Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes

Accelerated protein retention expansion microscopy using microwave radiation

Protein retention expansion microscopy (ExM) retains genetically encoded fluorescent proteins or antibody-conjugated fluorescent probes in fixed tissue and isotropically expands the tissue through a swellable polymer network to allow nanoscale (<70 nm) resolution on diffraction-limited confocal microscopes. Despite numerous advantages ExM brings to biological studies, the full protocol is time-consuming and can take multiple days to complete. Here, we adapted the ExM protocol to the vibratome-sectioned brain tissue of Xenopus laevis tadpoles and implemented a microwave-assisted protocol to reduce the workflow from days to hours. In addition to the significantly accelerated processing time, our microwave-assisted ExM (M/WExM) protocol maintains the superior resolution and signal-to-noise ratio of the original ExM protocol. Furthermore, the M/WExM protocol yields higher magnitude of expansion, suggesting that in addition to accelerating the process through increased diffusion rate of reagents, microwave radiation may also facilitate the expansion process. To demonstrate the applicability of this method to other specimens and protocols, we adapted the microwave-accelerated protocol to whole mount adult brain tissue of Drosophila melanogaster fruit flies, and successfully reduced the total processing time of a widely-used Drosophila IHC-ExM protocol from 6 days to 2 days. Our results demonstrate that with appropriate adjustment of the microwave parameters (wattage, pulse duration, interval, and number of cycles), this protocol can be readily adapted to different model organisms and tissue types to greatly increase the efficiency of ExM experiments.

Highly Accurate Profiling of Exosome Phenotypes Using Super-resolution Tricolor Fluorescence Co-localization

Exosomes contain a wealth of proteomic information, presenting promising biomarkers for the noninvasive early diagnosis of diseases, especially cancer. However, it remains a great challenge to accurately and reliably distinguish exosomes secreted from different types of cell lines. Fluorescence immunoassay is frequently used for exosome detection. Nonspecific adsorption in immunoassays is unavoidable and affects the reliability of assay results. Despite the fact that various methods have been proposed to reduce nonspecific adsorption, a more effective method that can eliminate the influence of nonspecific adsorption is still lacking. Here, we report a more convenient way (named SR-TFC) to remove the artifacts caused by nonspecific adsorption, which combines tricolor fluorescence labeling of target exosomes, tricolor super-resolution imaging, and pixel counting. The pixel counting method (named CFPP) is realized by MATLAB and can eliminate nonspecific binding sites at the single-pixel level, which has never been achieved before and could improve the reliability of detection to the maximum extent. Furthermore, as a proof-of-concept, profiling of exosomal membrane proteins and identification of breast cancer subpopulations are demonstrated. To enable multiplex breast cancer phenotypic analysis, three kinds of specific proteins are labeled to obtain the 3D phenotypic information on various exosomes. Breast cancer subtypes can be accurately identified according to the super-resolution images of some clinically relevant exosomal proteins. Worth mentioning is that, by selecting other biomarkers, classification of other cancers could also be realized using SR-TFC. Hence, the present work holds great potential in clinical cancer diagnosis and precision medicine.

Recent advances in super-resolution optical imaging based on aggregation-induced emission

Super-resolution imaging has rapidly emerged as an optical microscopy technique, offering advantages of high optical resolution over the past two decades; achieving improved imaging resolution requires significant efforts in developing super-resolution imaging agents characterized by high brightness, high contrast and high sensitivity to fluorescence switching. Apart from technical requirements in optical systems and algorithms, super-resolution imaging relies on fluorescent dyes with special photophysical or photochemical properties. The concept of aggregation-induced emission (AIE) was proposed in 2001, coinciding with unprecedented advancements and innovations in super-resolution imaging technology. AIE probes offer many advantages, including high brightness in the aggregated state, low background signal, a larger Stokes shift, ultra-high photostability, and excellent biocompatibility, making them highly promising for applications in super-resolution imaging. In this review, we summarize the progress in implementation methods and provide insights into the mechanism of AIE-based super-resolution imaging, including fluorescence switching resulting from photochemically-converted aggregation-induced emission, electrostatically controlled aggregation-induced emission and specific binding-regulated aggregation-induced emission. Particularly, the aggregation-induced emission principle has been proposed to achieve spontaneous fluorescence switching, expanding the selection and application scenarios of super-resolution imaging probes. By combining the aggregation-induced emission principle and specific molecular design, we offer some comprehensive insights to facilitate the applications of AIEgens (AIE-active molecules) in super-resolution imaging.

Photoactivatable Xanthone (PaX) Dyes Enable Quantitative, Dual Color, and Live-Cell MINFLUX Nanoscopy

The single-molecule localization concept MINFLUX has triggered a reevaluation of the features of fluorophores for attaining nanometer-scale resolution. MINFLUX nanoscopy benefits from temporally controlled fluorescence ("on"/"off") photoswitching. Combined with an irreversible switching behavior, the localization process is expected to turn highly efficient and quantitative data analysis simple. The potential in the recently reported photoactivable xanthone (PaX) dyes is recognized to extend the list of molecular switches used for MINFLUX with 561 nm excitation beyond the fluorescent protein mMaple. The MINFLUX localization success rates of PaX560 , PaX+560, and mMaple are quantitatively compared by analyzing the effective labeling efficiency of endogenously tagged nuclear pore complexes. The PaX dyes prove to be superior to mMaple and on par with the best reversible molecular switches routinely used in single-molecule localization microscopy. Moreover, the rationally designed PaX595 is introduced for complementing PaX560 in dual color 561 nm MINFLUX imaging based on spectral classification and the deterministic, irreversible, and additive-independent nature of PaX photoactivation is showcased in fast live-cell MINFLUX imaging. The PaX dyes meet the demands of MINFLUX for a robust readout of each label position and fill the void of reliable fluorophores dedicated to 561 nm MINFLUX imaging.

Frequency-dependent nonlinear optical response and refractive index investigation of lactone-derived thermochromic compounds

Nonlinear optical (NLO) switchable materials play a crucial role in the fields of electronics and optoelectronics. The selection of an appropriate switching approach is vital in designing such materials to enhance their NLO response. Among various approaches, thermos-switching materials have shown a 4-fold increase in NLO response compared to other photo-switching materials. In this study, we computationally investigated the geometric, electronic, and nonlinear optical properties of reversible lactone-based thermochromic compounds using the ωB97XD/6-311+G (d,p) level of theory. Molecular orbital studies are employed to analyze the electronic properties of the close and open isomers of these compounds, while time-dependent density functional theory (TD-DFT) analysis is utilized to evaluate their molecular absorption. Our findings reveal that the π-electronic conjugation-induced delocalization significantly influences the ON-OFF switchable nonlinear optical response of the lactone-based thermochromic compounds. Notably, among all compounds, the open isomer of lactone 2 exhibits the highest hyperpolarizability value (6596.69 au). Furthermore, we extended our analysis to investigate the frequency-dependent second and third-order hyperpolarizabilities. The most pronounced frequency-dependent NLO response is observed at 532 nm. Additionally, we calculated the refractive index of these thermochromic compounds to further assess their nonlinear optical response. The open isomer of lactone 1 demonstrates the highest refractive index value (3.99 × 10-14 cm2/W). Overall, our study highlights the excellent potential of reversible thermochromic compounds as NLO molecular thermos-switches for future applications.

Structured illumination contrast transfer function for high resolution quantitative phase imaging

We report a sub-diffraction resolution imaging of non-fluorescent samples through quantitative phase imaging. This is achieved through a novel application of structured illumination microscopy (SIM), a super-resolution imaging technique established primarily for fluorescence microscopy. Utilizing our contrast transfer function formalism with SIM, we extract the high spatial frequency components of the phase profile from the defocused intensity images, enabling the reconstruction of a quantitative phase image with a frequency spectrum that surpasses the diffraction limit imposed by the imaging system. Our approach offers several advantages including a deterministic, phase-unwrapping-free algorithm and an easily implementable, non-interferometric setup. We validate the proposed technique for high-resolution phase imaging through both simulation and experimental results, demonstrating a two-fold enhancement in resolution. A lateral resolution of 0.814 µm is achieved for the phase imaging of human cheek cells using a 0.42 NA objective lens and an illumination wavelength of 660 nm, highlighting the efficacy of our approach for high-resolution quantitative phase imaging.

Detecting continuous structural heterogeneity in single-molecule localization microscopy data

Fusion of multiple chemically identical complexes, so-called particles, in localization microscopy, can improve the signal-to-noise ratio and overcome under-labeling. To this end, structural homogeneity of the data must be assumed. Biological heterogeneity, however, could be present in the data originating from distinct conformational variations or (continuous) variations in particle shapes. We present a prior-knowledge-free method for detecting continuous structural variations with localization microscopy. Detecting this heterogeneity leads to more faithful fusions and reconstructions of the localization microscopy data as their heterogeneity is taken into account. In experimental datasets, we show the continuous variation of the height of DNA origami tetrahedrons imaged with 3D PAINT and of the radius of Nuclear Pore Complexes imaged in 2D with STORM. In simulation, we study the impact on the heterogeneity detection pipeline of Degree Of Labeling and of structural variations in the form of two independent modes.

Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging

In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.

Subtle Structural Translation Magically Modulates the Super-Resolution Imaging of Self-Blinking Rhodamines

The evolution of super-resolution imaging techniques is benefited from the ongoing competition for optimal rhodamine fluorophores. Yet, it seems blind to construct the desired rhodamine molecule matching the imaging need without the knowledge on imaging impact of even the minimum structural translation. Herein, we have designed a pair of self-blinking sulforhodamines (STMR and SRhB) with the bare distinction of methyl or ethyl substituents and engineered them with Halo protein ligands. Although the two possess similar spectral properties (λ_ab, λ_fl, ϕ, etc.), they demonstrated unique single-molecule characteristics preferring to individual imaging applications. Experimentally, STMR with high emissive rates was qualified for imaging structures with rapid dynamics (endoplasmic reticulum, and mitochondria), and SRhB with prolonged on-times and photostability was suited for relatively "static" nuclei and microtubules. Using this new knowledge, the mitochondrial morphology during apoptosis and ferroptosis was first super-resolved by STMR. Our study highlights the significance of even the smallest structural modification to the modulation of super-resolution imaging performance and would provide insights for future fluorophore design.

Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging

The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.

Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging

The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.

Mapping the Nicotinic Acetylcholine Receptor Nanocluster Topography at the Cell Membrane with STED and STORM Nanoscopies

The cell-surface topography and density of nicotinic acetylcholine receptors (nAChRs) play a key functional role in the synapse. Here we employ in parallel two labeling and two super-resolution microscopy strategies to characterize the distribution of this receptor at the plasma membrane of the mammalian clonal cell line CHO-K1/A5. Cells were interrogated with two targeted techniques (confocal microscopy and stimulated emission depletion (STED) nanoscopy) and single-molecule nanoscopy (stochastic optical reconstruction microscopy, STORM) using the same fluorophore, Alexa Fluor 647, tagged onto either α-bungarotoxin (BTX) or the monoclonal antibody mAb35. Analysis of the topography of nanometer-sized aggregates (“nanoclusters”) was carried out using STORMGraph, a quantitative clustering analysis for single-molecule localization microscopy based on graph theory and community detection, and ASTRICS, an inter-cluster similarity algorithm based on computational geometry. Antibody-induced crosslinking of receptors resulted in nanoclusters with a larger number of receptor molecules and higher densities than those observed in BTX-labeled samples. STORM and STED provided complementary information, STED rendering a direct map of the mesoscale nAChR distribution at distances ~10-times larger than the nanocluster centroid distances measured in STORM samples. By applying photon threshold filtering analysis, we show that it is also possible to detect the mesoscale organization in STORM images.

Optimal precision and accuracy in 4Pi-STORM using dynamic spline PSF models

Coherent fluorescence imaging with two objective lenses (4Pi detection) enables single-molecule localization microscopy with sub-10 nm spatial resolution in three dimensions. Despite its outstanding sensitivity, wider application of this technique has been hindered by complex instrumentation and the challenging nature of the data analysis. Here we report the development of a 4Pi-STORM microscope, which obtains optimal resolution and accuracy by modeling the 4Pi point spread function (PSF) dynamically while also using a simpler optical design. Dynamic spline PSF models incorporate fluctuations in the modulation phase of the experimentally determined PSF, capturing the temporal evolution of the optical system. Our method reaches the theoretical limits for precision and minimizes phase-wrapping artifacts by making full use of the information content of the data. 4Pi-STORM achieves a near-isotropic three-dimensional localization precision of 2–3 nm, and we demonstrate its capabilities by investigating protein and nucleic acid organization in primary neurons and mammalian mitochondria.

A dynamic model of the 4Pi point spread function enables localization microscopy with exceptional three-dimensional resolution and a simpler optical design. 4Pi-STORM images of neurons and mitochondria reveal new details of nanoscale protein and nucleic acid organization.

Fluorescence sensors for imaging membrane lipid domains and cholesterol

Lipid membrane domains are supramolecular lateral heterogeneities of biological membranes. Of nanoscopic dimensions, they constitute specialized hubs used by the cell as transient signaling platforms for a great variety of biologically important mechanisms. Their property to form and dissolve in the bulk lipid bilayer endow them with the ability to engage in highly dynamic processes, and temporarily recruit subpopulations of membrane proteins in reduced nanometric compartments that can coalesce to form larger mesoscale assemblies. Cholesterol is an essential component of these lipid domains; its unique molecular structure is suitable for interacting intricately with crevices and cavities of transmembrane protein surfaces through its rough β face while "talking" to fatty acid acyl chains of glycerophospholipids and sphingolipids via its smooth α face. Progress in the field of membrane domains has been closely associated with innovative improvements in fluorescence microscopy and new fluorescence sensors. These advances enabled the exploration of the biophysical properties of lipids and their supramolecular platforms. Here I review the rationale behind the use of biosensors over the last few decades and their contributions towards elucidation of the in-plane and transbilayer topography of cholesterol-enriched lipid domains and their molecular constituents. The challenges introduced by super-resolution optical microscopy are discussed, as well as possible scenarios for future developments in the field, including virtual ("no staining") staining.

Super-Resolution Imaging With Lanthanide Luminescent Nanocrystals: Progress and Prospect

Stimulated emission depletion (STED) nanoscopy has overcome a serious diffraction barrier on the optical resolution and facilitated new discoveries on detailed nanostructures in cell biology. Traditional fluorescence probes employed in the super-resolution imaging approach include organic dyes and fluorescent proteins. However, some limitations of these probes, such as photobleaching, short emission wavelengths, and high saturation intensity, still hamper the promotion of optical resolution and bio-applications. Recently, lanthanide luminescent probes with unique optical properties of non-photobleaching and sharp emissions have been applied in super-resolution imaging. In this mini-review, we will introduce several different mechanisms for lanthanide ions to achieve super-resolution imaging based on an STED-like setup. Then, several lanthanide ions used in super-resolution imaging will be described in detail and discussed. Last but not least, we will emphasize the future challenges and outlooks in hope of advancing the next-generation lanthanide fluorescent probes for super-resolution optical imaging.

Label-retention expansion microscopy

Expansion microscopy (ExM) increases the effective resolving power of any microscope by expanding the sample with swellable hydrogel. Since its invention, ExM has been successfully applied to a wide range of cell, tissue, and animal samples. Still, fluorescence signal loss during polymerization and digestion limits molecular-scale imaging using ExM. Here, we report the development of label-retention ExM (LR-ExM) with a set of trifunctional anchors that not only prevent signal loss but also enable high-efficiency labeling using SNAP and CLIP tags. We have demonstrated multicolor LR-ExM for a variety of subcellular structures. Combining LR-ExM with superresolution stochastic optical reconstruction microscopy (STORM), we have achieved molecular resolution in the visualization of polyhedral lattice of clathrin-coated pits in situ.

Analyzing Centrioles and Cilia by Expansion Microscopy

Expansion microscopy is an imaging method based on isotropic physical expansion of biological samples, which improves optical resolution and allows imaging of subresolutional cellular components by conventional microscopes. Centrioles are small microtubule-based cylindrical structures that build centrosomes and cilia, two organelles essential for vertebrates. Due to a centriole's small size, electron microscopy has traditionally been used to study centriole length and ultrastructural features. Recently, expansion microscopy has been successfully used as an affordable and accessible alternative to electron microscopy in the analysis of centriole and cilia length and structural features. Here, we describe an expansion microscopy approach for the analysis of centrioles and cilia in large populations of mammalian adherent and nonadherent cells and multiciliated cultures.

Silinanyl Rhodamines and Silinanyl Fluoresceins for Super-Resolution Microscopy

Single-molecule localization microscopy (SMLM) enables the visualization of biomolecules at unprecedented resolution and requires control of the fluorescent blinking (ON/OFF) states of fluorophores to detect single-molecule fluorescence without overlapping of the signals. Although SMLM probes based on the intramolecular spirocyclization of Si-xanthene fluorophores have been developed, fluorophores with lower ON/OFF ratios are required for SMLM visualization of high-density structures. Here, we describe a silinane structure that lowers the ON/OFF ratio of Si-xanthene fluorophores. On the basis of Mulliken population analysis, we replaced the dimethylsilane moiety in Si-rhodamine with a silinane moiety to increase the partial charge at the 9-position of the carbon atom in the Si-xanthene ring and to promote the ring-closure reaction. Evaluation of fluorescence properties in a solution and in single-molecule imaging indicated that introducing the silinane sufficiently stabilized the nonfluorescent spirocyclic forms, thus decreasing the fluorescence ON/OFF ratio. This novel substitution was applied to Si-rhodamines with various amine structures and to an Si-fluorescein to expand the color palette. We demonstrated SMLM observation of microtubules in fixed HeLa cells using the developed fluorophores in two color channels. The results demonstrated the feasibility of extending the design strategies of SMLM probes based on Si-xanthenes through modification of the substituents on the Si atom.

Nitric Oxide Photoreleasers with Fluorescent Reporting

Nitric oxide (NO) plays a multifaceted role in human physiology and pathophysiology, and its controlled delivery has great prospects in therapeutic applications. The light-activated uncaging of NO from NO caging compounds allows this free radical to be released with accurate control of site and dosage, which strictly determine its biological effects. Molecular constructs able to activate fluorescence concomitantly to NO release offer the important advantage of easy and real-time tracking of the amount of NO uncaged in a non-invasive fashion even in the cell environment. This contribution provides an overview of the advances in photoactivatable NO releasers bearing fluorescent reporting functionalities achieved in our and other laboratories, highlighting the rationale design and their potential therapeutic applications.

Advanced Static and Dynamic Fluorescence Microscopy Techniques to Investigate Drug Delivery Systems

In the past decade(s), fluorescence microscopy and laser scanning confocal microscopy (LSCM) have been widely employed to investigate biological and biomimetic systems for pharmaceutical applications, to determine the localization of drugs in tissues or entire organisms or the extent of their cellular uptake (in vitro). However, the diffraction limit of light, which limits the resolution to hundreds of nanometers, has for long time restricted the extent and quality of information and insight achievable through these techniques. The advent of super-resolution microscopic techniques, recognized with the 2014 Nobel prize in Chemistry, revolutionized the field thanks to the possibility to achieve nanometric resolution, i.e., the typical scale length of chemical and biological phenomena. Since then, fluorescence microscopy-related techniques have acquired renewed interest for the scientific community, both from the perspective of instrument/techniques development and from the perspective of the advanced scientific applications. In this contribution we will review the application of these techniques to the field of drug delivery, discussing how the latest advancements of static and dynamic methodologies have tremendously expanded the experimental opportunities for the characterization of drug delivery systems and for the understanding of their behaviour in biologically relevant environments.

3D particle averaging and detection of macromolecular symmetry in localization microscopy

Single molecule localization microscopy offers in principle resolution down to the molecular level, but in practice this is limited primarily by incomplete fluorescent labeling of the structure. This missing information can be completed by merging information from many structurally identical particles. In this work, we present an approach for 3D single particle analysis in localization microscopy which hugely increases signal-to-noise ratio and resolution and enables determining the symmetry groups of macromolecular complexes. Our method does not require a structural template, and handles anisotropic localization uncertainties. We demonstrate 3D reconstructions of DNA-origami tetrahedrons, Nup96 and Nup107 subcomplexes of the nuclear pore complex acquired using multiple single molecule localization microscopy techniques, with their structural symmetry deducted from the data.

Organic Nanoparticles-Assisted Low-Power STED Nanoscopy

Stimulated emission depletion (STED) nanoscopy plays a key role in achieving sub-50 nm high spatial resolution for subcellular live-cell imaging. To avoid re-excitation, the STED wavelength has to be tuned at the red tail of the emission spectrum of fluorescent probes, leading to high depletion laser power that might damage the cell viability and functionality. Herein, with the highly emissive silica-coated core-shell organic nanoparticles (CSONPs) enabling a giant Stokes shift of 150 nm, ultralow power STED is achieved by shifting the STED wavelength to the emission maximum at 660 nm. The stimulated emission cross section is increased by ∼20-fold compared to that at the emission red tail. The measured saturation intensity and lateral resolution of our CSONP are 0.0085 MW cm^-2 and 25 nm, respectively. More importantly, long-term (>3 min) dynamic super-resolution imaging of the lysosomal fusion-fission processes in living cells is performed with a resolution of 37 nm.

Rethinking resolution estimation in fluorescence microscopy: from theoretical resolution criteria to super-resolution microscopy

Resolution is undoubtedly the most important parameter in optical microscopy by providing an estimation on the maximum resolving power of a certain optical microscope. For centuries, the resolution of an optical microscope is generally considered to be limited only by the numerical aperture of the optical system and the wavelength of light. However, since the invention and popularity of various advanced fluorescence microscopy techniques, especially super-resolution fluorescence microscopy, many new methods have been proposed for estimating the resolution, leading to confusions for researchers who need to quantify the resolution of their fluorescence microscopes. In this paper, we firstly summarize the early concepts and criteria for predicting the resolution limit of an ideal optical system. Then, we discuss some important influence factors that deteriorate the resolution of a certain fluorescence microscope. Finally, we provide methods and examples on how to measure the resolution of a fluorescence microscope from captured fluorescence images. This paper aims to answer as best as possible the theoretical and practical issues regarding the resolution estimation in fluorescence microscopy.

Improving Brightness and Stability of Si-Rhodamine for Super-Resolution Imaging of Mitochondria in Living Cells

Photostable and bright organic dyes emitting in the near-infrared region are highly desirable for long-term dynamic bioimaging. Herein, we report a synthetic approach to build novel methoxy modified Si-rhodamine (SiRMO) dyes by introducing the methoxybenzene on the xanthene moiety. The brightness of SiRMO increased from 2300 M^-1 cm^-1 (SiRMO-0) to 49000 M^-1 cm^-1 (SiRMO-2) when the substituent 2,5-dimethoxybenzene was replaced with 2,6-dimethoxybenzene. Moreover, the stability of SiRMO-2 was significantly improved due to the steric hindrance protection of the two methoxy groups on the ninth carbon atom of the xanthene. After fast cellular uptake, the SiRMO dyes selectively stained the mitochondria with a low background in live cultured cells and primary neurons. The high brightness and stability of SiRMO-2 significantly improved the capability of monitoring mitochondria dynamic processes in living cells under super-resolution conditions. Moreover, with the fluorescence nanoscopy techniques, we observed the structure of mitochondrial cristae and mitochondria fission, fusion, and apoptosis with a high temporal resolution. Under two-photon illumination, SiRMO-2 showed also enhanced two-photon brightness and stability, which are important for imaging in thick tissue.

Live cell imaging of single RNA molecules with fluorogenic Mango II arrays

RNA molecules play vital roles in many cellular processes. Visualising their dynamics in live cells at single-molecule resolution is essential to elucidate their role in RNA metabolism. RNA aptamers, such as Spinach and Mango, have recently emerged as a powerful background-free technology for live-cell RNA imaging due to their fluorogenic properties upon ligand binding. Here, we report a novel array of Mango II aptamers for RNA imaging in live and fixed cells with high contrast and single-molecule sensitivity. Direct comparison of Mango II and MS2-tdMCP-mCherry dual-labelled mRNAs show marked improvements in signal to noise ratio using the fluorogenic Mango aptamers. Using both coding (β-actin mRNA) and long non-coding (NEAT1) RNAs, we show that the Mango array does not affect cellular localisation. Additionally, we can track single mRNAs for extended time periods, likely due to bleached fluorophore replacement. This property makes the arrays readily compatible with structured illumination super-resolution microscopy.

A special three-layer step-index fiber for building compact STED systems

Up to now, most of stimulated-emission-depletion (STED) systems were lens-based bulky systems. Exchanging some spatial light paths with optical fiber components will make the systems more flexible and will benefit various fields. A big problem to achieve this goal is that the STED beam generated by the traditional method of bulky systems cannot be maintained in an optical fiber due to its birefringence. In this article, we will introduce a type of special optical fiber. With the special fiber, a dark hollow beam with doughnut-shaped focal spot and a concentric beam with Gaussian-shaped focal spot can be generated at the same time. Parameters of a sample and a compact STED system based on it are demonstrated.

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.

Microscopy and Cell Biology: New Methods and New Questions

Understanding the cellular basis of human health and disease requires the spatial resolution of microscopy and the molecular-level details provided by spectroscopy. This review highlights imaging methods at the intersection of microscopy and spectroscopy with applications in cell biology. Imaging methods are divided into three broad categories: fluorescence microscopy, label-free approaches, and imaging tools that can be applied to multiple imaging modalities. Just as these imaging methods allow researchers to address new biological questions, progress in biological sciences will drive the development of new imaging methods. We highlight four topics in cell biology that illustrate the need for new imaging tools: nanoparticle-cell interactions, intracellular redox chemistry, neuroscience, and the increasing use of spheroids and organoids. Overall, our goal is to provide a brief overview of individual imaging methods and highlight recent advances in the use of microscopy for cell biology.

Small-Molecule Fluorescent Probes for Live-Cell Super-Resolution Microscopy

Super-resolution fluorescence microscopy is a powerful tool to visualize biomolecules and cellular structures at the nanometer scale. Employing these techniques in living cells has opened up the possibility to study dynamic processes with unprecedented spatial and temporal resolution. Different physical approaches to super-resolution microscopy have been introduced over the last years. A bottleneck to apply these approaches for live-cell imaging has become the availability of appropriate fluorescent probes that can be specifically attached to biomolecules. In this Perspective, we discuss the role of small-molecule fluorescent probes for live-cell super-resolution microscopy and the challenges that need to be overcome for their generation. Recent trends in the development of labeling strategies are reviewed together with the required chemical and spectroscopic properties of the probes. Finally, selected examples of the use of small-molecule fluorescent probes in live-cell super-resolution microscopy are given.

Method to identify and minimize artifacts induced by fluorescent impurities in single-molecule localization microscopy

The existence of fluorescent impurities has been a long-standing obstacle in single-molecule imaging, which results in sample misidentification and higher localization uncertainty. Spectroscopic single-molecule localization microscopy can record the full fluorescent spectrum of every stochastic single-molecule emission event. This capability allows us to quantify the spatial and spectral characteristics of fluorescent impurities introduced by sample preparation steps, based on which we developed a method to effectively separate fluorescent impurities from target molecules.

The actin cytoskeleton of the mouse sperm flagellum is organized in a helical structure

Conception in mammals is determined by the fusion of a sperm cell with an oocyte during fertilization. Motility is one of the features of sperm that allows them to succeed in fertilization, and their flagellum is essential for this function. Longitudinally, the flagellum can be divided into the midpiece, the principal piece and the end piece. A precise cytoskeletal architecture of the sperm tail is key for the acquisition of fertilization competence. It has been proposed that the actin cytoskeleton plays essential roles in the regulation of sperm motility; however, the actin organization in sperm remains elusive. In the present work, we show that there are different types of actin structures in the sperm tail by using three-dimensional stochastic optical reconstruction microscopy (STORM). In the principal piece, actin is radially distributed between the axoneme and the plasma membrane. The actin-associated proteins spectrin and adducin are also found in these structures. Strikingly, polymerized actin in the midpiece forms a double-helix that accompanies mitochondria. Our findings illustrate a novel specialized structure of actin filaments in a mammalian cell.

A toolbox of anti-mouse and anti-rabbit IgG secondary nanobodies

Pleiner, Bates, and Görlich introduce anti–mouse and anti–rabbit IgG nanobodies that can be produced in E. coli and fused to reporters or labeled fluorescently to create bright and specific detection reagents with unique advantages over conventional polyclonal secondary antibodies.

Polyclonal anti–immunoglobulin G (anti-IgG) secondary antibodies are essential tools for many molecular biology techniques and diagnostic tests. Their animal-based production is, however, a major ethical problem. Here, we introduce a sustainable alternative, namely nanobodies against all mouse IgG subclasses and rabbit IgG. They can be produced at large scale in Escherichia coli and could thus make secondary antibody production in animals obsolete. Their recombinant nature allows fusion with affinity tags or reporter enzymes as well as efficient maleimide chemistry for fluorophore coupling. We demonstrate their superior performance in Western blotting, in both peroxidase- and fluorophore-linked form. Their site-specific labeling with multiple fluorophores creates bright imaging reagents for confocal and superresolution microscopy with much smaller label displacement than traditional secondary antibodies. They also enable simpler and faster immunostaining protocols, and allow multitarget localization with primary IgGs from the same species and of the same class.

Gpufit: An open-source toolkit for GPU-accelerated curve fitting

We present a general purpose, open-source software library for estimation of non-linear parameters by the Levenberg-Marquardt algorithm. The software, Gpufit, runs on a Graphics Processing Unit (GPU) and executes computations in parallel, resulting in a significant gain in performance. We measured a speed increase of up to 42 times when comparing Gpufit with an identical CPU-based algorithm, with no loss of precision or accuracy. Gpufit is designed such that it is easily incorporated into existing applications or adapted for new ones. Multiple software interfaces, including to C, Python, and Matlab, ensure that Gpufit is accessible from most programming environments. The full source code is published as an open source software repository, making its function transparent to the user and facilitating future improvements and extensions. As a demonstration, we used Gpufit to accelerate an existing scientific image analysis package, yielding significantly improved processing times for super-resolution fluorescence microscopy datasets.

AIE Nanoparticles with High Stimulated Emission Depletion Efficiency and Photobleaching Resistance for Long-Term Super-Resolution Bioimaging

Stimulated emission depletion (STED) nanoscopy is a typical super-resolution imaging technique that has become a powerful tool for visualizing intracellular structures on the nanometer scale. Aggregation-induced emission (AIE) luminogens are ideal fluorescent agents for bioimaging. Herein, long-term super-resolution fluorescence imaging of cancer cells, based on STED nanoscopy assisted by AIE nanoparticles (NPs) is realized. 2,3-Bis(4-(phenyl(4-(1,2,2-triphenylvinyl)phenyl)amino)phenyl) fumaronitrile (TTF), a typical AIE luminogen, is doped into colloidal mesoporous silica to form fluorescent NPs. TTF@SiO₂ NPs bear three significant features, which are all essential for STED nanoscopy. First, their STED efficiency can reach more than 60%. Second, they are highly resistant to photobleaching, even under long-term and high-power STED light irradiation. Third, they have a large Stokes' shift of ≈150 nm, which is beneficial for restraining the fluorescence background induced by the STED light irradiation. STED nanoscopy imaging of TTF@SiO₂ -NPs-stained HeLa cells is performed, exhibiting a high lateral spatial resolution of 30 nm. More importantly, long-term (more than half an hour) super-resolution cell imaging is achieved with low fluorescence loss. Considering that AIE luminogens are widely used for organelle targeting, cellular mapping, and tracing, AIE-NPs-based STED nanoscopy holds great potential for many basic biomedical studies that require super-resolution and long-term imaging.

Polarized super-resolution structural imaging inside amyloid fibrils using Thioflavine T

Thioflavin T (ThT) is standardly used as a fluorescent marker to detect aggregation of amyloid fibrils by conventional fluorescence microscopy, including polarization resolved imaging that brings information on the orientational order of the fibrils. These techniques are however diffraction limited and cannot provide fine structural details at the fibrils scales of 10-100 nm, which lie beyond the diffraction limit. In this work, we evaluate the capacity of ThT to photoswitch when bound to insulin amyloids by adjusting the redox properties of its environment. We demonstrate that on-off duty cycles, intensity and photostability of the ThT fluorescence emission under adequate buffer conditions permit stochastic super-resolution imaging with a localization precision close to 20 nm. We show moreover that signal to noise conditions allow polarized orientational imaging of single ThT molecules, which reveals ultra-structure signatures related to protofilaments twisting within amyloid fibrils.

Super-resolution microscopy reveals functional organization of dopamine transporters into cholesterol and neuronal activity-dependent nanodomains

Dopamine regulates reward, cognition, and locomotor functions. By mediating rapid reuptake of extracellular dopamine, the dopamine transporter is critical for spatiotemporal control of dopaminergic neurotransmission. Here, we use super-resolution imaging to show that the dopamine transporter is dynamically sequestrated into cholesterol-dependent nanodomains in the plasma membrane of presynaptic varicosities and neuronal projections of dopaminergic neurons. Stochastic optical reconstruction microscopy reveals irregular dopamine transporter nanodomains (∼70 nm mean diameter) that were highly sensitive to cholesterol depletion. Live photoactivated localization microscopy shows a similar dopamine transporter membrane organization in live heterologous cells. In neurons, dual-color dSTORM shows that tyrosine hydroxylase and vesicular monoamine transporter-2 are distinctively localized adjacent to, but not overlapping with, the dopamine transporter nanodomains. The molecular organization of the dopamine transporter in nanodomains is reversibly reduced by short-term activation of NMDA-type ionotropic glutamate receptors, implicating dopamine transporter nanodomain distribution as a potential mechanism to modulate dopaminergic neurotransmission in response to excitatory input.The dopamine transporter (DAT) has a crucial role in the regulation of neurotransmission. Here, the authors use super-resolution imaging to show that DAT clusters into cholesterol-dependent membrane regions that are reversibly regulated by ionotropic glutamate receptors activation.

Single-molecule spectroelectrochemical cross-correlation during redox cycling in recessed dual ring electrode zero-mode waveguides

The ability of zero-mode waveguides (ZMW) to guide light into subwavelength-diameter nanoapertures has been exploited for studying electron transfer dynamics in zeptoliter-volume nanopores under single-molecule occupancy conditions. In this work, we report the spectroelectrochemical detection of individual molecules of the redox-active, fluorogenic molecule flavin mononucleotide (FMN) freely diffusing in solution. Our approach is based on an array of nanopore-confined recessed dual ring electrodes, wherein repeated reduction and oxidation of a single molecule at two closely spaced annular working electrodes yields amplified electrochemical signals. We have articulated these structures with an optically transparent bottom, so that the nanopores are bifunctional, exhibiting both nanophotonic and nanoelectrochemical behaviors allowing the coupling between electron transfer and fluorescence dynamics to be studied under redox cycling conditions. We also investigated the electric field intensity in electrochemical ZMWs (E-ZMW) through finite-element simulations, and the amplification of fluorescence by redox cycling agrees well with predictions based on optical confinement effects inside the E-ZMW. Proof-of-principle experiments are conducted showing that electrochemical and fluorescence signals may be correlated to reveal single molecule fluctuations in the array population. Cross-correlation of single molecule fluctuations in amperometric response and single photon emission provides unequivocal evidence of single molecule sensitivity.

New microscopy technique based on position localization of scattering particles

We introduce the Holographic - Single Scatterer Localization Microscopy in which we combine dynamical laser speckle illumination with centroid localization of backscattered light spots in order to localize isolated scattering particles. The reconstructed centroid images show very accurate particle localization, with precision much better than the width of diffraction-limited image of the particles recorded by the CCD. Furthermore, the method provides an improved resolution in distinguishing two very close scattering objects compared to the standard laser scanning techniques and can be assimilated to a confocal technique in the ability of light background rejection in three-dimensional disposition of scattering objects. The illumination is controlled via a digital holography setup based on the use of a spatial light modulator. This allows not only a high level of versatility in the illumination patterns, but also the remarkable characteristics of absence of moving mechanical parts, typical of the laser scanning techniques, and the possibility of strongly miniaturizing the setup.

Fluorescent Photoswitchable Diarylethenes for Biolabeling and Single-Molecule Localization Microscopies with Optical Superresolution

A modular assembly of water-soluble diarylethenes (DAEs), applicable as biomarkers for optical nanoscopy, is reported. Reversibly photoswitchable 1,2-bis(2-alkyl-6-phenyl-1-benzothiophene-1,1-dioxide-3-yl)perfluorocyclopentenes possessing a fluorescent "closed" form were decorated with one or two methoxy group(s) attached to the para-position(s) of phenyl ring(s) and two, four, or eight carboxylic acid groups. Antibody conjugates of these DAEs feature low aggregation, efficient photoswitching in aqueous buffers, specific staining of cellular structures, and photophysical properties (high emission efficiencies and low cycloreversion quantum yields) enabling their application in superresolution microscopy. Images of tubulin, vimentin, and nuclear pore complexes are presented. The superresolution images can also be acquired by using solely 488 nm light without additional photoactivation with UV light. These DAEs exhibit reversible photoswitching without requiring any additives to the imaging media and open new paths toward the modular design of fluorescent dyes for bioimaging with optical superresolution.

Hybrid Nanoscopy of Hybrid Nanomaterials

The combination of complementary techniques to characterize materials at the nanoscale is crucial to gain a more complete picture of their structure, a key step to design and fabricate new materials with improved properties and diverse functions. Here it is shown that correlative atomic force microscopy (AFM) and localization-based super-resolution microscopy is a useful tool that provides insight into the structure and emissive properties of fluorescent β-lactoglobulin (βLG) amyloid-like fibrils. These hybrid materials are made by functionalization of βLG with organic fluorophores and quantum dots, the latter being relevant for the production of 1D inorganic nanostructures templated by self-assembling peptides. Simultaneous functionalization of βLG fibers by QD655 and QD525 allows for correlative AFM and two-color super-resolution fluorescence imaging of these hybrid materials. These experiments allow the combination of information about the topography and number of filaments that compose a fibril, as well as the emissive properties and nanoscale spatial distribution of the attached fluorophores. This study represents an important step forward in the characterization of multifunctionalized hybrid materials, a key challenge in nanoscience.