Fluorescent probes and fluorescence (microscopy) techniques--illuminating biological and biomedical research

Copillar[5]arene Appended Pyrene Schiff Base: Photophysics, Aggregation Induced Emission and Picric Acid Recognition

Herein, we report the synthesis of copillar[5]arene-based pyrene Schiff base 1 and its characterization by using 1H, 13C NMR, FT-IR and mass spectrometry. UV-vis absorption, steady-state fluorescence and time-resolved fluorescence are done to elucidate the photophysical behaviors of 1. To understand the electronic structure of 1, density functional theory (DFT) calculations are performed. Owing to the presence of pyrene via a Schiff base linkage, compound 1 exhibits aggregation-induced emission (AIE) characteristics. It shows aggregation in aqueous THF and DMF. The aggregation behavior is successfully demonstrated by steady-state fluorescence, dynamic light scattering (DLS) and time-correlated single-photon counting (TCSPC) experiments. Experimental findings reveal that hydrophobic effect is the driving force in the formation of aggregates. As application, the aggregated state of 1 in aqueous THF fluorimetrically recognizes picric acid (PA) selectively over a series of nitro- and nonnitroaromatics with a detection limit of 1.62×10-7 M. The emission of the aggregated state is fully quenched upon interaction with PA.

Gold nanomaterials capped with bovine serum albumin for cell and extracellular vesicle imaging

Bovine serum albumin-capped gold nanoclusters (AuNC@BSA) are ionic, ultra-small, and eco-friendly nanomaterials that exhibit red fluorescence emission. Upon modification, these nanomaterials can serve as imaging probes with multimodal functionality. Owing to their nanoscale properties, AuNC@BSA-based nanomaterials can be readily endocytosed by cells for imaging. With the increasing interest in cell therapy, extracellular vesicles (EVs) have attracted considerable attention from researchers; however, effective methods for imaging EVs remain limited. Although several studies have explored imaging strategies for cells and EVs using compounds, nuclear pharmaceuticals, nanoparticles, or genetic constructs, the use of AuNC@BSA-based nanomaterials for labeling EVs and their parental cells has rarely been discussed, with even less attention paid to their multimodal potential. To address this gap, we utilized three types of AuNC@BSA-based derivatives: AuNC@BSA, AuNC@BSA-Gd, and AuNC@BSA-Gd-I. Our findings demonstrate that these derivatives can effectively label both cells and EVs using a simple direct labeling approach, which is particularly notable for EVs, as they typically require more complex labeling procedures. Furthermore, the multimodal potential of labeled cells and EVs was evaluated, revealing their capabilities for multimodal imaging. In summary, this study presents an effective strategy for labeling EVs and their parental cells using multimodal nanomaterials. These findings will contribute to accelerating the development of drug delivery systems, cell- and EV-based therapies, and advanced imaging strategies.

Exploring the landscape of FRET-based molecular sensors: Design strategies and recent advances in emerging applications

Probing biological processes in living organisms that could provide one-of-a-kind insights into real-time alterations of significant physiological parameters is a formidable task that calls for specialized analytic devices. Classical biochemical methods have significantly aided our understanding of the mechanisms that regulate essential biological processes. These methods, however, are typically insufficient for investigating transient molecular events since they focus primarily on the end outcome. Fluorescence resonance energy transfer (FRET) microscopy is a potent tool used for exploring non-invasively real-time dynamic interactions between proteins and a variety of biochemical signaling events using sensors that have been meticulously constructed. Due to their versatility, FRET-based sensors have enabled the rapid and standardized assessment of a large array of biological variables, facilitating both high-throughput research and precise subcellular measurements with exceptional temporal and spatial resolution. This review commences with a brief introduction to FRET theory and a discussion of the fluorescent molecules that can serve as tags in different sensing modalities for studies in chemical biology, followed by an outlining of the imaging techniques currently utilized to quantify FRET highlighting their strengths and shortcomings. The article also discusses the various donor-acceptor combinations that can be utilized to construct FRET scaffolds. Specifically, the review provides insights into the latest real-time bioimaging applications of FRET-based sensors and discusses the common architectures of such devices. There has also been discussion of FRET systems with multiplexing capabilities and multi-step FRET protocols for use in dual/multi-analyte detections. Future research directions in this exciting field are also mentioned, along with the obstacles and opportunities that lie ahead.

Hybrid plasmonic nanodiamonds for thermometry and local photothermal therapy of melanoma: a comparative study

Hyperthermia plays a significant role in cancer treatment by inducing cell damage through temperature elevation, often used alongside other treatment modalities. During hyperthermia therapy, temperature control is crucial. Here, we report on a simple synthesis route of hybrid plasmonic nanodiamonds either completely wrapped with an Au shell (NV@Au) or densely covered with Au NPs (NV@SiO 2 @Au). Such integration of nanodiamonds with Au NPs is advantageous both for heating and precise thermometry at nanoscale. After structural and optical investigations, heating abilities of the obtained plasmonic nanodiamonds were thoroughly inspected on glass, in association with living cells, and in tissue slices ex vivo, revealing their effective heat generation under excitation with light using a single excitation source. The developed hybrid plasmonic nanodiamonds were finally applied for local photothermal therapy of melanoma in vivo, demonstrating their efficacy in eradicating cancer cells and monitoring temperature during the process.

Response strategies and biological applications of organic fluorescent thermometry: cell- and mitochondrion-level detection

Temperature homeostasis is critical for cells to perform their physiological functions. Among the diverse methods for temperature detection, fluorescent temperature probes stand out as a proven and effective tool, especially for monitoring temperature in cells and suborganelles, with a specific emphasis on mitochondria. The utilization of these probes provides a new opportunity to enhance our understanding of the mechanisms and interconnections underlying various physiological activities related to temperature homeostasis. However, the complexity and variability of cells and suborganelles necessitate fluorescent temperature probes with high resolution and sensitivity. To meet the demanding requirements for intracellular/subcellular temperature detection, several strategies have been developed, offering a range of options to address this challenge. This review examines four fundamental temperature-response strategies employed by small molecule and polymer probes, including intramolecular rotation, polarity sensitivity, Förster resonance energy transfer, and structural changes. The primary emphasis was placed on elucidating molecular design and biological applications specific to each type of probe. Furthermore, this review provides an insightful discussion on factors that may affect fluorescent thermometry, providing valuable perspectives for future development in the field. Finally, the review concludes by presenting cutting-edge response strategies and research insights for mitigating biases in temperature sensing.

An "off-on" fluorescent nanosensor for the detection of cadmium ions based on APDC-etched CdTe/CdS/SiO2 quantum dots

In this study, we have developed a novel fluorescent "OFF-ON" quantum dots (QDs) sensor based on CdTe/CdS/SiO2 cores. Ammonium pyrrolidine dithiocarbamate (APDC), ethylenediamine tetraacetic acid (EDTA), and 1,10-phenanthroline (Phen) served as potential chemical etchants. Among these three etchants, APDC exhibited the most pronounced quenching effect (94.06%). The APDC-etched CdTe/CdS/SiO2 QDs demonstrated excellent optical properties: the fluorescence of the APDC-etched CdTe/CdS/SiO2 QDs system (excitation wavelength: 365 nm and emission wavelength: 622 nm) was significantly and selectively restored upon the addition of cadmium ions (Cd2+) (89.22%), compared to 15 other metal ions. The linear response of the APDC-etched CdTe/CdS/SiO2 QDs was observed within the cadmium ion (Cd2+) concentration ranges of 0-20 μmol L-1 and 20-160 μmol L-1 under optimized conditions (APDC: 300 μmol L-1, pH: 7.0, reaction time: 10 min). The detection limit (LOD) of the APDC-etched CdTe/CdS/SiO2 QDs for Cd2+ was 0.3451 μmol L-1 in the range of 0-20 μmol L-1. The LOD achieved by the QDs in this study surpasses that of the majority of previously reported nanomaterials. The feasibility of using APDC-etched CdTe/CdS/SiO2 QDs for Cd2+ detection in seawater, freshwater, and milk samples was verified, with average recoveries of 95.27%-110.68%, 92%-106.47%, and 90.73%-111.60%, respectively, demonstrating satisfactory analytical precision (RSD ≤ 8.26).

A Modular Approach for the Synthesis of Diverse Heterobifunctional Cyanine Dyes

Herein, we present a straightforward synthetic route for the design and synthesis of diverse heterobifunctional cyanine 5 dyes. We optimized the workup by harnessing the pH- and functional group-dependent solubility of the asymmetric cyanine 5 dyes. Therefore, purification through chromatography is deferred until the last synthesis step. Demonstrating successful large-scale synthesis, our modular approach prevents functional group degradation by introducing them in the last synthesis step. These modifiable heterobifunctional dyes offer significant utility in advancing biological studies.

Urban Flora Riches: Unraveling Metabolic Variation Along Altitudinal Gradients in Two Spontaneous Plant Species

Using resilient, self-sustaining plants in urban green spaces enhances environmental and cultural benefits and reduces management costs. We assessed two spontaneous plant species, Linaria vulgaris Mill. and Cichorium intybus L., in four sites from the surrounding urban areas, ranging in altitude from 78 to 1040 m. Protection against UV-B radiation is crucial for plants at higher altitudes, guiding our focus on UV-visible absorption spectra, fluorometric emission spectra, secondary metabolite accumulation, and pigment dynamics in leaves. Our findings revealed a slight increase in UV-absorbing compounds with altitude and species-specific changes in visible spectra. The UV-emission of fluorochromes decreased, while red emission increased with altitude but only in chicory. Polyphenols and flavonoids showed a slight upward trend with altitude. Divergent trends were observed in condensed tannin accumulation, with L. vulgaris decreasing and C. intybus increasing with altitude. Additionally, chicory leaves from higher altitudes (792 and 1040 m) contained significantly lower triterpene concentrations. In L. vulgaris, chlorophyll pigments and carotenoids varied with sites, contrasting with UV absorbance variations. For C. intybus, pigment variation was similar to absorbance changes in the UV and VIS range, except at the highest altitude. These observations provide valuable insights into species-specific strategies for adapting to diverse environmental contexts.

Detection of breast cancer cells by a near-infrared fluorescent probe targeting mitochondrial viscosity

Monitoring abnormal viscosity in biological systems is important for basic research and clinical applications. Fluorescence imaging technology is adaptable for the visualization of tumor tissues due to its comprehensive features. However, fluorescence detection of intracellular viscosity in clinical samples remains challenging. We developed a promising near-infrared fluorescent probe, M556, for viscosity measurement. M556, which targets mitochondria, was successfully applied to monitor the mitochondrial viscosity in living cells. Furthermore, M556 was demonstrated to effectively discriminate tumors from normal tissues in a mouse tumor model and in clinical specimens from breast cancer patients, thus indicating the potential perioperative use of this probe by clinicians to assist with biopsy procedures.

Non-Phenomenological Description of the Time-Resolved Emission in Solution with Quantum-Classical Vibronic Approaches-Application to Coumarin C153 in Methanol

We report a joint experimental and theoretical work on the steady-state spectroscopy and time-resolved emission of the coumarin C153 dye in methanol. The lowest energy excited state of this molecule is characterized by an intramolecular charge transfer thus leading to remarkable shifts of the time-resolved emission spectra, dictated by the methanol reorganization dynamics. We selected this system as a prototypical test case for the first application of a novel computational protocol aimed at the prediction of transient emission spectral shapes, including both vibronic and solvent effects, without applying any phenomenological broadening. It combines a recently developed quantum-classical approach, the adiabatic molecular dynamics generalized vertical Hessian method (Ad-MD|gVH), with nonequilibrium molecular dynamics simulations. For the steady-state spectra we show that the Ad-MD|gVH approach is able to reproduce quite accurately the spectral shapes and the Stokes shift, while a ∼0.15 eV error is found on the prediction of the solvent shift going from gas phase to methanol. The spectral shape of the time-resolved emission signals is, overall, well reproduced, although the simulated spectra are slightly too broad and asymmetric at low energies with respect to experiments. As far as the spectral shift is concerned, the calculated spectra from 4 ps to 100 ps are in excellent agreement with experiments, correctly predicting the end of the solvent reorganization after about 20 ps. On the other hand, before 4 ps solvent dynamics is predicted to be too fast in the simulations and, in the sub-ps timescale, the uncertainty due to the experimental time resolution (300 fs) makes the comparison less straightforward. Finally, analysis of the reorganization of the first solvation shell surrounding the excited solute, based on atomic radial distribution functions and orientational correlations, indicates a fast solvent response (≈100 fs) characterized by the strengthening of the carbonyl-methanol hydrogen bond interactions, followed by the solvent reorientation, occurring on the ps timescale, to maximize local dipolar interactions.

Triphenylamine-equipped 1,8-naphthaolactam: a versatile scaffold for the custom design of efficient subcellular imaging agents

Fluorescence imaging has enabled much progress in biological fields, while the evolution of commercially available dyes has lagged behind their advanced applications. Herein, we launch triphenylamine-equipped 1,8-naphthaolactam (NP-TPA) as a versatile scaffold for the custom design of an efficient subcellular imaging agent (NP-TPA-Tar), given its bright and constant emissions in various states, significant Stokes shifts, and facile modifiability. The resultant four NP-TPA-Tars maintain excellent emission behavior with targeted modifications and can map the spatial distribution of lysosomes, mitochondria, endoplasmic reticulum, and plasma membrane in Hep G2 cells. Compared to its commercial counterpart, NP-TPA-Tar has a 2.8-25.2 fold increase in Stokes shift, a 1.2-1.9 fold increase in photostability, enhanced targeting capability, and comparable imaging efficiency even at low concentrations of 50 nM. This work will help to accelerate the update of current imaging agents and super-resolution and real-time imaging in biological applications.

Red-Emitting Dithienothiophene S,S-Dioxide Dyes for Cellular Membrane Staining

A series of dithienothiophene S,S-dioxide (DTTDO) dyes was designed, synthesized, and investigated for their suitability in fluorescent cell imaging. Synthetized (D-π-A-π-D)-type DTTDO derivatives have molecule lengths close to the thickness of the phospholipid membrane, and they contain on both ends two positively charged or neutral polar groups to increase their solubility in water and to ensure simultaneous interaction with polar groups of the inner and outer part of the cellular membrane. DTTDO derivatives exhibit absorbance and emission maxima in the 517-538 nm and 622-694 nm range, respectively, and a large Stokes shift up to 174 nm. Fluorescence microscopy experiments revealed that these compounds selectively intercalate into cell membranes. Moreover, a cytotoxicity assay conducted on a model human live cells indicates low toxicity of these compounds at the concentrations required for effective staining. With suitable optical properties, low cytotoxicity, and high selectivity against cellular structures, DTTDO derivatives are proven to be attractive dyes for fluorescence-based bioimaging.

Lighting up Micro-/Nanorobots with Fluorescence

Micro-/nanorobots (MNRs) can be autonomously propelled on demand in complex biological environments and thus may bring revolutionary changes to biomedicines. Fluorescence has been widely used in real-time imaging, chemo-/biosensing, and photo-(chemo-) therapy. The integration of MNRs with fluorescence generates fluorescent MNRs with unique advantages of optical trackability, on-the-fly environmental sensitivity, and targeting chemo-/photon-induced cytotoxicity. This review provides an up-to-date overview of fluorescent MNRs. After the highlighted elucidation about MNRs of various propulsion mechanisms and the introductory information on fluorescence with emphasis on the fluorescent mechanisms and materials, we systematically illustrate the design and preparation strategies to integrate MNRs with fluorescent substances and their biomedical applications in imaging-guided drug delivery, intelligent on-the-fly sensing and photo-(chemo-) therapy. In the end, we summarize the main challenges and provide an outlook on the future directions of fluorescent MNRs. This work is expected to attract and inspire researchers from different communities to advance the creation and practical application of fluorescent MNRs on a broad horizon.

A library of Rhodamine6G-based pH-sensitive fluorescent probes with versatile in vivo and in vitro applications

Acidic pH is critical to the function of the gastrointestinal system, bone-resorbing osteoclasts, and the endolysosomal compartment of nearly every cell in the body. Non-invasive, real-time fluorescence imaging of acidic microenvironments represents a powerful tool for understanding normal cellular biology, defining mechanisms of disease, and monitoring for therapeutic response. While commercially available pH-sensitive fluorescent probes exist, several limitations hinder their widespread use and potential for biologic application. To address this need, we developed a novel library of pH-sensitive probes based on the highly photostable and water-soluble fluorescent molecule, Rhodamine 6G. We demonstrate versatility in terms of both pH sensitivity (i.e., pK a) and chemical functionality, allowing conjugation to small molecules, proteins, nanoparticles, and regenerative biomaterial scaffold matrices. Furthermore, we show preserved pH-sensitive fluorescence following a variety of forms of covalent functionalization and demonstrate three potential applications, both in vitro and in vivo, for intracellular and extracellular pH sensing. Finally, we develop a computation approach for predicting the pH sensitivity of R6G derivatives, which could be used to expand our library and generate probes with novel properties.

Multi-Modal Optical Imaging and Combined Phototherapy of Nasopharyngeal Carcinoma Based on a Nanoplatform

Nasopharyngeal carcinoma (NPC) is a common malignant tumor of the head and neck with a high incidence rate worldwide, especially in southern China. Phototheranostics in combination with nanoparticles is an integrated strategy for enabling simultaneous diagnosis, real-time monitoring, and administration of precision therapy for nasopharyngeal carcinoma (NPC). It has shown great potential in the field of cancer diagnosis and treatment owing to its unique noninvasive advantages. Many Chinese and international research teams have applied nano-targeted drugs to optical diagnosis and treatment technology to conduct multimodal imaging and collaborative treatment of NPC, which has become a hot research topic. In this review, we aimed to introduce the recent developments in phototheranostics of NPC based on a nanoplatform. This study aimed to elaborate on the applications of nanoplatform-based optical imaging strategies and treatment modalities, including fluorescence imaging, photoacoustic imaging, Raman spectroscopy imaging, photodynamic therapy, and photothermal therapy. This study is expected to provide a scientific basis for further research and development of NPC diagnosis and treatment.

Fluorescent probes for biomolecule detection under environmental stress

The use of fluorescent probes in visible detection has been developed over the last several decades. Biomolecules are essential in the biological processes of organisms, and their distribution and concentration are largely influenced by environmental factors. Significant advances have occurred in the applications of fluorescent probes for the detection of the dynamic localization and quantity of biomolecules during various environmental stress-induced physiological and pathological processes. Herein, we summarize representative examples of small molecule-based fluorescent probes that provide bimolecular information when the organism is under environmental stress. The discussion includes strategies for the design of smart small-molecule fluorescent probes, in addition to their applications in biomolecule imaging under environmental stresses, such as hypoxia, ischemia-reperfusion, hyperthermia/hypothermia, organic/inorganic chemical exposure, oxidative/reductive stress, high glucose stimulation, and drug treatment-induced toxicity. We believe that comprehensive insight into the beneficial applications of fluorescent probes in biomolecule detection under environmental stress should enable the further development and effective application of fluorescent probes in the biochemical and biomedical fields.

Fluorescence Microscopy Methods for the Analysis and Characterization of Lignin

Lignin is one of the most studied and analyzed materials due to its importance in cell structure and in lignocellulosic biomass. Because lignin exhibits autofluorescence, methods have been developed that allow it to be analyzed and characterized directly in plant tissue and in samples of lignocellulose fibers. Compared to destructive and costly analytical techniques, fluorescence microscopy presents suitable alternatives for the analysis of lignin autofluorescence. Therefore, this review article analyzes the different methods that exist and that have focused specifically on the study of lignin because with the revised methods, lignin is characterized efficiently and in a short time. The existing qualitative methods are Epifluorescence and Confocal Laser Scanning Microscopy; however, other semi-qualitative methods have been developed that allow fluorescence measurements and to quantify the differences in the structural composition of lignin. The methods are fluorescence lifetime spectroscopy, two-photon microscopy, Föster resonance energy transfer, fluorescence recovery after photobleaching, total internal reflection fluorescence, and stimulated emission depletion. With these methods, it is possible to analyze the transport and polymerization of lignin monomers, distribution of lignin of the syringyl or guaiacyl type in the tissues of various plant species, and changes in the degradation of wood by pulping and biopulping treatments as well as identify the purity of cellulose nanofibers though lignocellulosic biomass.

Prospects of Surface-Enhanced Raman Spectroscopy for Biomarker Monitoring toward Precision Medicine

Future precision medicine will be undoubtedly sustained by the detection of validated biomarkers that enable a precise classification of patients based on their predicted disease risk, prognosis, and response to a specific treatment. Up to now, genomics, transcriptomics, and immunohistochemistry have been the main clinically amenable tools at hand for identifying key diagnostic, prognostic, and predictive biomarkers. However, other molecular strategies, including metabolomics, are still in their infancy and require the development of new biomarker detection technologies, toward routine implementation into clinical diagnosis. In this context, surface-enhanced Raman scattering (SERS) spectroscopy has been recognized as a promising technology for clinical monitoring thanks to its high sensitivity and label-free operation, which should help accelerate the discovery of biomarkers and their corresponding screening in a simpler, faster, and less-expensive manner. Many studies have demonstrated the excellent performance of SERS in biomedical applications. However, such studies have also revealed several variables that should be considered for accurate SERS monitoring, in particular, when the signal is collected from biological sources (tissues, cells or biofluids). This Perspective is aimed at piecing together the puzzle of SERS in biomarker monitoring, with a view on future challenges and implications. We address the most relevant requirements of plasmonic substrates for biomedical applications, as well as the implementation of tools from artificial intelligence or biotechnology to guide the development of highly versatile sensors.

Computational Methods for Single-Cell Imaging and Omics Data Integration

Integrating single cell omics and single cell imaging allows for a more effective characterisation of the underlying mechanisms that drive a phenotype at the tissue level, creating a comprehensive profile at the cellular level. Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques such as MRI, CT, and PET. These imaging technologies complement omics-based data in biomedical research because they are helpful for identifying associations between genotype and phenotype, along with functional changes occurring at the tissue level. Single cell imaging can act as an intermediary between these levels. Meanwhile new technologies continue to arrive that can be used to interrogate the genome of single cells and its related omics datasets. As these two areas, single cell imaging and single cell omics, each advance independently with the development of novel techniques, the opportunity to integrate these data types becomes more and more attractive. This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further our understanding of complex biological phenomena like ageing. We include an emphasis on machine learning algorithms because of their ability to identify complex patterns in large multidimensional data.

Review on Optical Imaging Techniques for Multispectral Analysis of Nanomaterials

Biomedical imaging is an essential tool for investigating biological responses in vivo. Among the several imaging techniques, optical imaging systems with multispectral analysis of nanoparticles have been widely investigated due to their ability to distinguish the substances in biological tissues in vivo. This review article focus on multispectral optical imaging techniques that can provide molecular functional information. We summarize the basic principle of the spectral unmixing technique that enables the delineation of optical chromophores. Then, we explore the principle, typical system configuration, and biomedical applications of the representative optical imaging techniques, which are fluorescence imaging, two-photon microscopy, and photoacoustic imaging. The results in the recent studies show the great potential of the multispectral analysis techniques for monitoring responses of biological systems in vivo.

Biodegradable supramolecular micelles via host-guest interaction of cyclodextrin-terminated polypeptides and adamantane-terminated polycaprolactones

Biodegradable supramolecular micelles were prepared exploiting the host-guest interaction of cyclodextrin and adamantane. Cyclodextrin-initiated polypeptides acted as the hydrophilic corona, whereas adamantane-terminated polycaprolactones served as the hydrophobic core.

Quantum Dots Based Fluorescent Probe for the Selective Detection of Heavy Metal Ions

Heavy metal ions are one of the primary causes of environmental pollution. A marshal effect of heavy metal ions is a paramount ultimatum to humans, aquatic animals and other organisms present in nature. Multitude arrays of materials have been proclaimed for sensing of heavy metal ions and also many methodologies are applied for heavy metal ion sensing. Due to their toxicity and non-biodegradability, it is required to be perceived immediately prior to its manifestation of harmful effects. Quantum Dots (QDs) are zero-dimensional nanomaterial particles and owing to their distinctive optical and electronic properties, they are utilized as nanosensors. QDs have enriched fluorescence properties which includes broad excitation spectrum, narrow emission spectrum and photostability. QDs offer eclectic and sensitive detection of heavy metal ions due to presence of discrete capping agents and different functional groups present on the surface of the QDs. These capping layers and functional groups attune the sensing capability of the QDs, which leverages the interactions of QDs with various analytes by different mechanisms. This review, comprising of papers from 2011 to 2020,focuses on heavy metal ions sensing potential of various quantum dots and its applicability as a nanosensor for on field heavy metal ions detection in water. Quantum Dots (QDs) based Heavy Metal Detection.

Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality-Strong Affinity Nucleic Acids Binders

New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA-poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response. CD titrations showed aggregation along the polynucleotide with well-defined supramolecular chirality. The single dipyridinium-bridged dimer showed intercalation at low dye-DNA/RNA ratios. All new cyanine dyes showed potent micromolar antiproliferative activity against cancer cell lines, making them promising theranostic agents.

Straightforward Functionalization of Sulfur-Containing Peptides via 5- and 6-endo-dig Cyclization Reactions

We present a simple and convenient method for the generation of sulfenyl electrophiles from peptides containing S–S or S–H bonds by employing N-chlorosuccinimide. The corresponding sulfenyl electrophiles are further utilized in 5- and 6-endo-dig cyclization reactions yielding indolizinium salts, indoles, benzo[b]furans, polyaromatic hydrocarbons (PAHs) and isocoumarins, as well as quinolinones bearing a glutathione moiety. PAH derivatives can be used as selective fluorescent dyes for the visualization of lipid droplets in living cells.

Silicon-based fluorescent platforms for copper(ii) detection in water

The potential of silicon-based fluorescent platforms for the detection of trace toxic metal ions was investigated in an aqueous environment. To this aim, silicon chips were first functionalized with amino groups, and fluorescein organic dyes, used as sensing molecules, were then covalently linked to the surface via formation of thiourea groups. The obtained hybrid heterostructures exhibited high sensitivity and selectivity towards copper(ii), a limit of detection compatible with the recommended upper limits for copper in drinking water, and good reversibility using a standard metal-chelating agent. The fluorophore-analyte interaction mechanism at the basis of the reported fluorescence quenching, as well as the potential of performance improvement, were also studied. The herein presented sensing architecture allows, in principle, tailoring of the selectivity towards other metal ions by proper fluorophore selection, and provides a favorable outlook for integration of fluorescent chemosensors with silicon photonics technology.

Hypoxia-activated probe for NIR fluorescence and photoacoustic dual-mode tumor imaging

Construction of tumor microenvironment responsive probe with more than one imaging modality, in particular toward hypoxia of solid tumors, is an appealing yet significantly challenging task. In this work, we designed a hypoxia-activated probe TBTO (Triphenylamine-Benzothiadiazole-Triphenylamine derivative featuring four diethylamino N-Oxide groups) for in vivo imaging. TBTO could undergo bioreduction in a hypoxic microenvironment to yield compound TBT sharing both near-infrared (NIR) aggregation-induced emission and strong twisted intramolecular charge transfer features, which endows the probe with excellent performance in NIR fluorescence and photoacoustic dual-mode tumor imaging. This study offers useful insights into designing a new generation agent for clinical cancer diagnosis.

A fluorescent molecular rotor probe for tracking plasma membranes and exosomes in living cells

A rotor-based probe MRMP-1 was designed and synthesized. MRMP-1 can bind to plasma membranes very quickly and stably with remarkable fluorescence enhancement. It can be used to monitor the dynamic changes in cell membranes in real-time under stimuli conditions. Importantly, MRMP-1 is the first rotor-based fluorescent sensor to label exosomes in living cells.

Accuracy Meets Interpretability for Computational Spectroscopy by Means of Hybrid and Double-Hybrid Functionals

Accuracy and interpretability are often seen as the devil and holy grail in computational spectroscopy and their reconciliation remains a primary research goal. In the last few decades, density functional theory has revolutionized the situation, paving the way to reliable yet effective models for medium size molecules, which could also be profitably used by non-specialists. In this contribution we will compare the results of some widely used hybrid and double hybrid functionals with the aim of defining the most suitable recipe for all the spectroscopic parameters of interest in rotational and vibrational spectroscopy, going beyond the rigid rotor/harmonic oscillator model. We will show that last-generation hybrid and double hybrid functionals in conjunction with partially augmented double- and triple-zeta basis sets can offer, in the framework of second order vibrational perturbation theory, a general, robust, and user-friendly tool with unprecedented accuracy for medium-size semi-rigid molecules.

Fluorimetric and CD Recognition between Various ds-DNA/RNA Depends on a Cyanine Connectivity in Cyanine-guanidiniocarbonyl-pyrrole Conjugate

Two novel isosteric conjugates of guanidiniocarbonyl-pyrrole and 6-bromo-TO (thiazole orange) were prepared, differing only in linker connectivity to cyanine (benzothiazole nitrogen vs. quinoline nitrogen). The quinoline analog was significantly more susceptible to aggregation in an aqueous medium, which resulted in induced circular dichroism (ICD; λ = 450-550 nm) recognition between A-T(U) and G-C basepair containing polynucleotides. The benzothiazole-isostere showed pronounced (four-fold) fluorimetric selectivity toward ds-RNA in comparison to any ds-DNA, at variance to its quinoline-analogue fluorescence being weakly selective to GC-DNA. Preliminary screening on human tumor and normal lung cell lines showed that both dyes very efficiently enter living cells and accumulate in mitochondria, causing moderate cytotoxic effects, and thus could be considered as lead compounds toward novel theragnostic mitochondrial dyes.

BatchDeconvolution: a Fiji plugin for increasing deconvolution workflow

Deconvolution microscopy is a very useful, software-based technique allowing to deblur microscopy images and increase both lateral and axial resolutions. It can be used along with many of fluorescence microscopy imaging techniques. By increasing axial resolution, it also enables three-dimensional imaging using a basic wide-field fluorescence microscope. Unfortunately, commercially available deconvolution software is expensive, while freely available programs have limited capabilities of a batch file processing. In this work we present BatchDeconvolution, a Fiji plugin that bridges two programs that we used subsequently in an image deconvolution pipeline: PSF Generator and DeconvolutionLab2, both from Biomedical Imaging Group, EPFL. Our software provides a simple way to perform a batch processing of multiple microscopy files with minimal working time required from the user.

Fluorophore-Labeled Cyclic Nucleotides as Potent Agonists of Cyclic Nucleotide-Regulated Ion Channels

High-affinity fluorescent derivatives of cyclic adenosine and guanosine monophosphate are powerful tools for investigating their natural targets. Cyclic nucleotide-regulated ion channels belong to these targets and are vital for many signal transduction processes, such as vision and olfaction. The relation of ligand binding to activation gating is still challenging, and there is a need for fluorescent probes that enable the process to be broken down to the single-molecule level. This inspired us to prepare fluorophore-labeled cyclic nucleotides, which are composed of a bright dye and a nucleotide derivative with a thiophenol motif at position 8 that has already been shown to enable superior binding affinity. These bioconjugates were prepared by a novel cross-linking strategy that involves substitution of the nucleobase with a modified thiophenolate in good yield. Both fluorescent nucleotides are potent activators of different cyclic nucleotide-regulated ion channels with respect to the natural ligand and previously reported substances. Molecular docking of the probes excluding the fluorophore reveals that the high potency can be attributed to additional hydrophobic and cation-π interactions between the ligand and the protein. Moreover, the introduced substances have the potential to investigate related target proteins, such as cAMP- and cGMP-dependent protein kinases, exchange proteins directly activated by cAMP or phosphodiesterases.

Discrimination of live and dead cells with two different sets of signals and unique application in vivo imaging

Discriminating living and dead cells is of great significance for the study of apoptosis. In this work, we have developed a unique fluorescent probe (RPIC) for discriminating live and dead cells with duel-channel fluorescence imaging under double excitation and double emission mode. Dead cells treated with RPIC shows weak fluorescence signals in red channel, however, strong fluorescence signals are appeared in red channel in live cells. Weak and strong green fluorescence signals present at live cells and dead cells, respectively. Moreover, RPIC can detect successfully apoptosis of cancer cells. For in-vivo imaging, RPIC can discriminate successfully live and dead zebrafish with the same method. More interestingly, it is found that RPIC possesses the ability of discriminating normal mice and tumor mice.

Conjugating a groove binder analogue to a styryl-quinolinium scaffold for the light-up detection of duplex and G-Quadruplex DNA with different binding modes

The rational design of novel small molecules, which can target specific DNA sequences or secondary structural DNAs, is one of the most important goals in medicinal chemistry. Also the studies of DNA binding potency which can give fundamental insight into binding mechanisms and specificity are essential. In this paper, a N-methylated quinolinium probe NSQ functionalized with a G-Quadruplex DNA groove binder analogue was designed and synthesized. NSQ was found to express selective and sensitive for "light-up" detection of both G-Quadruplex and duplex DNAs over RNA and other biomolecules. The characteristics of NSQ and its interactions with DNAs were comprehensively evaluated by means of fluorescence, UV-Vis, circular dichroism, FID assay, DFT calculation and molecular docking. NSQ exhibited higher binding affinity to G-Quadruplex than to duplex DNA. Binding mechanism analysis indicated NSQ interacted with G-Quadruplex DNA mainly through end-stacking mode, while bound with duplex DNA into the minor groove of AT-rich regions. Further, NSQ exhibited potent in vitro anti-tumor activity, and to elucidate the cellular applications, confocal cell imaging was carried out and validated its mainly nuclear localization.

Discriminating normal and inflammatory models by viscosity changes with a mitochondria-targetable fluorescent probe

Intracellular viscosity abnormalities can lead to diabetes, neurodegenerative diseases and cancer. In this work, we developed a mitochondria-targetable fluorescent probe (EIMV) for discriminating normal and inflammatory models by viscosity changes. It was found that EIMV showed excellent properties, including high photostability, low cytotoxicity, red emission and favorable biocompatibility. In view of these unique features, this probe could successfully identify normal and cancer cells via viscosity changes. Furthermore, the EIMV probe successfully identified zebrafish with different viscosities by the same method. Moreover, EIMV exhibited different fluorescence signals in normal and inflammatory mice due to changes in viscosity. Therefore, the probe provides a new method to study the relationship between diseases and viscosity in the fields of biology and medicine.

FluoroCalins: engineered lipocalins with novel binding functions fused to a fluorescent protein for applications in biomolecular imaging and detection

FluoroCalins represent novel bifunctional protein reagents derived from engineered lipocalins fused to a fluorescent reporter protein, here the enhanced green fluorescent protein (eGFP). We demonstrate the construction, facile bacterial production and broad applicability of FluoroCalins using two Anticalin® molecules directed against the tumor vasculature-associated extra domain B of fibronectin (ED-B) and the vascular endothelial growth factor receptor 3, a marker of tumor and lymphangiogenesis. FluoroCalins were prepared with two different spacers: (i) a short Ser3Ala linker and (ii) a long hydrophilic and conformationally unstructured PASylation® polypeptide comprising 200 Pro, Ala and Ser residues. These FluoroCalins were applied for direct target quantification in enzyme-linked immunosorbent assay as well as target detection by flow cytometry and fluorescence microscopy of live and fixed cells, respectively, demonstrating high specificity and signal-to-noise ratio. Hence, FluoroCalins offer a promising alternative to antibody-based reagents for state of the art fluorescent in vitro detection and biomolecular imaging.

A Software Tool for High-Throughput Real-Time Measurement of Intensity-Based Ratio-Metric FRET

Förster resonance energy transfer (FRET) is increasingly used for non-invasive measurement of fluorescently tagged molecules in live cells. In this study, we have developed a freely available software tool MultiFRET, which, together with the use of a motorised microscope stage, allows multiple single cells to be studied in one experiment. MultiFRET is a Java plugin for Micro-Manager software, which provides real-time calculations of ratio-metric signals during acquisition and can simultaneously record from multiple cells in the same experiment. It can also make other custom-determined live calculations that can be easily exported to Excel at the end of the experiment. It is flexible and can work with multiple spectral acquisition channels. We validated this software by comparing the output of MultiFRET to that of a previously established and well-documented method for live ratio-metric FRET experiments and found no significant difference between the data produced with the use of the new MultiFRET and other methods. In this validation, we used several cAMP FRET sensors and cell models: i) isolated adult cardiomyocytes from transgenic mice expressing the cytosolic epac1-camps and targeted pmEpac1 and Epac1-PLN sensors, ii) isolated neonatal mouse cardiomyocytes transfected with the AKAP79-CUTie sensor, and iii) human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) transfected with the Epac-S^H74 sensor. The MultiFRET plugin is an open source freely available package that can be used in a wide area of live cell imaging when live ratio-metric calculations are required.

Protein-like Enwrapped Perylene Bisimide Chromophore as a Bright Microcrystalline Emitter Material

Strongly emissive solid-state materials are mandatory components for many emerging optoelectronic technologies, but fluorescence is often quenched in the solid state owing to strong intermolecular interactions. The design of new organic pigments, which retain their optical properties despite their high tendency to crystallize, could overcome such limitations. Herein, we show a new material with monomer-like absorption and emission profiles as well as fluorescence quantum yields over 90 % in its crystalline solid state. The material was synthesized by attaching two bulky tris(4-tert-butylphenyl)phenoxy substituents at the perylene bisimide bay positions. These substituents direct a packing arrangement with full enwrapping of the chromophore and unidirectional chromophore alignment within the crystal lattice to afford optical properties that resemble those of their natural pigment counterparts, in which chromophores are rigidly embedded in protein environments.

A 2-(benzo[d]thiazol-2-yl)phenol based on conjugated polymer: Highly selective colorimetric fluorescent chemosensor for F-depending on Si–O bond cleavage reaction

Design and synthesis of highly selective fluorine ion probes become particularly important owing to the specific role of fluorine ion in chemical and biomedical progresses. As a new-type of fluorescent material, conjugated polymers with unique photometric properties have been widely researched by scientists in the field of the fluorescence sensors. In this study, the polymer PBTPV-OSi containing benzothiazole moiety is synthesized via palladium-catalyzed Heck coupling reaction. This polymer not only exhibits good solubility in organic solvents but also shows high selectivity for fluorine ion detection in comparison to other anions. Upon addition of F− to PBTPV-OSi solution, Si–O cleavage of PBTPV-OSi leads to the fluorescence quenching of the polymer in tetrahydrofuran dramatically, and the detection limit is 8 × 10−6 mol/L. Moreover, besides detecting fluorine ion from organic phase, the probe can also effectively detect potassium fluoride from inorganic phase. More importantly, a naked-eye detectable chromogenic and fluorogenic dual response to fluorine ion (F−) can be visibly noted and the detection process of fluorine ion is relatively fast.

Ratiometric Fluorescent Nanoprobe for Highly Sensitive Determination of Mercury Ions

In this study, a novel dual-emission ratiometric fluorescent nanoprobe (RFN) was synthesized and ultilized for highly sensitive determination of mercury ions. In this nanoprobe, fluorescein isothiocyanate (FITC) doped silica (SiO₂) served as a reference signal, FITC–SiO₂ microspheres were synthesized and modified with amino groups, and then Au Nanoclusters (AuNCs) were combined with the amino groups on the surface of the FITC–SiO₂ microspheres to obtain the RFN. The selectivity, stability, and pH of the RFN were then optimized, and the determination of mercury ions was performed under optimal conditions. The probe fluorescence intensity ratio (F₅₂₀ nm/F₆₈₀ nm) and Hg²⁺ concentration (1.0 × 10⁻¹⁰ mol/L to 1.0 × 10⁻⁸ mol/L) showed a good linear relationship, with a correlation coefficient of R² = 0.98802 and a detection limit of 1.0 × 10⁻¹⁰ mol/L, respectively. The probe was used for the determination of trace mercury ion in water samples, and the recovery rate was 98.15~100.45%, suggesting a wide range of applications in monitoring pollutants, such as heavy metal ion and in the area of environmental protection.

Advances in Cyanine - Amino Acid Conjugates and Peptides for Sensing of DNA, RNA and Protein Structures

Small molecule spectrophotometric probes for DNA/RNA and proteins are of the utmost importance for diagnostics in biochemical and biomedical research. Both, naturally occurring and synthetic probes, often include peptide sequence responsible for the selectivity toward the particular target; however, commercially available dyes are restricted to single point attachment to the peptide (having one reactive group). Here presented are our recent advances in the development of novel amino acidfluorophore probes, with the unique characteristic of free N- and C-terminus available for incorporation at any peptide backbone position. Intriguingly, already monomeric amino acid-fluorophores showed recognition among various DNA/RNA, whereby steric impact and contribution of halogens is systematically studied. Moreover, some dyes revealed intracellular mitochondria specificity. Further, several hetero-dimeric chromophore systems were prepared, demonstrating that synergistic effect can lead to simultaneous DNA, RNA and protein fluorimetric recognition, combined with enzyme inhibition. Also, homodimeric cyanines equipped with chlorine revealed intriguing DNA/RNA selectivity in respect to well-known parent TOTO and YOYO dyes.

Boron-Containing Probes for Non-optical High-Resolution Imaging of Biological Samples

Boron has been employed in materials science as a marker for imaging specific structures by electron energy loss spectroscopy (EELS) or secondary ion mass spectrometry (SIMS). It has a strong potential in biological analyses as well; however, the specific coupling of a sufficient number of boron atoms to a biological structure has proven challenging. Herein, we synthesize tags containing closo-1,2-dicarbadodecaborane, coupled to soluble peptides, which were integrated in specific proteins by click chemistry in mammalian cells and were also coupled to nanobodies for use in immunocytochemistry experiments. The tags were fully functional in biological samples, as demonstrated by nanoSIMS imaging of cell cultures. The boron signal revealed the protein of interest, while other SIMS channels were used for imaging different positive ions, such as the cellular metal ions. This allows, for the first time, the simultaneous imaging of such ions with a protein of interest and will enable new biological applications in the SIMS field.