Author Correction: Self-assembled poly-catenanes from supramolecular toroidal building blocks.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Self-assembled poly-catenanes from supramolecular toroidal building blocks.

Mechanical interlocking of molecules (catenation) is a nontrivial challenge in modern synthetic chemistry and materials science1,2. One strategy to achieve catenation is the design of pre-annular molecules that are capable of both efficient cyclization and of pre-organizing another precursor to engage in subsequent interlocking3-9. This task is particularly difficult when the annular target is composed of a large ensemble of molecules, that is, when it is a supramolecular assembly. However, the construction of such unprecedented assemblies would enable the visualization of nontrivial nanotopologies through microscopy techniques, which would not only satisfy academic curiosity but also pave the way to the development of materials with nanotopology-derived properties. Here we report the synthesis of such a nanotopology using fibrous supramolecular assemblies with intrinsic curvature. Using a solvent-mixing strategy, we kinetically organized a molecule that can elongate into toroids with a radius of about 13 nanometres. Atomic force microscopy on the resulting nanoscale toroids revealed a high percentage of catenation, which is sufficient to yield 'nanolympiadane'10, a nanoscale catenane composed of five interlocked toroids. Spectroscopic and theoretical studies suggested that this unusually high degree of catenation stems from the secondary nucleation of the precursor molecules around the toroids. By modifying the self-assembly protocol to promote ring closure and secondary nucleation, a maximum catenation number of 22 was confirmed by atomic force microscopy.

Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly Polarized Light.

Control over the stereochemistry of metal-organic cages can give rise to useful functions that are entwined with chirality, such as stereoselective guest binding and chiroptical applications. Here, we report a chiral CuI12L4 pseudo-octahedral cage that self-assembled from condensation of triaminotriptycene, aminoquinaldine, and diformylpyridine subcomponents around CuI templates. The corners of this cage consist of six head-to-tail dicopper(I) helicates whose helical chirality can be controlled by the addition of enantiopure 1,1'-bi-2-naphthol (BINOL) during the assembly process. Chiroptical and nuclear magnetic resonance (NMR) studies elucidated the process and mechanism of stereochemical information transfer from BINOL to the cage during the assembly process. Initially formed CuI(BINOL)2 thus underwent stereoselective ligand exchange during the formation of the chiral helicate corners of the cage, which determined the overall cage stereochemistry. The resulting dicopper(I) helicate corners of the cage were also shown to generate circularly polarized luminescence.

Pioglitazone Phases and Metabolic Effects in Nanoparticle-Treated Cells Analyzed via Rapid Visualization of FLIM Images.

Fluorescence lifetime imaging microscopy (FLIM) has proven to be a useful method for analyzing various aspects of material science and biology, like the supramolecular organization of (slightly) fluorescent compounds or the metabolic activity in non-labeled cells; in particular, FLIM phasor analysis (phasor-FLIM) has the potential for an intuitive representation of complex fluorescence decays and therefore of the analyzed properties. Here we present and make available tools to fully exploit this potential, in particular by coding via hue, saturation, and intensity the phasor positions and their weights both in the phasor plot and in the microscope image. We apply these tools to analyze FLIM data acquired via two-photon microscopy to visualize: (i) different phases of the drug pioglitazone (PGZ) in solutions and/or crystals, (ii) the position in the phasor plot of non-labelled poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs), and (iii) the effect of PGZ or PGZ-containing NPs on the metabolism of insulinoma (INS-1 E) model cells. PGZ is recognized for its efficacy in addressing insulin resistance and hyperglycemia in type 2 diabetes mellitus, and polymeric nanoparticles offer versatile platforms for drug delivery due to their biocompatibility and controlled release kinetics. This study lays the foundation for a better understanding via phasor-FLIM of the organization and effects of drugs, in particular, PGZ, within NPs, aiming at better control of encapsulation and pharmacokinetics, and potentially at novel anti-diabetics theragnostic nanotools.

Subtle Stereochemical Effects Influence Binding and Purification Abilities of an FeII4L4 Cage.

A tetrahedral FeII4L4 cage assembled from the coordination of triangular chiral, face-capping ligands to iron(II). This cage exists as two diastereomers in solution, which differ in the stereochemistry of their metal vertices, but share the same point chirality of the ligand. The equilibrium between these cage diastereomers was subtly perturbed by guest binding. This perturbation from equilibrium correlated with the size and shape fit of the guest within the host; insight as to the interplay between stereochemistry and fit was provided by atomistic well-tempered metadynamics simulations. The understanding thus gained as to the stereochemical impact on guest binding enabled the design of a straightforward process for the resolution of the enantiomers of a racemic guest.

Studying the trafficking of labeled trodusquemine and its application as nerve marker for light-sheet and expansion microscopy.

Trodusquemine is an aminosterol with a variety of biological and pharmacological functions, such as acting as an antimicrobial, stimulating body weight loss and interfering with the toxicity of proteins involved in the development of Alzheimer's and Parkinson's diseases. The mechanisms of interaction of aminosterols with cells are, however, still largely uncharacterized. Here, by using fluorescently labeled trodusquemine (TRO-A594 and TRO-ATTO565), we show that trodusquemine binds initially to the plasma membrane of living cells, that the binding affinity is dependent on cholesterol, and that trodusquemine is then internalized and mainly targeted to lysosomes after internalization. We also found that TRO-A594 is able to strongly and selectively bind to myelinated fibers in fixed mouse brain slices, and that it is a marker compatible with tissue clearing and light-sheet fluorescence microscopy or expansion microscopy. In conclusion, this work contributes to further characterize the biology of aminosterols and provides a new tool for nerve labeling suitable for the most advanced microscopy techniques.

Innate dynamics and identity crisis of a metal surface unveiled by machine learning of atomic environments.

Metals are traditionally considered hard matter. However, it is well known that their atomic lattices may become dynamic and undergo reconfigurations even well below the melting temperature. The innate atomic dynamics of metals is directly related to their bulk and surface properties. Understanding their complex structural dynamics is, thus, important for many applications but is not easy. Here, we report deep-potential molecular dynamics simulations allowing to resolve at an atomic resolution the complex dynamics of various types of copper (Cu) surfaces, used as an example, near the Hüttig (∼1/3 of melting) temperature. The development of deep neural network potential trained on density functional theory calculations provides a dynamically accurate force field that we use to simulate large atomistic models of different Cu surface types. A combination of high-dimensional structural descriptors and unsupervized machine learning allows identifying and tracking all the atomic environments (AEs) emerging in the surfaces at finite temperatures. We can directly observe how AEs that are non-native in a specific (ideal) surface, but that are, instead, typical of other surface types, continuously emerge/disappear in that surface in relevant regimes in dynamic equilibrium with the native ones. Our analyses allow estimating the lifetime of all the AEs populating these Cu surfaces and to reconstruct their dynamic interconversions networks. This reveals the elusive identity of these metal surfaces, which preserve their identity only in part and in part transform into something else under relevant conditions. This also proposes a concept of "statistical identity" for metal surfaces, which is key to understanding their behaviors and properties.

Investigating the mechanism of action of DNA-loaded PEGylated lipid nanoparticles.

PEGylated lipid nanoparticles (LNPs) are commonly used to deliver bioactive molecules, but the role of PEGylation in DNA-loaded LNP interactions at the cellular and subcellular levels remains poorly understood. In this study, we investigated the mechanism of action of DNA-loaded PEGylated LNPs using gene reporter technologies, dynamic light scattering (DLS), synchrotron small angle X-ray scattering (SAXS), and fluorescence confocal microscopy (FCS). We found that PEG has no significant impact on the size or nanostructure of DNA LNPs but reduces their zeta potential and interaction with anionic cell membranes. PEGylation increases the structural stability of LNPs and results in lower DNA unloading. FCS experiments revealed that PEGylated LNPs are internalized intact inside cells and largely shuttled to lysosomes, while unPEGylated LNPs undergo massive destabilization on the plasma membrane. These findings can inform the design, optimization, and validation of DNA-loaded LNPs for gene delivery and vaccine development.

A Guide to Perform 3D Histology of Biological Tissues with Fluorescence Microscopy.

The analysis of histological alterations in all types of tissue is of primary importance in pathology for highly accurate and robust diagnosis. Recent advances in tissue clearing and fluorescence microscopy made the study of the anatomy of biological tissue possible in three dimensions. The combination of these techniques with classical hematoxylin and eosin (H&E) staining has led to the birth of three-dimensional (3D) histology. Here, we present an overview of the state-of-the-art methods, highlighting the optimal combinations of different clearing methods and advanced fluorescence microscopy techniques for the investigation of all types of biological tissues. We employed fluorescence nuclear and eosin Y staining that enabled us to obtain hematoxylin and eosin pseudo-coloring comparable with the gold standard H&E analysis. The computational reconstructions obtained with 3D optical imaging can be analyzed by a pathologist without any specific training in volumetric microscopy, paving the way for new biomedical applications in clinical pathology.

A robust and versatile platform for image scanning microscopy enabling super-resolution FLIM.

Image scanning microscopy (ISM) can improve the effective spatial resolution of confocal microscopy to its theoretical limit. However, current implementations are not robust or versatile, and are incompatible with fluorescence lifetime imaging (FLIM). We describe an implementation of ISM based on a single-photon detector array that enables super-resolution FLIM and improves multicolor, live-cell and in-depth imaging, thereby paving the way for a massive transition from confocal microscopy to ISM.

Measuring Molecular Diffusion in Dynamic Subcellular Nanostructures by Fast Raster Image Correlation Spectroscopy and 3D Orbital Tracking.

Here we provide demonstration that fast fluorescence fluctuation spectroscopy is a fast and robust approach to extract information on the dynamics of molecules enclosed within subcellular nanostructures (e.g., organelles or vesicles) which are also moving in the complex cellular environment. In more detail, Raster Image Correlation Spectroscopy (RICS) performed at fast timescales (i.e., microseconds) reveals the fast motion of fluorescently labeled molecules within two exemplary dynamic subcellular nanostructures of biomedical interest, the lysosome and the insulin secretory granule (ISG). The measurement of molecular diffusion is then used to extract information on the average properties of subcellular nanostructures, such as macromolecular crowding or molecular aggregation. Concerning the lysosome, fast RICS on a fluorescent tracer allowed us to quantitatively assess the increase in organelle viscosity in the pathological condition of Krabbe disease. In the case of ISGs, fast RICS on two ISG-specific secreting peptides unveiled their differential aggregation propensity depending on intragranular concentration. Finally, a combination of fast RICS and feedback-based 3D orbital tracking was used to subtract the slow movement of subcellular nanostructures from the fast diffusion of molecules contained within them and independently validate the results. Results presented here not only demonstrate the acquired ability to address the dynamic behavior of molecules in moving, nanoscopic reference systems, but prove the relevance of this approach to advance our knowledge on cell function at the subcellular scale.

ß-Cell Pathophysiology: A Review of Advanced Optical Microscopy Applications.

ß-cells convert glucose (input) resulting in the controlled release of insulin (output), which in turn has the role to maintain glucose homeostasis. ß-cell function is regulated by a complex interplay between the metabolic processing of the input, its transformation into second-messenger signals, and final mobilization of insulin-containing granules towards secretion of the output. Failure at any level in this process marks ß-cell dysfunction in diabetes, thus making ß-cells obvious potential targets for therapeutic purposes. Addressing quantitatively ß-cell (dys)function at the molecular level in living samples requires probing simultaneously the spatial and temporal dimensions at the proper resolution. To this aim, an increasing amount of research efforts are exploiting the potentiality of biophysical techniques. In particular, using excitation light in the visible/infrared range, a number of optical-microscopy-based approaches have been tailored to the study of ß-cell-(dys)function at the molecular level, either in label-free mode (i.e., exploiting intrinsic autofluorescence of cells) or by the use of organic/genetically-encoded fluorescent probes. Here, relevant examples from the literature are reviewed and discussed. Based on this, new potential lines of development in the field are drawn.

Non-uniform Photoinduced Unfolding of Supramolecular Polymers Leading to Topological Block Nanofibers.

Synthesis of one-dimensional nanofibers with distinct topological (higher-order structural) domains in the same main chain is one of the challenging topics in modern supramolecular polymer chemistry. Non-uniform structural transformation of supramolecular polymer chains by external stimuli may enable preparation of such nanofibers. To demonstrate feasibility of this post-polymerization strategy, we prepared a photoresponsive helically folded supramolecular polymers from a barbiturate monomer containing an azobenzene-embedded rigid π-conjugated scaffold. In contrast to previous helically folded supramolecular polymers composed of a more flexible azobenzene monomer, UV-light induced unfolding of the newly prepared helically folded supramolecular polymers occurred nonuniformly, affording topological block copolymers consisting of folded and unfolded domains. The formation of such blocky copolymers indicates that the photoinduced unfolding of the helically folded structures initiates from relatively flexible parts such as termini or defects. Spontaneous refolding of the unfolded domains was observed after visible-light irradiation followed by aging to restore fully folded structures.

Solvent-Driven Supramolecular Wrapping of Self-Assembled Structures.

Self-assembly relies on the ability of smaller and discrete entities to spontaneously arrange into more organized systems by means of the structure-encoded information. Herein, we show that the design of the media can play a role even more important than the chemical design. The media not only determines the self-assembly pathway at a single-component level, but in a very narrow solvent composition, a supramolecular homo-aggregate can be non-covalently wrapped by a second component that possesses a different crystal lattice. Such a process has been followed in real time by confocal microscopy thanks to the different emission colors of the aggregates formed by two isolated PtII complexes. This coating is reversible and controlled by the media composition. Single-crystal X-ray diffraction and molecular simulations based on coarse-grained (CG) models allowed the understanding of the properties displayed by the different aggregates. Such findings could result in a new method to construct hierarchical supramolecular structures.

Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage.

Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host-guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host-guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host-guest interactions.

Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage.

Photochromic molecules undergo reversible isomerization upon irradiation with light at different wavelengths, a process that can alter their physical and chemical properties. For instance, dihydropyrene (DHP) is a deep-colored compound that isomerizes to light-brown cyclophanediene (CPD) upon irradiation with visible light. CPD can then isomerize back to DHP upon irradiation with UV light or thermally in the dark. Conversion between DHP and CPD is thought to proceed via a biradical intermediate; bimolecular events involving this unstable intermediate thus result in rapid decomposition and poor cycling performance. Here, we show that the reversible isomerization of DHP can be stabilized upon confinement within a PdII6L4 coordination cage. By protecting this reactive intermediate using the cage, each isomerization reaction proceeds to higher yield, which significantly decreases the fatigue experienced by the system upon repeated photocycling. Although molecular confinement is known to help stabilize reactive species, this effect is not typically employed to protect reactive intermediates and thus improve reaction yields. We envisage that performing reactions under confinement will not only improve the cyclic performance of photochromic molecules, but may also increase the amount of product obtainable from traditionally low-yielding organic reactions.

Biomimetic Synthesis of Sub-20 nm Covalent Organic Frameworks in Water.

Covalent organic frameworks (COFs) are commonly synthesized under harsh conditions yielding unprocessable powders. Control in their crystallization process and growth has been limited to studies conducted in hazardous organic solvents. Herein, we report a one-pot synthetic method that yields stable aqueous colloidal solutions of sub-20 nm crystalline imine-based COF particles at room temperature and ambient pressure. Additionally, through the combination of experimental and computational studies, we investigated the mechanisms and forces underlying the formation of such imine-based COF colloids in water. Further, we show that our method can be used to process the colloidal solution into 2D and 3D COF shapes as well as to generate a COF ink that can be directly printed onto surfaces. These findings should open new vistas in COF chemistry, enabling new application areas.

Hypericin-Apomyoglobin: An Enhanced Photosensitizer Complex for the Treatment of Tumor Cells.

Bioavailability of photosensitizers for cancer photodynamic therapy is often hampered by their low solubility in water. Here, we overcome this issue by using the water-soluble protein apomyoglobin (apoMb) as a carrier for the photosensitizer hypericin (Hyp). The Hyp-apoMb complex is quickly uptaken by HeLa and PC3 cells at submicromolar concentrations. Fluorescence emission of Hyp-apoMb is exploited to localize the cellular distribution of the photosensitizer. The plasma membrane is rapidly and efficiently loaded, and fluorescence is observed in the cytoplasm only at later times and to a lesser extent. Comparison with cells loaded with Hyp alone demonstrates that the uptake of the photosensitizer without the protein carrier is a slower, less efficient process, that involves the whole cell structure without preferential accumulation at the plasma membrane. Cell viability assays demonstrate that the Hyp-apoMb exhibits superior performance over Hyp. Similar results were obtained using tumor spheroids as three-dimensional cell culture models.

The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease.

NEET proteins comprise a new class of [2Fe-2S] cluster proteins. In human, three genes encode for NEET proteins: cisd1 encodes mitoNEET (mNT), cisd2 encodes the Nutrient-deprivation autophagy factor-1 (NAF-1) and cisd3 encodes MiNT (Miner2). These recently discovered proteins play key roles in many processes related to normal metabolism and disease. Indeed, NEET proteins are involved in iron, Fe-S, and reactive oxygen homeostasis in cells and play an important role in regulating apoptosis and autophagy. mNT and NAF-1 are homodimeric and reside on the outer mitochondrial membrane. NAF-1 also resides in the membranes of the ER associated mitochondrial membranes (MAM) and the ER. MiNT is a monomer with distinct asymmetry in the molecular surfaces surrounding the clusters. Unlike its paralogs mNT and NAF-1, it resides within the mitochondria. NAF-1 and mNT share similar backbone folds to the plant homodimeric NEET protein (At-NEET), while MiNT's backbone fold resembles a bacterial MiNT protein. Despite the variation of amino acid composition among these proteins, all NEET proteins retained their unique CDGSH domain harboring their unique 3Cys:1His [2Fe-2S] cluster coordination through evolution. The coordinating exposed His was shown to convey the lability to the NEET proteins' [2Fe-2S] clusters. In this minireview, we discuss the NEET fold and its structural elements. Special attention is given to the unique lability of the NEETs' [2Fe-2S] cluster and the implication of the latter to the NEET proteins' cellular and systemic function in health and disease.