Thiophene-based dyes for probing membranes

Core-Alkynylated Fluorescent Flippers: Altered Ultrafast Photophysics to Track Thick Membranes

Fluorescent flippers have been introduced as small-molecule probes to image membrane tension in living systems. This study describes the design, synthesis, spectroscopic and imaging properties of flippers that are elongated by one and two alkynes inserted between the push and the pull dithienothiophene domains. The resulting mechanophores combine characteristics of flippers, reporting on physical compression in the ground state, and molecular rotors, reporting on torsional motion in the excited state, to take their photophysics to new level of sophistication. Intensity ratios in broadened excitation bands from differently twisted conformers of core-alkynylated flippers thus report on mechanical compression. Lifetime boosts from ultrafast excited-state planarization and lifetime drops from competitive intersystem crossing into triplet states report on viscosity. In standard lipid bilayer membranes, core-alkynylated flippers are too long for one leaflet and tilt or extend into disordered interleaflet space, which preserves rotor-like torsional disorder and thus weak, blue-shifted fluorescence. Flipper-like planarization occurs only in highly ordered membranes of matching leaflet thickness, where they light up and selectively report on these thick membranes with red-shifted, sharpened excitation maxima, high intensity and long lifetime.

Fluorescent Molecular Rotors Quantify an Adjuvant-Induced Softening of Plant Wax

Epicuticular wax is the outmost layer of plant leaves that protects them from desiccation and penetration of harmful reagents. There is an intense industrial effort in the development of softening agents, adjuvants, that can adjust the permeability of the wax toward pesticides and, thus, play an important role in sustainable agriculture. However, mechanistic understanding of the structure and dynamic properties within the plant wax, particularly upon the application of adjuvants, is currently lacking. In this work, we demonstrate that fluorescence lifetime imaging microscopy (FLIM) combined with molecular rotors, fluorescent probes sensitive to viscosity, can directly probe the microviscosity of amorphous and crystalline phases of model plant wax layers. Moreover, this approach is able to quantify the changes in viscosity in both phases upon the addition of water and adjuvant solutions on top of the wax. We show that water permeation mostly perturbs the crystalline phase of the wax, while our chosen adjuvant, Plurafac LF431, mainly softens the amorphous phase of the wax. Our technique provides a facile and quantitative way to monitor dynamic properties within plant waxes with diffraction-limited resolution and reveals the effect of organic substances on wax structure and rigidity, crucial for designing next-generation agents to improve agricultural efficiency.

Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules

The viscosity and crowding of biological environment are considered vital for the correct cellular function, and alterations in these parameters are known to underly a number of pathologies including diabetes, malaria, cancer and neurodegenerative diseases, to name a few. Over the last decades, fluorescent molecular probes termed molecular rotors proved extremely useful for exploring viscosity, crowding, and underlying molecular interactions in biologically relevant settings. In this review, we will discuss the basic principles underpinning the functionality of these probes and will review advances in their use as sensors for lipid order, protein crowding and conformation, temperature and non-canonical nucleic acid structures in live cells and other relevant biological settings.

Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes

A multistep computational approach has been employed to study a multimillion all-atom dyed plasma membrane, with no less than 42 different lipid species spanning the major head groups and a variety of fatty acids, as well as cholesterol, with the objective of investigating its structure and dynamics, as well as its impact on the embedded di-8-ANEPPS dyes. The latter are commonly used as bioimaging probes and serve as local microscopes. So, they provide information on membrane morphology via their second harmonic nonlinear optical (NLO) responses, which have the advantage of being specific to interface regions and sensitive to the chromophore environment. In previous studies, this chromophore has only been studied in simpler membrane models, far from the complexity of real lipid bilayers, while, owing to the ever-increasing computational resources, multimillion lipid bilayers have been studied, giving access to the effects of its heterogeneity. First, using molecular dynamics (MD) simulations, it is found that the combination of lipids produces a more ordered and denser membrane compared to its homogeneous model counterparts, while the local environment of the embedded dyes becomes enriched in phosphatidylcholine. Subsequently, the second harmonic first hyperpolarizability of the probes was calculated at the TDDFT level on selected frames of MD, highlighting the influence of the lipid environment. Due to the complexity of the system, machine learning (ML) tools have been employed to establish relationships between the membrane structural parameters, the orientation of the probes, and their NLO responses. These ML approaches have revealed influential features, including the presence of diacylglycerol lipids close to the dye. On the whole, this work provides a first step toward understanding the cooperation, synergy, and interactions that occur in such complex guest-host environments, which have emerged as new targets for drug design and membrane lipid therapy.

Long-term spatiotemporal and highly specific imaging of the plasma membrane of diverse plant cells using a near-infrared AIE probe

Fluorescent probes are valuable tools to visualize plasma membranes intuitively and clearly and their related physiological processes in a spatiotemporal manner. However, most existing probes have only realized the specific staining of the plasma membranes of animal/human cells within a very short time period, while almost no fluorescent probes have been developed for the long-term imaging of the plasma membranes of plant cells. Herein, we designed an AIE-active probe with NIR emission to achieve four-dimensional spatiotemporal imaging of the plasma membranes of plant cells based on a collaboration approach involving multiple strategies, demonstrated long-term real-time monitoring of morphological changes of plasma membranes for the first time, and further proved its wide applicability to plant cells of different types and diverse plant species. In the design concept, three effective strategies including the similarity and intermiscibility principle, antipermeability strategy and strong electrostatic interactions were combined to allow the probe to specifically target and anchor the plasma membrane for an ultralong amount of time on the premise of guaranteeing its sufficiently high aqueous solubility. The designed APMem-1 can quickly penetrate cell walls to specifically stain the plasma membranes of all plant cells in a very short time with advanced features (ultrafast staining, wash-free, and desirable biocompatibility) and the probe shows excellent plasma membrane specificity without staining other areas of the cell in comparison to commercial FM dyes. The longest imaging time of APMem-1 can be up to 10 h with comparable performance in both imaging contrast and imaging integrity. The validation experiments on different types of plant cells and diverse plants convincingly proved the universality of APMem-1. The development of plasma membrane probes with four-dimensional spatial and ultralong-term imaging ability provides a valuable tool to monitor the dynamic processes of plasma membrane-related events in an intuitive and real-time manner.

Directly imaging emergence of phase separation in peroxidized lipid membranes

Lipid peroxidation is a process which is key in cell signaling and disease, it is exploited in cancer therapy in the form of photodynamic therapy. The appearance of hydrophilic moieties within the bilayer's hydrocarbon core will dramatically alter the structure and mechanical behavior of membranes. Here, we combine viscosity sensitive fluorophores, advanced microscopy, and X-ray diffraction and molecular simulations to directly and quantitatively measure the bilayer's structural and viscoelastic properties, and correlate these with atomistic molecular modelling. Our results indicate an increase in microviscosity and a decrease in the bending rigidity upon peroxidation of the membranes, contrary to the trend observed with non-oxidized lipids. Fluorescence lifetime imaging microscopy and MD simulations give evidence for the presence of membrane regions of different local order in the oxidized membranes. We hypothesize that oxidation promotes stronger lipid-lipid interactions, which lead to an increase in the lateral heterogeneity within the bilayer and the creation of lipid clusters of higher order.

Two-Photon Absorption: An Open Door to the NIR-II Biological Window?

The way in which photons travel through biological tissues and subsequently become scattered or absorbed is a key limitation for traditional optical medical imaging techniques using visible light. In contrast, near-infrared wavelengths, in particular those above 1000 nm, penetrate deeper in tissues and undergo less scattering and cause less photo-damage, which describes the so-called "second biological transparency window". Unfortunately, current dyes and imaging probes have severely limited absorption profiles at such long wavelengths, and molecular engineering of novel NIR-II dyes can be a tedious and unpredictable process, which limits access to this optical window and impedes further developments. Two-photon (2P) absorption not only provides convenient access to this window by doubling the absorption wavelength of dyes, but also increases the possible resolution. This review aims to provide an update on the available 2P instrumentation and 2P luminescent materials available for optical imaging in the NIR-II window.

Synthesis, X-ray structure, antimicrobial activity, DFT and molecular docking studies of N-(thiophen-2-ylmethyl)thiophene-2-carboxamide

In the present study, N-(thiophen-2-ylmethyl)thiophene-2-carboxamide, C10H9NOS2, (I), was obtained by the reaction of thiophene-2-carbonyl chloride and thiophen-2-ylmethanamine. Characterization of (I) was carried out using X-ray diffraction, spectroscopic techniques and elemental analyses. The DFT/B3LYP/6-311++G(d,p) theoretical level was successfully applied to calculate the optimized geometry and the local and global chemical activity parameters. The results obtained show good agreement between the experimental and theoretical geometrical parameters. The local and global chemical activity parameters were examined to determine the electrophilic and nucleophilic sites in (I). The natural bond orbital (NBO) analysis of (I) gives an efficient methodology for investigating the inter- and intramolecular bonding, as well as giving a convenient basis for investigating charge transfer or conjugative interactions in molecular systems. Also, the antimicrobial activity of (I) was investigated against eight microorganisms using the microdilution method and it is found to have an effective antibacterial activity. In addition, molecular docking studies were calculated in order to understand the nature of the binding of (I) with a lung cancer protein (PDB entry 1x2j).

Small molecule based fluorescent chemosensors for imaging the microenvironment within specific cellular regions

The microenvironment (local environment), including viscosity, temperature, polarity, hypoxia, and acidic-basic status (pH), plays indispensable roles in cellular processes. Significantly, organelles require an appropriate microenvironment to perform their specific physiological functions, and disruption of the microenvironmental homeostasis could lead to malfunctions of organelles, resulting in disorder and disease development. Consequently, monitoring the microenvironment within specific organelles is vital to understand organelle-related physiopathology. Over the past few years, many fluorescent probes have been developed to help reveal variations in the microenvironment within specific cellular regions. Given that a comprehensive understanding of the microenvironment in a particular cellular region is of great significance for further exploration of life events, a thorough summary of this topic is urgently required. However, there has not been a comprehensive and critical review published recently on small-molecule fluorescent chemosensors for the cellular microenvironment. With this review, we summarize the recent progress since 2015 towards small-molecule based fluorescent probes for imaging the microenvironment within specific cellular regions, including the mitochondria, lysosomes, lipid drops, endoplasmic reticulum, golgi, nucleus, cytoplasmic matrix and cell membrane. Further classifications at the suborganelle level, according to detection of microenvironmental factors by probes, including polarity, viscosity, temperature, pH and hypoxia, are presented. Notably, in each category, design principles, chemical synthesis, recognition mechanism, fluorescent signals, and bio-imaging applications are summarized and compared. In addition, the limitations of the current microenvironment-sensitive probes are analyzed and the prospects for future developments are outlined. In a nutshell, this review comprehensively summarizes and highlights recent progress towards small molecule based fluorescent probes for sensing and imaging the microenvironment within specific cellular regions since 2015. We anticipate that this summary will facilitate a deeper understanding of the topic and encourage research directed towards the development of probes for the detection of cellular microenvironments.

Imaging non-classical mechanical responses of lipid membranes using molecular rotors

Lipid packing in cellular membranes has a direct effect on membrane tension and microviscosity, and plays a central role in cellular adaptation, homeostasis and disease. According to conventional mechanical descriptions, viscosity and tension are directly interconnected, with increased tension leading to decreased membrane microviscosity. However, the intricate molecular interactions that combine to build the structure and function of a cell membrane suggest a more complex relationship between these parameters. In this work, a viscosity-sensitive fluorophore ('molecular rotor') is used to map changes in microviscosity in model membranes under conditions of osmotic stress. Our results suggest that the relationship between membrane tension and microviscosity is strongly influenced by the bilayer's lipid composition. In particular, we show that the effects of increasing tension are minimised for membranes that exhibit liquid disordered (Ld) - liquid ordered (Lo) phase coexistence; while, surprisingly, membranes in pure gel and Lo phases exhibit a negative compressibility behaviour, i.e. they soften upon compression.

Fluorescent Membrane Tension Probes for Super-Resolution Microscopy: Combining Mechanosensitive Cascade Switching with Dynamic-Covalent Ketone Chemistry

We report the design, synthesis, and evaluation of fluorescent flipper probes for single-molecule super-resolution imaging of membrane tension in living cells. Reversible switching from bright-state ketones to dark-state hydrates, hemiacetals, and hemithioacetals is demonstrated for twisted and planarized mechanophores in solution and membranes. Broadband femtosecond fluorescence up-conversion spectroscopy evinces ultrafast chalcogen-bonding cascade switching in the excited state in solution. According to fluorescence lifetime imaging microscopy, the new flippers image membrane tension in live cells with record red shifts and photostability. Single-molecule localization microscopy with the new tension probes resolves membranes well below the diffraction limit.

Multimodal optical contrast agents as new tools for monitoring and tuning nanoemulsion internalisation into cancer cells. From live cell imaging to in vivo imaging of tumours

Tailor-made NIR emitting dyes were designed as multimodal optical probes. These asymmetric amphiphilic compounds show combined intense absorption in the visible region, NIR fluorescence emission, high two-photon absorption in the NIR (with the maximum located around 1000 nm) as well as large Stokes' shift values and second-harmonic generation ability. Thanks to their structure, high loading into nanoemulsions (NEs) could be achieved leading to very high one- and two-photon brightness. These dyes were demonstrated to act as multimodal contrast agents able to generate different optical modalities of interest for bioimaging. Indeed, the uptake and carrier behaviour of the dye-loaded NEs into cancer cells could be monitored by simultaneous two-photon fluorescence and second-harmonic generation optical imaging. Multimodal imaging provided deep insight into the mechanism and kinetics of dye internalisation. Quite interestingly, the nature of the dyes was also found to influence both the kinetics of endocytosis and the internalisation pathways in glioblastoma cancer cells. By modulating the charge distribution within the dyes, the NEs can be tuned to escape lysosomes and enter the mitochondria. Moreover, surface functionalization with PEG macromolecules was realized to yield stealth NIRF-NEs which could be used for in vivo NIRF imaging of subcutaneous tumours in mice.

Second Harmonic Generation Spectroscopy of Membrane Probe Dynamics in Gram-Positive Bacteria

Bacterial membranes are complex mixtures with dispersity that is dynamic over scales of both space and time. To capture adsorption onto and transport within these mixtures, we conduct simultaneous second harmonic generation (SHG) and two-photon fluorescence measurements on two different gram-positive bacterial species as the cells uptake membrane-specific probe molecules. Our results show that SHG not only can monitor the movement of small molecules across membrane leaflets but also is sensitive to higher-level ordering of the molecules within the membrane. Further, we show that the membranes of Staphylococcus aureus remain more dynamic after longer times at room temperature in comparison to Enterococcus faecalis. Our findings provide insight into the variability of activities seen between structurally similar molecules in gram-positive bacteria while also demonstrating the power of SHG to examine these dynamics.

The synthesis and photophysical properties of tris-coumarins

A structurally unique cyclic tris-coumarin possessing three identical coumarin units bridged by amide linkers as well as two linear analogs has been synthesized. There is a remarkable agreement between crystallographic data, 1H NMR and results of calculations for the cyclic tris-coumarin, showing in all cases a non-symmetric arrangement of identical coumarin moieties. Weak polarization of the coumarin subunits, resulting from the presence of only CONH- groups as electron-donors, results in a hypsochromic shift of both absorption and emission in this dye. We have proven that in non-cyclic, head-to-tail linked tris-coumarins, the photophysics is controlled not only by the substituents but also by the conformation of the molecule, which in turn depends on the nature of the linker's interactions. These can be controlled by the presence/absence of an amide-type hydrogen atom responsible for the formation of intramolecular hydrogen bonds. The presence of a hydrogen bond favors a stretched trans conformation of the dye, while in its absence, folding of the molecule occurs leading to a more compact conformation. Although, the increased number of covalently linked coumarin units does not drastically change the preferred conformation, the fluorescence quantum yields of tris-coumarins are significantly lower than for analogous bis-coumarins composed of the same units.

Solvent-dependent photophysics of a red-shifted, biocompatible coumarin photocage

A novel coumarin photocage with long-wavelength and high photolysis quantum yield shows solvent dependent photolysis.

Push-pull pyropheophorbides for nonlinear optical imaging

Pyropheophorbide-a methyl ester (PPa-OMe) has been modified by attaching electron-donor and -acceptor groups to alter its linear and nonlinear optical properties. Regioselective bromination of the terminal vinyl position and Suzuki coupling were used to attach a 4-(N,N-diethylaminophenyl) electron-donor group. The electron-acceptor dicyanomethylene was attached at the cyclic ketone position through a Knoevenagel condensation. Four different derivatives of PPa-OMe, containing either electron-donor or electron-acceptor groups, or both, were converted to hydrophilic bis-TEG amides to generate a series of amphiphilic dyes. The absorption and emission properties of all the dyes were compared to a previously reported push-pull type porphyrin-based dye and a commercial push-pull styryl dye, FM4-64. Electrochemical measurements reveal that the electron donor group causes a greater decrease in HOMO-LUMO gap than the electron-acceptor. TD-DFT calculations on optimized geometries (DFT) of all four dyes show that the HOMO is mostly localized on the donor, 4-(N,N-diethylaminophenyl), while the LUMO is distributed around the chlorin ring and the electron-acceptor. Hyper-Rayleigh scattering experiments show that the first-order hyperpolarizabilities of the dyes increase on attaching either electron-donor or -acceptor groups, having the highest value when both the donor and acceptor groups are attached. Two-photon excited fluorescence (TPEF) and second harmonic generation (SHG) images of the bis-TEG amide attached dyes in lipid monolayer-coated droplets of water-in-oil reveal that the TPEF and SHG involve transition dipole moments in different orientations.

Effect of conformational flexibility on photophysics of bis-coumarins

The fluorescence of bis-coumarins linked via CONH and COO functionalities is strongly dependant on solvent polarity.

Planarizable Push-Pull Probes: Overtwisted Flipper Mechanophores

Planarizable push-pull fluorescent probes, also referred to as flipper probes, have been introduced as conceptually innovative mechanophores that report on forces in their local environment in lipid bilayer membranes. The best flipper probes respond to a change from liquid disordered to solid ordered membranes with a red shift in excitation of 50-90 nm. A simultaneous increase in fluorescence lifetime and negligible background fluorescence from the aqueous phase qualifies these fluorescent probes for meaningful imaging in live cells. Here, we report that the replacement of methyl with isobutyl substituents along the scaffold of a dithienothiophene dimer strongly reduces fluorescence intensity but increases solvatochromism slightly. These trends imply that the large substituents in "leucine flippers" hinder the planarization in the first excited state to result in twisted intramolecular charge transfer (TICT). As a result of this overtwisting, the leucine flippers form interesting fluorescent micelles in water but fail to respond to changes in membrane order. These dramatic changes in function provide one of the most impressive illustrations for the hypersensitivity of fluorescent membrane probes toward small changes in their structure.

Visualising the membrane viscosity of porcine eye lens cells using molecular rotors

The plasma membranes of cells within the eye lens play an important role in metabolite transport within the avascular tissue of the lens, maintaining its transparency over the entire lifespan of an individual. Here we use viscosity-sensitive 'molecular rotors' to map the microscopic viscosity within these unusual cell membranes, establishing that they are characterised by an unprecedentedly high degree of lipid organisation.

Non-linear optical, electrochemical and spectroelectrochemical properties of amphiphilic inner salt porphyrinic systems

Three zwitterionic meso-substituted A3B- and AB2C-porphyrins containing one sulfonato alkylpyridinium substituent and three or two alkoxy-substituted phenyl groups were synthesized in good yield and fully characterized as to their physicochemical properties by a variety of techniques. This new series of inner salt donor-acceptor meso-substituted porphyrin derivatives were prepared for possible application as amphiphilic probes for membrane insertion in the area of combined second-harmonic and two-photon fluorescence cellular microscopy. To this end, the linear and nonlinear optical properties of the compounds were characterized, together with their electrochemical and spectroelectrochemical properties in non-aqueous media. The neutral design of such molecules enabled us to determine their second order non-linear properties, both by Electric Field Induced Second Harmonic Generation and Hyper–Rayleigh Scattering. Two-photon absorption cross sections of these dyes were also measured by the two-photon induced fluorescence method. The zwitterionic nature of the inner salt results in very specific solvent-dependent redox-properties, which could be rationalized in terms of solvent-dependent ion-pairing. The overall data electrochemical and photophysical data indicates that these new porphyrinic systems should be good probes for membrane potential sensing.

Dipolar Dyes with a Pyrrolo[2,3-b]quinoxaline Skeleton Containing a Cyano Group and a Bridged Tertiary Amino Group: Synthesis, Solvatofluorochromism, and Bioimaging

Two strongly polarized dipolar chromophores possessing a cyclic tertiary amino group at one terminus of the molecule and a CN group at the opposite terminus were designed and synthesized. Their rigid skeleton contains the rarely studied pyrrolo[2,3-b]quinoxaline ring system. The photophysical properties of these regioisomeric dyes were different owing to differing π conjugation between the CN group and the electron-donor moiety. These dipolar molecules showed very intense emission, strong solvatofluorochromism, and sufficient two-photon brightness for bioimaging. One of these regioisomeric dyes, namely, 11-carbonitrile-2,3,4,5,6,7-hexahydro-1H-3a,8,13,13b-tetraazabenzo[b]cyclohepta[1,2,3-jk]fluorene, was successfully utilized in two-photon imaging of mouse organ tissues and showed distinct tissue morphology with high resolution.

Multimodal two-photon imaging using a second harmonic generation-specific dye

Second harmonic generation (SHG) imaging can be used to visualize unique biological phenomena, but currently available dyes limit its application owing to the strong fluorescent signals that they generate together with SHG. Here we report the first non-fluorescent and membrane potential-sensitive SHG-active organic dye Ap3. Ap3 is photostable and generates SH signals at the plasma membrane with virtually no fluorescent signals, in sharp contrast to the previously used fluorescent dye FM4-64. When tested in neurons, Ap3-SHG shows linear membrane potential sensitivity and fast responses to action potentials, and also shows significantly reduced photodamage compared with FM4-64. The SHG-specific nature of Ap3 allows simultaneous and completely independent imaging of SHG signals and fluorescent signals from various reporter molecules, including markers of cellular organelles and intracellular calcium. Therefore, this SHG-specific dye enables true multimodal two-photon imaging in biological samples.

Current dyes for second harmonic generation (SHG) imaging strongly fluoresce, limiting their application. Here the authors develop a SHG-specific dye, Ap3, that partitions into cell membranes, displays sensitivity to membrane potential and has virtually no fluorescence emission at SHG imaging wavelengths.

Imaging plasma membrane phase behaviour in live cells using a thiophene-based molecular rotor

A thiophene-based molecular rotor was used to probe ordering and viscosity within artificial lipid bilayers and live cell plasma membranes.

Headgroup engineering in mechanosensitive membrane probes

Tricky chemistry had to be addressed to make mechanosensitive membrane probes ready for use, including a chalcogen-bond mediated “molecular guillotinylation”.

Solvatofluorochromic, non-centrosymmetric π-expanded diketopyrrolopyrrole

A donor–acceptor type π-expanded diketopyrrolopyrrole behaves as non-centrosymmetric as far as linear optical properties are concerned but as ‘pseudo-symmetric’ for two-photon absorption.

Strong solvent dependence of linear and non-linear optical properties of donor–acceptor type pyrrolo[3,2-b]pyrroles

The pyrrolo[3,2-b]pyrrole core was determined to be an efficient linker allowing the conjugation of peripheral benzene rings. The resulting dipolar compounds displayed strong solvatochromism of fluorescence.