Publications by authors named "Andrey S Klymchenko"

Article Synopsis
  • Current single-molecule imaging methods are slow and complicated, making it hard to use them in biology.*
  • POLCAM is a new, simpler way to detect molecules using a special camera that works quickly and easily on regular microscopes.*
  • To help others use POLCAM, free software and instructions were created, and it has been tested on important biological samples like human cells.*
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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.

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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.

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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.

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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 VHs on NP surfaces.

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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.

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Article Synopsis
  • The study examines how the polarity of lipid membranes influences cellular functions, particularly in neurons, where different subregions may exhibit varying membrane characteristics.
  • Researchers used a specialized membrane probe to measure local polarity in the plasma membranes of neuronal cells, finding that growth cones had higher polarity compared to cell bodies.
  • The results indicate that the unique membrane polarity in growth cones could play a crucial role in their structure and function, highlighting differences compared to non-neuronal cells.
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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.

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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.

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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.

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Article Synopsis
  • A variety of protein tags enable precise tracking and localization of proteins within cells, enhanced by combining them with polarity-sensitive fluorescent probes for deeper insights into protein environments in organelles.
  • Researchers designed three fluorescent probes using solvatochromic nile red dye linked to HaloTag, with one probe (NR12-Halo) successfully labeling various proteins across key cell compartments, distinguishing between apolar lipid membranes and other proteins.
  • This method revealed important dynamics in protein environments during their lifecycle and how factors like mechanical stress and dietary fats influence protein behavior and interactions within cellular structures.
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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. In this work, FRET between fluorescent organic nanoparticles (NPs) is studied 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.

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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.

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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).

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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.

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Article Synopsis
  • Biomembranes are essential structures around cells and organelles that play key roles in various biological processes, motivating the development of chemical tools like fluorescent probes for studying them.
  • Recent advancements in these probes allow researchers to target specific membrane types—such as plasma membranes and organelles—using various design principles, including different targeting ligands.
  • Different types of membrane probes have been created for specific uses, like sensing polarity, viscosity, and voltage, which help visualize and study membrane properties, detect cellular changes, and measure the presence of ions and proteins.
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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.

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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.

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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.

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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.

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Super-resolution fluorescence imaging based on single-molecule localization microscopy (SMLM) enables visualizing cellular structures with nanometric precision. However, its spatial and temporal resolution largely relies on the brightness of ON/OFF switchable fluorescent dyes. Moreover, in cell plasma membranes, the single-molecule localization is hampered by the fast lateral diffusion of membrane probes.

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Sphingomyelin is a dominant sphingolipid in mammalian cells. Its production in the Golgi traps cholesterol synthesized in the ER to promote formation of a sphingomyelin/sterol gradient along the secretory pathway. This gradient marks a fundamental transition in physical membrane properties that help specify organelle identify and function.

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Osteosarcoma (OS) is the most common primary bone cancer, where the overall 5-year surviving rate is below 20% in resistant forms. Accelerating cures for those poor outcome patients remains a challenge. Nevertheless, several studies of agents targeting abnormal cancerous pathways have yielded disappointing results when translated into clinic because of the lack of accurate OS preclinical modeling.

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Over the last decade fluorescence-guided surgery has been primarily focused on the NIR-I window. However, the NIR-I window has constraints, such as limited penetration and scattering. Consequently, exploring the performance of NIR-I dyes at longer wavelengths (i.

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Nanoprecipitation is a facile and efficient approach to the assembly of loaded polymer nanoparticles (NPs) for applications in bioimaging and targeted drug delivery. Their successful use in clinics requires reproducible and scalable synthesis, for which microfluidics appears as an attractive technique. However, in the case of nanoprecipitation, particle formation depends strongly on mixing.

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