A new pentacyclic pyrylium fluorescent probe that responds to pH imbalance during apoptosis

Efficient fluorophores with easy synthetic routes and fast responses are of great importance in clinical diagnostics. Herein, we report a new, rigid pentacyclic pyrylium fluorophore, PS-OMe, synthesised in a single step by a modified Vilsmeier–Haack reaction. Insights into the reaction mechanism facilitated a new reaction protocol for the efficient synthesis of PS-OMe which upon demethylation resulted in a “turn-on” pH sensor, PS-OH. This new fluorescent probe has been successfully used to monitor intracellular acidification at physiological pH. From the fluorescence image analysis, we were able to quantify the intracellular dynamic pH change during apoptosis. This new pH probe is a potential chemical tool for screening, drug discovery and dose determination in cancer therapy.

A modified Vilsmeier–Haack reaction resulted in the synthesis of a pyrylium based turn-on fluorescent pH probe. The probe can monitor minute acidification and dynamic pH variation in cells during apoptosis with therapeutic chemo drugs.     

A facile combinatorial approach to construct a ratiometric fluorescent sensor: application for the real-time sensing of cellular pH changes

Realtime monitoring of the cellular environment, such as the intracellular pH, in a defined cellular space provides a comprehensive understanding of the dynamics processes in a living cell. Considering the limitation of spatial resolution in conventional microscopy measurements, multiple types of fluorophores assembled within that space would behave as a single fluorescent probe molecule. Such a character of microscopic measurements enables a much more flexible combinatorial design strategy in developing fluorescent probes for given targets. Nanomaterials with sizes smaller than the microscopy spatial resolution provide a scaffold to assemble several types of fluorophores with a variety of optical characteristics, therefore providing a convenient strategy for designing fluorescent pH sensors. In this study, fluorescein (CF) and tetramethylrhodamine (CR) were assembled on a DNA nanostructure with controlling the number of each type of fluorophore. By taking advantage of the different responses of CF and CR emissions to the pH environment, an appropriate assembly of both CF and CR on DNA origami enabled a controlled intensity of fluorescence emission and ratiometric pH monitoring within the space defined by DNA origami. The CF and CR-assembled DNA origami was successfully applied for monitoring the intracellular pH changes.

A combinatorial assembly of two types of intensity-based fluorophores on a DNA nanostructure provided a ratiometric pH probe with high emission intensity for monitoring intracellular pH changes.     

Interrogating surface versus intracellular transmembrane receptor populations using cell-impermeable SNAP-tag substrates

Employing self-labelling protein tags for the attachment of fluorescent dyes has become a routine and powerful technique in optical microscopy to visualize and track fused proteins. However, membrane permeability of the dyes and the associated background signals can interfere with the analysis of extracellular labelling sites. Here we describe a novel approach to improve extracellular labelling by functionalizing the SNAP-tag substrate benzyl guanine (“BG”) with a charged sulfonate (“SBG”). This chemical manipulation can be applied to any SNAP-tag substrate, improves solubility, reduces non-specific staining and renders the bioconjugation handle impermeable while leaving its cargo untouched. We report SBG-conjugated fluorophores across the visible spectrum, which cleanly label SNAP-fused proteins in the plasma membrane of living cells. We demonstrate the utility of SBG-conjugated fluorophores to interrogate class A, B and C G protein-coupled receptors (GPCRs) using a range of imaging approaches including nanoscopic superresolution imaging, analysis of GPCR trafficking from intra- and extracellular pools, in vivo labelling in mouse brain and analysis of receptor stoichiometry using single molecule pull down.

Impermeable SNAP-tag substrates allow exclusive labelling of receptors on the cell membrane for nanoscopy, SiMPull and in vivo use.     

Multiplexed optical barcoding of cells via photochemical programming of bioorthogonal host–guest recognition

Modern chemical and biological studies are undergoing a paradigm shift, where understanding the fate of individual cells, in an apparently homogeneous population, is becoming increasingly important. This has inculcated a growing demand for developing strategies that label individual cells with unique fluorescent signatures or barcodes so that their spatiotemporal trajectories can be mapped in real time. Among various approaches, light-regulated methods employing photocaged fluorophores have received particular attention, owing to their fine spatiotemporal control over labelling. However, their multiplexed use to barcode large numbers of cells for interrogating cellular libraries or complex tissues remains inherently challenging, due to the lack of multiple spectrally distinct photoactivated states in the currently available photocaged fluorophores. We report here an alternative multiplexable strategy based on optically controlled host–guest recognition in the cucurbit[7]uril (CB[7]) system that provides spatial control over the positioning of fluorophores to generate distinct barcodes in ‘user-defined’ cells. Using a combination of three spectrally distinct CB[7]-conjugated fluorophores and by sequentially performing cycles of photoactivation and fluorophore encoding, we demonstrate 10-color barcoding in microtubule-targeted fixed cells as well as 7-color barcoding in cell surface glycan targeted live MCF7 cells.

Barcoding provides abilities to learn about individual species within an apparently homogeneous population. We describe a light-mediated multiplexed cellular barcoding strategy through spatial programming of cucurbit[7]uril molecular recognition.     

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.

Overtones and combinations of O–H vibrations in the solvent efficiently quench red-emitting fluorophores by resonant energy transfer.     

Carbon nanodots revised: the thermal citric acid/urea reaction

Luminescent compounds obtained from the thermal reaction of citric acid and urea have been studied and utilized in different applications in the past few years. The identified reaction products range from carbon nitrides over graphitic carbon to distinct molecular fluorophores. On the other hand, the solid, non-fluorescent reaction product produced at higher temperatures has been found to be a valuable precursor for the CO₂-laser-assisted carbonization reaction in carbon laser-patterning. This work addresses the question of structural identification of both, the fluorescent and non-fluorescent reaction products obtained in the thermal reaction of citric acid and urea. The reaction products produced during autoclave–microwave reactions in the melt were thoroughly investigated as a function of the reaction temperature and the reaction products were subsequently separated by a series of solvent extractions and column chromatography. The evolution of a green molecular fluorophore, namely HPPT, was confirmed and a full characterization study on its structure and photophysical properties was conducted. The additional blue fluorescence is attributed to oligomeric ureas, which was confirmed by complementary optical and structural characterization. These two components form strong hydrogen-bond networks which eventually react to form solid, semi-crystalline particles with a size of ∼7 nm and an elemental composition of 46% C, 22% N, and 29% O. The structural features and properties of all three main components were investigated in a comprehensive characterization study.

Products of the thermal reaction of citric acid and urea have been identified as a complex mixture of fluorophores and particles.     

Singlet fission in a hexacene dimer: energetics dictate dynamics

Singlet fission (SF) is an exciton multiplication process with the potential to raise the efficiency limit of single junction solar cells from 33% to up to 45%. Most chromophores generally undergo SF as solid-state crystals. However, when such molecules are covalently coupled, the dimers can be used as model systems to study fundamental photophysical dynamics where a singlet exciton splits into two triplet excitons within individual molecules. Here we report the synthesis and photophysical characterization of singlet fission of a hexacene dimer. Comparing the hexacene dimer to analogous tetracene and pentacene dimers reveals that excess exoergicity slows down singlet fission, similar to what is observed in molecular crystals. Conversely, the lower triplet energy of hexacene results in an increase in the rate of triplet pair recombination, following the energy gap law for radiationless transitions. These results point to design rules for singlet fission chromophores: the energy gap between singlet and triplet pair should be minimal, and the gap between triplet pair and ground state should be large.

We report the synthesis and photophysical characterization of highly exoergic singlet fission in a hexacene dimer revealing exciton dynamics that follow the energy gap law.     

“Eggs in egg cartons”: co-crystallization to embed molecular cages into crystalline lattices

Discrete (M₃L₂)_n cages assembled from a tripodal ligand (L) and metal ions (M: Cu(i) or Ag(i)) are embedded in networked coordination hosts formed by partial dissociation of the same discrete cages during the crystallization process. The resulting “eggs-in-an-egg-carton” structures provide unique examples of the co-crystallization of discrete and infinite coordination frameworks.

Discrete coordination cages were connected into the infinite lattices via shape-complementary co-crystallization with networked coordination hosts in the “eggs-in-an-egg-carton” styles.     

Development of photo- and chemo-stable near-infrared-emitting dyes: linear-shape benzo-rosol and its derivatives as unique ratiometric bioimaging platforms

Microscopic imaging aided with fluorescent probes has revolutionized our understanding of biological systems. Organic fluorophores and probes thus continue to evolve for bioimaging applications. Fluorophores such as cyanines and hemicyanines emit in the near-infrared (NIR) region and thus allow deeper imaging with minimal autofluorescence; however, they show limited photo- and chemo-stability, demanding new robust NIR fluorophores. Such photo- and chemo-stable NIR fluorophores, linear-shape π-extended rosol and rosamine analogues, are disclosed here which provide bright fluorescence images in cells as well as in tissues by confocal laser-scanning microscopy. Furthermore, they offer unique ratiometric imaging platforms for activatable probes with dual excitation and dual emission capability, as demonstrated with a 2,4-dinitrophenyl ether derivative of benzo-rosol.

NIR-emitting benzo-rosol and -rosamine dyes offer novel ratiometric imaging platforms with high pohoto- and chemo-stability.     

N-Methyl deuterated rhodamines for protein labelling in sensitive fluorescence microscopy

Rhodamine fluorophores are setting benchmarks in fluorescence microscopy. Herein, we report the deuterium (d12) congeners of tetramethyl(silicon)rhodamine, obtained by isotopic labelling of the four methyl groups, show improved photophysical parameters (i.e. brightness, lifetimes) and reduced chemical bleaching. We explore this finding for SNAP- and Halo-tag labelling in live cells, and highlight enhanced properties in several applications, such as fluorescence activated cell sorting, fluorescence lifetime microscopy, stimulated emission depletion nanoscopy and single-molecule Förster-resonance energy transfer. We finally extend this idea to other dye families and envision deuteration as a generalizable concept to improve existing and to develop new chemical biology probes.

Deuteration enhances photophysical and chemical properties of fluorescent rhodamine dyes for higher brightness in sensitive microscopy.     

Towards photoswitchable quadruple hydrogen bonds via a reversible “photolocking” strategy for photocontrolled self-assembly

Developing new photoswitchable noncovalent interaction motifs with controllable bonding affinity is crucial for the construction of photoresponsive supramolecular systems and materials. Here we describe a unique “photolocking” strategy for realizing photoswitchable control of quadruple hydrogen-bonding interactions on the basis of modifying the ureidopyrimidinone (UPy) module with an ortho-ester substituted azobenzene unit as the “photo-lock”. Upon light irradiation, the obtained Azo-UPy motif is capable of unlocking/locking the partial H-bonding sites of the UPy unit, leading to photoswitching between homo- and heteroquadruple hydrogen-bonded dimers, which has been further applied for the fabrication of novel tunable hydrogen bonded supramolecular systems. This “photolocking” strategy appears to be broadly applicable in the rational design and construction of other H-bonding motifs with sufficiently photoswitchable noncovalent interactions.

A photolocking strategy is described to achieve the construction of effectively photoswitchable quadruple hydrogen bonds featuring with photoregulable H-bonding affinities, which is further applied in the photocontrollable H-bonded self-assemblies.     

3-Bromotetrazine: labelling of macromolecules via monosubstituted bifunctional s-tetrazines

We report the synthesis and first characterisation of the novel chemical probe 3-bromotetrazine and establish its reactivity towards nucleophiles. This led to the synthesis of several novel classes of 3-monosubstituted s-tetrazines. A remarkable functional group selectivity is observed and is utilised to site-selectively functionalise different complex molecules. The stability of 3-bromotetrazine under the reaction conditions facilitated the development of a protocol for protein functionalisation, which enabled a “minimal”, bifunctional tetrazine unit as a bio-orthogonal handle for inverse electron demand Diels–Alder reactions. Additionally, a novel tetrazine-based chemical probe was developed and its application in the context of thiol-targeted natural product isolation and labelling of mammalian cells is demonstrated.

3-Bromotetrazine selectively labels small and macromolecules up to proteins and can then be used as a fluorophore or as a bio-orthogonal handle for downstream functionalisation.     

Bright luminescent lithium and magnesium carbene complexes

We report on the convenient synthesis of a CNC pincer ligand composed of carbazole and two mesoionic carbenes, as well as the corresponding lithium- and magnesium complexes. Mono-deprotonation affords a rare “naked” amide anion. In contrast to the proligand and its mono-deprotonated form, tri-deprotonated s-block complexes show bright luminescence, and their photophysical properties were therefore investigated by absorption- and luminescence spectroscopy. They reveal a quantum yield of 16% in solution at ambient temperature. Detailed quantum-chemical calculations assist in rationalizing the emissive properties based on an Intra-Ligand-Charge-Transfer (ILCT) between the carbazolido- and mesoionic carbene ligands. (Earth-)alkali metals prevent the distortion of the ligand following excitation and, thus, by avoiding non-radiative deactivation support bright luminescence.

Lithium- and magnesium complexes of a CNC pincer ligand composed of carbazole and two mesoionic carbenes are bright luminescent, because the metals prevent molecular distortions upon excitation.     

Long-lived lanthanide emission via a pH-sensitive and switchable LRET complex

Lanthanide-based luminescence resonance energy transfer (LRET) can be used as a tool to enhance lanthanide emission for time-resolved cellular imaging applications. By shortening lanthanide emission lifetimes whilst providing an alternative radiative pathway to the formally forbidden, weak lanthanide-only emission, the photon flux of such systems is increased. With this aim in mind, we investigated energy transfer in differently spaced donor–acceptor terbium–rhodamine pairs with the LRET “on” (low pH) and LRET “off” (high pH). Results informed the design, preparation and characterisation of a compound containing terbium, a spectrally-matched pH-responsive fluorophore and a receptor-targeting group. By combining these elements, we observed switchable LRET, where the targeting group sensitises lanthanide emission, resulting in an energy transfer to the rhodamine dye with an efficiency of E = 0.53. This strategy can be used to increase lanthanide emission rates for brighter optical probes.

A pH-sensitive luminescence resonance energy transfer (LRET) was explored as a method to increase photon flux in a terbium-rhodamine-receptor targeting group construct. At low pH, long-lived dye emission and shorter terbium lifetimes were observed.     

What is the role of acid–acid interactions in asymmetric phosphoric acid organocatalysis? A detailed mechanistic study using interlocked and non-interlocked catalysts

Organocatalysis has revolutionized asymmetric synthesis. However, the supramolecular interactions of organocatalysts in solution are often neglected, although the formation of catalyst aggregates can have a strong impact on the catalytic reaction. For phosphoric acid based organocatalysts, we have now established that catalyst–catalyst interactions can be suppressed by using macrocyclic catalysts, which react predominantly in a monomeric fashion, while they can be favored by integration into a bifunctional catenane, which reacts mainly as phosphoric acid dimers. For acyclic phosphoric acids, we found a strongly concentration dependent behavior, involving both monomeric and dimeric catalytic pathways. Based on a detailed experimental analysis, DFT-calculations and direct NMR-based observation of the catalyst aggregates, we could demonstrate that intermolecular acid–acid interactions have a drastic influence on the reaction rate and stereoselectivity of asymmetric transfer-hydrogenation catalyzed by chiral phosphoric acids.

Supramolecular acid–acid interactions lead to competing monomeric and dimeric pathways in phosphoric acid catalysis – so that stereoselectivities depend on catalyst concentration.     

Oxime as a general photocage for the design of visible light photo-activatable fluorophores

Photoactivatable fluorophores have been widely used for tracking molecular and cellular dynamics with subdiffraction resolution. In this work, we have prepared a series of photoactivatable probes using the oxime moiety as a new class of photolabile caging group in which the photoactivation process is mediated by a highly efficient photodeoximation reaction. Incorporation of the oxime caging group into fluorophores results in loss of fluorescence. Upon light irradiation in the presence of air, the oxime-caged fluorophores are oxidized to their carbonyl derivatives, restoring strong fluorophore fluorescence. To demonstrate the utility of these oxime-caged fluorophores, we have created probes that target different organelles for live-cell confocal imaging. We also carried out photoactivated localization microscopy (PALM) imaging under physiological conditions using low-power light activation in the absence of cytotoxic additives. Our studies show that oximes represent a new class of visible-light photocages that can be widely used for cellular imaging, sensing, and photo-controlled molecular release.

Photoactivatable fluorophores have been widely used for tracking molecular and cellular dynamics with subdiffraction resolution.     

Pinkment: a synthetic platform for the development of fluorescent probes for diagnostic and theranostic applications

Reaction-based fluorescent-probes have proven successful for the visualisation of biological species in various cellular processes. Unfortunately, in order to tailor the design of a fluorescent probe to a specific application (i.e. organelle targeting, material and theranostic applications) often requires extensive synthetic efforts and the synthetic screening of a range of fluorophores to match the required synthetic needs. In this work, we have identified Pinkment-OH as a unique “plug-and-play” synthetic platform that can be used to develop a range of ONOO⁻ responsive fluorescent probes for a variety of applications. These include theranostic-based applications and potential material-based/bioconjugation applications. The as prepared probes displayed an excellent sensitivity and selectivity for ONOO⁻ over other ROS. In vitro studies using HeLa cells and RAW 264.7 macrophages demonstrated their ability to detect exogenously and endogenously produced ONOO⁻. Evaluation in an LPS-induced inflammation mouse model illustrated the ability to monitor ONOO⁻ production in acute inflammation. Lastly, theranostic-based probes enabled the simultaneous evaluation of indomethacin-based therapeutic effects combined with the visualisation of an inflammation biomarker in RAW 264.7 cells.

Pinkment, a resorufin based ONOO⁻ selective and sensitive ‘plug and play’ fluorescence-based platform for in vitro and in vivo use, enables facile functionalisation for various imaging and theranostic applications.     

A modular and divergent approach to spirocyclic pyrrolidines

An efficient three-step sequence to afford a valuable class of spirocyclic pyrrolidines is reported. A reductive cleavage/Horner–Wadsworth–Emmons cascade facilitates the spirocyclisation of a range of isoxazolines bearing a distal β-ketophosphonate. The spirocyclisation precursors are elaborated in a facile and modular fashion, via a [3 + 2]-cycloaddition followed by the condensation of a phosphonate ester, introducing multiple points of divergence. The synthetic utility of this protocol has been demonstrated in the synthesis of a broad family of 1-azaspiro[4,4]nonanes and in a concise formal synthesis of the natural product (±)-cephalotaxine.

A three-step, modular and divergent sequence accessing challenging spirocyclic pyrrolidines has been developed, featuring a novel reductive spirocyclization cascade.     

Fluorogenic probes for detecting deacylase and demethylase activity towards post-translationally-modified lysine residues

Reversible enzymatic post-translational modification of the ε-amino groups of lysine residues (e.g. N-acylation reactions) plays an important role in regulating the cellular activities of numerous proteins. This study describes how enzyme catalyzed N-deprotection of lysine residues of non-fluorescent peptide-coumarin probes can be used to generate N-deprotected peptides that undergo spontaneous O- to N-ester transfer reactions (uncatalyzed) to generate a highly fluorescent N-carbamoyl peptide. This enables detection of enzyme catalyzed N-deacetylation, N-demalonylation, N-desuccinylation and N-demethylation reactions activities towards the N-modified lysine residues of these probes using simple ‘turn on’ fluorescent assays.

We developed “turn-on” fluorescent probes that detect enzymatic lysine deacylation and demethylation critical for epigenetic and other cellular phenomena, using intramolecular O- to N-ester transfer reactions.     

Discrete Helmholtz model: a single layer of correlated counter-ions. Metal oxides and silica interfaces,ion-exchange and biological membranes

The mechanism by which interfaces in solution can be polarised depends on the nature of the charge carriers. In the case of a conductor, the charge carriers are electrons and the polarisation is homogeneous in the plane of the electrode. In the case of an insulator covered by ionic moieties, the polarisation is inhomogeneous and discrete in the plane of the interface. Despite these fundamental differences, these systems are usually treated in the same theoretical framework that relies on the Poisson–Boltzmann equation for the solution side. In this perspective, we show that interfaces polarised by discrete charge distributions are rather ubiquitous and that their associated potential drop significantly differs from those of conductor–electrolyte interfaces. We show that these configurations, spanning liquid–liquid interfaces, charged silica–water interfaces, metal oxide interfaces, supercapacitors, ion-exchange membranes and even biological membranes can be uniformly treated under a common “Discrete Helmholtz” model where the discrete charges are compensated by a single layer of correlated counter-ions, thereby generating a sharp potential drop at the interface.

Electrolytes in solution are strongly correlated with discrete charges at insulating interfaces inducing a behavior significantly different from that of conducting interfaces.