Super-resolution microscopy with DNA-PAINT

A CRISPR/Cas13a system based on a dumbbell-shaped hairpin combined with DNA-PAINT to establish the DCP-platform for highly sensitive detection of Hantaan virus RNA

Rapid and sensitive detection of specific RNA sequences is crucial for clinical diagnosis, surveillance, and biotechnology applications. Currently, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the gold standard for RNA detection; however, it is associated with long processing time, complex procedures, and a high false-positive rate. To address these challenges, we developed a novel sensing platform based on CRISPR/Cas13a that incorporates a dumbbell-shaped hairpin and DNA-PAINT for rapid, highly specific, and sensitive RNA analysis. By leveraging the CRISPR/Cas13a system, this platform enables the cleavage of dumbbell-shaped hairpins, which subsequently allows the cleaved primers to initiate cyclic amplification of fluorescent signals. These signals are further enhanced by the binding and dissociation phenomena inherent to DNA-PAINT technology, ultimately achieving remarkable triple signal amplification. Additionally, the system effectively discriminates Hantaan virus RNA from Seoul virus in real samples. Importantly, the platform can be easily adapted for the detection of other RNAs by simply reconfiguring the hybridization region of crRNA. In conclusion, this platform represents a "five-in-one" RNA detection approach that integrates reliability, versatility, robustness, high specificity, and superior quantitative capabilities. It provides novel insights for direct RNA detection based on CRISPR/Cas13a and demonstrates significant potential for advancement in viral diagnostics.

DNA-PAINT Imaging with Hydrogel Imprinting and Clearing

Hydrogel-embedding is a versatile technique in fluorescence microscopy, offering stabilization, optical clearing, and the physical expansion of biological specimens. DNA-PAINT is a super-resolution microscopy approach based on the diffusion and transient binding of fluorescently labeled oligos, but its feasibility in hydrogels has not yet been explored. In this study, we demonstrate that polyacrylamide hydrogels support sufficient diffusion for effective DNA-PAINT imaging. Using acrydite-anchored oligonucleotides imprinted from patterned DNA origami nanostructures and microtubule filaments in fixed cells, we find that hydrogel embedding preserves docking strand positioning at the nanoscale. Sample clearing via protease treatment had minor structural effects on the microtubule structure and enhanced diffusion and accessibility to hydrogel-imprinted docking strands. Our work demonstrates promising potential for diffusion and binding-based fluorescence imaging applications in hydrogel-embedded samples.

Model-free machine learning-based 3D single molecule localisation microscopy

Single molecule localisation microscopy (SMLM) can provide two-dimensional super-resolved image data from conventional fluorescence microscopes, while three dimensional (3D) SMLM usually involves a modification of the microscope, for example, to engineer a predictable axial variation in the point spread function. Here we demonstrate a 3D SMLM approach (we call 'easyZloc') utilising a lightweight Convolutional Neural Network that is generally applicable, including with 'standard' (unmodified) fluorescence microscopes, and which we consider may be practically useful in a high throughput SMLM workflow. We demonstrate the reconstruction of nuclear pore complexes with comparable performance to previously reported methods but with a significant reduction in computational power and execution time. 3D reconstructions of the nuclear envelope and an actin sample over a larger axial range are also shown.

Spatial and stoichiometric in situ analysis of biomolecular oligomerization at single-protein resolution

Latest advances in super-resolution microscopy allow the study of subcellular features at the level of single proteins, which could lead to discoveries in fundamental biological processes, specifically in cell signaling mediated by membrane receptors. Despite these advances, accurately extracting quantitative information on molecular arrangements of proteins at the 1-20 nm scale through rigorous image analysis remains a significant challenge. Here, we present SPINNA (Single-Protein Investigation via Nearest-Neighbor Analysis): an analysis framework that compares nearest-neighbor distances from experimental single-protein position data with those obtained from realistic simulations based on a user-defined model of protein oligomerization states. We demonstrate SPINNA in silico, in vitro, and in cells. In particular, we quantitatively assess the oligomerization of the epidermal growth factor receptor (EGFR) upon EGF treatment and investigate the dimerization of CD80 and PD-L1, key surface ligands involved in immune cell signaling. Importantly, we offer an open-source Python implementation and a GUI to facilitate SPINNA's widespread use in the scientific community.

IFITM2 Modulates Endocytosis Maintaining Neural Stem Cells in Developing Neocortex

Brain development is orchestrated by a complex interplay of genetic and environmental signals, with endocytosis serving as a pivotal process in integrating extracellular cues. However, the specific role of endocytosis in neurogenesis remains unclear. We uncover a critical function of the interferon-induced transmembrane protein, IFITM2, essential for endocytic processes in radial glial cells (RGCs). IFITM2 is highly expressed near the ventricular surface in the developing brain. Loss of IFITM2 impairs endosome formation and disrupts RGC maintenance. Mechanistically, we confirmed that the YXXø endocytic motif on IFITM2 is essential for its subcellular localization, with mutations in this motif reducing endocytic vesicles. Additionally, the K82 and K87 residues of IFITM2 interact with phosphoinositides to promote endocytic vesicle formation. Polarized localization of phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) on the ventricular side suggests its role in vesicle formation. IFITM2 deficiency also leads to reduced phosphorylation of AKT and GSK3β. These findings highlight the essential role of IFITM2 in regulating endocytosis in RGCs, which is critical for maintaining neural stem cells and proper brain development, offering new insights into the connection between cellular signaling and neurogenesis in both mouse and human models.

Live imaging of the extracellular matrix with a glycan-binding fluorophore

All multicellular systems produce and dynamically regulate extracellular matrices (ECMs) that play essential roles in both biochemical and mechanical signaling. Though the spatial arrangement of these extracellular assemblies is critical to their biological functions, visualization of ECM structure is challenging, in part because the biomolecules that compose the ECM are difficult to fluorescently label individually and collectively. Here, we present a cell-impermeable small-molecule fluorophore, termed Rhobo6, that turns on and red shifts upon reversible binding to glycans. Given that most ECM components are densely glycosylated, the dye enables wash-free visualization of ECM, in systems ranging from in vitro substrates to in vivo mouse mammary tumors. Relative to existing techniques, Rhobo6 provides a broad substrate profile, superior tissue penetration, non-perturbative labeling, and negligible photobleaching. This work establishes a straightforward method for imaging the distribution of ECM in live tissues and organisms, lowering barriers for investigation of extracellular biology.

MINFLUX nanoscopy: Visualising biological matter at the nanoscale level

Since its introduction in 2017, MINFLUX nanoscopy has shown that it can visualise fluorescent molecules with an exceptional localisation precision of a few nanometres. In this overview, we provide a brief insight into technical implementations, fluorescent marker developments and biological studies that have been conducted in connection with MINFLUX imaging and tracking. We also formulate ideas on how MINFLUX nanoscopy and derived technologies could influence bioimaging in the future. This insight is intended as a general starting point for an audience looking for a brief overview of MINFLUX nanoscopy from theory to application.

Advancements in fluorescent nanobiosensors for HPV detection: from integrating nanomaterials to DNA nanotechnology

Human papillomavirus (HPV) is a leading cause of cervical cancer and other malignancies, necessitating the development of highly sensitive and specific detection tools. This review explores recent advancements in fluorescent nanobiosensors (FNBS) for HPV detection, focusing on the integration of nanomaterials and DNA nanotechnology, highlighting their contributions to improving sensitivity, specificity, and point-of-care (POC) usability. The review critically evaluates a range of nanomaterial-based FNBS, including those employing quantum and carbon dots, nanoclusters, nanosheets, and nanoparticles, discussing their underlying signal amplification mechanisms, target recognition strategies, and limitations related to toxicity, stability, and reproducibility. Furthermore, it examines the application of diverse DNA nanotechnology, such as DNA origami, DNAzyme, catalytic hairpin assembly (CHA), hybridization chain reaction (HCR), and DNA hydrogel in improving FNBS performance. It also addresses the current challenges in clinical translation, emphasizing the necessity for large-scale production methods and thorough clinical validation to ensure biosafety. It also outlines the potential of innovative technologies, such as CRISPR-Cas-based diagnostics and artificial intelligence, to further revolutionize HPV detection and enable accessible, cost-effective screening, particularly in resource-limited settings. This review provides a valuable resource for researchers and clinicians seeking to develop next-generation FNBS for improved HPV diagnostics and cervical cancer prevention.

Effects of DNA Origami-Based Nanoagent Design on Apoptosis Induction in a Large 3D Cancer Spheroid Model

DNA origami offers highly accurate control over shape and addressability on the nanoscale. This precise control makes it highly valuable in various fields, particularly precision nanotherapeutics. For cancer treatment, the extrinsic activation of programmed cell death by Fas receptor (FasR)/CD95-based nanoagents is a promising, minimally invasive strategy. However, treating large, solid tumors poses challenges for the design of DNA origami-based therapeutics, including drug distribution and altered cellular behavior. Here, these challenges are addressed by establishing design principles for nanoagents and testing them in a 3D cancer spheroid model. First, the ability of DNA origami nanostructures are assessed to penetrate large cancer spheroids, finding that penetration is influenced by the DNA origami size rather than its structural flexibility. Second, the capability of FasL-DNA origami-based nanoagents are evaluated to induce apoptosis in cancer spheroids, representing a more biologically relevant environment, compared to 2D studies. It is found that apoptosis induction is primarily determined by the FasL attachment strategy rather than the underlying DNA origami structure. The most effective nanoagents constructed in this study halted spheroid growth and eradicated all cancer cells within the spheroids. This study offers important insights into critical design considerations for DNA-based therapeutics for complex cellular environments, advancing DNA origami nanotherapeutic development.

Single Molecule Localization Super-resolution Dataset for Deep Learning with Paired Low-resolution Images

Deep learning super-resolution microscopy has advanced rapidly in recent years. Super-resolution images acquired by single molecule localization microscopy (SMLM) are ideal sources for high-quality datasets. However, the scarcity of public datasets limits the development of deep learning methods. Here, we describe a biological image dataset, DL-SMLM, which provides paired low-resolution fluorescence images and super-resolution SMLM data for training super-resolution models. DL-SMLM consists of six different subcellular structures, including microtubules, lumen and membrane of endoplasmic reticulum (ER), Clathrin coated pits (CCPs), outer membrane of mitochondria (OMM) and inner membrane of mitochondria (IMM). There are 188 sets of raw SMLM data and 100 signal levels for each low-resolution image. This allows software developers to generate thousands of training pairs through data segmentation. The performance of the imaging system was further evaluated using DNA origami samples. Finally, we demonstrated examples of super-resolution models trained using data from DL-SMLM, highlighting the effectiveness of DL-SMLM for developing deep learning super-resolution microscopy.

A method for site-specifically tethering the enzyme urease to DNA origami with sustained activity

Attaching enzymes to nanostructures has proven useful to the study of enzyme functionality under controlled conditions and has led to new technologies. Often, the utility and interest of enzyme-tethered nanostructures lie in how the enzymatic activity is affected by how the enzymes are arranged in space. Therefore, being able to conjugate enzymes to nanostructures while preserving the enzymatic activity is essential. In this paper, we present a method to conjugate single-stranded DNA to the enzyme urease while maintaining enzymatic activity. We show evidence of successful conjugation and quantify the variables that affect the conjugation yield. We also show that the enzymatic activity is unchanged after conjugation compared to the enzyme in its native state. Finally, we demonstrate the tethering of urease to nanostructures made using DNA origami with high site-specificity. Decorating nanostructures with enzymatically-active urease may prove to be useful in studying, or even utilizing, the functionality of urease in disciplines ranging from biotechnology to soft-matter physics. The techniques we present in this paper will enable researchers across these fields to modify enzymes without disrupting their functionality, thus allowing for more insightful studies into their behavior and utility.

The nucleoid of rapidly growing Escherichia coli localizes close to the inner membrane and is organized by transcription, translation, and cell geometry

Bacterial chromosomes are spatiotemporally organized and sensitive to environmental changes. However, the mechanisms underlying chromosome configuration and reorganization are not fully understood. Here, we use single-molecule localization microscopy and live-cell imaging to show that the Escherichia coli nucleoid adopts a condensed, membrane-proximal configuration during rapid growth. Drug treatment induces a rapid collapse of the nucleoid from an apparently membrane-bound state within 10 min of halting transcription and translation. This hints toward an active role of transertion (coupled transcription, translation, and membrane insertion) in nucleoid organization, while cell wall synthesis inhibitors only affect nucleoid organization during morphological changes. Further, we provide evidence that the nucleoid spatially correlates with elongasomes in unperturbed cells, suggesting that large membrane-bound complexes might be hotspots for transertion. The observed correlation diminishes in cells with changed cell geometry or upon inhibition of protein biosynthesis. Replication inhibition experiments, as well as multi-drug treatments highlight the role of entropic effects and transcription in nucleoid condensation and positioning. Thus, our results indicate that transcription and translation, possibly in the context of transertion, act as a principal organizer of the bacterial nucleoid, and show that an altered metabolic state and antibiotic treatment lead to major changes in the spatial organization of the nucleoid.

One-click image reconstruction in single-molecule localization microscopy via deep learning

Deep neural networks have led to significant advancements in microscopy image generation and analysis. In single-molecule localization based super-resolution microscopy, neural networks are capable of predicting fluorophore positions from high-density emitter data, thus reducing acquisition time, and increasing imaging throughput. However, neural network-based solutions in localization microscopy require intensive human intervention and computation expertise to address the compromise between model performance and its generalization. For example, researchers manually tune parameters to generate training images that are similar to their experimental data; thus, for every change in the experimental conditions, a new training set should be manually tuned, and a new model should be trained. Here, we introduce AutoDS and AutoDS3D, two software programs for reconstruction of single-molecule super-resolution microscopy data that are based on Deep-STORM and DeepSTORM3D, that significantly reduce human intervention from the analysis process by automatically extracting the experimental parameters from the imaging raw data. In the 2D case, AutoDS selects the optimal model for the analysis out of a set of pre-trained models, hence, completely removing user supervision from the process. In the 3D case, we improve the computation efficiency of DeepSTORM3D and integrate the lengthy workflow into a graphic user interface that enables image reconstruction with a single click. Ultimately, we demonstrate superior performance of both pipelines compared to Deep-STORM and DeepSTORM3D for single-molecule imaging data of complex biological samples, while significantly reducing the manual labor and computation time.

A Bayesian Model to Count the Number of Two-State Emitters in a Diffraction Limited Spot

We address the problem of inferring the number of independently blinking fluorescent light emitters, when only their combined intensity contributions can be observed. This problem occurs regularly in light microscopy of objects smaller than the diffraction limit, where one wishes to count the number of fluorescently labeled subunits. Our proposed solution directly models the photophysics of the system, as well as the blinking kinetics of the fluorescent emitters as a fully differentiable hidden Markov model, estimating a posterior distribution of the total number of emitters. We show that our model is more accurate and increases the range of countable subunits by a factor of 2 compared to current state-of-the-art methods. Furthermore, we demonstrate that our model can be used to investigate the effect of blinking kinetics on counting ability and therefore can inform optimal experimental conditions.

High-Throughput Single-Molecule Microscopy with Adaptable Spatial Resolution Using Exchangeable Oligonucleotide Labels

Super-resolution microscopy facilitates the visualization of cellular structures at a resolution approaching the molecular level. Especially, super-resolution techniques based on the localization of single molecules have relatively modest instrument requirements and are thus good candidates for adoption in bioimaging. However, their low-throughput nature hampers their applicability in biomolecular research and screening. Here, we propose a workflow for more efficient data collection, starting with the scanning of large areas using fast fluctuation-based imaging, followed by single-molecule localization microscopy of selected cells. To achieve this workflow, we exploit the versatility of DNA oligo hybridization kinetics with DNA-PAINT probes to tailor the fluorescent blinking toward high-throughput and high-resolution imaging. Additionally, we employ super-resolution optical fluctuation imaging (SOFI) to analyze statistical fluctuations in the DNA-PAINT binding kinetics, thereby tolerating much denser blinking and facilitating accelerated imaging speeds. Thus, we demonstrate 30-300-fold faster imaging of different cellular structures compared to conventional DNA-PAINT imaging, albeit at a lower resolution. Notably, by tuning the image medium and data processing though, we can flexibly switch between high-throughput SOFI (scanning an FOV of 0.65 mm × 0.52 mm within 4 min of total acquisition time) and super-resolution DNA-PAINT microscopy and thereby demonstrate that combining DNA-PAINT and SOFI enables one to adapt image resolution and acquisition time based on the imaging needs. We envision this approach to be especially powerful when combined with multiplexing and 3D imaging.

Engineering a custom-sized DNA scaffold for more efficient DNA origami-based nucleic acid data storage

DNA has emerged as a promising material to address growing data storage demands. We recently demonstrated a structure-based DNA data storage approach where DNA probes are spatially oriented on the surface of DNA origami and decoded using DNA-PAINT. In this approach, larger origami structures could improve the efficiency of reading and writing data. However, larger origami require long single-stranded DNA scaffolds that are not commonly available. Here, we report the engineering of a novel longer DNA scaffold designed to produce a larger rectangle origami needed to expand the origami-based digital nucleic acid memory (dNAM) approach. We confirmed that this scaffold self-assembled into the correct origami platform and correctly positioned DNA data strands using atomic force microscopy and DNA-PAINT super-resolution microscopy. This larger structure enables a 67% increase in the number of data points per origami and will support efforts to efficiently scale up origami-based dNAM.

Redox signaling modulates axonal microtubule organization and induces a specific phosphorylation signature of microtubule-regulating proteins

Many life processes are regulated by physiological redox signaling, but excessive oxidative stress can damage biomolecules and contribute to disease. Neuronal microtubules are critically involved in axon homeostasis, regulation of axonal transport, and neurodegenerative processes. However, whether and how physiological redox signaling affects axonal microtubules is largely unknown. Using live cell imaging and super-resolution microscopy, we show that subtoxic concentrations of the central redox metabolite hydrogen peroxide increase axonal microtubule dynamics, alter the structure of the axonal microtubule array, and affect the efficiency of axonal transport. We report that the mitochondria-targeting antioxidant SkQ1 and the microtubule stabilizer EpoD abolish the increase in microtubule dynamics. We found that hydrogen peroxide specifically modulates the phosphorylation state of microtubule-regulating proteins, which differs from arsenite as an alternative stress inducer, and induces a largely non-overlapping phosphorylation pattern of MAP1B as a main target. Cell-wide phosphoproteome analysis revealed signaling pathways that are inversely activated by hydrogen peroxide and arsenite. In particular, hydrogen peroxide treatment was associated with kinases that suppress apoptosis and regulate brain metabolism (PRKDC, CK2, PDKs), suggesting that these pathways play a central role in physiological redox signaling and modulation of axonal microtubule organization. The results suggest that the redox metabolite and second messenger hydrogen peroxide induces rapid and local reorganization of the microtubule array in response to mitochondrial activity or as a messenger from neighboring cells by activating specific signaling cascades.

Advanced fluorescence lifetime-enhanced multiplexed nanoscopy of cells

In this review paper, we summarize the significant advancements in the field of fluorescence lifetime imaging microscopy (FLIM), particularly wide-field FLIM with single-molecule sensitivity, achieved using the time-correlated single-photon counting-based position-sensitive LINCam system. Fluorescence lifetime adds valuable information beyond conventional intensity-based imaging, enabling diverse applications across research fields. Here, we focus on three primary bioimaging applications: (I) single-molecule FLIM in the far-red spectral region, (II) fast and multiplexed super-resolution imaging of cells, and (III) three-dimensional super-resolution imaging with high axial localization precision. Recent advances in position-sensitive detector technologies offer exciting opportunities for high-throughput super-resolution imaging with enhanced localization precision.

ATG2A engages Rab1a and ARFGAP1 positive membranes during autophagosome biogenesis

Autophagosomes form from seed membranes that expand through bulk-lipid transport via the bridge-like lipid transporter ATG2. The origins of the seed membranes and their relationship to the lipid transport machinery are poorly understood. Using proximity labeling and a variety of fluorescence microscopy techniques, we show that ATG2A localizes to extra-Golgi ARFGAP1 puncta during autophagosome biogenesis. ARFGAP1 itself is dispensable during macroautophagy, but among other proteins associating to these membranes, we find that Rab1 is essential. ATG2A co-immunoprecipitates strongly with Rab1a, and siRNA-mediated depletion of Rab1 blocks autophagy downstream of LC3B lipidation, similar to ATG2A depletion. Further, when either autophagosome formation or the early secretory pathway is perturbed, ARFGAP1 and Rab1a accumulate at ectopic locations with autophagic machinery. Our results suggest that ATG2A engages a Rab1a complex on select early secretory membranes at an early stage in autophagosome biogenesis.

Protocol for SUM-PAINT spatial proteomic imaging generating neuronal architecture maps in rat hippocampal neurons

To unravel the complexity of biological processes, it is necessary to resolve the underlying protein organization down to single proteins. Here, we present a protocol for secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a DNA-PAINT-based super-resolution microscopy technique that is capable of resolving virtually unlimited protein species with single-protein resolution. We describe the steps to prepare neuronal cultures, troubleshoot and conduct SUM-PAINT experiments, and analyze the resulting feature-rich neuronal cell atlases using unsupervised machine learning approaches. For complete details on the use and execution of this protocol, please refer to Unterauer et al.1.

Three-color single-molecule localization microscopy in chromatin

Super-resolution microscopy has revolutionized our ability to visualize structures below the diffraction limit of conventional optical microscopy and is particularly useful for investigating complex biological targets like chromatin. Chromatin exhibits a hierarchical organization with structural compartments and domains at different length scales, from nanometers to micrometers. Single molecule localization microscopy (SMLM) methods, such as STORM, are essential for studying chromatin at the supra-nucleosome level due to their ability to target epigenetic marks that determine chromatin organization. Multi-label imaging of chromatin is necessary to unpack its structural complexity. However, these efforts are challenged by the high-density nuclear environment, which can affect antibody binding affinities, diffusivity and non-specific interactions. Optimizing buffer conditions, fluorophore stability, and antibody specificity is crucial for achieving effective antibody conjugates. Here, we demonstrate a sequential immunolabeling protocol that reliably enables three-color studies within the dense nuclear environment. This protocol couples multiplexed localization datasets with a robust analysis algorithm, which utilizes localizations from one target as seed points for distance, density and multi-label joint affinity measurements to explore complex organization of all three targets. Applying this multiplexed algorithm to analyze distance and joint density reveals that heterochromatin and euchromatin are not-distinct territories, but that localization of transcription and euchromatin couple with the periphery of heterochromatic clusters. This work is a crucial step in molecular imaging of the dense nuclear environment as multi-label capacity enables for investigation of complex multi-component systems like chromatin with enhanced accuracy.

Oxygen-excluded nanoimaging of polymer blend films

Polymer blend films exhibit unique properties and have applications in various fields. However, understanding their nanoscale structures and polymer component distributions remains a challenge. To address this limitation, we have developed a super-resolution fluorescence microscopy-based technique called oxygen-excluded nanoimaging. By using point accumulation for imaging in nanoscale topography with sulfonate-based dye molecules, we achieved nanoscale imaging of polymer blend films while specifically labeling non-oxygen domains and excluding oxygen-containing domains. This selectivity is attributed to the electrostatic repulsion between the negatively charged sulfonate groups in the dye molecules and the oxygen atoms in the polymer side chains. We demonstrate the applicability of oxygen-excluded nanoimaging to various polymer blend films, enabling domain identification and visualization of nanoscale structures. Our oxygen-excluded nanoimaging technique provides unique insights into the complex phase separation behavior of polymer blends at the nanoscale, opening possibilities for the nanoscale characterization of a wide range of materials beyond polymer blends.

Emerging protein sequencing technologies: proteomics without mass spectrometry?

INTRODUCTION

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics for 30 years. Advantages provided by LC-MS/MS are offset by significant disadvantages, including cost. Recently, several non-mass spectrometric methods have emerged, but little information is available about their capacity to analyze the complex mixtures routine for mass spectrometry.

AREAS COVERED

We review recent non-mass-spectrometric methods for sequencing proteins and peptides, including those using nanopores, sequencing by degradation, reverse translation, and short-epitope mapping, with comments on bioinformatics challenges, fundamental limitations, and areas where new technologies will be more or less competitive with LC-MS/MS. In addition to conventional literature searches, instrument vendor websites, patents, webinars, and preprints were also consulted to give a more up-to-date picture.

EXPERT OPINION

Many new technologies are promising. However, demonstrations that they outperform mass spectrometry in terms of peptides and proteins identified have not yet been published, and astute observers note important disadvantages, especially relating to the dynamic range of single-molecule measurements of complex mixtures. Still, even if the performance of emerging methods proves inferior to LC-MS/MS, their low cost could create a different kind of revolution: a dramatic increase in the number of biology laboratories engaging in new forms of proteomics research.

Subcellular dynamics in unicellular parasites

Bioimaging has made tremendous advances in this century. Innovations in high- and super-resolution microscopy are well established, and live-cell imaging is extensively used to gain an overview of dynamic processes. But the combination of high spatial and temporal resolution necessary to capture intracellular dynamics is rarely achieved. Further, efficient software pipelines - that can handle the recorded data and allow comprehensive analyses - are being developed but lag behind other technical innovations in applicability for broad groups of researchers. Especially in parasites, which offer great potential for studying subcellular dynamics, the possibilities have only begun to be probed. In all cases, the complete description of dynamic molecular movement in 3D space remains a challenging necessity.

Molecular Determinants of Protein Pathogenicity at the Single-Aggregate Level

Determining the structure-function relationships of protein aggregates is a fundamental challenge in biology. These aggregates, whether formed in vitro, within cells, or in living organisms, present significant heterogeneity in their molecular features such as size, structure, and composition, making it difficult to determine how their structure influences their functions. Interpreting how these molecular features translate into functional roles is crucial for understanding cellular homeostasis and the pathogenesis of various debilitating diseases like Alzheimer's and Parkinson's. In this study, a bottom-up approach is introduced to explore how variations in protein aggregates' size, composition, post-translational modifications and point mutations profoundly influence their biological functions. Applying this method to Alzheimer's and Parkinson's associated proteins, novel disease-relevant pathways are uncovered, demonstrating how subtle alterations in composition and morphology can shift the balance between healthy and pathological states. This findings provide deeper insights into the molecular basis of protein's functions at the single-aggregate level, enhancing the knowledge of their roles in health and disease.

Single Objective Light Sheet Microscopy allows high-resolution in vivo brain imaging of Drosophila

In vivo imaging of dynamic sub-cellular brain structures in Drosophila melanogaster is key to understanding several phenomena in neuroscience. However, its implementation has been hindered by a trade-off between spatial resolution, speed, photobleaching, phototoxicity, and setup complexity required to access the specific target regions of the small brain of Drosophila . Here, we present a single objective light-sheet microscope, customized for in vivo imaging of adult flies and optimized for maximum resolution. With it, we imaged the axonal projections of small lateral ventral neurons (known as s-LNvs) in intact adult flies. We imaged the plasma membrane, mitochondria, and dense-core vesicles with high spatial resolution up to 370 nm, ten times lower photobleaching than confocal microscopy, lower invasiveness and complexity in sample mounting than alternative light-sheet technologies, and without relying on phototoxic pulsed infrared lasers. This unique set of features paves the way for new long-term, dynamic studies in the brains of living flies.

Nanosized core-shell bio-hybrid microgels and their internal structure

Microgels are versatile materials with applications across biomedicine, materials science, and beyond. Their controllable size and composition enables tailoring specific properties, yet characterizing their internal structures on the nanoscale remains challenging. Super-resolution fluorescence microscopy (SRFM) effectively analyzes sub-μm structures, including microgels, offering a tool for investigating more complex systems such as core-shell microgels. Understanding their internal structure, in particular interpenetration at the soft-soft interface between core and shell and accessibility for guest molecules, is vital for rationally designing predictable functionalities. This study examines the core-shell morphology and the accessibility for guest molecules of bio-hybrid DNA-poly(N-isopropylmethacrylamide) microgels at three stages of shell polymerization using SRFM. Covalent fluorescence labeling probes the core polymer, co-polymerized with N,N'-bis(acryloyl)cystamine, which provides visual insight into core and shell compartmentalization. The results demonstrate core polymer interpenetration into the shell without compromising its original structure, and additionally allow us to determine the size- and hydrophobicity dependent accessibility of the microgel core. This, offering new perspectives on the internal architecture of core-shell microgels, contributes to the in-depth understanding of their complex behavior, potentially guiding the rational design of new microgel drug delivery systems, taking into account the complex interplay of polarity, size and charge of guest molecules.

Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues

DNA-PAINT enables nanoscale imaging with virtually unlimited multiplexing and molecular counting. Here, we address challenges, such as variable imaging performance and target accessibility, that can limit its broader applicability. Specifically, we enhance its capacity for robust single-protein imaging and molecular counting by optimizing the integration of TIRF microscopy with physical sectioning, in particular, Tokuyasu cryosectioning. Our method, tomographic & kinetically enhanced DNA-PAINT (tkPAINT), achieves 3 nm localization precision across diverse samples, enhanced imager binding, and improved cellular integrity. tkPAINT can facilitate molecular counting with DNA-PAINT inside the nucleus, as demonstrated through its quantification of the in situ abundance of RNA Polymerase II in both HeLa cells as well as mouse tissues. Anticipating that tkPAINT could become a versatile tool for the exploration of biomolecular organization and interactions across cells and tissues, we also demonstrate its capacity to support multiplexing, multimodal targeting of proteins and nucleic acids, and 3D imaging.

Data Readout Techniques for DNA-Based Information Storage

DNA is a natural chemical substrate that carries genetic information, which also serves as a powerful toolkit for storing digital data. Compared to traditional storage media, DNA molecules offer higher storage density, longer lifespan, and lower maintenance energy consumption. In DNA storage process, data readout is a critical step that bridges the gap between DNA molecular/structures with stored digital information. With the continued development of strategies in DNA data storage technology, the readout techniques have evolved. However, there is a lack of systematic introduction and discussion on the readout techniques for reported DNA data storage systems, especially the correlation between the design of the data storage system and the corresponding selection of readout techniques. This review first introduces two main categories of DNA data storage units (i.e., sequence and structure) and their corresponding readout techniques (i.e., sequencing and nonsequencing methods), and then reviewed representative examples of notable advancements in DNA data storage technology, focusing on data storage unit design, and readout technique selection. It also introduces emerging approaches to assist data readout techniques, such as implementation of microfluidic and fluorescent probes. Finally, the paper discusses the limitations, challenges, and potential of DNA data readout approaches.

Nanoscale Cellular Traction Force Quantification: CRISPR-Cas12a Supercharged DNA Tension Sensors in Nanoclustered Ligand Patterns

High-throughput measurement of cellular traction forces at the nanoscale remains a significant challenge in mechanobiology, limiting our understanding of how cells interact with their microenvironment. Here, we present a novel technique for fabricating protein nanopatterns in standard multiwell microplate formats (96/384-wells), enabling the high-throughput quantification of cellular forces using DNA tension gauge tethers (TGTs) amplified by CRISPR-Cas12a. Our method employs sparse colloidal lithography to create nanopatterned surfaces with feature sizes ranging from sub 100 to 800 nm on transparent, planar, and fully PEGylated substrates. These surfaces allow for the orthogonal immobilization of two different proteins or biomolecules using click-chemistry, providing precise spatial control over cellular signaling cues. We demonstrate the robustness and versatility of this platform through imaging techniques, including total internal reflection fluorescence microscopy, confocal laser scanning microscopy, and high-throughput imaging. Applying this technology, we measured the early stage mechanical forces exerted by 3T3 fibroblasts across different nanoscale features, detecting forces ranging from 12 to 56 pN. By integrating the Mechano-Cas12a Assisted Tension Sensor (MCATS) system, we achieved rapid and high-throughput quantification of cellular traction forces, analyzing over 2 million cells within minutes. Our findings reveal that nanoscale clustering of integrin ligands significantly influences the mechanical responses of cells. This platform offers a powerful tool for mechanobiology research, facilitating the study of cellular forces and mechanotransduction pathways in a high-throughput manner compatible with standard cell culture systems.

Chromato-kinetic fingerprinting enables multiomic digital counting of single disease biomarker molecules

Early and personalized intervention in complex diseases requires robust molecular diagnostics, yet the simultaneous detection of diverse biomarkers-microRNAs (miRNAs), mutant DNAs, and proteins-remains challenging due to low abundance and preprocessing incompatibilities. We present Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE), a next-generation, triple-modality, multiplexed detection platform that integrates both chromatic and kinetic fingerprinting for molecular profiling through digital encoding. Bio-SCOPE achieves femtomolar sensitivity, single-base mismatch specificity, and minimal matrix interference, enabling precise, parallel quantification of up to six biomarkers in a single sample with single-molecule resolution. We demonstrate its versatility in accurately detecting low-abundance miRNA signatures from human tissues, identifying upregulated miRNAs in the plasma of prostate cancer patients, and measuring elevated interleukin-6 (IL-6) and hsa-miR-21 levels in cytokine release syndrome patients. By seamlessly integrating multiomic biomarker panels on a unified, high-precision platform, Bio-SCOPE provides a transformative tool for molecular diagnostics and precision medicine.

Monitoring Dynamic Conformations of a Single Fluorescent Molecule Inside a Protein Cavity

Fluorescence nanoscopy and single-molecule methods are entering the realm of structural biology, breaking new ground for dynamic structural measurements at room temperature and liquid environments. Here, single-molecule localization microscopy, polarization-dependent single-molecule excitation, and protein engineering are combined to determine the orientation of a fluorophore forming hydrogen bonds inside a protein cavity. The observed conformations are in good agreement with molecular dynamics simulations, enabling a new, more realistic interplay between experiments and simulations to identify stable conformations and the key interactions involved. Furthermore, jumps between conformations can be monitored with a precision of 3° and a time resolution of a few seconds, confirming the potential of this methodology for retrieving dynamic structural information of nanoscopic biological systems under physiologically compatible conditions.

Trans-synaptic molecular context of NMDA receptor nanodomains

Tight coordination of the spatial relationships between protein complexes is required for cellular function. In neuronal synapses, many proteins responsible for neurotransmission organize into subsynaptic nanoclusters whose trans-cellular alignment modulates synaptic signal propagation. However, the spatial relationships between these proteins and NMDA receptors (NMDARs), which are required for learning and memory, remain undefined. Here, we mapped the relationship of key NMDAR subunits to reference proteins in the active zone and postsynaptic density using multiplexed super-resolution DNA-PAINT microscopy. GluN2A and GluN2B subunits formed nanoclusters with diverse configurations that, surprisingly, were not localized near presynaptic vesicle release sites marked by Munc13-1. Despite this, we found a subset of release sites was enriched with NMDARs, and modeling of glutamate release and receptor activation in measured synapses indicated this nanotopography promotes NMDAR activation. This subset of release sites was internally denser with Munc13-1, aligned with abundant PSD-95, and associated closely with specific NMDAR nanodomains. Further, NMDAR activation drove rapid reorganization of this release site/receptor relationship, suggesting a structural mechanism for tuning NMDAR-mediated synaptic transmission. This work reveals a new principle regulating NMDAR signaling and suggests that synaptic functional architecture depends on the assembly of and trans-cellular spatial relationships between multiprotein nanodomains.

A Versatile Drift-Free Super-Resolution Imaging Method via Oblique Bright-Field Correlation

High-resolution optical microscopy, particularly super-resolution localization microscopy, requires precise real-time drift correction to maintain constant focus at nanoscale precision during the prolonged data acquisition. Existing methods, such as fiducial marker tracking, reflection monitoring, and bright-field image correlation, each provide certain advantages but are limited in their broad applicability. In this work, a versatile and robust drift correction technique is presented for single-molecule localization-based super-resolution microscopy. It is based on the displacement analysis of bright-field image features of the specimen with oblique illumination. By leveraging the monotonic relationship between the displacement of image features and axial positions, this method can precisely measure the drift of the imaging system in real-time with sub-nanometer precision in all three dimensions, over a broad axial range, and for various samples, including those with closely matched refractive indices. The performance of this method is validated against conventional marker-assisted techniques and demonstrates its high precision in super-resolution imaging across various biological samples. This method paves the way for fully automated drift-free super-resolution imaging systems.

Understanding the molecular diversity of synapses

Synapses are composed of thousands of proteins, providing the potential for extensive molecular diversity to shape synapse type-specific functional specializations. In this Review, we explore the landscape of synaptic diversity and describe the mechanisms that expand the molecular complexity of synapses, from the genotype to the regulation of gene expression to the production of specific proteoforms and the formation of localized protein complexes. We emphasize the importance of examining every molecular layer and adopting a systems perspective to understand how these interconnected mechanisms shape the diverse functional and structural properties of synapses. We explore current frameworks for classifying synapses and methodologies for investigating different synapse types at varying scales, from synapse-type-specific proteomics to advanced imaging techniques with single-synapse resolution. We highlight the potential of synapse-type-specific approaches for integrating molecular data with cellular functions, circuit organization and organismal phenotypes to enable a more holistic exploration of neuronal phenomena across different scales.

Peptide nucleic acids: Recent advancements and future opportunities in biomedical applications

Peptide nucleic acids (PNA), synthetic molecules comprising a peptide-like backbone and natural and unnatural nucleobases, have garnered significant attention for their potential applications in gene editing and other biomedical fields. The unique properties of PNA, particularly enhanced stability/specificity/affinity towards targeted DNA and RNA sequences, achieved significant attention recently for gene silencing, gene correction, antisense therapy, drug delivery, biosensing and other various diagnostic aspects. This review explores the structure, properties, and potential of PNA in transforming genetic engineering including potent biomedical challenges. In Addition, we explore future perspectives and potential limitations of PNA-based technologies, highlighting the need for further research and development to fully realize their therapeutic and biotechnological potential.

Nanobody-Oligonucleotide Conjugates (NucleoBodies): The Next Frontier in Oligonucleotide Therapy

As of now, more than 15 oligonucleotide drugs, primarily small interfering RNAs and antisense oligonucleotide classes, have been approved by the US FDA for therapeutic use, and many more are under clinical trials. However, safe and effective delivery of the oligonucleotide-based drugs to the target tissue still remains a major challenge. For enhanced plasma half-life, effective endosomal release, and other multiple functionalities, various carrier molecules have been used over the years. The successful therapeutic application of antibody-drug conjugates has made antibodies a popular choice for the delivery of oligonucleotide payloads into the target tissues. Single-chain variable domains of heavy chain antibodies (nanobodies) have proven a promising alternative to antibodies in recent years due to their small size, high affinity for the target, cell-penetrating potency, simple and easy production. The present review highlights the oligonucleotide drug types and their conjugation with nanobodies called NucleoBodies for effective targeted delivery, detection and diagnostics.

Super-resolution imaging of proteins inside live mammalian cells with mLIVE-PAINT

Super-resolution microscopy has revolutionized biological imaging, enabling the visualization of structures at the nanometer length scale. Its application in live cells, however, has remained challenging. To address this, we adapted LIVE-PAINT, an approach we established in yeast, for application in live mammalian cells. Using the 101A/101B coiled-coil peptide pair as a peptide-based targeting system, we successfully demonstrate the super-resolution imaging of two distinct proteins in mammalian cells, one localized in the nucleus, and the second in the cytoplasm. This study highlights the versatility of LIVE-PAINT, suggesting its potential for live-cell super-resolution imaging across a range of protein targets in mammalian cells. We name the mammalian cell version of our original method mLIVE-PAINT.

Transplantation of gasdermin pores by extracellular vesicles propagates pyroptosis to bystander cells

Pyroptosis mediated by gasdermins (GSDMs) plays crucial roles in infection and inflammation. Pyroptosis triggers the release of inflammatory molecules, including damage-associated molecular patterns (DAMPs). However, the consequences of pyroptosis-especially beyond interleukin (IL)-1 cytokines and DAMPs-that govern inflammation are poorly defined. Here, we show intercellular propagation of pyroptosis from dying cells to bystander cells in vitro and in vivo. We identified extracellular vesicles (EVs) released by pyroptotic cells as the propagator of lytic death to naive cells, promoting inflammation. DNA-PAINT super-resolution and immunoelectron microscopy revealed GSDMD pore structures on EVs released by pyroptotic cells. Importantly, pyroptotic EVs transplant GSDMD pores on the plasma membrane of bystander cells and kill them. Overall, we demonstrate that cell-to-cell vesicular transplantation of GSDMD pores disseminates pyroptosis, revealing a domino-like effect governing disease-associated bystander cell death.

Immobile Integrin Signaling Transit and Relay Nodes Organize Mechanosignaling through Force-Dependent Phosphorylation in Focal Adhesions

Transmembrane signaling receptors, such as integrins, organize as nanoclusters that provide several advantages, including increasing avidity, sensitivity (increasing the signal-to-noise ratio), and robustness (signaling threshold) of the signal in contrast to signaling by single receptors. Furthermore, compared to large micron-sized clusters, nanoclusters offer the advantage of rapid turnover for the disassembly of the signal. However, whether nanoclusters function as signaling hubs remains poorly understood. Here, we employ fluorescence nanoscopy combined with photoactivation and photobleaching at subdiffraction limited resolution of ∼100 nm length scale within a focal adhesion to examine the dynamics of diverse focal adhesion proteins. We show that (i) subregions of focal adhesions are enriched in an immobile population of integrin β3 organized as nanoclusters, which (ii) in turn serve to organize nanoclusters of associated key adhesome proteins-vinculin, focal adhesion kinase (FAK) and paxillin, demonstrating that signaling proceeds by formation of nanoclusters rather than through individual proteins. (iii) Distinct focal adhesion protein nanoclusters exhibit distinct protein dynamics, which is closely correlated to their function in signaling. (iv) Long-lived nanoclusters function as signaling hubs─wherein immobile integrin nanoclusters organize phosphorylated FAK to form stable nanoclusters in close proximity to them, which are disassembled in response to inactivation signal by removal of force and in turn activation of phosphatase PTPN12. (v) Signaling takes place in response to external signals such as force or geometric arrangement of the nanoclusters and when the signal is removed, these nanoclusters disassemble. We term these functional nanoclusters as integrin signaling transit and relay nodes (STARnodes). Taken together, these results demonstrate that integrin STARnodes seed signaling downstream of the integrin receptors by organizing hubs of signaling proteins (FAK, paxillin, vinculin) to relay the incoming signal intracellularly and bring about robust function.

Leveraging Synthetic Antibody-DNA Conjugates to Expand the CRISPR-Cas12a Biosensing Toolbox

We report here the use of antibody-DNA conjugates (Ab-DNA) to activate the collateral cleavage activity of the CRISPR-Cas12a enzyme. Our findings demonstrate that Ab-DNA conjugates effectively trigger the collateral cleavage activity of CRISPR-Cas12a, enabling the transduction of antibody-mediated recognition events into fluorescence outputs. We developed two different immunoassays using an Ab-DNA as activator of Cas12a: the CRISPR-based immunosensing assay (CIA) for detecting SARS-CoV-2 spike S protein, which shows superior sensitivity compared with the traditional enzyme-linked immunosorbent assay (ELISA), and the CRISPR-based immunomagnetic assay (CIMA). Notably, CIMA successfully detected the SARS-CoV-2 spike S protein in undiluted saliva with a limit of detection (LOD) of 890 pM in a 2 h assay. Our results underscore the benefits of integrating Cas12a-based signal amplification with antibody detection methods. The potential of Ab-DNA conjugates, combined with CRISPR technology, offers a promising alternative to conventional enzymes used in immunoassays and could facilitate the development of versatile CRISPR analytical platforms for the detection of non-nucleic acid targets.

Unveiling nanoparticle-immune interactions: how super-resolution imaging illuminates the invisible

Nanoparticles (NPs) have attracted considerable attention in nanomedicine, particularly in harnessing and manipulating immune cells. However, the current understanding of the interactions between NPs and immune cells at the nanoscale remains limited. Advancing this knowledge guides the design principles of NPs. This review offers a historical perspective on the synergistic evolution of immunology and optical microscopy, examines the current landscape of NP applications in immunology, and explores the advancements in super-resolution imaging techniques, which provide new insights into nanoparticle-immune cell interactions. Key findings from recent studies are discussed, along with challenges and future directions in this rapidly evolving field.

Optimized molecule detection in localization microscopy with selected false positive probability

Single-molecule localization microscopy (SMLM) allows imaging beyond the diffraction limit. Detection of molecules is a crucial initial step in SMLM. False positive detections, which are not quantitatively controlled in current methods, are a source of artifacts that affect the entire SMLM analysis pipeline. Furthermore, current methods lack standardization, which hinders reproducibility. Here, we present an optimized molecule detection method which combines probabilistic thresholding with theoretically optimal filtering. The probabilistic thresholding enables control over false positive detections while optimal filtering minimizes false negatives. A theoretically optimal Poisson matched filter is used as a performance benchmark to evaluate existing filtering methods. Overall, our approach allows the detection of molecules in a robust, single-parameter and user-unbiased manner. This will minimize artifacts and enable data reproducibility in SMLM.

Decoding the molecular interplay of CD20 and therapeutic antibodies with fast volumetric nanoscopy

Elucidating the interaction between membrane proteins and antibodies requires whole-cell imaging at high spatiotemporal resolution. Lattice light-sheet (LLS) microscopy offers fast volumetric imaging but suffers from limited spatial resolution. DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT) achieves molecular resolution but is restricted to two-dimensional imaging owing to long acquisition times. We have developed two-dye imager (TDI) probes that enable ~15-fold faster imaging. Combining TDI-DNA-PAINT and LLS microscopy on immunological B cells revealed the oligomeric states and interaction of endogenous CD20 with the therapeutic monoclonal antibodies (mAbs) rituximab, ofatumumab, and obinutuzumab. Our results demonstrate that CD20 is abundantly expressed on microvilli that bind mAbs, which leads to an antibody concentration-dependent B cell polarization and stabilization of microvilli protrusions. These findings could aid rational design of improved immunotherapies targeting tumor-associated antigens.

Super-Resolved Fluorescence Lifetime Imaging of Single Cy3 Molecules and Quantum Dots Using Time-Correlated Single Photon Counting with a Four-Pixel Fiber Optic Array Camera

Time-resolved single molecule localization microscopy (TR-SMLM) with a 2 × 2 pixel fiber optic array camera was combined with time-correlated single photon counting (TCSPC) to obtain super-resolved fluorescence lifetime images of individual Cy3 dye molecules and individual colloidal CdSe/CdS/ZnS core/shell/shell semiconductor quantum dots (QDs). The characteristic blinking and bleaching behavior of the Cy3 and the blinking behavior of the QD emitters were used as distinguishing optical characteristics to isolate them and determine their centroid locations with spatial resolution below the optical diffraction limit. TCSPC was used to characterize the fluorescence lifetime and intensity corresponding to each emitter location. The mean centroid locations of the QDs could be determined with a precision of ∼1-4 nm, and the mean centroid locations of the Cy3 molecules could be determined with a precision of ∼2-9 nm, depending on the number of photons collected during the observation time. In a super-resolved fluorescence lifetime image with a single Cy3 dye molecule and a single QD separated by ∼34 nm, the two emitters were distinguished based on the average photon arrival times with respect to the excitation laser pulse observed during time intervals when only one emitter was in the on state, ∼6 ns for Cy3 and ∼17 ns for the QD. The mean distance between the two emitters was determined with a precision of ∼8 nm. The feasibility of using this super-resolved fluorescence lifetime imaging technique to investigate QD-dye complexes that use Förster resonance energy transfer (FRET) and/or electron transfer to form optical biosensors is discussed.

Heterogeneity of late endosome/lysosomes shown by multiplexed DNA-PAINT imaging

Late endosomes/lysosomes (LELs) are crucial for numerous physiological processes and their dysfunction is linked to many diseases. Proteomic analyses have identified hundreds of LEL proteins; however, whether these proteins are uniformly present on each LEL, or if there are cell-type-dependent LEL subpopulations with unique protein compositions is unclear. We employed quantitative, multiplexed DNA-PAINT super-resolution imaging to examine the distribution of seven key LEL proteins (LAMP1, LAMP2, CD63, Cathepsin D, TMEM192, NPC1, and LAMTOR4). While LAMP1, LAMP2, and Cathepsin D were abundant across LELs, marking a common population, most analyzed proteins were associated with specific LEL subpopulations. Our multiplexed imaging approach identified up to eight different LEL subpopulations based on their unique membrane protein composition. Additionally, our analysis of the spatial relationships between these subpopulations and mitochondria revealed a cell-type-specific tendency for NPC1-positive LELs to be closely positioned to mitochondria. Our approach will be broadly applicable to determining organelle heterogeneity with single organelle resolution in many biological contexts.

Polymer Nano-Carrier-Mediated Gene Delivery: Visualizing and Quantifying DNA Encapsulation Using dSTORM

The success of gene therapy hinges on the effective encapsulation, protection, and compression of genes. These processes deliver therapeutic genes into designated cells for genetic repair, cellular behavior modification, or therapeutic effect induction. However, quantifying the encapsulation efficiency of small molecules of interest like DNA or RNA into delivery carriers remains challenging. This work shows how super-resolution microscopy, specifically direct stochastic optical reconstruction microscopy (dSTORM), can be employed to visualize and measure the quantity of DNA entering a single carrier. Utilizing pNIPAM/bPEI microgels as model nano-carriers to form polyplexes, DNA entry into the carrier is revealed across different charge ratios at temperatures below and above the volume phase transition of the microgel core. The encapsulation efficiency also depends on DNA length and shape. This work demonstrates the uptake of the carrier entity by primary derived macro-phages and showcases the cell viability of the polyplexes. The study shows that dSTORM is a potent tool for fine-tuning and creating polyplex microgel carrier systems with precise size, shape, and loading capacity at the individual particle level. This advancement shall contribute significantly to optimizing gene delivery systems.

DNA Origami Multicolor Quantum Dot Platforms for Sub-diffraction Spectral Separation Imaging

Super-resolution optical imaging techniques rely on validation standards. In this regard, it is of paramount importance to develop consistent and reliable well-defined reference samples. In this study, we employ a DNA origami scaffold to engineer a multicolor quantum dot hybrid nanostructure, and evaluate it through a recently proposed quantum dot-based spectral separation technique. Our findings underscore the utility of multivalent DNA structures, which serve as a robust and precise scaffold for the nanoscale placement of quantum dots. The employed spectral resolution method offers a straightforward and rapid means of imaging acquisition, compatible with standard confocal or fluorescence microscopes possessing spectral signal separation capabilities and a single excitation laser wavelength. This combined methodology represents a promising avenue for advancing super-resolution optical imaging techniques.

Analyzing Point Accumulation in Nanoscale Topography (PAINT) Data to Decipher T Cell Receptor Cluster Signalling

Upon activation via antigen binding, T cell receptors (TCRs) become phosphorylated and cluster, initiating a signalling cascade which ultimately leads to T cell activation. Single-Molecule Localization Microscopy (SMLM) is an essential tool for studying nanoclusters and quantifying the TCR activation pathway, as these events take place at a molecular level beneath the resolution limit of conventional optical microscopes. SMLM achieves high molecular precision by employing switchable fluorescent signals and identifies individual molecules within a diffraction-limited area. Points accumulation in nanoscale topography (PAINT), including DNA-PAINT and protein-PAINT (pPAINT), offers even greater quantification of SMLM data. Unlike traditional SMLM techniques, PAINT is not limited by spectral limitations or bleaching, allowing for more accurate quantification of TCR clustering and molecular organization at the plasma membrane. Here we present a pipeline to analyze PAINT data collected in T cells, using the Picasso software package, to quantify the nanoclusters in activated cells.

Engineering GID4 for use as an N-terminal proline binder via directed evolution

Nucleic acid sequencing technologies have gone through extraordinary advancements in the past several decades, significantly increasing throughput while reducing cost. To create similar advancement in proteomics, numerous approaches are being investigated to advance protein sequencing. One of the promising approaches uses N-terminal amino acid binders (NAABs), also referred to as recognizers, that selectively can identify amino acids at the N-terminus of a peptide. However, there are only a few engineered NAABs currently available that bind to specific amino acids and meet the requirements of a biotechnology reagent. Therefore, additional NAABs need to be identified and engineered to enable confident identification and, ultimately, de novo protein sequencing. To fill this gap, a human protein GID4 was engineered to create a NAAB for N-terminal proline (Nt-Pro). While native GID4 binds Nt-Pro, its binding is weak (µmol/L) and greatly influenced by the identity of residues following the Nt-Pro. Through directed evolution, yeast-surface display, and fluorescence-activated cell sorting, we identified sequence variants of GID4 with increased binding response to Nt-Pro. Moreover, variants with an A252V mutation showed a reduced influence from residues in the second and third positions of the target peptide when binding to Nt-Pro. The workflow outlined here is shown to be a viable strategy for engineering NAABs, even when starting from native Nt-binding proteins whose binding is strongly impacted by the identity of residues following Nt-amino acid.