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Centeno SP, Nothdurft K, Klymchenko AS, Pich A, Richtering W, Wöll D. FLIM nanoscopy resolves the structure and preferential adsorption in the co-nonsolvency of PNIPAM microgels in methanol-water. J Colloid Interface Sci 2025; 678:210-220. [PMID: 39243721 DOI: 10.1016/j.jcis.2024.08.235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024]
Abstract
Polymer microgels are swollen macromolecular networks with a typical size of hundred of nanometers to several microns that show an extraordinary open and responsive architecture to different external stimuli, being therefore important candidates for nanobiotechnology and nanomedical applications such as biocatalysis, sensing and drug delivery. It is therefore crucial to understand the delicate balance of physical-chemical interactions between the polymer backbone and solvent molecules that to a high extent determine their responsivity. In particular, the co-nonsolvency effect of poly(N-isopropylacrylamide) in aqueous alcohols is highly discussed, and there is a disagreement between molecular dynamics (MD) simulations (from literature) of the preferential adsorption of alcohol on the polymer chains and the values obtained by several empirical methods that mostly probe the bulk solvent properties. It is our contention that the most efficacious method for addressing this problem requires a nanoscopic method that can be combined with spectroscopy and record fluorescence spectra and super-resolved fluorescence lifetime images of microgels labeled covalently with the solvatochromic dye Nile Red. By employing this approach, we could simultaneously resolve the structure of sub-micron size objects in the swollen and in the collapsed state and estimate the solvent composition inside of them in - mixtures for two very different polymer architectures. We found an outstanding agreement between the MD simulations and our results that estimate a co-solvent molar fraction excess of approximately 3 with a very flat profile in the lateral direction of the microgel.
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Bruggeman E, Zhang O, Needham LM, Körbel M, Daly S, Cheetham M, Peters R, Wu T, Klymchenko AS, Davis SJ, Paluch EK, Klenerman D, Lew MD, O'Holleran K, Lee SF. POLCAM: instant molecular orientation microscopy for the life sciences. Nat Methods 2024; 21:1873-1883. [PMID: 39375574 PMCID: PMC11466833 DOI: 10.1038/s41592-024-02382-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/17/2024] [Indexed: 10/09/2024]
Abstract
Current methods for single-molecule orientation localization microscopy (SMOLM) require optical setups and algorithms that can be prohibitively slow and complex, limiting widespread adoption for biological applications. We present POLCAM, a simplified SMOLM method based on polarized detection using a polarization camera, which can be easily implemented on any wide-field fluorescence microscope. To make polarization cameras compatible with single-molecule detection, we developed theory to minimize field-of-view errors, used simulations to optimize experimental design and developed a fast algorithm based on Stokes parameter estimation that can operate over 1,000-fold faster than the state of the art, enabling near-instant determination of molecular anisotropy. To aid in the adoption of POLCAM, we developed open-source image analysis software and a website detailing hardware installation and software use. To illustrate the potential of POLCAM in the life sciences, we applied our method to study α-synuclein fibrils, the actin cytoskeleton of mammalian cells, fibroblast-like cells and the plasma membrane of live human T cells.
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Kislinger G, Fabig G, Wehn A, Rodriguez L, Jiang H, Niemann C, Klymchenko AS, Plesnila N, Misgeld T, Müller-Reichert T, Khalin I, Schifferer M. Combining array tomography with electron tomography provides insights into leakiness of the blood-brain barrier in mouse cortex. eLife 2024; 12:RP90565. [PMID: 39102289 PMCID: PMC11299977 DOI: 10.7554/elife.90565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024] Open
Abstract
Like other volume electron microscopy approaches, automated tape-collecting ultramicrotomy (ATUM) enables imaging of serial sections deposited on thick plastic tapes by scanning electron microscopy (SEM). ATUM is unique in enabling hierarchical imaging and thus efficient screening for target structures, as needed for correlative light and electron microscopy. However, SEM of sections on tape can only access the section surface, thereby limiting the axial resolution to the typical size of cellular vesicles with an order of magnitude lower than the acquired xy resolution. In contrast, serial-section electron tomography (ET), a transmission electron microscopy-based approach, yields isotropic voxels at full EM resolution, but requires deposition of sections on electron-stable thin and fragile films, thus making screening of large section libraries difficult and prone to section loss. To combine the strength of both approaches, we developed 'ATUM-Tomo, a hybrid method, where sections are first reversibly attached to plastic tape via a dissolvable coating, and after screening detached and transferred to the ET-compatible thin films. As a proof-of-principle, we applied correlative ATUM-Tomo to study ultrastructural features of blood-brain barrier (BBB) leakiness around microthrombi in a mouse model of traumatic brain injury. Microthrombi and associated sites of BBB leakiness were identified by confocal imaging of injected fluorescent and electron-dense nanoparticles, then relocalized by ATUM-SEM, and finally interrogated by correlative ATUM-Tomo. Overall, our new ATUM-Tomo approach will substantially advance ultrastructural analysis of biological phenomena that require cell- and tissue-level contextualization of the finest subcellular textures.
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Aknine N, Klymchenko AS. Push-Pull Fluorescent Dyes with Trifluoroacetyl Acceptor for High-Fidelity Sensing of Polarity and Heterogeneity of Lipid Droplets. Anal Chem 2024. [PMID: 39083638 DOI: 10.1021/acs.analchem.4c02322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Imaging and sensing of lipid droplets (LDs) attracted significant attention due to growing evidence for their important role in cell life. Solvatochromic dyes are promising tools to probe LDs' local polarity, but this analysis is biased by their non-negligible emission from intracellular membranes and capacity to emit from both the apolar core and polar interface of LDs. Here, we developed two push-pull solvatochromic dyes based on naphthalene and fluorene cores bearing an exceptionally strong electron acceptor, the trifluoroacetyl group. The latter was found to boost the optical properties of the dyes by shifting their absorption and emission to red and increasing their extinction coefficient, photostability, and sensitivity to solvent polarity (solvatochromism). In contrast to classical solvatochromic dyes, such as parent aldehydes and reference Nile Red, the new dyes exhibited strong fluorescence quenching by millimolar water concentrations in organic solvents. In live cells, the trifluoroacetyl dyes exhibited high specificity to LDs, whereas the parent aldehydes and Nile Red showed a detectable backgrounds from intracellular membranes. Experiments in model lipid membranes and nanoemulsion droplets confirmed the high selectivity of new probes to LDs in contrast to classical solvatochromic dyes. Moreover, the new probes were found to be selective to the LDs oil core, where they can sense lipid unsaturation and chain length. Their ratiometric imaging in cells revealed strong heterogeneity in polarity within LDs, which covered the range of polarities of unsaturated triglyceride oils, whereas Nile Red failed to properly estimate the local polarity of LDs. Finally, the probes revealed that LDs core polarity can be altered by fatty acid diets, which correlates with their chain length and unsaturation.
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Cruz Da Silva E, Gaki P, Flieg F, Messmer M, Gucciardi F, Markovska Y, Reisch A, Fafi-Kremer S, Pfeffer S, Klymchenko AS. Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404167. [PMID: 39011971 DOI: 10.1002/smll.202404167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/05/2024] [Indexed: 07/17/2024]
Abstract
Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.
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Mathieu C, Ghosh S, Draussin J, Gasser A, Jacquot G, Banerjee M, Gupta T, Schmutz M, Mirjolet C, Tillement O, Lux F, Klymchenko AS, Donzeau M, Pivot X, Harlepp S, Detappe A. Supramolecular Heterodimer Peptides Assembly for Nanoparticles Functionalization. Adv Healthc Mater 2024; 13:e2304250. [PMID: 38444191 PMCID: PMC11468928 DOI: 10.1002/adhm.202304250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/22/2024] [Indexed: 03/07/2024]
Abstract
Nanoparticle (NP) surface functionalization with proteins, including monoclonal antibodies (mAbs), mAb fragments, and various peptides, has emerged as a promising strategy to enhance tumor targeting specificity and immune cell interaction. However, these methods often rely on complex chemistry and suffer from batch-dependent outcomes, primarily due to limited control over the protein orientation and quantity on NP surfaces. To address these challenges, a novel approach based on the supramolecular assembly of two peptides is presented to create a heterotetramer displaying VHHs on NP surfaces. This approach effectively targets both tumor-associated antigens (TAAs) and immune cell-associated antigens. In vitro experiments showcase its versatility, as various NP types are biofunctionalized, including liposomes, PLGA NPs, and ultrasmall silica-based NPs, and the VHHs targeting of known TAAs (HER2 for breast cancer, CD38 for multiple myeloma), and an immune cell antigen (NKG2D for natural killer (NK) cells) is evaluated. In in vivo studies using a HER2+ breast cancer mouse model, the approach demonstrates enhanced tumor uptake, retention, and penetration compared to the behavior of nontargeted analogs, affirming its potential for diverse applications.
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Pivovarenko VG, Klymchenko AS. Fluorescent Probes Based on Charge and Proton Transfer for Probing Biomolecular Environment. CHEM REC 2024; 24:e202300321. [PMID: 38158338 DOI: 10.1002/tcr.202300321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Fluorescent probes for sensing fundamental properties of biomolecular environment, such as polarity and hydration, help to study assembly of lipids into biomembranes, sensing interactions of biomolecules and imaging physiological state of the cells. Here, we summarize major efforts in the development of probes based on two photophysical mechanisms: (i) an excited-state intramolecular charge transfer (ICT), which is represented by fluorescent solvatochromic dyes that shift their emission band maximum as a function of environment polarity and hydration; (ii) excited-state intramolecular proton transfer (ESIPT), with particular focus on 5-membered cyclic systems, represented by 3-hydroxyflavones, because they exhibit dual emission sensitive to the environment. For both ICT and ESIPT dyes, the design of the probes and their biological applications are summarized. Thus, dyes bearing amphiphilic anchors target lipid membranes and report their lipid organization, while targeting ligands direct them to specific organelles for sensing their local environment. The labels, amino acid and nucleic acid analogues inserted into biomolecules enable monitoring their interactions with membranes, proteins and nucleic acids. While ICT probes are relatively simple and robust environment-sensitive probes, ESIPT probes feature high information content due their dual emission. They constitute a powerful toolbox for addressing multitude of biological questions.
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Combes A, Rieb C, Haye L, Klymchenko AS, Serra CA, Reisch A. Mixing versus Polymer Chemistry in the Synthesis of Loaded Polymer Nanoparticles through Nanoprecipitation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:16532-16542. [PMID: 37955543 DOI: 10.1021/acs.langmuir.3c02468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Polymer nanoparticles (NPs) loaded with drugs and contrast agents have become key tools in the advancement of nanomedicine, requiring robust technologies for their synthesis. Nanoprecipitation is a particularly interesting technique for the assembly of loaded polymer NPs, which is well-known to proceed under kinetic control, with a strong influence of the assembly conditions. On the other hand, the nature of the used polymer also influences the outcome of nanoprecipitation. Here, we investigated systematically the relative effects of mixing of the organic and aqueous phases and polymer chemistry on the formation of polymer nanocarriers. For this, two mixing schemes, manual mixing and microfluidic mixing using an impact-jet micromixer, were first evaluated, showing mixing times of several tens of milliseconds and a few milliseconds, respectively. Copolymers of ethyl methacrylate with charged and hydrophilic groups and different polyesters (poly(d-l-lactide-co-glycolide) and poly(lactic acid)) were combined with a fluorescent dye salt and tested for particle assembly using these "slow" and "fast" mixing methods. Our results showed that in the case of the most hydrophobic polymers, the speed of mixing had no significant influence on the size and loading of the formed NPs. In contrast, in the case of less hydrophobic polymers, faster mixing led to smaller NPs with better encapsulation. The switch between mixing and polymer-controlled assembly was directly correlated to the solubility limit of the polymers in acetonitrile-water mixtures, with a critical point for solubility limits between 15 and 20 vol % of water. Our results provide simple guidelines on how to evaluate the possible influence of polymer chemistry and mixing on the formation of loaded NPs, opening the way to fine-tune their properties and optimize their large-scale production.
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Ashoka AH, Aparin IO, Reisch A, Klymchenko AS. Brightness of fluorescent organic nanomaterials. Chem Soc Rev 2023. [PMID: 37338018 DOI: 10.1039/d2cs00464j] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Brightness is a fundamental property of fluorescent nanomaterials reflecting their capacity to absorb and emit light. In sensing materials, brightness is crucial for high-sensitivity (bio)molecular detection, while in optical bioimaging it ensures high spatial and temporal resolution. Fluorescent organic nanoparticles (NPs) are particularly attractive because of their superior brightness compared to organic dyes. With the ever-growing diversity of organic nanomaterials, it is important to establish universal principles for measuring and estimating their brightness. This tutorial review provides definitions of brightness and describes the major approaches to its analysis based on ensemble and single-particle techniques. We present the current chemical approaches to fight Aggregation-Caused Quenching (ACQ) of fluorophores, which is a major challenge in the design of bright organic nanomaterials. The main classes of fluorescent organic NPs are described, including conjugated polymer NPs, aggregation-induced emission NPs, and NPs based on neutral and ionic dyes. Their brightness and other properties are systematically compared. Some brightest examples of bulk solid-state emissive organic materials are also mentioned. Finally, we analyse the importance of brightness and other particle properties in biological applications, such as bioimaging and biosensing. This tutorial will provide guidelines for chemists on the design of fluorescent organic NPs with improved performance and help them to estimate and compare the brightness of new nanomaterials with literature reports. Moreover, it will help biologists to select appropriate materials for sensing and imaging applications.
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Fanciullo G, Orlandi S, Klymchenko AS, Muccioli L, Rivalta I. Characterizing Counterion-Dependent Aggregation of Rhodamine B by Classical Molecular Dynamics Simulations. Molecules 2023; 28:4742. [PMID: 37375296 DOI: 10.3390/molecules28124742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The aggregation in a solution of charged dyes such as Rhodamine B (RB) is significantly affected by the type of counterion, which can determine the self-assembled structure that in turn modulates the optical properties. RB aggregation can be boosted by hydrophobic and bulky fluorinated tetraphenylborate counterions, such as F5TPB, with the formation of nanoparticles whose fluorescence quantum yield (FQY) is affected by the degree of fluorination. Here, we developed a classical force field (FF) based on the standard generalized Amber parameters that allows modeling the self-assembling process of RB/F5TPB systems in water, consistent with experimental evidence. Namely, the classical MD simulations employing the re-parametrized FF reproduce the formation of nanoparticles in the RB/F5TPB system, while in the presence of iodide counterions, only RB dimeric species can be formed. Within the large, self-assembled RB/F5TPB aggregates, the occurrence of an H-type RB-RB dimer can be observed, a species that is expected to quench RB fluorescence, in agreement with the experimental data of FQY. The outcome provides atomistic details on the role of the bulky F5TPB counterion as a spacer, with the developed classical FF representing a step towards reliable modeling of dye aggregation in RB-based materials.
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Pelletier R, Danylchuk DI, Benaissa H, Broch F, Vauchelles R, Gautier A, Klymchenko AS. Genetic Targeting of Solvatochromic Dyes for Probing Nanoscale Environments of Proteins in Organelles. Anal Chem 2023. [PMID: 37229557 DOI: 10.1021/acs.analchem.3c00515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A variety of protein tags are available for genetically encoded protein labeling, which allow their precise localization and tracking inside the cells. A new dimension in protein imaging can be offered by combining protein tags with polarity-sensitive fluorescent probes, which provide information about local nanoscale environments of target proteins within the subcellular compartments (organelles). Here, we designed three fluorescent probes based on solvatochromic nile red dye, conjugated to a HaloTag reactive targeting group through polyethylene glycol linkers of varying lengths. The probe with medium linker length, NR12-Halo, was found to label specifically a large variety of proteins localized in defined cell compartments, such as plasma membranes (outer and inner leaflets), endoplasmic reticulum, Golgi apparatus, cytosol, microtubules, actin, and chromatin. Owing to its polarity-sensitive fluorophore, the probe clearly distinguished the proteins localized within apolar lipid membranes from other proteins. Moreover, it revealed dramatic changes in the environment during the life cycle of proteins from biosynthesis to their expected localization and, finally, to recycling inside lysosomes. Heterogeneity in the local polarity of some membrane proteins also suggested a formation of low-polar protein aggregates, for example, within cell-cell contacts. The approach also showed that mechanical stress (cell shrinking by osmotic shock) induced a general polarity decrease in membrane proteins, probably due to the condensation of biomolecules. Finally, the nanoenvironment of some membrane proteins was affected by a polyunsaturated fatty acid diet, which provided the bridge between organization of lipids and proteins. The developed solvatochromic HaloTag probe constitutes a promising tool for probing nanoscale environments of proteins and their interactions within subcellular structures.
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Biswas DS, Gaki P, Da Silva EC, Combes A, Reisch A, Didier P, Klymchenko AS. Long-range Energy Transfer Between Dye-loaded Nanoparticles: Observation and Amplified Detection of Nucleic Acids. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2301402. [PMID: 37073109 DOI: 10.1002/adma.202301402] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Förster resonance energy transfer (FRET) is essential in optical materials for light-harvesting, photovoltaics and biosensing, but its operating range is fundamentally limited by the Förster radius of ∼5 nm. Here, FRET between fluorescent organic nanoparticles (NPs) is studied for the first time in order to break this limit. The donor and acceptor NPs are built from charged hydrophobic polymers loaded with cationic dyes and bulky hydrophobic counterions. Their surface is functionalized with DNA in order to control surface-to-surface distance. It is found that the FRET efficiency does not follow the canonic Förster law, reaching 0.70 and 0.45 values for NP-NP distance of 15 and 20 nm, respectively. This corresponds to the FRET efficiency decay as power four of the surface-to-surface NP-NP distance. Based on this long-distance FRET, a DNA nanoprobe is developed, where a target DNA fragment, encoding cancer marker survivin, brings together donor and acceptor NPs at ∼15 nm distance. In this nanoprobe, a single molecular recognition results in unprecedented color switch for >5000 dyes, yielding a simple and fast assay with 18 attomoles limit of detection. Breaking the Förster distance limit for ultrabright NPs opens the route to advanced optical nanomaterials for amplified FRET-based sensing of biomolecules. This article is protected by copyright. All rights reserved.
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Yudhistira T, Da Silva EC, Combes A, Lehmann M, Reisch A, Klymchenko AS. Biotinylated Fluorescent Polymeric Nanoparticles for Enhanced Immunostaining. SMALL METHODS 2023; 7:e2201452. [PMID: 36808832 DOI: 10.1002/smtd.202201452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/29/2022] [Indexed: 06/18/2023]
Abstract
The performance of fluorescence immunostaining is physically limited by the brightness of organic dyes, whereas fluorescence labeling with multiple dyes per antibody can lead to dye self-quenching. The present work reports a methodology of antibody labeling by biotinylated zwitterionic dye-loaded polymeric nanoparticles (NPs). A rationally designed hydrophobic polymer, poly(ethyl methacrylate) bearing charged, zwitterionic and biotin groups (PEMA-ZI-biotin), enables preparation of small (14 nm) and bright fluorescent biotinylated NPs loaded with large quantities of cationic rhodamine dye with bulky hydrophobic counterion (fluorinated tetraphenylborate). The biotin exposure at the particle surface is confirmed by Förster resonance energy transfer with dye-streptavidin conjugate. Single-particle microscopy validates specific binding to biotinylated surfaces, with particle brightness 21-fold higher than quantum dot-585 (QD-585) at 550 nm excitation. The nanoimmunostaining method, which couples biotinylated antibody (cetuximab) with bright biotinylated zwitterionic NPs through streptavidin, significantly improves fluorescence imaging of target epidermal growth factor receptors (EGFR) on the cell surface compared to a dye-based labeling. Importantly, cetuximab labeled with PEMA-ZI-biotin NPs can differentiate cells with distinct expression levels of EGFR cancer marker. The developed nanoprobes can greatly amplify the signal from labeled antibodies, and thus become a useful tool in the high-sensitivity detection of disease biomarkers.
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Saladin L, Dal Pra O, Klymchenko AS, Didier P, Collot M. Tuning Directed Photooxidation-Induced Conversion of Pyrrole-Based Styryl Coumarin Dual-Color Photoconverters. Chemistry 2023; 29:e202300685. [PMID: 36919917 DOI: 10.1002/chem.202300685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
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.
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Saladin L, Dal Pra O, Klymchenko AS, Didier P, Collot M. Tuning Directed Photooxidation‐Induced Conversion of Pyrrole‐Based Styryl Coumarin Dual‐Color Photoconverters. Chemistry 2023. [DOI: 10.1002/chem.202300684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Ragaller F, Andronico L, Sykora J, Kulig W, Rog T, Urem YB, Abhinav A, Danylchuk DI, Hof M, Klymchenko AS, Amaro M, Vattulainen I, Sezgin E. Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. Biophys J 2023; 122:224a. [PMID: 36783097 DOI: 10.1016/j.bpj.2022.11.1332] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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Saladin L, Dal Pra O, Klymchenko AS, Didier P, Collot M. Tuning Directed Photooxidation-Induced Conversion of Pyrrole-Based Styryl Coumarin Dual-Color Photoconverters. Chemistry 2023; 29:e202203933. [PMID: 36719328 DOI: 10.1002/chem.202203933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/01/2023]
Abstract
Dual-emissive photoconvertible fluorophores (DPCFs) are powerful tools to unambiguously track labeled cells in bioimaging. We recently introduced a new rational mechanism called directed photooxidation-induced conversion (DPIC) enabling efficient DPCFs to be obtained by conjugating a coumarin to aromatic singlet-oxygen reactive moieties (ASORMs). Pyrrole was found to be a suitable ASORM as it provided a high hypsochromic shift along with a fast and efficient conversion. By synthesizing various pyrrole-based styryl coumarin dyes, we showed that the photoconversion properties, including the quantum yield of photoconversion and the chemical yield of conversion can be tuned by chemical modification of the pyrrole. These modifications led to an improved dual emissive converter, SCP-Boc, which displayed a high brightness and an enhanced photoconversion yield of 63 %. SCP-Boc was successfully used to sequentially photoconvert cells by laser scanning confocal microscopy.
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Saladin L, Breton V, Dal Pra O, Klymchenko AS, Danglot L, Didier P, Collot M. Dual-Color Photoconvertible Fluorescent Probes Based on Directed Photooxidation Induced Conversion for Bioimaging. Angew Chem Int Ed Engl 2023; 62:e202215085. [PMID: 36420823 PMCID: PMC10107923 DOI: 10.1002/anie.202215085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
Abstract
We herein present a new concept to produce dual-color photoconvertible probes based on a mechanism called Directed Photooxidation Induced Conversion (DPIC). As a support of this mechanism, styryl-coumarins (SCs) bearing Aromatic Singlet Oxygen Reactive Moieties (ASORMs) like furan and pyrrole have been synthesized. SCs are bright fluorophores, which undergo a hypsochromic conversion upon visible light irradiation due to directed photooxidation of the ASORM that leads to the disruption of conjugation. SC-P, a yellow emitting probe bearing a pyrrole moiety, converts to a stable blue emitting coumarin with a 68 nm shift allowing the photoconversion and tracking of lipid droplet in live cells. This new approach might pave the way to a new generation of photoconvertible dyes for advanced bioimaging applications.
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Liu F, Anton N, Niko Y, Klymchenko AS. Controlled Release and Capture of Aldehydes by Dynamic Imine Chemistry in Nanoemulsions: From Delivery to Detoxification. ACS APPLIED BIO MATERIALS 2023; 6:246-256. [PMID: 36516427 DOI: 10.1021/acsabm.2c00861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Current biomedical applications of nanocarriers are focused on drug delivery, where encapsulated cargo is released in the target tissues under the control of external stimuli. Here, we propose a very different approach, where the active toxic molecules are removed from biological tissues by the nanocarrier. It is based on the drug-sponge concept, where specific molecules are captured by the lipid nanoemulsion (NE) droplets due to dynamic covalent chemistry inside their oil core. To this end, we designed a highly lipophilic amine (LipoAmine) capable of reacting with a free cargo-aldehyde (fluorescent dye and 4-hydroxynonenal toxin) directly inside lipid NEs, yielding a lipophilic imine conjugate well encapsulated in the oil core. The formation of imine bonds was first validated using a push-pull pyrene aldehyde dye, which changes its emission color during the reaction. The conjugate formation was independently confirmed by mass spectrometry. As a result, LipoAmine-loaded NEs spontaneously loaded cargo-aldehydes, yielding formulations stable against leakage at pH 7.4, which can further release the cargo in a low pH range (4-6) in solutions and living cells. Using fluorescence microscopy, we showed that LipoAmine NEs can extract pyrene aldehyde dye from cells as well as from an epithelial tissue (chicken skin). Moreover, successful extraction from cells was also achieved for a highly toxic aliphatic aldehyde 4-hydroxynonenal, which allowed obtaining the proof of concept for detoxification of living cells. Taken together, these results show that the dynamic imine chemistry inside NEs can be used to develop detoxification platforms.
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Brou GA, Gbassi GK, Shulov I, Seralin A, Klymchenko AS, Vandamme TF, Anton N. Study of surfactant cross-linking by click chemistry on a model water/oil interface. Phys Chem Chem Phys 2023; 25:1177-1186. [PMID: 36519558 DOI: 10.1039/d2cp02146c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we explored how chemical reactions of amphiphile compounds can be characterized and followed-up on model interfaces. A custom-made surfactant containing three alkyne sites was first adsorbed and characterized at a water/oil interface. These amphiphiles then underwent interfacial crosslinking by click chemistry upon the addition of a second reactive agent. The monolayer properties and dilatational elasticity, were compared before and after the polymerization. Using bulk phase exchange, the composition of the aqueous bulk phase was finely controlled and washed to specifically measure the interfacial effects of the entities adsorbed and trapped at the interface. In this study, we aim to emphasize an original experimental approach to follow complex phenomena occurring on model interfaces, and also show the potential of this method to characterize multifactorial processes.
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Abstract
Biomembranes are ubiquitous lipid structures that delimit the cell surface and organelles and operate as platforms for a multitude of biomolecular processes. The development of chemical tools─fluorescent probes─for the sensing and imaging of biomembranes is a rapidly growing research direction, stimulated by a high demand from cell biologists and biophysicists. This Account focuses on advances in these smart molecules, providing a voyage from the cell frontier─plasma membranes (PM)─toward intracellular membrane compartments─organelles. General classification of the membrane probes can be based on targeting principles, sensing profile, and optical response. Probes for PM and organelle membranes are designed based on multiple targeting principles: conjugation with natural lipids or synthetic targeting ligands and in situ cell labeling by bio-orthogonal chemistry, conjugation to protein tags, and receptor-ligand interactions. Thus, to obtain membrane probes targeting PM with selectivity to one leaflet, we designed membrane anchor ligands based on a charged group and an alkyl chain. According to the sensing profile, we define basic membrane markers with constant emission and probes for biophysical and chemical sensing. The markers are built from classical fluorophores, exemplified by a series of bright cyanines and BODIPY dyes bearing the PM anchors (MemBright). Membrane probes for biophysical sensing are based on environment-sensitive fluorophores: (1) polarity-sensitive solvatochromic dyes; (2) viscosity-sensitive fluorescent molecular rotors; (3) mechanosensitive fluorescent flippers; and (4) voltage-sensitive electrochromic dyes. Our solvatochromic probes based on Nile Red (NR12S, NR12A, NR4A), Laurdan (Pro12A), and 3-hydroxyflavone (F2N12S) through polarity-sensing can visualize liquid ordered and disordered phases of lipid membranes, sense lipid order and its heterogeneity in cell PM, detect apoptosis, etc. Chemically sensitive probes, combining a dye, membrane-targeting ligand, and molecular recognition unit, enable the detection of pH, ions, redox species, lipids, and proteins at the biomembrane surface. In terms of the optical response profile, we can identify (1) fluorogenic (turn-on) probes, allowing background-free imaging; (2) ratiometric probes, e.g., solvatochromic probes, which enable ratiometric imaging by changing their emission/excitation color; (3) fluorescence lifetime-responsive probes, e.g., fluorescence molecular rotors and flippers, suitable for fluorescence lifetime imaging (FLIM); and (4) switchable probes, important for single-molecule localization microscopy. We showed that combining solvatochromic probes with on-off switching through a reversible binding specifically to cell PM enables the mapping of their biophysical properties with superior resolution. While the majority of efforts have been focused on PM, the probes for cellular organelles, such as endoplasmic reticulum, mitochondria, Golgi apparatus, etc., emerge rapidly. Thus, nontargeted solvatochromic probes can distinguish organelles by the emission color. Targeted solvatochromic probes based on Nile Red revealed unique signatures of polarity and lipid order of individual organelles and their different sensitivities to oxidative or mechanical stress. Lipid droplets, which are membraneless lipidic structures, constitute another interesting organelle target for probing the cell stress. Currently, we stand at the beginning of a long route with big challenges ahead, in particular (1) to achieve superior organelle specificity; (2) to label specific biomembrane leaflets, notably the inner leaflet of PM; (3) to detect lipid organization in a proximity of specific proteins; and (4) to probe biomembranes in tissues and animals.
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Oya S, Korogi K, Kohno T, Tsuiji H, Danylchuk DI, Klymchenko AS, Niko Y, Hattori M. The Plasma Membrane Polarity Is Higher in the Neuronal Growth Cone than in the Cell Body of Hippocampal and Cerebellar Granule Neurons. Biol Pharm Bull 2023; 46:1820-1825. [PMID: 38044101 DOI: 10.1248/bpb.b23-00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The polarity of the biological membrane, or lipid order, regulates many cellular events. It is generally believed that the plasma membrane polarity is regulated according to cell type and function, sometimes even within a cell. Neurons have a variety of functionally specialized subregions, each of which bears distinct proteins and lipids, and the membrane polarity of the subregions may differ accordingly. However, no direct experimental evidence of it has been presented to date. In the present study, we used a cell-impermeable solvatochromic membrane probe NR12A to investigate the local polarity of the plasma membrane of neurons. Both in hippocampal and cerebellar granule neurons, growth cones have higher membrane polarity than the cell body. In addition, the overall variation in the polarity value of each pixel was greater in the growth cone than in cell bodies, suggesting that the lateral diffusion and/or dynamics of the growth cone membrane are greater than other parts of the neuron. These tendencies were much less notably observed in the lamellipodia of a non-neuronal cell. Our results suggest that the membrane polarity of neuronal growth cones is unique and this characteristic may be important for its structure and function.
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Moskalevska I, Faure V, Haye L, Mercey-Ressejac M, Dey AK, Chovelon B, Soro LK, Charbonnière LJ, Reisch A, Klymchenko AS, Marche PN, Coll JL, Macek Jilkova Z, le Guével X. Intracellular accumulation and immunological response of NIR-II polymeric nanoparticles. Int J Pharm 2022; 630:122439. [PMID: 36503846 DOI: 10.1016/j.ijpharm.2022.122439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/06/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
Polymeric nanoparticles (NPs) are extremely promising for theranostic applications. However, their interest depends largely on their interactions with immune system, including the capacity to activate inflammation after their capture by macrophages. In the present study, we generated monodisperse poly(ethyl methacrylate) (PEMA) NPs loaded with hydrophobic photoluminescent gold nanoclusters (Au NCs) emitting in the NIR-II optical windows and studied their interaction in vitro with J774.1A macrophages. PEMA NPs showed an efficient time and dose dependent cellular uptake with up to 70 % of macrophages labelled in 24 h without detectable cell death. Interestingly, PEMA and Au-PEMA NPs induced an anti-inflammatory response and a strong down-regulation of nitric oxide level on lipopolysacharides (LPS) activated macrophages, but without influence on the levels of reactive oxygen species (ROS). These polymeric NPs may thus present a potential interest for the treatment of inflammatory diseases.
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Saladin L, Breton V, Dal Pra O, Klymchenko AS, Danglot L, Didier P, Collot M. Dual‐Color Photoconvertible Fluorescent Probes Based on Directed Photooxidation Induced Conversion for bioimaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202215085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rodik RV, Cherenok SO, Postupalenko VY, Oncul S, Brusianska V, Borysko P, Kalchenko VI, Mely Y, Klymchenko AS. Anionic amphiphilic calixarenes for peptide assembly and delivery. J Colloid Interface Sci 2022; 624:270-278. [PMID: 35660896 DOI: 10.1016/j.jcis.2022.05.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
Shape-persistent macrocycles enable superior control on molecular self-assembly, allowing the preparation of well-defined nanostructures with new functions. Here, we report on anionic amphiphilic calixarenes of conic shape and their self-assembly behavior in aqueous media for application in intracellular delivery of peptides. Newly synthesized calixarenes bearing four phosphonate groups and two or four long alkyl chains were found to form micelles of ∼ 10 nm diameter, in contrast to an analogue with short alkyl chains. These amphiphilic calixarenes are able to complex model (oligo-lysine) and biologically relevant (HIV-1 nucleocapsid peptide) cationic peptides into small nanoparticles (20-40 nm). By contrast, a control anionic calixarene with short alkyl chains fails to form small nanoparticles with peptides, highlighting the importance of micellar assembly of amphiphilic calixarenes for peptide complexation. Cellular studies reveal that anionic amphiphilic calixarenes exhibit low cytotoxicity and enable internalization of fluorescently labelled peptides into live cells. These findings suggest anionic amphiphilic macrocycles as promising building blocks for the preparation of peptide delivery vehicles.
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