Environment-sensitive Probe Research Articles

VISION - an open-source software for automated multi-dimensional image analysis of cellular biophysics.

Environment-sensitive probes are frequently used in spectral and multi-channel microscopy to study alterations in cell homeostasis. However, the few open-source packages available for processing of spectral images are limited in scope. Here, we present VISION, a stand-alone software based on Python for spectral analysis with improved applicability. In addition to classical intensity-based analysis, our software can batch-process multidimensional images with an advanced single-cell segmentation capability and apply user-defined mathematical operations on spectra to calculate biophysical and metabolic parameters of single cells. VISION allows for 3D and temporal mapping of properties such as membrane fluidity and mitochondrial potential. We demonstrate the broad applicability of VISION by applying it to study the effect of various drugs on cellular biophysical properties. the correlation between membrane fluidity and mitochondrial potential, protein distribution in cell-cell contacts and properties of nanodomains in cell-derived vesicles. Together with the code, we provide a graphical user interface for easy adoption.

Novel insights into the modulation of the voltage-gated potassium channel KV1.3 activation gating by membrane ceramides

Membrane lipids extensively modulate the activation gating of voltage-gated potassium channels (KV), however, much less is known about the mechanisms of ceramide and glucosylceramide actions including which structural element is the main intramolecular target and whether there is any contribution of indirect, membrane biophysics-related mechanisms to their actions. We used two-electrode voltage-clamp fluorometry capable of recording currents and fluorescence signals to simultaneously monitor movements of the pore domain (PD) and the voltage sensor domain (VSD) of the KV1.3 ion channel after attaching an MTS-TAMRA fluorophore to a cysteine introduced into the extracellular S3-S4 loop of the VSD. We observed rightward shifts in the conductance-voltage (G-V) relationship, slower current activation kinetics, and reduced current amplitudes in response to loading the membrane with C16-ceramide (Cer) or C16-glucosylceramide (GlcCer). When analyzing VSD movements, only Cer induced a rightward shift in the fluorescence signal-voltage (F-V) relationship and slowed fluorescence activation kinetics, whereas GlcCer exerted no such effects. These results point at a distinctive mechanism of action with Cer primarily targeting the VSD, while GlcCer only the PD of KV1.3. Using environment-sensitive probes and fluorescence-based approaches, we show that Cer and GlcCer similarly increase molecular order in the inner, hydrophobic regions of bilayers, however, Cer induces a robust molecular reorganization at the membrane-water interface. We propose that this unique ordering effect in the outermost membrane layer in which the main VSD rearrangement involving an outward sliding of the top of S4 occurs can explain the VSD targeting mechanism of Cer, which is unavailable for GlcCer.

Fluorescence Lifetime Imaging of Lipid Heterogeneity in the Inner Mitochondrial Membrane with a Super-photostable Environment-Sensitive Probe.

The inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red-emissive IMM-labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super-resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling.

A study of hydrophobic domain formation of polymeric drug precipitation inhibitors in aqueous solution

Despite the widespread use of polymers as precipitation inhibitors in supersaturating drug formulations, the current understanding of their mechanisms of action is still incomplete. Specifically, the role of hydrophobic drug interactions with polymers by considering possible supramolecular conformations in aqueous dispersion is an interesting topic. Accordingly, this study investigated the tendency of polymers to create hydrophobic domains, where lipophilic compounds may nest to support drug solubilisation and supersaturation. Fluorescence spectroscopy with the environment-sensitive probe pyrene was compared with atomistic molecular dynamics simulations of the model drug fenofibrate (FENO). Subsequently, kinetic drug supersaturation and thermodynamic solubility experiments were conducted. As a result, the different polymers showed hydrophobic domain formation to a varying degree and the molecular simulations supported interpretation of fluorescence spectroscopy data. Molecular insights were gained into the conformational structure of how the polymers interacted with FENO in solution phase, which apart from nucleation and crystal growth effects, determined drug concentrations in solution. Notable was that even at the lowest polymer concentration of 0.01 %, w/v, there were polymer-specific solubilisation effects of FENO observed and the resulting reduction in apparent drug supersaturation provided relevant knowledge both from a mechanistic and practical perspective.

Quantifying Fluorescence Lifetime Responsiveness of Environment-Sensitive Probes for Membrane Fluidity Measurements.

The structural diversity of different lipid species within the membrane defines its biophysical properties such as membrane fluidity, phase transition, curvature, charge distribution, and tension. Environment-sensitive probes, which change their spectral properties in response to their surrounding milieu, have greatly contributed to our understanding of such biophysical properties. To realize the full potential of these probes and avoid misinterpretation of their spectral responses, a detailed investigation of their fluorescence characteristics in different environments is necessary. Here, we examined the fluorescence lifetime of two newly developed membrane order probes, NR12S and NR12A, in response to alterations in their environments such as the degree of lipid saturation, cholesterol content, double bond position and configuration, and phospholipid headgroup. As a comparison, we investigated the lifetime sensitivity of the membrane tension probe Flipper in these environments. Applying fluorescence lifetime imaging microscopy (FLIM) in both model membranes and biological membranes, all probes distinguished membrane phases by lifetime but exhibited different lifetime sensitivities to varying membrane biophysical properties (e.g., cholesterol). While the lifetime of Flipper is particularly sensitive to the membrane cholesterol content, the NR12S and NR12A lifetimes are moderately sensitive to both the cholesterol content and lipid acyl chains. Moreover, all of the probes exhibit longer lifetimes at longer emission wavelengths in membranes of any complexity. This emission wavelength dependency results in varying lifetime resolutions at different spectral regions, which are highly relevant for FLIM data acquisition. Our data provide valuable insights on how to perform FLIM with these probes and highlight both their potential and limitations.

Use of DFT Calculations as a Tool for Designing New Solvatochromic Probes for Biological Applications

The intramolecular charge transfer behavior of push–pull dyes is the origin of their sensitivity to environment. Such compounds are of interest as probes for bioimaging and as biosensors to monitor cellular dynamics and molecular interactions. Those that are solvatochromic are of particular interest in studies of lipid dynamics and heterogeneity. The development of new solvatochromic probes has been driven largely by the need to tune desirable properties such as solubility, emission wavelength, or the targeting of a particular cellular structure. DFT calculations are often used to characterize these dyes. However, if a correlation between computed (dipole moment) and experimentally measured solvatochromic behavior can be established, they can also be used as a design tool that is accessible to students. Here, we examine this correlation and include case studies of the effects of probe modifications and conformation on dipole moments within families of solvatochromic probes. Indeed, the ground state dipole moment, an easily computed parameter, is correlated with experimental solvatochromic behavior and can be used in the design of new environment-sensitive probes before committing resources to synthesis.

Characterization of environment-sensitive probes to study membrane biophysical properties

Characterization of environment-sensitive probes to study membrane biophysical properties

Fluorescent Probes Based on Charge and Proton Transfer for Probing Biomolecular Environment.

Fluorescent probes for sensing fundamental properties of biomolecular environment, such as polarity and hydration, help to study assembly of lipids into biomembranes, sensing interactions of biomolecules and imaging physiological state of the cells. Here, we summarize major efforts in the development of probes based on two photophysical mechanisms: (i) an excited-state intramolecular charge transfer (ICT), which is represented by fluorescent solvatochromic dyes that shift their emission band maximum as a function of environment polarity and hydration; (ii) excited-state intramolecular proton transfer (ESIPT), with particular focus on 5-membered cyclic systems, represented by 3-hydroxyflavones, because they exhibit dual emission sensitive to the environment. For both ICT and ESIPT dyes, the design of the probes and their biological applications are summarized. Thus, dyes bearing amphiphilic anchors target lipid membranes and report their lipid organization, while targeting ligands direct them to specific organelles for sensing their local environment. The labels, amino acid and nucleic acid analogues inserted into biomolecules enable monitoring their interactions with membranes, proteins and nucleic acids. While ICT probes are relatively simple and robust environment-sensitive probes, ESIPT probes feature high information content due their dual emission. They constitute a powerful toolbox for addressing multitude of biological questions.

Establishment of environment-sensitive probes targeting BRD3/BRD4 for imaging and therapy of tumor

The BET (bromo and extra-terminal) family proteins are epigenetic readers and master transcription coactivators, which have attracted great interests as cancer therapeutic targets. However, there are few developed labeling toolkits that can be applied for the dynamic studies of BET family proteins in living cells and tissue slices. In order to label and study the distribution of the BET family proteins in tumor cells and tumor tissues, a novel series of environment-sensitive fluorescent probes (6a-6c) were designed and evaluated for their labeling properties. Interestingly, 6a is capable of identifying tumor tissue slices and making a distinction between the tumor and normal tissues. Moreover, it can localize to the nuclear bodies in tumor slices just like BRD3 antibody. In addition, it also played an anti-tumor role through the induction of apoptosis. All these features render 6a may compatible for immunofluorescent studies and future cancer diagnosis, and guide for the discovery of new anticancer drugs.

Spatiotemporal single-cell phenotyping in living 3D skin organoids.

Continuous monitoring of cell states in living tissues remains elusive despite the explosion of single cell technologies. Here, we use organelle-specific environment-sensitive probes (ESPs) combined with hyperspectral imaging and a dedicated quantitative analysis pipeline to spatially and temporally track keratinocyte cell states in living 3D skin organoids. Our technique, named ESPRESSO (Environmental Sensors Profiling Relayed by Subcellular Structures and Organelles) combines hyperspectral imaging and phasor unmixing, enabling imaging of up to 6 ESPs (targeting chromatin, mitochondria, lysosomes, tubulin, Golgi apparatus and lipid droplets) at the same time with a single laser excitation. The quantification of morphological (e.g., number, size, organization) and functional (e.g., membrane potential, pH, polarity) characteristics of the organelles and subcellular structures allows us to identify the cell state at the single-cell level and is applicable to living cells in 2D and 3D. Cell state and cell-cell interactions are tightly regulated in space and time to determine tissue function. However, the spatiotemporal regulation of cell states and their interactions at the systems level during skin development and dysfunction remains poorly understood. Determination of cell states is routinely achieved by high-dimensional methods such as single-cell RNA sequencing (scRNA-seq), which yields the transcriptional profile at the single cell level of cell cultures and tissue. However, processing of the sample is required with consequent loss of spatial information. Genetic modification to include fluorescent tagging of a biomarker of interest can sometimes be used for living samples, although this approach is limited to observing a few parameters at one time and it may not be applicable to primary cells due to difficulty in transfection and early loss of proliferative capacity. Here, we demonstrate the capability of ESPRESSO to characterize keratinocyte differentiation as a function of space and time in living 3D skin organoid.

Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties.

The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis vs. trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.

Investigation of breast cancer metabolic plasticity in the tumor microenvironment by single-cell organelle phenotyping.

Metabolic plasticity, i.e., the capability of cells to modify their metabolic state, is a hallmark of cancer and an important factor in the formation of metastases as well as a major contributor to chemoresistance and tumor recurrence. Furthermore, the tumor microenvironment, namely the collection of environmental properties (pH, nutrient availability, fatty acids) and cell types that surround the main tumor mass, is regarded to as the main driver of the metabolic state of tumor cells. Unfortunately, no technique can non-invasively assess the metabolic state of single cells in living samples, limiting our understanding of the heterogeneity and dynamics of metabolic state transitions. Here, we apply a technique, named ESPRESSO (Environmental Sensors Profiling Relayed by Subcellular Structures and Organelles) that combines organelle-specific environment-sensitive probes (ESPs) with hyperspectral imaging and quantitative bioimage analysis. We use a mixture of lipid droplet-, mitochondria- and lysosome-specific ESPs to quantify of morphological (e.g., number, size, organization) and functional (e.g., membrane potential, pH, polarity) characteristics to identify the metabolic state in single, living cells. To understand the differences in metabolic plasticity of non-tumorigenic breast epithelial (MCF10a) and triple negative breast cancer (MDA-MB-231) cells, we determined their metabolic state with ESPRESSO under a variety of stress and environmental conditions, identifying the characteristic metabolic signature of the cell lines under those conditions. We further investigated the response to diverse chemotherapy drugs (doxorubicin, paclitaxel, curcumin) in an effort to understand their effect on cancer and healthy cells, highlighting the environmental conditions that would favor the resistance to a specific drug treatment. Taken together, we provide a framework to identify the metabolic response of cancer and non-tumorigenic cells under different drugs, stressors and environmental conditions, providing in-depth characterization of their metabolic response at the single cell level.

Ultrafast fluorescence depolarisation in green fluorescence protein tandem dimers as hydrophobic environment sensitive probes.

Advances in ultra-fast photonics have enabled monitoring of biochemical interactions on a sub nano-second time scale. In addition, picosecond dynamics of intermolecular energy transfer in fluorescent proteins has been observed. Here, we present the development of a genetically encoded fluorescent sensor that can detect changes in hydrophobicity by monitoring ultrafast fluorescence depolarisation. Our sensor is composed of a pair of dimeric enhanced green fluorescent proteins (dEGFPs) linked by a flexible amino-acid linker. We show dimerisation is perturbed by the addition of glycerol which interferes with the hydrophobic interaction of the two proteins. Time-resolved fluorescence anisotropy revealed a systematic attenuation of ultrafast fluorescence depolarisation when the sensor was exposed to increasing glycerol concentrations. This suggests that as hydrophobicity increases, dEGFP pairing decreases within a tandem dimer. Un-pairing of the protein fluorophores dramatically alters the rate of energy transfer between the proteins, resulting in an increase in the limiting anisotropy of the sensor.

Membrane interactions of apoptotic inhibitor Bcl-xL: What can be learned using fluorescence spectroscopy

Permeabilization of the mitochondrial outer membrane–a point of no return in apoptotic regulation–is tightly controlled by proteins of the Bcl-2 family. Apoptotic inhibitor Bcl-xL is an important member of this family, responsible for blocking the permeabilization, and is also a promising target for anti-cancer drugs. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (i) a soluble folded conformation, (ii) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (iii) refolded membrane-inserted conformations, for which no structural data are available. In this review, we present the summary of the application of various methods of fluorescence spectroscopy for studying membrane interaction of Bcl-xL, and specifically the formation of the refolded inserted conformation. We discuss the application of environment-sensitive probes, Förster resonance energy transfer, fluorescence correlation spectroscopy, and fluorescent quenching for structural, thermodynamic, and functional characterization of protein-lipid interactions, which can benefit studies of other members of Bcl-2 (e.g., Bax, BAK, Bid). The conformational switching between various conformations of Bcl-xL depends on the presence of divalent cations, pH and lipid composition. This insertion-refolding transition also results in the release of the BH4 regulatory domain from the folded structure of Bcl-xL, which is relevant to the lipid-regulated conversion between canonical and non-canonical modes of apoptotic inhibition.

8-Aminoquinoline-containing squaric acid congeners as polarity and viscosity probes

Squaraine-type dyes are privileged motifs and scaffolds with valuable and tunable photophysical properties, and have found numerous applications in various areas of chemical and biological sciences. Yet, environment-sensing capabilities of squaraine dyes have not been widely explored. This study illustrates how selective incorporation of a readily available 8-aminoquinoline moiety onto squaric acid or squarate scaffolds fine-tunes environment-sensing capabilities of these dyes. The squaraine motif is required for achieving meaningful correlations between probe’s photophysical properties and media’s properties, whereas semi-squaraine and squaramide analogues exhibit inferior environment-sensing capabilities. The 1,3-bis(8-aminoquinolinyl)squaraine dye shows potential as a multiplexing environment-sensitive probe that could sense media’s polarity variations via absorption changes, and environmental viscosity via amplitude-weighted fluorescence lifetime changes.

Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties.

The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades, several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis versus trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.

4-Azidocinnoline-Cinnoline-4-amine Pair as a New Fluorogenic and Fluorochromic Environment-Sensitive Probe.

A new type of fluorogenic and fluorochromic probe based on the reduction of weakly fluorescent 4-azido-6-(4-cyanophenyl)cinnoline to the corresponding fluorescent cinnoline-4-amine was developed. We found that the fluorescence of 6-(4-cyanophenyl)cinnoline-4-amine is strongly affected by the nature of the solvent. The fluorogenic effect for the amine was detected in polar solvents with the strongest fluorescence increase in water. The environment-sensitive fluorogenic properties of cinnoline-4-amine in water were explained as a combination of two types of fluorescence mechanisms: aggregation-induced emission (AIE) and excited state intermolecular proton transfer (ESPT). The suitability of an azide–amine pair as a fluorogenic probe was tested using a HepG2 hepatic cancer cell line with detection by fluorescent microscopy, flow cytometry, and HPLC analysis of cells lysates. The results obtained confirm the possibility of the transformation of the azide to amine in cells and the potential applicability of the discovered fluorogenic and fluorochromic probe for different analytical and biological applications in aqueous medium.

Environment-sensitive emission of anionic hydrogen-bonded urea-derivative\u2013acetate-ion complexes and their aggregation-induced emission enhancement

Anions often quench fluorescence (FL). However, strong ionic hydrogen bonding between fluorescent dyes and anion molecules has the potential to control the electronic state of FL dyes, creating new functions via non-covalent interactions. Here, we propose an approach, utilising ionic hydrogen bonding between urea groups and anions, to control the electronic states of fluorophores and develop an aggregation-induced emission enhancement (AIEE) system. The AIEE ionic hydrogen-bonded complex (IHBC) formed between 1,8-diphenylnaphthalene (p-2Urea), with aryl urea groups at the para-positions on the peri-phenyl rings, and acetate ions exhibits high environmental sensitivities in solution phases, and the FL quantum yield (QY) in ion-pair assemblies of the IHBC and tetrabutylammonium cations is more than five times higher than that of the IHBC in solution. Our versatile and simple approach for the design of AIEE dye facilitates the future development of environment-sensitive probes and solid-state emitting materials.

Exhibiting environment sensitive optical properties through multiscale modelling: A study of photoactivatable probes

To assess a tumor biomarker like the cyclooxygenase-2 enzyme (COX-2), non-invasive imaging techniques are powerful tools. The (non-) linear optical properties of activatable fluorescent probes which are selectively bound to the biomarker can therefore be exploited. The here presented molecular modelling results based on multi-scale modelling techniques highlight the importance of the conformational versatility and of changes in the electronic interactions of such probes when they are embedded in water or in the COX-2 homodimer enzyme. The ANQ-IMC-6 probe, which combines the binding domain/scaffold of indomethacin (IMC) on COX-2 with the optical properties of acenaphtho[1,2-b]quinoxaline (ANQ), is found to be folded in the solvent and unfolded in the enzyme. A concerted movement of the probe and the protein is seen, while the rotational autocorrelation function exhibits also the intrinsic properties of the probe. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) calculations are used to simulate the one-photon and two-photon absorption spectra along with the first hyperpolarizability. The transition has a local character in vacuum, but changes to a charge transfer one in the presence of the microenvironment of the enzyme. This is also visible through a change of the shape of the absorption spectrum, while at the same time the simulated signals of second harmonic generation experiments are strongly enhanced. The results of this work prove that an environment sensitive probe with an anchoring group and an optical active part can be constructed for use in absorption spectroscopy, without the need to revert to fluorescence experiments.

Impact of Hydroxypropyl Methylcellulose Acetate Succinate Critical Aggregation Concentration on Celecoxib Supersaturation.

Polymers play an important role in amorphous solid dispersions (ASDs), enhancing stability in the solid state and maintaining supersaturation in aqueous solutions of intrinsically low-water-soluble drug candidates. Hydroxypropyl methylcellulose acetate succinate (HPMCAS) is widely used in ASDs due to its hydrophobic/hydrophilic balance and ionizability of the substituent functionalities. While colloid formation of HPMCAS in solution due to this hydrophobic/hydrophilic balance has been studied, the impact of the polymer conformation (random coil vs aggregated) on drug supersaturation of ASDs is not well understood. To our knowledge, this is the first report where the critical aggregation concentration for three grades of HPMCAS (HF/MF/LF) has been determined via fluorescence spectroscopy using the environment-sensitive probe pyrene. The specific impact of polymer conformation (random coil vs aggregate) on the model drug celecoxib (CLX) has been elucidated with fluorescence quenching and nuclear magnetic resonance (NMR) spectroscopy. A negative deviation of the Stern-Volmer plot indicated that aggregated HPMCAS effectively blocked the quencher's access to CLX. This is further supported by NMR observations, where NMR spectra indicate a larger change of chemical shift of the -NH group of CLX when HPMCAS is above its aggregated concentration, suggesting strong H-bonding interactions between aggregated HPMCAS and CLX. Finally, the supersaturation-precipitation study shows that all three grades of HPMCAS in the aggregated state significantly enhanced CLX supersaturation compared to the nonaggregated state, indicating that polymer aggregation plays a critical role in maintaining drug supersaturation.