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Two-photon (TP) excitation of organic chromophores is of great interest for decades, as applications of such phenomena from 3-dimentional (3D) microfabrication to optical limiting and optical data storage, are of increasing importance. More recently, two-photon excitation found important applications in biology, notably in two-photon excited microscopy (TPEM) or two-photon photodynamic therapy (2P-PDT). Nevertheless, these techniques were using dyes or sensitizers designed for one-photon processes with low two-photon response. The lack of efficient molecules specifically designed for two-photon applications has led us to design new chromophores for biological applications with increased sensitivity to two-photon excitation and specifically added properties useful in biological media, such as water solubility. Here we describe the molecular engineering of such dyes mainly for cell and small animal observation by TPEM and their conjugation to magnetic nanoparticles and bio-nanoparticles such as viruses. We will then focus on the possibility to use photochemical reaction for cell triggering by two-photon photorelease of biologically active substances the so-called two-photon uncaging. [ABSTRACT FROM AUTHOR]

Photoactivatable fluorescent probes are valuable tools in bioimaging for tracking cells down to single molecules and for single molecule localization microscopy. For the latter application, green emitting dyes are in demand. We herein developed an efficient green‐emitting photoactivatable furanyl‐BODIPY (PFB) and we established a new mechanism of photoactivation called Directed Photooxidation Induced Activation (DPIA) where the furan is photo‐oxidized in a directed manner by the singlet oxygen produced by the probe. The efficient photoconverter (93‐fold fluorescence enhancement at 510 nm, 49 % yield conversion) is functionalizable and allowed targeting of several subcellular structures and organelles, which were photoactivated in live cells. Finally, we demonstrated the potential of PFB in super‐resolution imaging by performing PhotoActivated Localization Microscopy (PALM) in live cells. [ABSTRACT FROM AUTHOR]

DNA origami nanostructures (DOs) are promising tools for applications including drug delivery, biosensing, detecting biomolecules, and probing chromatin substructures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing, visualizing, and controlling biomolecular processes within live cells. We present an approach to deliver DOs into live-cell nuclei. We show that these DOs do not undergo detectable structural degradation in cell culture media or cell extracts for 24 hours. To deliver DOs into the nuclei of human U2OS cells, we conjugated 30-nanometer DO nanorods with an antibody raised against a nuclear factor, specifically the largest subunit of RNA polymerase II (Pol II). We find that DOs remain structurally intact in cells for 24 hours, including inside the nucleus. We demonstrate that electroporated anti-Pol II antibody-conjugated DOs are piggybacked into nuclei and exhibit subdiffusive motion inside the nucleus. Our results establish interfacing DOs with a nuclear factor as an effective method to deliver nanodevices into live-cell nuclei. [ABSTRACT FROM AUTHOR]

We report a universal smart probe (SP) that is capable of detecting several homologous let-7 microRNAs (miRNAs). While the SP is complementary to let-7a, and therefore, strongly binds to this target, due to sequence homology, the SP also has equal propensity to non-specifically hybridize with let-7b and let-7c, which are homologous to let-7a. The fluorescence signal of the SP was switched off in the absence of any homologous member target, but the signal was switched on when any of the three homologous members was present. With the assistance of nucleic acid blockers (NABs), this SP system can discriminate between homologous miRNAs. We show that the SP can discriminate between let-7a and the other two sequences by using linear NABs (LNABs) to block non-specific interactions between the SP and these sequences. We also found that LNABs used do not cross-react with the let-7a target due to the low LNABs:SP molar ratio of 6:1 used. Overall, this SP represents a universal probe for the recognition of a homologous miRNA family. The assay is sensitive, providing a detection limit of 6 fmol. The approach is simple, fast, usable at room temperature, and represents a general platform for the in vitro detection of homologous microRNAs by a single fluorescent hairpin probe. [ABSTRACT FROM AUTHOR]

Cationic carbon dots (CDs) have been recently described as nucleic acid carriers with high in vitro and in vivo transfection efficiency and imaging properties. However, developing nanoparticles (NPs) for biomedical applications requires assessing their safety. In the present study, we characterized the cell uptake and trafficking, as well as the cell viability loss, oxidative stress, inflammation, and mitochondrial and lysosomal perturbations evoked by cationic CDs prepared by microwave-assisted pyrolysis of citric acid and high molecular weight branched polyethyleneimine (bPEI25k), using THP-1-derived macrophages. CDs were rapidly internalized by cells and addressed to the lysosomes after their cell entry. The NPs induced a dose- and time-dependent loss in cell viability that was associated with oxidative stress and IL-8 release. The CDs triggered also a dose-dependent loss in lysosome integrity, mitochondrial dysfunction, and NLRP3 inflammasome activation. Inhibition of the lysosomal protease cathepsin B significantly reduced CD-induced mitochondrial dysfunction and NLRP3 inflammasome activation, suggesting a pivotal role of the lysosome in the toxicological effects of the NPs. Our study provides for the first time a mechanistic pathway for the toxicological effects of bPEI25k-based cationic CDs. [ABSTRACT FROM AUTHOR]

Overexpression of EGFR drives glioblastomas (GBM) cell invasion but these tumours remain resistant to EGFR-targeted therapies such as tyrosine kinase inhibitors (TKIs). Endocytosis, an important modulator of EGFR function, is often dysregulated in glioma cells and is associated with therapy resistance. However, the impact of TKIs on EGFR endocytosis has never been examined in GBM cells. In the present study, we showed that gefitinib and other tyrosine kinase inhibitors induced EGFR accumulation in early-endosomes as a result of an increased endocytosis. Moreover, TKIs trigger early-endosome re-localization of another membrane receptor, the fibronectin receptor alpha5beta1 integrin, a promising therapeutic target in GBM that regulates physiological EGFR endocytosis and recycling in cancer cells. Super-resolution dSTORM imaging showed a close-proximity between beta1 integrin and EGFR in intracellular membrane compartments of gefitinib-treated cells, suggesting their potential interaction. Interestingly, integrin depletion delayed gefitinib-mediated EGFR endocytosis. Co-endocytosis of EGFR and alpha5beta1 integrin may alter glioma cell response to gefitinib. Using an in vitro model of glioma cell dissemination from spheroid, we showed that alpha5 integrin-depleted cells were more sensitive to TKIs than alpha5-expressing cells. This work provides evidence for the first time that EGFR TKIs can trigger massive EGFR and alpha5beta1 integrin co-endocytosis, which may modulate glioma cell invasiveness under therapeutic treatment. [ABSTRACT FROM AUTHOR]

[Display omitted] • Isothiazologuanosine (tzG) is an isofunctional fluorescent analogue of Guanosine. • tzG contains the N7 atom involved in Hoogsteen base pairs and enzyme recognition. • tzG photophysics is studied by fluorescence spectroscopy and quantum mechanics. • tzG tautomer equilibrium and non-radiative paths are polarity/proticity sensitive. • tzG can monitor nucleic acid conformational changes and interaction with proteins. Application of fluorescence techniques to investigate molecular interactions with nucleic acids is complicated by their poor emission, making the substitution of natural nucleobases by fluorescent nucleoside analogues (FNAs) a useful strategy. A breakthrough in fluorescent nucleoside analogues has been the development of thienoguanosine (thG) and isothiazologuanosine (tzG), two isosteric mimics of guanosine (G). Due to its N7 atom needed in Hoogsteen base pairs and enzyme recognition, tzG is also an isofunctional G surrogate. Herein, we integrated fluorescence spectroscopy measurements with quantum mechanical (QM) calculations to characterize the mechanisms underlying tzG photophysics in different solvents. In dioxane and ethyl acetate, tzG existed primarily as a H1 keto-amino tautomer with short fluorescence lifetime (τ ∼ 2 ns) and low quantum yield (ϕ ∼ 0.10). In buffer, the H1 tautomer (ϕ = 0.36, τ = 8.84 ns) coexisted with a weakly emissive H3 keto-amino tautomer. The two tautomers were also observed in methanol, but with a 30% decrease in ϕ and τ values for the major H1 tautomer. QM calculations suggested that the main non-radiative pathway of tzG-H1 involves NS bond loosening and is responsible for the more solvent-sensitive ϕ and τ values compared to thG. This pathway is much more efficient for tzG-H3, for which an additional pathway to a dark nπ* state and a large coupling with triplet states further explain its very low emission. This study lays the ground for rationally using tzG as a sensitive FNA. [ABSTRACT FROM AUTHOR]

The realm of self-healing materials integrates chemical and physical mechanisms that prevent wear and fracturing and extend the operational lifetime. Unlike the favorable rheology of amorphous soft materials that facilitates efficient contact between fragments, the efficiency of recovery of atomistically ordered materials is restricted by slower interfacial mass transport and the need for ideal physical alignment, which limits their real-world application. We report drastic enhancements in efficiency and recovery time in the self-healing of anilinium bromide, challenging these limitations. Crystals of this material recovered up to 49% within seconds and up to 95% after 100 min via ferroelastic detwinning. The spatial evolution of strain during cracking and healing was measured in real time using digital image correlation. Favorable alignment and strong ionic bonding across the interface of partially fractured crystals facilitate self-healing. This study elevates organic crystals close to the best-in-class self-healing polymers and sets an approach for durable crystal-based optoelectronics., (© 2024. The Author(s).)

HIV-1 Gag polyprotein plays a pivotal role in assembly and budding of new particles, by specifically packaging two copies of viral gRNA in the host cell cytoplasm and selecting the cell plasma membrane for budding. Both gRNA and membrane selections are thought to be mediated by the compact form of Gag. This compact form binds to gRNA through both its matrix (MA) and nucleocapsid (NC) domains in the cytoplasm. At the plasma membrane, the membrane competes with gRNA for Gag binding, resulting in a transition to the extended form of Gag found in immature particles with MA bound to membrane lipids and NC to gRNA. The Gag compact form was previously evidenced in vitro. Here, we demonstrated the compact form of Gag in cells by confocal microscopy, using a bimolecular fluorescence complementation approach with a split-GFP bipartite system. Using wild-type Gag and Gag mutants, we showed that the compact form is highly dependent on the binding of MA and NC domains to RNA, as well as on interactions between MA and CA domains. In contrast, Gag multimerization appears to be less critical for the accumulation of the compact form. Finally, mutations altering the formation of Gag compact form led to a strong reduction in viral particle production and infectivity, revealing its key role in the production of infectious viral particles., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The viscosity that ensures the controlled diffusion of biomolecules in cells is a crucial biophysical parameter. Consequently, fluorescent probes capable of reporting viscosity variations are valuable tools in bioimaging. In this field, red-shifted probes are essential, as the widely used and gold standard probe remains green-emitting molecular rotors based on BODIPY. Here, we demonstrate that pyrrolyl squaraines, red-emissive fluorophores, exhibit high sensitivity over a wide viscosity range from 30 to 4890 mPa·s. Upon alkylation of the pyrrole moieties, the probes improve their sensitivity to viscosity through an enhanced twisted intramolecular charge transfer phenomenon. We utilized this scaffold to develop a plasma membrane probe, pSQ-PM, that efficiently stains the plasma membrane in a fluorogenic manner. Using fluorescence lifetime imaging, pSQ-PM enabled efficient sensing of viscosity variations in the plasma membrane under various conditions and in different cell lines (HeLa, U2OS, and NIH/3T3). Moreover, upon incubation, pSQ-PM stained the membrane of intracellular vesicles and suggested that the lysosomal membranes displayed enhanced fluidity.

Photomodulable fluorescent probes are drawing increasing attention due to their applications in advanced bioimaging. Whereas photoconvertible probes can be advantageously used in tracking, photoswitchable probes constitute key tools for single-molecule localization microscopy to perform super-resolution imaging. Herein, we shed light on a red and far-red BODIPY, namely, BDP-576 and BDP-650, which possess both properties of conversion and switching. Our study demonstrates that these pyrrolyl-BODIPYs convert into typical green- and red-emitting BODIPYs that are perfectly adapted to microscopy. We also showed that this pyrrolyl-BODIPYs undergo Directed Photooxidation Induced Conversion, a photoconversion mechanism that we recently introduced, where the pyrrole moiety plays a central role. These unique features were used to develop targeted photoconvertible probes toward different organelles or subcellular units (plasma membrane, mitochondria, nucleus, actin, Golgi apparatus, etc. ) using chemical targeting moieties and a Halo tag. We notably showed that BDP-650 could be used to track intracellular vesicles over more than 20 min in two-color imagings with laser scanning confocal microscopy, demonstrating its robustness. The switching properties of these photoconverters were studied at the single-molecule level and were then successfully used in live single-molecule localization microscopy in epithelial cells and neurons. Both membrane- and mitochondria- targeted probes could be used to decipher membrane 3D architecture and mitochondrial dynamics at the nanoscale. This study builds a bridge between the photoconversion and photoswitching properties of probes undergoing directed photooxidation and shows the versatility and efficacy of this mechanism in advanced live imaging.

Efficient exciton transport is the essential property of natural and synthetic light-harvesting (LH) devices. Here we investigate exciton transport properties in LH organic polymer nanoparticles (ONPs) of 40 nm diameter. The ONPs are loaded with a rhodamine B dye derivative and bulky counterion, enabling dye loadings as high as 0.3 M, while preserving fluorescence quantum yields larger than 30%. We use time-resolved fluorescence spectroscopy to monitor exciton-exciton annihilation (EEA) kinetics within the ONPs dispersed in water. We demonstrate that unlike the common practice for photoluminescence investigations of EEA, the non-uniform intensity profile of the excitation light pulse must be taken into account to analyse reliably intensity-dependent population dynamics. Alternatively, a simple confocal detection scheme is demonstrated, which enables (i) retrieving the correct value for the bimolecular EEA rate which would otherwise be underestimated by a typical factor of three, and (ii) revealing minor EEA by-products otherwise unnoticed. Considering the ONPs as homogeneous rigid solutions of weakly interacting dyes, we postulate an incoherent exciton hoping mechanism to infer a diffusion constant exceeding 0.003 cm 2 s -1 and a diffusion length as large as 70 nm. This work demonstrates the success of the present ONP design strategy at engineering efficient exciton transport in disordered multichromophoric systems.

Although the human immunodeficiency virus type 1 lipid envelope has been reported to be enriched with host cell sphingomyelin and cholesterol, the molecular mechanism of the enrichment is not well understood. Viral Gag protein plays a central role in virus budding. Here, we report the interaction between Gag and host cell lipids using different quantitative and super-resolution microscopy techniques in combination with specific probes that bind endogenous sphingomyelin and cholesterol. Our results indicate that Gag in the inner leaflet of the plasma membrane colocalizes with the outer leaflet sphingomyelin-rich domains and cholesterol-rich domains, enlarges sphingomyelin-rich domains, and strongly restricts the mobility of sphingomyelin-rich domains. Moreover, Gag multimerization induces sphingomyelin-rich and cholesterol-rich lipid domains to be in close proximity in a curvature-dependent manner. Our study suggests that Gag binds, coalesces, and reorganizes pre-existing lipid domains during assembly., (© 2023. The Author(s).)

Invited for the cover of this issue is the group of Mayeul Collot at the University of Strasbourg (CNRS). The image depicts the effect of simple chemical tuning on coumarin dyes to tune and improve the DPIC photoconversion mechanism. Read the full text of the article at 10.1002/chem.202203933., (© 2023 Wiley-VCH GmbH.)

Time-resolved fluorescence anisotropy (TRFA) provides key information on the dynamics of biomolecules and their interaction with ligands. However, since natural nucleosides are almost non-fluorescent, its application to DNA duplexes (dsDNA) requires fluorescent labels, which can alter dsDNA stability, hinder protein binding, and complicate interpretation of TRFA experiments due to their local motion. As shown here, thienoguanosine ( th G), a fluorescent analogue of guanosine, overcomes all these limitations. We recorded the TRFA decays of th G-labelled dsDNA of different lengths. th G behaved as a rigid, non-perturbing reporter, since no fast correlation time was recorded for any tested dsDNA. Due to its perfect stacking, only two correlation times, instead of the typical three, describe th G-labelled dsDNA rotational dynamics. Thanks to these features, we provided a complete description of the tumbling of the different dsDNA and their complexes with the Set and Ring Associated (SRA) domain of UHRF1, a key epigenetic regulator, obtaining values in excellent agreement with theoretical predictions. Moreover, th G was also found sensitive to SRA-induced base flipping of neighboring nucleobases. In the DNA label toolbox, th G thus stands out as a unique reporter for investigating the rotational dynamics of dsDNA and protein/dsDNA complexes., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Very few proteins are reported to bind specific lipids. Because of the high selectivity and strong binding to specific lipids, lipid-targeting pore forming toxins (PFTs) have been employed to study the distribution of lipids in cell- and model-membranes. Non-toxic and monomeric PFT-derivatives are especially useful to study living cells. In this chapter we highlight sphingomyelin (SM)-binding PFT, lysenin (Lys), its derivatives, and newly identified SM/cholesterol binding protein, nakanori. We describe the preparation of non-toxic mutant of Lys (NT-Lys) and its application in optical and super resolution microscopy. We also discuss the observation of nanometer scale lipid domains labeled with nakanori and maltose-binding protein (MBP)-Lys in electron microscopy., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Thienoguanosine ( th G) is an isomorphic guanosine (G) surrogate that almost perfectly mimics G in nucleic acids. To exploit its full potential and lay the foundation for future applications, 20 DNA duplexes, where the bases facing and neighboring th G were systematically varied, were thoroughly studied using fluorescence spectroscopy, molecular dynamics simulations, and mixed quantum mechanical/molecular mechanics calculations, yielding a comprehensive understanding of its photophysics in DNA. In matched duplexes, th G's hypochromism was larger for flanking G/C residues but its fluorescence quantum yield (QY) and lifetime values were almost independent of the flanking bases. This was attributed to high duplex stability, which maintains a steady orientation and distance between nucleobases, so that a similar charge transfer (CT) mechanism governs the photophysics of th G independently of its flanking nucleobases. th G can therefore replace any G residue in matched duplexes, while always maintaining similar photophysical features. In contrast, the local destabilization induced by a mismatch or an abasic site restores a strong dependence of th G's QY and lifetime values on its environmental context, depending on the CT route efficiency and solvent exposure of th G. Due to this exquisite sensitivity, th G appears ideal for monitoring local structural changes and single nucleotide polymorphism. Moreover, th G's dominant fluorescence lifetime in DNA is unusually long (9-29 ns), facilitating its selective measurement in complex media using a lifetime-based or a time-gated detection scheme. Taken together, our data highlight th G as an outstanding emissive substitute for G with good QY, long fluorescence lifetimes, and exquisite sensitivity to local structural changes.

The human immunodeficiency virus type 1 Gag precursor specifically selects the unspliced viral genomic RNA (gRNA) from the bulk of cellular and spliced viral RNAs via its nucleocapsid (NC) domain and drives gRNA encapsidation at the plasma membrane (PM). To further identify the determinants governing the intracellular trafficking of Gag-gRNA complexes and their accumulation at the PM, we compared, in living and fixed cells, the interactions between gRNA and wild-type Gag or Gag mutants carrying deletions in NC zinc fingers (ZFs) or a nonmyristoylated version of Gag. Our data showed that the deletion of both ZFs simultaneously or the complete NC domain completely abolished intracytoplasmic Gag-gRNA interactions. Deletion of either ZF delayed the delivery of gRNA to the PM but did not prevent Gag-gRNA interactions in the cytoplasm, indicating that the two ZFs display redundant roles in this respect. However, ZF2 played a more prominent role than ZF1 in the accumulation of the ribonucleoprotein complexes at the PM. Finally, the myristate group, which is mandatory for anchoring the complexes at the PM, was found to be dispensable for the association of Gag with the gRNA in the cytosol., (Copyright © 2020 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

The thienoguanine nucleobase ( th G b ) is an isomorphic fluorescent analogue of guanine. In aqueous buffer at neutral pH, th G b exists as a mixture of two ground-state H1 and H3 keto-amino tautomers with distinct absorption and emission spectra and high quantum yield. In this work, we performed the first systematic photophysical characterization of th G b as a function of pH (2 to 12). Steady-state and time-resolved fluorescence spectroscopies, supplemented with theoretical calculations, enabled us to identify three additional th G b forms, resulting from pH-dependent ground-state and excited-state reactions. Moreover, a thorough analysis allowed us to retrieve their individual absorption and emission spectra as well as the equilibrium constants which govern their interconversion. From these data, the complete photoluminescence pathway of th G b in aqueous solution and its dependence as a function of pH was deduced. As the identified forms differ by their spectra and fluorescence lifetime, th G b could be used as a probe for sensing local pH changes under acidic conditions.

The neuropeptide Y (NPY) plays numerous biological roles that are mediated by a family of G-protein-coupled receptors. Among the latter, the NPY Y 1 subtype receptor undergoes a rapid desensitization following agonist exposure. This desensitization was suggested to result from a rapid clathrin-dependent internalization of Y 1 and its recycling at the plasma membrane via sorting/early endosomes (SE/EE) and recycling endosomes (RE). Herein, to validate and quantitatively consolidate the mechanism of NPY internalization, we quantitatively investigated the NPY-induced internalization of the Y 1 receptor by direct stochastic optical reconstruction microscopy (dSTORM), a super-resolution imaging technique that can resolve EE and SE, which are below the resolution limit of conventional optical microscopes. Using Cy5-labeled NPY, we could monitor with time the internalization and recycling of NPY on HEK293 cells stably expressing eGFP-labeled Y 1 receptors. Furthermore, by discriminating the SE/EE from the larger RE by their sizes and monitoring these two populations as a function of time, we could firmly consolidate the kinetic model describing the internalization mechanism of the Y 1 receptors as the basis for their rapid desensitization following agonist exposure.

[reaction: see text] The synthesis and photonic and liquid-crystalline properties of a novel oligo biphenylene vinylene (OBV) chromophore with an extended pi-electron system are reported; the compound exhibits high fluorescence, a large two-photon absorption cross-section, and two- and three-dimensional liquid-crystalline mesophases.