Why fluorescent probes for endoplasmic reticulum are selective: an experimental and QSAR-modelling study

The basis of the selectivity of fluorochromes routinely used to visualize the endoplasmic reticulum (ER) in live cells remains obscure. To clarify this, interactions of living cells with fluorochromes of varied physicochemical properties were analyzed experimentally and numerically using a quantitative structure activity relationship analysis (QSAR). Routine selective ER probes were found to be amphipathic, lipophilic cations with moderate-sized conjugated systems. The moderately lipophilic character permits probe uptake by passive diffusion without nonspecific accumulation in biomembranes. The moderately amphipathic character favors uptake into the ER, perhaps owing to its high concentration of zwitterionic lipid head-groups. The QSAR model rationalizes the impractical character of some ER probes mentioned in the literature, and could permit design of novel ER probes with different emission colors. The possibility of using the QSAR model as a tool to predict the accumulation of xenobiotics in the ER of living cells is illustrated by the localization of certain antipsychotic drugs in cultured cells.     

Why fluorescent probes for endoplasmic reticulum are selective: an experimental and QSAR-modelling study

The basis of the selectivity of fluorochromes routinely used to visualize the endoplasmic reticulum (ER) in live cells remains obscure. To clarify this, interactions of living cells with fluorochromes of varied physicochemical properties were analyzed experimentally and numerically using a quantitative structure activity relationship analysis (QSAR). Routine selective ER probes were found to be amphipathic, lipophilic cations with moderate-sized conjugated systems. The moderately lipophilic character permits probe uptake by passive diffusion without nonspecific accumulation in biomembranes. The moderately amphipathic character favors uptake into the ER, perhaps owing to its high concentration of zwitterionic lipid head-groups. The QSAR model rationalizes the impractical character of some ER probes mentioned in the literature, and could permit design of novel ER probes with different emission colors. The possibility of using the QSAR model as a tool to predict the accumulation of xenobiotics in the ER of living cells is illustrated by the localization of certain antipsychotic drugs in cultured cells.     

Interactions of molecular probes with living cells and tissues. Part 1. Some general mechanistic proposals,making use of a simplistic Chinese box model

Summary A simple and generalised model — termed the simplistic Chinese box [SCB] model — for the interaction of molecular probes with living systems is described. The SCB model includes the following assumptions. That living systems may be considered as built from biologically defined boxes, e.g. whole cell nucleus nucleoli. That movement of molecular probes into and through these boxes is strongly infuenced by box wall permeability, which in turn is largely dependent on the simple physicochemical properties of probe and wall. That retention of probes in boxes is influenced by permeability of the walls and by trapping of probes by boxes and walls, the latter effect also being strongly dependent on simple physicochemical, properties. That important physicochemical properties include electric charge, hydrophilicity/lipophilicity, non-specific protein binding, and molecular size. That, since all these factors can be expressed or modelled numerically, SAR methodology is an appropriate technique for analysing molecular probe investigations. This paper is dedicated to the memory of Prof. A.W. Rogers     

Perturbing probes and the study of lipid-protein bilayer membranes

Recent experimental and theoretical developments concerning perturbing probes are outlined. The fluorescent probe 1,6-diphenyl-1,3,5-hexatriene and nitroxide electron paramagnetic resonance spin labels attached to lipid hydrocarbon chains are taken as the most widely used examples of such probes. The reliability of these probes as indicators of the statics and dynamics of unlabelled lipid hydrocarbon chains is discussed, and the use of such probes in giving information about protein size, protein oligomerization and protein lateral distribution is outlined. Examples are given of studies to determine protein packing in lipid bilayers membranes.     

Comparative study on fluorescent probes distributed in human erythrocytes and platelets

Important cellular functions, such as rheological properties of cells are presumably related to the membrane lipid fluidity which may be approached by the use of fluorescence polarization method. However, biological membranes represent very heterogeneous media and the knowledge of the fluidity of membrane compartments requires the use of different probes. Two fluorescent probes, DPH and its cationic derivative, TMA-DPH, have been employed to probe the lipid fluidity of human platelets and red cell membranes. The results show that the informations given by DPH and TMA-DPH can present important differences, suggesting that DPH and TMA-DPH are localized in different regions of cell membranes. In an attempt to investigate relations between lipid fluidity and rheological properties of red cells, the behavior of probes was studied in a "Couette" viscometer with a device for studying the emissive properties of probes when red cell membranes are under shear conditions.     

Optical probes and transducers

Biosensors are by definition a combination of a biological receptor compound and a physical or physicochemical transducer. Therefore, the transducing structure is a critical part of every biosensor. In the development of new and improved biosensing layers the importance of the transducing structure is not restricted to the substrate to which biological structures have to be coupled. A field of even greater importance is the use of transducers as probes providing information on the structure and function of biosensing layers, and their relation to a transducer surface.

The aim of this paper is to give an overview on optical transducer principles and optical (surface) analytical techniques relevant as part of biosensing structures as well as probes in the development and optimisation of biosensing layers. Categories discussed are basic optical effects, materials involved, surface chemistry, the principal and technological limits of spatial resolution, and sensitivity. The intimate relation between the spatial resolution of a probe, the resulting size of interaction areas, and the feasibility of array structures is pointed out.

Two interferometric methods are presented in principle, and their application to biosensing and some results are discussed in detail. The necessity to characterise receptor layers to get detailed information about the interaction process is pointed out. The close relationship between optimal characterisation of layers by selection of adequate probe technologies and improvement of probe performance, and the development of new biosensing layers is discussed. Finally an outlook is given for future aspects of improved spatial resolution and multianalyte detection.     

Fluorescent lipid probes: properties and application

This review is devoted to fluorescent lipid probes: the characteristics of their fluorophores; the main methods of their synthesis; and the potentialities, scope, and limitations of their use in studies of biological systems (cells, membranes and their models, enzymes of lipid metabolism, etc.). Particular attention is paid to the lipid specificity of the probes, i.e., the correspondence of their physicochemical characteristics and behavior in biological systems to those of natural lipids.     

Interactions of molecular probes with living cells and tissues. Part 1. Some general mechanistic proposals, making use of a simplistic Chinese box model

A simple and generalised model-termed the simplistic Chinese box [SCB] model-for the interaction of molecular probes with living systems is described. The SCB model includes the following assumptions. That living systems may be considered as built from biologically defined boxes, e.g. whole cell, nucleus, nucleoli. That movement of molecular probes into and through these boxes is strongly influenced by box wall permeability, which in turn is largely dependent on the simple physicochemical properties of probe and wall. That retention of probes in boxes is influenced by permeability of the walls and by trapping of probes by boxes and walls, the latter effect also being strongly dependent on simple physicochemical properties. That important physicochemical properties include electric charge, hydrophilicity/lipophilicity, non-specific protein binding, and molecular size. That, since all these factors can be expressed or modelled numerically, SAR methodology is an appropriate technique for analysing molecular probe investigations.     

Multivalent carbocyanine molecular probes: synthesis and applications

Synergistic multivalent interactions can amplify desired chemical or biological molecular recognitions. We report a new class of multicarboxylate-containing carbocyanine dye constructs for use as optical scaffolds that not only serve as fluorescent antennas but also participate in structural assembly of the multivalent molecular construct. Three generations of carboxylate-terminating multivalent near-infrared carbocyanine probes from a dicarboxylic acid precursor dye (cypate) were prepared via its imino diacetic acid derivatives. Conjugation of the probes with D-(+)-glucosamine afforded dendritic arrays of the carbohydrates on an inner NIR chromophore core. All the multicarboxylate probes and their glucosamine conjugates have similar NIR spectral properties because conjugation occurred at distal positions to the inner chromophore core, thereby providing consistent and predictable spectral properties for their biological applications. Although light-induced photodamage equally affected the precursor dye, multicarboxylate probes, and their glucosamine derivatives, we observed that octacarboxylcypate (multivalent probe) was remarkably stable in different mediums at physiologically relevant temperatures relative to cypate, especially in basic mediums. Biodistribution studies in tumor-bearing nude mice show that all the glucosamine conjugates localized in the tumor but cypate was almost exclusively retained in the liver at 24 h postinjection. The tumor uptake does not correlate with the number of glucosamine tether on the multicarboxylate probe. Overall, the triglucosamine derivative appears to offer the best balance between high tumor uptake and low retention in nontarget tissues. These results suggest that multivalent molecular beacons are useful for assessing the beneficial effects of multivalency and for optimizing the biological and chemical properties of tissue-specific molecular probes.     

Predicting and avoiding subcellular compartmentalization artifacts arising from acetoxymethyl ester calcium imaging probes. The case of fluo-3 AM and a general account of the phenomenon including a problem avoidance chart

Abstract

Stimulated by difficulties experienced when using fluo-3 AM, we developed a general mechanistic model to aid understanding and practical application of calcium probes applied as acetoxymethyl (AM) esters. Several practical issues previously overlooked or under-emphasized are considered by this model. First, some AM ester probes are “super” lipophilic, e.g., calcium orange, fluo-3, fura red, and these are trapped in the plasma membrane. Entry of such compounds into cells requires the presence of serum albumin in the incubation medium or esterase in the plasma membrane or both. Second, visible cytosolic calcium signals require significant cytosolic esterase, which varies considerably among cell lines and within cell populations of a single cell line. Finally, compartmentalization artefacts are most likely when incompletely hydrolyzed esters are present in the cytosol. This can occur because of low cytosolic esterase concentration or activity, and especially when long incubation times or high extracellular probe concentrations are used. An additional factor favoring compartmentalization is the presence of the “salt” form of the probe in the cytosol in the absence of significant concentrations of calcium ions. We provide an algorithmic chart to aid assessment of possible compartmentalization, guides to relevant QSAR models, and notes on estimation of the structural parameters required when using these models.     

Fluorescent lipid probes: some properties and applications (a review)

Odd as it may seem, experimental challenges in lipid research are often hampered by the simplicity of the lipid structure. Since, as in protein research, mutants or overexpression of lipids are not realistic, a considerable amount of lipid research relies on the use of tagged lipid analogues. However, given the size of an average lipid molecule, special care is needed for the selection of probes, since if the size and intramolecular localization of the probe is not specifically taken into account, it may dramatically affect the properties of the lipids. The latter is particularly important in cell biological studies of lipid trafficking and sorting, where the probed lipid should resemble its natural counterpart as closely as possible. On the other hand, for biophysical applications, these considerations may be less critical. Here we provide a brief overview of the application of several lipid probes in cell biological and biophysical research, and critically analyze their validity in the various fields.     

Fluorescent probes in membrane studies.

A number of spectroscopic techniques are suitable for studying biological membranes. Of these, fluorescence has the sensitivity and time resolution for following membrane events associated with nerve excitation. In this paper, the nature of the information derived from measurements of the fluorescence properties of externally introduced chromophores in membranes is examined. In particular, the locations of various probes are described on the basis of nuclear magnetic resonance (n.m.r.) experiments in model situations. Then the motional characteristics of the probe molecules (rotation and diffusion) are discussed. Finally experiments designed to relate the detailed observations that can be made in lipid bilayers using n.m.r. and fuorescence measurements to those (more limited in nature) that can be made in membranes are described.     

Interaction of molecular probes with living cells and tissues. Part 2. A structure-activity analysis of mitochondrial staining by cationic probes, and a discussion of the synergistic nature of image-based and biochemical approaches.

Cultured rat fibroblasts were exposed to 41 cationic fluorescent probes of very varied hydrophilicity/lipophilicity. Outcome of probe-cell interaction fell into one of the following categories: probe failed to enter the cells; probe accumulated on cell surfaces; probe accumulated in mitochondria, and/or in other intracellular regions. The observations were analysed using a Simplistic Chinese Box (SCB) approach, and the following conclusions were reached. It was the hydrophilic probes which failed to enter cells, whilst extremely lipophilic probes were retained on the cell surfaces. Only the slightly lipophilic cationic probes were permeant, and accumulated in mitochondria. Using the probes log P values to model hydrophilicity/lipophilicity, effective cationic mitochondrial stains can be specified numerically so: 0 less than log P probe less than +5. This SCB model was used to rationalise a variety of earlier observations on the action of mitochondrial probes. The applicability of the SCB approach to integrate image-based and biochemical investigations was demonstrated by using the action of chlorpromazine on mitochondrial action as a case example.     

Critical effects of polar fluorescent probes on the interaction of DHA with POPC supported lipid bilayers

The understanding of lipid bilayer structure and function has been advanced by the application of molecular fluorophores. However, the effects of these probe molecules on the physicochemical properties of membranes being studied are poorly understood. A quartz crystal microbalance with dissipation monitoring instrument was used in this work to investigate the impact of two commonly used fluorescent probes, 1‑palmitoyl‑2‑{12‑[(7‑nitro‑2‑1,3‑benzoxadiazol‑4‑yl)amino]dodecanoyl}‑sn‑glycero‑3‑phosphocholine (NBD-PC) and 1,2‑dipalmitoyl‑sn‑glycero‑3‑phosphoethanolamine‑n‑(lissamine rhodamine‑B‑sulfonyl) (Lis-Rhod PE), on the formation and physicochemical properties of a 1‑palmitoyl‑2‑oleoyl‑sn‑glycero‑3‑phosphocholine supported lipid bilayer (POPC-SLB). The interaction of the POPC-SLB and fluorophore-modified POPC-SLB with docosahexaenoic acid, DHA, was evaluated. The incorporation of DHA into the POPC-SLB was observed to significantly decrease in the presence of the Lis-Rhod PE probe compared with the POPC-SLB. In addition, it was observed that the small concentration of DHA incorporated into the POPC:NBD-PC SLB can produce rearrangement processes followed by the lost not only of DHA but also of POPC or NBD-PC molecules or both during the washing step. This work has significant implications for the interpretation of data employing fluorescent reporter molecules within SLBs.     

Chemistry and biology of N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-labeled lipids: fluorescent probes of biological and model membranes

Lipids that are covalently labeled with the 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) group are widely used as fluorescent analogues of native lipids in model and biological membranes to study a variety of processes. The fluorescent NBD group may be attached either to the polar or the apolar regions of a wide variety of lipid molecules. Synthetic routes for preparing the lipids, and spectroscopic and ionization properties of these probes are reviewed in this report. The orientation of various NBD-labeled lipids in membranes, as indicated by the location of the NBD group, is also discussed. The NBD group is uncharged at neutral pH in membranes, but loops up to the surface if attached to acyl chains of phospholipids. These lipids find applications in a variety of membrane-related studies which include membrane fusion, lipid motion and dynamics, organization of lipids and proteins in membranes, intracellular lipid transfer, and bilayer to hexagonal phase transition in liposomes. Use of NBD-labeled lipids as analogues of natural lipids is critically evaluated.     

A DIE responsive NIR-fluorescent cell membrane probe

It is challenging to achieve selective off to on modulation of the emissive state of a fluorophore within a complex and heterogeneous cellular environment. Herein we show that the dis-assembly of a non-fluorescent aggregate to produce individual fluorescent molecules, termed disaggregation induced emission (DIE), can be utilised to achieve this goal with an amphiphilic BF₂-azadipyrromethene (NIR-AZA) probe. Optical near-infrared properties of the NIR-AZA probe used in this study include absorption and emission maxima at 700 and 726 nm respectively when in the emissive non-aggregated state. Key to the success of the probe is the bis-sulfonic acid substitution of the NIR-AZA fluorophore, which is atypical for membrane probes as it does not contain zwitterionic lipid substituents. The aggregation/disaggregation properties of the NIR-fluorophore have been investigated in model surfactant and synthetic liposomal systems and shown to be emissive responsive to both. Real-time live cell imaging experiments in HeLa Kyoto and MC3T3 cells showed a rapid switch on of emission specific to the plasma membrane of viable and apoptotic cells attributable to a disaggregation-induced emission of the probe. Image analysis software confirmed localisation of fluorescence to the plasma membrane. Cell membrane staining was also effective for formaldehyde fixed cells, with staining possible either before or after fixation. This study adds new and important findings to recent developments of DIE responsive probes and further applications of this controllable emission-switching event are anticipated.     

New covalent capture probes for imaging and therapy, based on a combination of binding affinity and disulfide bond formation

We describe the synthesis and development of new reactive DOTA-metal complexes for covalently targeting engineered receptors in vivo, which have superior tumor uptake and clearance properties for biomedical applications. These probes are found to clear efficiently through the kidneys and minimally through other routes, but bind persistently in the tumor target. We also explore the new technique of Cerenkov luminescence imaging to optically monitor radiolabeled probe distribution and kinetics in vivo. Cerenkov luminescence imaging uniquely enables sensitive noninvasive in vivo imaging of a β(-) emitter such as (90)Y with an optical imager.     

Recent progress on small molecular temperature-sensitive fluorescent probes

Temperature is an important biophysical parameter that is closely related with the metabolic activity in living cells. Therefore, the detection of intracellular temperature changes is crucial for exploring temperature-related biological processes. Fluorescence probe is an ideal tool for observing temperature changes in cells, which has many advantages, such as high sensitivity, good selectivity, and noninvasive, and thus aroused the great interest of researchers. In this paper, we summarize the recent progress of organic small molecule temperature-sensitive fluorescence probes in recent years was reviewed. Particularly, we describe the common response mode to the temperature and the practical applications of the probe in living cells and even animal models. Moreover, an outlook regarding temperature detection in clinical applications is discussed. The temperature-sensitive fluorescent probe is a “black box” to many researchers. This review aims to open a window on the prospect of the noninvasive in vivo detection of temperature which is helpful to deeper understand this rich research area.