Subsurface Super-resolution Imaging of Unstained Polymer Nanostructures

Super-Resolution Fluorescence Imaging for Semiconductor Nanoscale Metrology and Inspection

The increase in the number and complexity of process levels in semiconductor production has driven the need for the development of new measurement methods that can evaluate semiconductor devices at the critical dimensions of fine patterns and simultaneously inspect nanoscale contaminants or defects. However, conventional optical inspection methods often fail to resolve device patterns or defects at the level of tens of nanometers required for device development owing to their diffraction-limited resolutions. In this study, we used the stochastic optical reconstruction microscopy (STORM) technique to image semiconductor nanostructures with feature sizes as small as 30 nm and detect individual 20 nm-diameter contaminants. STORM imaging of semiconductor nanopatterns is based on the development of a selective labeling method of fluorophores for a negative silicon oxide surface using the charge interaction of positive polyethylenimine molecules. This study demonstrates the potential of STORM for nanoscale metrology and in-line defect inspection of semiconductor integrated circuits.

Surface Preparation for Single-Molecule Fluorescence Imaging in Organic Solvents

The development of single-molecule techniques provides opportunities to investigate the properties and heterogeneities of individual molecules, which are almost impossible to be obtained in ensemble measurements. Recently, single-molecule fluorescence microscopy is being applied more and more to study chemical reactions in organic solvents. However, little has been done to optimize the surface preparation procedures for single-molecule fluorescence imaging in organic solvents. In this work, we developed a method to prepare the surface for single-molecule fluorescence imaging in organic solvents with a well-controlled surface density of chemically immobilized dye molecules and a low density of nonspecifically adsorbed impurities. We also compared the surfaces prepared by two different procedures and studied the impacts of the polarities of the solvent and the surface functionality on the quality of prepared surface. We found that higher polarities of both the solvent and the surface functionality provided better control of the surface density of chemically immobilized dyes and helped reduce the nonspecific adsorption of both dyes and fluorescent impurities in organic solvents. We further performed single-molecule fluorescence imaging in DMF and investigated the photophysical properties of dyes and fluorescent impurities, which could be used to filter out false counts in single-molecule fluorescence measurements.

Polarity Nano-Mapping of Polymer Film Using Spectrally Resolved Super-Resolution Imaging

With the rapid development of the nanofabrication of polymer materials, the local measurement of the chemical properties of polymer nanostructures has become crucial because they can be highly heterogeneous at the nanoscale. We developed a spectroscopic imaging approach to characterize the nanoscale local polarity of polymer films via spectrally resolved super-resolution microscopy. We demonstrate the capability of the recently developed single-molecule sensing and imaging method to probe the polarity of polymers either inside a polymer matrix or on the external surface of a polymer. The nanoscale polarity sensing capability of our method facilitates the differentiation of various polymer surfaces based on chemical polarities, and it can further differentiate the polarity of functional side chain groups. Moreover, we demonstrate that a two-component polymer mixture can be locally distinguished based on the contrasting polarities of the lateral phase separation, further allowing for the investigation of nanoscale phase separation depending on the composition of the polymer blend film. This approach is anticipated to open the door to further characterizations of various nanocomposite materials.

Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy

The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.

100th Anniversary of Macromolecular Science Viewpoint: Single-Molecule Studies of Synthetic Polymers

Single polymer studies have revealed unexpected and heterogeneous dynamics among identical or seemingly similar macromolecules. In recent years, direct observation of single polymers has uncovered broad distributions in molecular behavior that play a key role in determining bulk properties. Early single polymer experiments focused primarily on biological macromolecules such as DNA, but recent advances in synthesis, imaging, and force spectroscopy have enabled broad exploration of chemically diverse polymer systems. In this Viewpoint, we discuss the recent study of synthetic polymers using single-molecule methods. In terms of polymer synthesis, direct observation of single chain polymerization has revealed heterogeneity in monomer insertion events at catalytic centers and decoupling of local and global growth kinetics. In terms of single polymer visualization, recent advances in super-resolution imaging, atomic force microscopy (AFM), and liquid-cell transmission electron microscopy (LC-TEM) can resolve structure and dynamics in single synthetic chains. Moreover, single synthetic polymers can be probed in the context of bulk material environments, including hydrogels, nanostructured polymers, and crystalline polymers. In each area, we highlight key challenges and exciting opportunities in using single polymer techniques to enhance our understanding of polymer science. Overall, the expanding versatility of single polymer methods will enable the molecular-scale design and fundamental understanding of a broad range of chemically diverse and functional polymeric materials.

100th Anniversary of Macromolecular Science Viewpoint: Enabling Advances in Fluorescence Microscopy Techniques

In the past few decades there has been a revolution in the field of optical microscopy with emerging capabilities such as super-resolution and single-molecule fluorescence techniques. Combined with the classical advantages of fluorescence imaging, such as chemical labeling specificity, and noninvasive sample preparation and imaging, these methods have enabled significant advances in our polymer community. This Viewpoint discusses several of these capabilities and how they can uniquely offer information where other characterization techniques are limited. Several examples are highlighted that demonstrate the ability of fluorescence microscopy to understand key questions in polymer science such as single-molecule diffusion and orientation, 3D nanostructural morphology, and interfacial and multicomponent dynamics. Finally, we briefly discuss opportunities for further advances in techniques that may allow them to make an even greater contribution in polymer science.

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.

Quantitative Comparison of Dye and Ultrasmall Fluorescent Silica Core-Shell Nanoparticle Probes for Optical Super-Resolution Imaging of Model Block Copolymer Thin Film Surfaces

In recent years, high-resolution optical imaging in the far field has provided opportunities for alternative approaches to nanocharacterization traditionally dominated by electron and scanning probe microscopies. Here, we report the optical super-resolution imaging of model block copolymer (BCP) thin film surface nanostructures through stochastic optical reconstruction microscopy (STORM). We compare a set of surface-functionalized fluorescent core-shell silica nanoparticles encapsulating two different organic dyes, Cy3 and Cy5, with the corresponding free dyes in STORM. Using various click-type chemistries, these probes are covalently attached to the surface of specific blocks of BCP thin films, enabling selective block labeling and optical visualization. We demonstrate that the enhanced brightness of these particle probes offers distinct advantages over conventional dye labeling, outperforming one of the best STORM dyes available (Cy5).

Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion

We developed transmission diffraction grating-based spectroscopic single-molecule localization microscopy (sSMLM) to collect the spatial and spectral information of single-molecule blinking events concurrently. We characterized the spectral heterogeneities of multiple far-red emitting dyes in a high-throughput manner using sSMLM. We also investigated the influence of spectral dispersion on the single-molecule identification performance of fluorophores with large spectral overlapping. The careful tuning of spectral dispersion in grating-based sSMLM permitted simultaneous three-color super-resolution imaging in fixed cells with a single objective lens at a relatively low photon budget. Our sSMLM has a compact optical design and can be integrated with conventional localization microscopy to provide add-on spectroscopic analysis capability.

Super-resolution Imaging of Proton Sponge-Triggered Rupture of Endosomes and Cytosolic Release of Small Interfering RNA

The intracellular delivery of nucleic acids and proteins remains a key challenge in the development of biological therapeutics. In gene therapy, the inefficient delivery of small interfering RNA (siRNA) to the cytosol by lipoplexes or polyplexes is often ascribed to the entrapment and degradation of siRNA payload in the endosomal compartments. A possible mechanism by which polyplexes rupture the endosomal membrane and release their nucleic acid cargo is commonly defined as the "proton sponge effect". This is an osmosis-driven process triggered by the proton buffering capacity of polyplexes. Herein, we investigate the molecular basis of the "proton sponge effect" through direct visualization of the siRNA trafficking process, including analysis of individual polyplexes and endosomes, using stochastic optical reconstruction microscopy. We probe the sequential siRNA trafficking steps through single molecule super-resolution analysis of subcellular structures, polyplexes, and silencing RNA molecules. Specifically, individual intact polyplexes released in the cytosol upon rupture of the endosomes, the damaged endosomal vesicles, and the disassembly of the polyplexes in the cytosol are examined. We find that the architecture of the polyplex and the rigidity of the cationic polymer chains are crucial parameters that control the mechanism of endosomal escape driven by the proton sponge effect. We provide evidence that in highly branched and rigid cationic polymers, such as glycogen or polyethylenimine, immobilized on silica nanoparticles, the proton sponge effect is effective in inducing osmotic swelling and rupture of endosomes.

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.

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.

Spectroscopic analysis beyond the diffraction limit

The recent surge in spectroscopic Single-Molecule Localization Microscopy (sSMLM) offers exciting new capabilities for combining single molecule imaging and spectroscopic analysis. Through the synergistic integration of super-resolution optical microscopy and single-molecule spectroscopy, sSMLM offers combined strengths from both fields. By capturing the full spectra of single molecule fluorescent emissions, sSMLM can distinguish minute spectroscopic variations from individual fluorescent molecules while preserving nanoscopic spatial localization precision. It can significantly extend the coding space for multi-molecule super-resolution imaging. Furthermore, it has the potential to detect spectroscopic variations in fluorescence emission associated with molecular interactions, which further enables probing local chemical and biochemical inhomogeneities of the nano-environments. In this review, we seek to explain the working principle of sSMLM technologies and the status of sSMLM techniques towards new super-resolution imaging applications.

Spatial and spectral imaging of point-spread functions using a spatial light modulator

We develop a point-spread function (PSF) engineering approach to imaging the spatial and spectral information of molecular emissions using a spatial light modulator (SLM). We show that a dispersive grating pattern imposed upon the emission reveals spectral information. We also propose a deconvolution model that allows the decoupling of the spectral and 3D spatial information in engineered PSFs. The work is readily applicable to single-molecule measurements and fluorescent microscopy.

Super-Resolution Imaging and Plasmonics

This review describes the growing partnership between super-resolution imaging and plasmonics, by describing the various ways in which the two topics mutually benefit one another to enhance our understanding of the nanoscale world. First, localization-based super-resolution imaging strategies, where molecules are modulated between emissive and nonemissive states and their emission localized, are applied to plasmonic nanoparticle substrates, revealing the hidden shape of the nanoparticles while also mapping local electromagnetic field enhancements and reactivity patterns on their surface. However, these results must be interpreted carefully due to localization errors induced by the interaction between metallic substrates and single fluorophores. Second, plasmonic nanoparticles are explored as image contrast agents for both superlocalization and super-resolution imaging, offering benefits such as high photostability, large signal-to-noise, and distance-dependent spectral features but presenting challenges for localizing individual nanoparticles within a diffraction-limited spot. Finally, the use of plasmon-tailored excitation fields to achieve subdiffraction-limited spatial resolution is discussed, using localized surface plasmons and surface plasmon polaritons to create confined excitation volumes or image magnification to enhance spatial resolution.

Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast

Visualizing the nanoscale intracellular structures formed by nucleic acids, such as chromatin, in nonperturbed, structurally and dynamically complex cellular systems, will help expand our understanding of biological processes and open the next frontier for biological discovery. Traditional superresolution techniques to visualize subdiffractional macromolecular structures formed by nucleic acids require exogenous labels that may perturb cell function and change the very molecular processes they intend to study, especially at the extremely high label densities required for superresolution. However, despite tremendous interest and demonstrated need, label-free optical superresolution imaging of nucleotide topology under native nonperturbing conditions has never been possible. Here we investigate a photoswitching process of native nucleotides and present the demonstration of subdiffraction-resolution imaging of cellular structures using intrinsic contrast from unmodified DNA based on the principle of single-molecule photon localization microscopy (PLM). Using DNA-PLM, we achieved nanoscopic imaging of interphase nuclei and mitotic chromosomes, allowing a quantitative analysis of the DNA occupancy level and a subdiffractional analysis of the chromosomal organization. This study may pave a new way for label-free superresolution nanoscopic imaging of macromolecular structures with nucleotide topologies and could contribute to the development of new DNA-based contrast agents for superresolution imaging.

Super-resolution spectroscopic microscopy via photon localization

Traditional photon localization microscopy analyses only the spatial distributions of photons emitted by individual molecules to reconstruct super-resolution optical images. Unfortunately, however, the highly valuable spectroscopic information from these photons have been overlooked. Here we report a spectroscopic photon localization microscopy that is capable of capturing the inherent spectroscopic signatures of photons from individual stochastic radiation events. Spectroscopic photon localization microscopy achieved higher spatial resolution than traditional photon localization microscopy through spectral discrimination to identify the photons emitted from individual molecules. As a result, we resolved two fluorescent molecules, which were 15 nm apart, with the corresponding spatial resolution of 10 nm-a four-fold improvement over photon localization microscopy. Using spectroscopic photon localization microscopy, we further demonstrated simultaneous multi-colour super-resolution imaging of microtubules and mitochondria in COS-7 cells and showed that background autofluorescence can be identified through its distinct emission spectra.