Imaging Nanostructures by Single-Molecule Localization Microscopy in Organic Solvents

Super-Resolution Microscopy as a Versatile Tool in Probing Molecular Assembly

Molecular assembly is promising in the construction of advanced materials, obtaining structures with specific functions. In-depth investigation of the relationships between the formation, dynamics, structure, and functionality of the specific molecular assemblies is one of the greatest challenges in nanotechnology and chemistry, which is essential in the rational design and development of functional materials for a variety of applications. Super-resolution microscopy (SRM) has been used as a versatile tool for investigating and elucidating the structures of individual molecular assemblies with its nanometric resolution, multicolor ability, and minimal invasiveness, which are also complementary to conventional optical or electronic techniques that provide the direct observation. In this review, we will provide an overview of the representative studies that utilize SRM to probe molecular assemblies, mainly focusing on the imaging of biomolecular assemblies (lipid-based, peptide-based, protein-based, and DNA-based), organic-inorganic hybrid assemblies, and polymer assemblies. This review will provide guidelines for the evaluation of the dynamics of molecular assemblies, assembly and disassembly processes with distinct dynamic behaviors, and multicomponent assembly through the application of these advanced imaging techniques. We believe that this review will inspire new ideas and propel the development of structural analyses of molecular assemblies to promote the exploitation of new-generation functional materials.

Organelle Proximity Analysis for Enhanced Quantification of Mitochondria-Endoplasmic Reticulum Interactions in Single Cells via Super-Resolution Microscopy

Mitochondria (MT) and the endoplasmic reticulum (ER) maintain lipid and calcium homeostasis through membrane contacts, particularly MT-ER contacts (MERCs), spanning distances from 10 to 50 nm. However, the variation of different distance ranges and the metabolic factors influencing this variation remain poorly understood. This study employed microfluidic chip-based super-resolution microscopy in conjunction with a Moore-Neighbor tracing-incorporated organelle proximity analysis algorithm. This approach enabled precise three-dimensional localization of single-fluorescence protein molecules within narrow and irregular membrane proximities. It achieved lateral localization precision of less than 20 nm, resulting in a minimum MERC distance of approximately 8 nm in spatial and mean distances across multiple threshold ranges. Additionally, we demonstrated that the MERC distance variation was correlated with MT size rather than ER width. The proportion of each distance range varied significantly after the stimuli. Free cholesterol showed a negative correlation with various distances, while distances of 10-30 nm were associated with glucose, glutamine, and pyruvic acid. Furthermore, the 30-40 nm range was influenced by citric acid. These results underscore the role of advanced subcellular organelle analysis in elucidating the single-molecule behavior and organelle morphology in single-cell studies.

Discordant Supramolecular Fibres Reversibly Depolymerised by Temperature and Light

Synthetic stimuli responsive supramolecular polymers attract increasing interest for their ability to mimic the unique properties of natural assemblies. Here we focus on the well-studied benzene-1,3,5-tricarboxamide (BTA) motif, and substitute it with two (S)-3,7-dimethyloctyl groups and an azobenzene photoswitch. We demonstrate the UV (λ=365 nm) induced depolymerisation of the helical hydrogen-bonded polymers in methylcyclohexane (MCH) through circular dichroism and UV-vis spectroscopy in dilute solution (15 μm), and NMR and iPAINT super-resolution microscopy in concentrated solution (300 μm). The superstructure can be regenerated after thermal depolymerization, whilst repeated depolymerisation can be reversed without degradation by irradiating at λ=455 nm. Molecular dynamics simulations show that the most energetically favourable configuration for these polymers in MCH is a left-handed helical network of hydrogen-bonds between the BTA cores surrounded by two right-handed helices of azobenzenes. The responsiveness to two orthogonal triggers across a broad concentration range holds promise for use in, for example, photo-responsive gelation.

Transforming Separation Science with Single-Molecule Methods

Empirical optimization of the multiscale parameters underlying chromatographic and membrane separations leads to enormous resource waste and production costs. A bottom-up approach to understand the physical phenomena underlying challenges in separations is possible with single-molecule observations of solute-stationary phase interactions. We outline single-molecule fluorescence techniques that can identify key interactions under ambient conditions. Next, we describe how studying increasingly complex samples heightens the relevance of single-molecule results to industrial applications. Finally, we illustrate how separation methods that have not been studied at the single-molecule scale can be advanced, using chiral chromatography as an example case. We hope new research directions based on a molecular approach to separations will emerge based on the ideas, technologies, and open scientific questions presented in this Perspective.

Super-Resolution Imaging of Self-Assembled Nanocarriers Using Quantitative Spectroscopic Analysis for Cluster Extraction

Self-assembled nanocarriers have inspired a range of applications for bioimaging, diagnostics, and drug delivery. The noninvasive visualization and characterization of these nanocarriers are important to understand their structure to function relationship. However, the quantitative visualization of nanocarriers in the sample's native environment remains challenging with the use of existing technologies. Single-molecule localization microscopy (SMLM) has the potential to provide both high-resolution visualization and quantitative analysis of nanocarriers in their native environment. However, nonspecific binding of fluorescent probes used in SMLM can introduce artifacts, which imposes challenges in the quantitative analysis of SMLM images. We showed the feasibility of using spectroscopic point accumulation for imaging in nanoscale topography (sPAINT) to visualize self-assembled polymersomes (PS) with molecular specificity. Furthermore, we analyzed the unique spectral signatures of Nile Red (NR) molecules bound to the PS to reject artifacts from nonspecific NR bindings. We further developed quantitative spectroscopic analysis for cluster extraction (qSPACE) to increase the localization density by 4-fold compared to sPAINT; thus, reducing variations in PS size measurements to less than 5%. Finally, using qSPACE, we quantitatively imaged PS at various concentrations in aqueous solutions with ∼20 nm localization precision and 97% reduction in sample misidentification relative to conventional SMLM.

Direct Observation of Nanoparticles within Cells at Subcellular Levels by Super-Resolution Fluorescence Imaging

Direct observation of nanoparticles with high spatial resolution at subcellular levels is of great importance to understand the nanotoxicology and promote the biomedical applications of nanoparticles. Super-resolution fluorescence microscopy can break the diffraction resolution limit to achieve spatial resolution of tens of nanometers, making it ideal for highly accurate observation of nanoparticles in the cellular world. In this study, we introduced the employment of super-resolution fluorescence imaging for monitoring nanoparticles within cells. Carbocyanine dyes Alexa Flour 647 labeled mesoporous silica nanoparticles (designated as MSNs-AF647) were constructed as the super-resolution imaging nanoplatform in this work as proof of concept. The MSNs-AF647 were incubated with Hela cells, and the nanoparticles within cells were further monitored by super-resolution fluorescence microscopy. The fluorescence images of MSNs-AF647 within cells captured with the super-resolution fluorescence microscopy showed a much higher spatial resolution than that obtained using conventional fluorescence microscopy, showing that super-resolution fluorescence images can provide more accurate information to locate the nanoparticles at the subcellular levels. Moreover, other functional molecules can be easily loaded into the MSNs-AF647 super-resolution imaging nanoplatform, which suggested that super-resolution fluorescence imaging can further be applied to various bioimaging-related areas, such as imaging-guided therapy, with the aid of the MSNs-AF647 nanoplatform. This study demonstrates that super-resolution fluorescence microscopy offers a highly accurate method to study nanoparticles in the cellular world. We anticipate this strategy may further be applied to research areas such as studying the nanotoxicology and optimization of nanoparticle-based bioprobes or drugs by designing new nanostructured materials with multifunctional properties based on MSNs-AF647.

A Polymerizable Photoswitchable Fluorophore for Super-Resolution Imaging of Polymer Self-Assembly and Dynamics

Single-molecule super-resolution microscopy has become a standard imaging tool in the life sciences for visualizing nanostructures in situ, but the application of this technique in polymer science is much less explored. A key bottleneck is the lack of fluorophores and simple covalent attachment strategies onto polymer chains. Here, we report a functional diarylethene-based photoswitchable fluorophore that can be directly incorporated into polymer backbones through copolymerization, which significantly streamlines the labeling strategy, with no further postcoupling reactions or purifications needed. The attachment of fluorophores onto selectively labeled polymers enables super-resolution imaging of a series of model polymer blend systems with different nanostructures and chemical compositions. As each individual fluorophore is able to switch several times on average between its bright and dark state, multiple time-lapse images can be acquired to observe the dynamic nanostructural evolution of polymer blends upon solvent vapor annealing. With this demonstration of a universal, simplified labeling strategy and the ability to image polymer assembly under native conditions, this reported fluorophore may promote the widespread use of super-resolution microscopy in the polymer community.

Painting Supramolecular Polymers in Organic Solvents by Super-resolution Microscopy

Despite the rapid development of complex functional supramolecular systems, visualization of these architectures under native conditions at high resolution has remained a challenging endeavor. Super-resolution microscopy was recently proposed as an effective tool to unveil one-dimensional nanoscale structures in aqueous media upon chemical functionalization with suitable fluorescent probes. Building upon our previous work, which enabled photoactivation localization microscopy in organic solvents, herein, we present the imaging of one-dimensional supramolecular polymers in their native environment by interface point accumulation for imaging in nanoscale topography (iPAINT). The noncovalent staining, typical of iPAINT, allows the investigation of supramolecular polymers' structure in situ without any chemical modification. The quasi-permanent adsorption of the dye to the polymer is exploited to identify block-like arrangements within supramolecular fibers, which were obtained upon mixing homopolymers that were prestained with different colors. The staining of the blocks, maintained by the lack of exchange of the dyes, permits the imaging of complex structures for multiple days. This study showcases the potential of PAINT-like strategies such as iPAINT to visualize multicomponent dynamic systems in their native environment with an easy, synthesis-free approach and high spatial resolution.

Supramolecular Block Copolymers under Thermodynamic Control

Supramolecular block copolymers are becoming attractive materials in nascent optoelectronic and catalytic technologies. However, their dynamic nature precludes the straightforward tuning and analysis of the polymer’s structure. Here we report the elucidation on the microstructure of triarylamine triamide-based supramolecular block copolymers through a comprehensive battery of spectroscopic, theoretical, and super-resolution microscopic techniques. Via spectroscopic analysis we demonstrate that the direct mixing of preassembled homopolymers and the copolymerization induced by slow cooling of monomers lead to the formation of the same copolymer’s architecture. The small but pronounced deviation of the experimental spectra from the linear combination of the homopolymers’ spectra hints at the formation of block copolymers. A mass balance model is introduced to further unravel the microstructure of the copolymers formed, and it confirms that stable multiblock supramolecular copolymers can be accessed from different routes. The multiblock structure of the supramolecular copolymers originates from the fine balance between favorable hydrogen-bonding interactions and a small mismatch penalty between two different monomers. Finally, we visualized the formation of the supramolecular block copolymers by adapting a recently developed super-resolution microscopy technique, interface point accumulation for imaging in nanoscale topography (iPAINT), for visualizing the architectures formed in organic media. Combining multiple techniques was crucial to unveil the microstructure of these complex dynamic supramolecular systems.

Fluorescent Diarylethene Photoswitches-A Universal Tool for Super-Resolution Microscopy in Nanostructured Materials

Super-resolution fluorescence microscopy allows for unprecedented in situ visualization of biological structures, but its application to materials science has so far been comparatively limited. One of the main reasons is the lack of powerful dyes that allow for labeling and photoswitching in materials science systems. In this study it is shown that appropriate substitution of diarylethenes bearing a fluorescent closed and dark open form paves the way for imaging nanostructured materials with three of the most popular super-resolution fluorescence microscopy methods that are based on different concepts to achieve imaging beyond the diffraction limit of light. The key to obtain optimal resolution lies in a proper control over the photochemistry of the photoswitches and its adaption to the system to be imaged. It is hoped that the present work will provide researchers with a guide to choose the best photoswitch derivative for super-resolution microscopy in materials science, just like the correct choice of a Swiss Army Knife's tool is essential to fulfill a given task.

Inhibition of cancer cell migration with CuS@ mSiO2-PEG nanoparticles by repressing MMP-2/MMP-9 expression

The metastasis of cancer cells is a vital aspect of disease progression and therapy. Although a few nanoparticles (NPs) aimed at controlling metastasis in cancer therapy have been reported, the NPs are normally combined with drugs, yet the direct therapeutic effects of the NPs are not reported. To study the direct influence of NPs on cancer metastasis, the potential suppression capacity of CuS@mSiO₂-PEG NPs to tumor cell migration, a kind of typical photothermal NPs, was systemically evaluated in this study. Using CuS@mSiO₂-PEG NP stimulation and a transwell migration assay, we found that the migration of HeLa cells was significantly decreased. This phenomenon may be associated with two classical proteins in metastasis: matrix metalloproteinase 2 (MMP-2) and matrix metalloproteinase 9 (MMP-9). In addition, the mechanism may closely associate with non-receptor tyrosine kinase protein (SRC)/focal adhesion kinase (FAK) signaling pathway which varies in vivo and in vitro. To confirm the differences in the expression of SRC and FAK, related inhibitors were studied for additional comparison. Also, the results indicated that even though the migration inhibition was closely related to SRC and FAK signaling pathway, there may be another unknown regulation mechanism existing and its metastasis inhibition was significant. Confirmed by long-term survival curve study, CuS@mSiO₂-PEG NPs significantly reduced the metastasis of cancer cells and improved the survival rates of metastasis in a mouse model. Thus, we believe that the direct influence of NPs on cancer cell metastasis is a promising study topic.

Studying structure and dynamics of self-assembled peptide nanostructures using fluorescence and super resolution microscopy

Understanding the formation and properties of self-assembled peptide nanostructures is the basis for the design of new architectures for various applications. Here we show the potential of fluorescence and super resolution imaging to unveil the structural and dynamic features of peptide nanofibers with high spatiotemporal resolution.

Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments

Caged organic fluorophores are established tools for localization-based super-resolution imaging. Their use relies on reversible deactivation of standard organic fluorophores by chemical reduction or commercially available caged dyes with ON switching of the fluorescent signal by ultraviolet (UV) light. Here, we establish caging of cyanine fluorophores and caged rhodamine dyes, i.e., chemical deactivation of fluorescence, for single-molecule Förster resonance energy transfer (smFRET) experiments with freely diffusing molecules. They allow temporal separation and sorting of multiple intramolecular donor–acceptor pairs during solution-based smFRET. We use this “caged FRET” methodology for the study of complex biochemical species such as multisubunit proteins or nucleic acids containing more than two fluorescent labels. Proof-of-principle experiments and a characterization of the uncaging process in the confocal volume are presented. These reveal that chemical caging and UV reactivation allow temporal uncoupling of convoluted fluorescence signals from, e.g., multiple spectrally similar donor or acceptor molecules on nucleic acids. We also use caging without UV reactivation to remove unwanted overlabeled species in experiments with the homotrimeric membrane transporter BetP. We finally outline further possible applications of the caged FRET methodology, such as the study of weak biochemical interactions, which are otherwise impossible with diffusion-based smFRET techniques because of the required low concentrations of fluorescently labeled biomolecules.

Nanoscopic Visualization of Soft Matter Using Fluorescent Diarylethene Photoswitches

The in situ imaging of soft matter is of paramount importance for a detailed understanding of functionality on the nanoscopic scale. Although super-resolution fluorescence microscopy methods with their unprecedented imaging capabilities have revolutionized research in the life sciences, this potential has been far less exploited in materials science. One of the main obstacles for a more universal application of super-resolved fluorescence microscopy methods is the limitation of readily available suitable dyes to overcome the diffraction limit. Here, we report a novel diarylethene-based photoswitch with a highly fluorescent closed and a nonfluorescent open form. Its photophysical properties, switching behavior, and high photostability make the dye an ideal candidate for photoactivation localization microscopy (PALM). It is capable of resolving apolar structures with an accuracy far beyond the diffraction limit of optical light in cylindrical micelles formed by amphiphilic block copolymers.