Uptake and localisation of small-molecule fluorescent probes in living cells: a critical appraisal of QSAR models and a case study concerning probes for DNA and RNA

A Cyanine Dye for Highly Specific Recognition of Parallel G-Quadruplex Topology and Its Application in Clinical RNA Detection for Cancer Diagnosis

G-quadruplex (G4), an unconventional nucleic acid structure, shows polymorphism in its topological morphology. The parallel G4 topology is the most prevalent form in organisms and plays a regulatory role in many biological processes. Designing fluorescent probes with high specificity for parallel G4s is important but challenging. Herein, a supramolecular assembly of the anionic cyanine dye SCY-5 is reported, which selectively identifies parallel G4 topology. SCY-5 can clearly distinguish parallel G4s from other G4s and non-G4s, even including hybrid-type G4s with parallel characteristics. The high specificity mechanism of SCY-5 involves a delicate balance between electrostatic repulsion and π-π interaction between SCY-5 and G4s. Using SCY-5, cellular RNA extracted from peripheral venous blood was quantitatively detected, and a remarkable increase in RNA G4 content in cancer patients compared to healthy volunteers was confirmed for the first time. This study provides new insights for designing specific probes for parallel G4 topology and opens a new path for clinical cancer diagnosis using RNA G4 as a biomarker.

Cellular Visualization of G-Quadruplex RNA via Fluorescence- Lifetime Imaging Microscopy

Over the past decade, appreciation of the roles of G-quadruplex (G4) structures in cellular regulation and maintenance has rapidly grown, making the establishment of robust methods to visualize G4s increasingly important. Fluorescent probes are commonly used for G4 detection in vitro; however, achieving sufficient selectivity to detect G4s in a dense and structurally diverse cellular environment is challenging. The use of fluorescent probes for G4 detection is further complicated by variations of probe uptake into cells, which may affect fluorescence intensity independently of G4 abundance. In this work, we report an alternative small-molecule approach to visualize G4s that does not rely on fluorescence intensity switch-on and, thus, does not require the use of molecules with exclusive G4 binding selectivity. Specifically, we have developed a novel thiazole orange derivative, TOR-G4, that exhibits a unique fluorescence lifetime when bound to G4s compared to other structures, allowing G4 binding to be sensitively distinguished from non-G4 binding, independent of the local probe concentration. Furthermore, TOR-G4 primarily colocalizes with RNA in the cytoplasm and nucleoli of cells, making it the first lifetime-based probe validated for exploring the emerging roles of RNA G4s in cellulo.

Specific Fluorescent Probes for Imaging DNA in Cell-Free Solution and in Mitochondria in Living Cells

New styryl dyes consisting of N-methylpyridine or N-methylquinoline scaffolds were synthesized, and their binding affinities for DNA in cell-free solution were studied. The replacement of heterocyclic residue from the pyridine to quinoline group as well as variation in the phenyl part strongly influenced their binding modes, binding affinities, and spectroscopic responses. Biological experiments showed the low toxicity of the obtained dyes and their applicability as selective dyes for mitochondria in living cells.

The potential of phenothiazinium dyes as cytotoxicity markers in cisplatin-treated cells

Assessing the in vitro toxicity of compounds on cell cultures is an important step during the screening of candidate molecules for diverse applications. Among the strategies employed to determine cytotoxicity, MTT, neutral red, and resazurin are commonly used. Methylene blue (MB), a phenothiazinium salt, has several uses, such as dye, redox indicator, and even as treatment for human disease and health conditions, such as malaria and methemoglobinemia. However, MB has only been sparsely used as a cellular toxicity indicator. As a viability indicator, MB is mostly applied to fixed cultures at high concentrations, especially when compared to MTT or neutral red. Here we show that MB and its related compounds new methylene blue (NMB), toluidine blue O (TBO), and dimethylmethylene blue (DMMB) can be used as cytotoxicity indicators in live (non-fixed) cells treated for 72 h with DMSO and cisplatin. We compared dye uptake between phenothiazinium dyes and neutral red by analyzing supernatant and cell content via visible spectra scanning and microscopy. All dyes showed a similar ability to assess cell toxicity compared to either MTT or neutral red. Our method represents a cost-effective alternative to in vitro cytotoxicity assays using cisplatin or DMSO, indicating the potential of phenothiazinium dyes for the screening of candidate drugs and other applications.

RNA G-quadruplex in live cells lighted-up by a thiazole orange analogue for SCA36 identification

SCA36 is a neurodegenerative disease mainly caused by the abnormal expansion of the GGGCCT repeat sequence in intron 1 of NOP56. The RNA sequences of this gene are expected to form large amounts of G-quadruplexes in the cytoplasm, which may be a potential intervention and detection target for SCA36. Here, we have developed a small-molecular compound named TCB-1, which shows good selectivity to the G-quadruplex structure, and its fluorescence can be enhanced by hundreds of folds. Interestingly, TCB-1 can avoid lysosome capture, evenly disperse in the cytoplasm, and selectively light up the cytoplasmic RNA G-quadruplexes. This property allows TCB-1 to sensitively detect the increased formation of cytoplasmic RNA G-quadruplexes in SCA36 model cells. This work not only provides new ideas for the design of small-molecule compounds targeting RNA G-quadruplexes in living cells, but also intuitively demonstrates the increased formation of RNA G-quadruplexes caused by NOP56 gene mutation, providing a possible tool for the detection of SCA36.

Single-molecule photosensitizers for NIR-II fluorescence and photoacoustic imaging guided precise anticancer phototherapy

It is ideal yet challenging to achieve precise tumor targeting and high-quality imaging guided combined photodynamic and photothermal therapy (PDT and PTT). In this study, we synthesized a series of D-π-A-type single-molecule photosensitizers (CyE-TT, CyQN-TT, and CyQN-BTT) based on quaternized 1,1,2-trimethyl-1H-benz[e]indoles as acceptors by introducing π-bridges to elongate their emission wavelength and triphenylamine as a donor to construct a twisted molecular conformation. We found that the 1O2 generation ability and the photothermal conversion efficiency (PCE) are directly correlated with the π-bridge between donors and acceptors in these molecules. When a 2,1,3-benzothiadiazole group as a π-bridge was introduced into CyQN-BTT, the singlet oxygen yield enhanced to 27.1%, PCE to 37.8%, and the emission wavelength was red-shifted to near-infrared II (NIR-II). Importantly, double-cationic CyQN-BTT displays structure-inherent cancer cell targeting ability instead of targeting normal cells. Consequently, relying on NIR-II fluorescence imaging (NIR-II FLI) and photoacoustic imaging (PAI) guided PDT and PTT, CyQN-BTT can accurately locate solid tumors in mice and effectively eliminate them with good biocompatibility and biosafety to normal tissues. This study provides insights into the design and development of a tumor-specific targeting multifunctional photosensitizer for precise cancer phototherapy.

Organosulfur/selenium-based Highly Fluorogenic Molecular Probes for Live-Cell Nucleolus Imaging

We present rationally designed cationic organochalcogens highly selective to RNA. We have demonstrated that the conformational dynamics and subsequently the optical properties of these dyes can be controlled to facilitate efficient bioimaging. We report organoselenium and organosulfur-based cell-permeable red-emissive probes bearing favorable cyclic sidearm with potential for selective and high contrast imaging of cell nucleoli. The probes exhibit high quantum yield upon interaction with RNA in an aqueous solution. An in-depth multiscale simulation study reveals that the prominent rotational freezing of the electron-donating sidearm of the probes in the microenvironment of RNA helps in attaining more planar conformation when compared to DNA. It exerts a greater extent of intramolecular charge transfer and hence leads to enhanced fluorescence emission. A systematic structure-interaction relationship study highlighted the impact of heavy-chalcogens toward the improved emissive properties of the probes.

Squaraine probes for the bimodal staining of lipid droplets and endoplasmic reticulum imaging in live cells

We report the synthesis of a library of asymmetric squaraines and their application as superior bimodal “on-demand” fluorescence probes for lipid drolet and endoplasmic reticulum in cancer cells.

An organic molecular compound for in situ identification of mitochondrial G-quadruplexes in live cells

Emerging studies have shown that mitochondrial G-quadruplex plays a critical role in regulating mitochondrial gene replication and transcription, which makes it a promising target for the diagnosis and treatment of cancer or other major diseases. Molecular compounds that can highly target the mitochondrial G-quadruplexes in live cells are essential for further revealing the function and mechanism of these G-quadruplexes. Here, we have developed an organic molecular compound that can highly target the mitochondria of living cells by virtue of the membrane potential mechanism. Then it shows high selectivity to the G-quadruplex structure in the mitochondria, and its fluorescence overlaps well with that of the BG4 antibody. Moreover, the compound has extremely low cytotoxicity and does not interfere with the natural state of G-quadruplex structure. With these good properties, this compound will have great potential in mitochondrial G-quadruplex tracking research or targeted drug screening.

A hybrid aggregate FRET probe from the mixed assembly of cyanine dyes for highly specific monitoring of mitochondria autophagy

Mitochondria autophagy, also known as mitophagy, is a process in which mitochondria are wrapped by autophagosomes and fused with lysosomes for degradation. This process is essential for mitochondrial quality control. Here, we developed a hybrid aggregate FRET probe through mixed assembly of two cyanine dyes FMOTY and AMTC. In live cells, FMOTY and AMTC exist independently in lysosomes and mitochondria and will not produce interfering FRET background signals. The FRET signal is only generated when mitochondria is transported to lysosomes during mitophagy. This allows the hybridized aggregate to be used as a highly specific probe for monitoring mitophagy.

Lipid Peroxidation Assay Using BODIPY-Phenylbutadiene Probes: A Methodological Overview

The assessment of reactive oxygen species has increasing importance in biomedical sciences, due to their biological role in signaling pathways and induction of cell damage at low and high concentrations, respectively. Detection of lipid peroxidation with sensing probes such as some BODIPY dyes has now wide application in studies using fluorescent microplate readers, flow cytometry, and fluorescence microscopy. Two phenylbutadiene derivatives of BODIPY are commonly used as peroxidation probes, non-oxidized probes and oxidized products giving red and green fluorescence, respectively. Peculiar features of lipoperoxidation and BODIPY dye properties make this assessment a rather complex process, not exempt of doubts and troubles. Color changes and fluorescence fading that are not due to lipid peroxidation must be taken into account to avoid misleading results. As a characteristic feature of lipoperoxidation is the propagation of peroxyl radicals, pitfalls and advantages of a delayed detection by BODIPY probes should be considered.

Real-time monitoring of DNA G-quadruplexes in living cells with a small-molecule fluorescent probe

G-quadruplex DNA has been viewed as a prospective anti-cancer target owing to its potential biological relevance. Real-time monitoring of DNA G-quadruplex structures in living cells can provide valuable insights into the relationship between G-quadruplex formation and its cellular consequences. However, the probes capable of detecting DNA G-quadruplexes in living cells are still very limited. Herein, we reported a new fluorescent probe, IMT, for real-time visualization of DNA G-quadruplex structures in living cells. Using IMT as a fluorescent indicator, the quantity changes of DNA G-quadruplex at different points in time during continuous cellular progression responding to Aphidicolin and Hydroxyurea treatment have been directly visualized. Our data demonstrate that IMT will be a valuable tool for exploring DNA G-quadruplexes in live cells. Further application of IMT in fluorescence imaging may reveal more information on the roles of DNA G-quadruplexes in biological systems.

Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures

Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures.

Nuclear cytometry and chromatin organization

The nuclear-targeting chemical probe, for the detection and quantification of DNA within cells, has been a mainstay of cytometry-from the colorimetric Feulgen stain to smart fluorescent agents with tuned functionality. The level of nuclear structure and function at which the probe aims to readout, or indeed at which a DNA-targeted drug acts, is shadowed by a wide range of detection modalities and analytical methods. These methods are invariably limited in terms of the resolution attainable versus the volume occupied by targeted chromatin structures. The scalar challenge arises from the need to understand the extent and different levels of compaction of genomic DNA and how such structures can be re-modeled, reported, or even perturbed by both probes and drugs. Nuclear cytometry can report on the complex levels of chromatin order, disorder, disassembly, and even active disruption by probes and drugs. Nuclear probes can report defining features of clinical and therapeutic interest as in NETosis and other cell death processes. New cytometric approaches continue to bridge the scalar challenges of analyzing chromatin organization. Advances in super-resolution microscopy address the resolution and depth of analysis issues in cellular systems. Typical of recent insights into chromatin organization enabled by exploiting a DNA interacting probe is ChromEM tomography (ChromEMT). ChromEMT uses the unique properties of the anthraquinone-based cytometric dye DRAQ5™ to reveal that local and global 3D chromatin structures effect differences in compaction. The focus of this review is nuclear and chromatin cytometry, with linked reference to DNA targeting probes and drugs as exemplified by the anthracenediones.

MitoNeoD: A Mitochondria-Targeted Superoxide Probe

Mitochondrial superoxide (O₂^⋅-) underlies much oxidative damage and redox signaling. Fluorescent probes can detect O₂^⋅-, but are of limited applicability in vivo, while in cells their usefulness is constrained by side reactions and DNA intercalation. To overcome these limitations, we developed a dual-purpose mitochondrial O₂^⋅- probe, MitoNeoD, which can assess O₂^⋅- changes in vivo by mass spectrometry and in vitro by fluorescence. MitoNeoD comprises a O₂^⋅--sensitive reduced phenanthridinium moiety modified to prevent DNA intercalation, as well as a carbon-deuterium bond to enhance its selectivity for O₂^⋅- over non-specific oxidation, and a triphenylphosphonium lipophilic cation moiety leading to the rapid accumulation within mitochondria. We demonstrated that MitoNeoD was a versatile and robust probe to assess changes in mitochondrial O₂^⋅- from isolated mitochondria to animal models, thus offering a way to examine the many roles of mitochondrial O₂^⋅- production in health and disease.

Hydrophobicity determines the fate of self-assembled fluorescent nanoparticles in cells

The fate of small molecule nanoparticles (SMNPs) composed of self-assembling intrinsically fluorescent π-conjugated oligomers was studied in cells as a function of side-chain hydrophobicity. While the hydrophobic SMNPs remained intact upon cellular uptake, the more hydrophilic SMNPs disassembled and dispersed throughout the cytosol.

Hydrophobic resorufamine derivatives: potent and selective red fluorescent probes of the endoplasmic reticulum of mammalian cells

The endoplasmic reticulum (ER) of eukaryotic cells plays critical roles in the processing of secreted and transmembrane proteins. Defects in these functions are associated with a wide range of pathologies. To image this organelle, cells are often treated with fluorescent ER-Tracker dyes. Although these compounds are selective, existing red fluorescent probes of the ER are costly glibenclamide derivatives that inhibit ER-associated sulphonylurea receptors. To provide simpler and more cost-effective red fluorescent probes of the ER, we synthesized amino analogues of the fluorophore resorufin. By varying the polarity of linked substituents, we identified hexyl resorufamine (HRA) as a novel hydrophobic (cLogD (pH 7.4) = 3.8) red fluorescent (Ex. 565 nm; Em. 614 nm in ethanol) molecular probe. HRA is exceptionally bright in organic solvents (quantum yield = 0.70), it exclusively localizes to the ER of living HeLa cells as imaged by confocal microscopy, it is effective at concentrations as low as 100 nM, and it is non-toxic under these conditions. To examine its utility, we used HRA to facilitate visualization of small molecule-mediated release of a GFP-GPI fusion protein from the ER into the secretory pathway. HRA represents a potent, selective, and cost-effective probe for imaging and labeling the ER.

Establishing the subcellular localization of photodynamically-induced ROS using 3,3'-diaminobenzidine: A methodological proposal, with a proof-of-concept demonstration

The critical involvement of reactive oxygen species (ROS) in both physiological and pathological processes in cell biology makes their detection and assessment a fundamental topic in biomedical research. Established methodologies to study ROS in cell biology take advantage of oxidation reactions between the ROS and a reduced probe. After reacting the probe reveals the presence of ROS either by the appearance of colour (chromogenic reaction) or fluorescence (fluorogenic reaction). However current methodologies rarely allow for a site-specific detection of ROS production. Here we propose a colorimetric reaction driven by the oxidation of 3,3'-diaminobenzidine (DAB) by photodynamically-produced ROS that allows for fine detection of the ROS production site. The introduced methodology is fast, easy to implement and permits cellular resolution at the submicrometric level. Although the basic protocol is proved in a photodynamic model of ROS generation, the principle is applicable to many different scenarios of intracellular ROS production. As a consequence this proposed methodology should greatly complement other techniques aiming at establishing a precise subcellular localization of ROS generation.

Fluorescence-based bioassays for the detection and evaluation of food materials

We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.

Nucleus-staining with biomolecule-mimicking nitrogen-doped carbon dots prepared by a fast neutralization heat strategy

Biomolecule-mimicking nitrogen-doped carbon dots (N-Cdots) were synthesized from dopamine by a neutralization heat strategy. Fluorescence imaging of various cells validated their nucleus-staining efficiency. The dopamine-mimicking N-Cdots "trick" nuclear membranes to achieve nuclear localization and imaging.

Synthesis of Fluorophores that Target Small Molecules to the Endoplasmic Reticulum of Living Mammalian Cells

The endoplasmic reticulum (ER) plays critical roles in the processing of secreted and transmembrane proteins. To deliver small molecules to this organelle, we synthesized fluorinated hydrophobic analogues of the fluorophore rhodol. These cell-permeable fluorophores are exceptionally bright, with quantum yields of around 0.8, and they were found to specifically accumulate in the ER of living HeLa cells, as imaged by confocal laser scanning microscopy. To target a biological pathway controlled by the ER, we linked a fluorinated hydrophobic rhodol to 5-nitrofuran-2-acrylaldehyde. In contrast to an untargeted nitrofuran warhead, delivery of this electrophilic nitrofuran to the ER by the rhodol resulted in cytotoxicity comparable to the ER-targeted cytotoxin eeyarestatin I, and specifically inhibited protein processing by the ubiquitin-proteasome system. Fluorinated hydrophobic rhodols are outstanding fluorophores that enable the delivery of small molecules for targeting ER-associated proteins and pathways.

Luminescent probes for the bioimaging of small anionic species in vitro and in vivo

This comprehensive review examines recent developments in the use of fluorescent/luminescent probes for the bioimaging of anionic species. Images in cover art reproduced with permission from ref. 290 and 306.

The Histochem Cell Biol conspectus: the year 2013 in review

Herein, we provide a brief synopsis of all manuscripts published in Histochem Cell Biol in the year 2013. For ease of reference, we have divided the manuscripts into the following categories: Advances in Methodologies; Molecules in Health and Disease; Organelles, Subcellular Structures and Compartments; Golgi Apparatus; Intermediate Filaments and Cytoskeleton; Connective Tissue and Extracellular Matrix; Autophagy; Stem Cells; Musculoskeletal System; Respiratory and Cardiovascular Systems; Gastrointestinal Tract; Central Nervous System; Peripheral Nervous System; Excretory Glands; Kidney and Urinary Bladder; and Male and Female Reproductive Systems. We hope that the readership will find this annual journal synopsis of value and serve as a quick, categorized reference guide for “state-of-the-art” manuscripts in the areas of histochemistry, immunohistochemistry, and cell biology.

A bright red fluorescent cyanine dye for live-cell nucleic acid imaging, with high photostability and a large Stokes shift

TO3-CN is a bright red fluorescent cyanine dye for live-cell nucleic acid imaging, with high photostability and a large Stokes shift.

Predictive binding geometry of ligands to DNA minor groove: isohelicity and hydrogen-bonding pattern

The interaction of drugs and dyes with nucleic acids, particularly when binding to DNA minor groove occurs, has increasing importance in biomedical sciences. This is due to the resulting biological activity and to the possibility of recognizing AT and GC base pairs. In such cases, DNA binding can be predicted if appropriate helical and hydrogen-bonding parameters are deduced from DNA models, and a simplified geometrical rule in the form of a stencil is then applied on computer-drawn molecules of interest. Relevant structure parameter values for minor groove binders are the length (4.6 < L < 5.4 Å) and angle (152 < σ < 156.5°) between three consecutive units, measured at the level of hydrogen donor or acceptor groups. Application of the stencil shows that predictive methods can aid in the design of new compounds, by checking the possible binding of isohelical sequence-specific ligands along the DNA minor groove.

Computational approaches to analyse and predict small molecule transport and distribution at cellular and subcellular levels

Quantitative structure-activity relationship (QSAR) studies and mechanistic mathematical modeling approaches have been independently employed for analysing and predicting the transport and distribution of small molecule chemical agents in living organisms. Both of these computational approaches have been useful for interpreting experiments measuring the transport properties of small molecule chemical agents, in vitro and in vivo. Nevertheless, mechanistic cell-based pharmacokinetic models have been especially useful to guide the design of experiments probing the molecular pathways underlying small molecule transport phenomena. Unlike QSAR models, mechanistic models can be integrated from microscopic to macroscopic levels, to analyse the spatiotemporal dynamics of small molecule chemical agents from intracellular organelles to whole organs, well beyond the experiments and training data sets upon which the models are based. Based on differential equations, mechanistic models can also be integrated with other differential equations-based systems biology models of biochemical networks or signaling pathways. Although the origin and evolution of mathematical modeling approaches aimed at predicting drug transport and distribution has occurred independently from systems biology, we propose that the incorporation of mechanistic cell-based computational models of drug transport and distribution into a systems biology modeling framework is a logical next step for the advancement of systems pharmacology research.