to produce a brilliant 110-fold increase in fluorescence, resulting in the highest quantum yield molecular fluorophore thus far. The bright molecular complex allowed for the fastest video-rate imaging in the second NIR window with ∼50-fold reduced exposure times at a fast 50 frames-per-second (FPS) capable of resolving mouse cardiac cycles. In addition, we demonstrate that the NIR-II molecular complexes are superior to clinically approved ICG for lymph node imaging deep within the mouse body.

Near-infrared (NIR) fluorescence imaging >1,000 nm allows deep tissue imaging, but available organic dyes display poor brightness and temporal resolution. Here, the authors synthesize a NIR dye that, upon binding serum proteins, exhibits a 110-fold increase in intensity, giving an 11% quantum yield.