DNA origami-based standards for quantitative fluorescence microscopy

Self-folding RCA product into a parallel monolayer DNA nanoribbon and woven into a nano-fence structure by a short bridge strand

The universal programmed construction of patterned periodic self-assembled nanostructures is a technical challenge in DNA origami nanotechnology but has numerous potential applications in biotechnology and biomedicine. In order to circumvent the dilemma that traditional DNA origami requires a long unusual single-stranded virus DNA as the scaffold and hundreds or even thousands of short strands as staples, we report a method for constructing periodically-self-folded rolling circle amplification products (RPs). The repeating unit is designed to have 3 intra-unit duplexes (inDP1,2,3) and 2 between-unit duplexes (buDP1,2). Based on the complementary pairing of bases, RPs each can self-fold into a periodic grid-patterned ribbon (GR) without the help of any auxiliary oligonucleotide staple. Moreover, by using only an oligonucleotide bridge strand, the GRs are connected together into the larger and denser planar nano-fence-shaped product (FP), which substantially reduces the number of DNA components compared with DNA origami and eliminates the obstacles in the practical application of DNA nanostructures. More interestingly, the FP-based DNA framework can be easily functionalized to offer spatial addressability for the precise positioning of nanoparticles and guest proteins with high spatial resolution, providing a new avenue for the future application of DNA assembled framework nanostructures in biology, material science, nanomedicine and computer science that often requires the ordered organization of functional moieties with nanometer-level and even molecular-level precision.

Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC)

Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is, however, a growing gap between the state of the art and what is accessible to biologists, biochemists, medical researchers, or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed microspectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy, time-correlated single-photon counting and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines, are provided, to allow non-optics specialists to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and open-source Brick-MIC platform will be a valuable tool for many laboratories worldwide.

MultiMatch: geometry-informed colocalization in multi-color super-resolution microscopy

With recent advances in multi-color super-resolution light microscopy, it is possible to simultaneously visualize multiple subunits within biological structures at nanometer resolution. To optimally evaluate and interpret spatial proximity of stainings on such an image, colocalization analysis tools have to be able to integrate prior knowledge on the local geometry of the recorded biological complex. We present MultiMatch to analyze the abundance and location of chain-like particle arrangements in multi-color microscopy based on multi-marginal optimal unbalanced transport methodology. Our object-based colocalization model statistically addresses the effect of incomplete labeling efficiencies enabling inference on existent, but not fully observable particle chains. We showcase that MultiMatch is able to consistently recover existing chain structures in three-color STED images of DNA origami nanorulers and outperforms geometry-uninformed triplet colocalization methods in this task. MultiMatch generalizes to an arbitrary number of color channels and is provided as a user-friendly Python package comprising colocalization visualizations.

Visualization of the hepatic and renal cell uptake and trafficking of tetrahedral DNA origami in tumour

DNA nanostructures, known for their programmability, ease of modification, and favourable biocompatibility, have gained widespread application in the biomedical field. Among them, Tetrahedral DNA Origami (TDOs), as a novel DNA nanostructure, possesses well-defined structures, multiple modification sites, and large cavities, making it a promising drug carrier. However, current understanding of TDOs' interactions with biological systems, particularly with target cells and organs, remains unexplored, limiting its further applications in biomedicine. In this work, we prepared TDOs with an average particle size of 40 nm and labelled them with Cy5 fluorescent molecules. Following intravenous injection in mice, the uptake of TDOs by different types of liver and kidney cells was observed. Results indicated that TDOs accumulate in renal tubules and are metabolized by Kupffer cells, epithelial cells, and hepatocytes in the liver. Additionally, in a tumour-bearing mouse model, TDOs passively targeted tumour tissues and exhibited excellent tumour penetration and retention after rapid metabolism in hepatocytes. Our findings provide crucial insights for the development of TDO-based drug delivery systems.

Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads

Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.

Fluorophore multimerization on a PEG backbone as a concept for signal amplification and lifetime modulation

Fluorescent labels have strongly contributed to many advancements in bioanalysis, molecular biology, molecular imaging, and medical diagnostics. Despite a large toolbox of molecular and nanoscale fluorophores to choose from, there is still a need for brighter labels, e.g., for flow cytometry and fluorescence microscopy, that are preferably of molecular nature. This requires versatile concepts for fluorophore multimerization, which involves the shielding of dyes from other chromophores and possible quenchers in their neighborhood. In addition, to increase the number of readout parameters for fluorescence microscopy and eventually also flow cytometry, control and tuning of the labels' fluorescence lifetimes is desired. Searching for bright multi-chromophoric or multimeric labels, we developed PEGylated dyes bearing functional groups for their bioconjugation and explored their spectroscopic properties and photostability in comparison to those of the respective monomeric dyes for two exemplarily chosen fluorophores excitable at 488 nm. Subsequently, these dyes were conjugated with anti-CD4 and anti-CD8 immunoglobulins to obtain fluorescent conjugates suitable for the labeling of cells and beads. Finally, the suitability of these novel labels for fluorescence lifetime imaging and target discrimination based upon lifetime measurements was assessed. Based upon the results of our spectroscopic studies including measurements of fluorescence quantum yields (QY) and fluorescence decay kinetics we could demonstrate the absence of significant dye-dye interactions and self-quenching in these multimeric labels. Moreover, in a first fluorescence lifetime imaging (FLIM) study, we could show the future potential of this multimerization concept for lifetime discrimination and multiplexing.

Dominant Analytical Techniques in DNA Nanotechnology for Various Applications

DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite the distinct objectives of each application, they are united in their reliance on essential analytical techniques, such as purification and characterization. This tutorial aims to guide the reader through the current state of DNA nanotechnology analytical chemistry, outlining important factors to consider when designing, assembling, purifying, and characterizing a DNA nanostructure for downstream applications.

Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA

The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.

Advancing Spectrally-Resolved Single Molecule Localization Microscopy with Deep Learning

Spectrally-resolved single molecule localization microscopy (srSMLM) is a recent technique enriching single molecule localization microscopy with the simultaneous recording of spectra of the single emitters. srSMLM resolution is limited by the number of photons collected per emitters. Sharing a photon budget to record the localization and the spectroscopic information results in a loss of spatial and spectral resolution-or forces the sacrifice of one at the expense of the other. Here, srUnet-a deep-learning Unet-based image processing routine trained to increase the spectral and spatial signals to compensate for the resolution loss inherent in additionally recording the spectral component is reported. Both localization and spectral precision are improved by srUnet-particularly for the low-emitting species. srUnet increases the fraction of localization whose signal can be both spatially and spectrally characterized. It preserves spectral shifts and the linearity of the dispersion of light. It strongly facilitates wavelength assignment in multicolor experiments. srUnet is a simple post-processing add-on boosting srSMLM performance close to conventional SMLM with the potential to turn srSMLM into the new standard for multicolor single molecule imaging.

Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions

Programmable, custom-shaped, and nanometer-precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnology and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiological conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct molecular-level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Additionally, specific issues demanding further investigation are identified. This review - through its specific viewpoint - may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiological media.

Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components by rate-zonal centrifugation

DNA origami purification is essential for many fields, including biophysics, molecular engineering, and therapeutics. The increasing interest in DNA origami has led to the development of rate-zonal centrifugation (RZC) as a scalable, high yield, and contamination-free method for purifying DNA origami nanostructures. RZC purification uses a linear density gradient of viscous media, such as glycerol or sucrose, to separate molecules according to their mass and shape. However, many methods for creating density gradients are time-consuming because they rely on slow passive diffusion. To expedite the preparation time, we used a LEGO gradient mixer to generate rotational motion and rapidly create a quasi-continuous density gradient with a minimal layering of the viscous media. Rotating two layers of differing concentrations at an angle decreases the time needed to form the density gradient from a few hours to minutes. In this study, the density gradients created by the LEGO gradient mixer were used to purify 3 DNA origami shapes that have different aspect ratios and numbers of components, with an aspect ratio ranging from 1:1 to 1:100 and the number of components up to 2. The gradient created by our LEGO gradient mixer is sufficient to purify folded DNA origami nanostructures from excess staple strands, regardless of their aspect ratios. Moreover, the gradient was able to separate DNA origami dimers from DNA origami monomers. In light of recent advances in large-scale DNA origami production, our method provides an alternative for purifying DNA origami nanostructures in large (gram) quantities in resource-limited settings.

Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures

DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.

Quantitative Single-Molecule Localization Microscopy

Super-resolution fluorescence microscopy allows the investigation of cellular structures at nanoscale resolution using light. Current developments in super-resolution microscopy have focused on reliable quantification of the underlying biological data. In this review, we first describe the basic principles of super-resolution microscopy techniques such as stimulated emission depletion (STED) microscopy and single-molecule localization microscopy (SMLM), and then give a broad overview of methodological developments to quantify super-resolution data, particularly those geared toward SMLM data. We cover commonly used techniques such as spatial point pattern analysis, colocalization, and protein copy number quantification but also describe more advanced techniques such as structural modeling, single-particle tracking, and biosensing. Finally, we provide an outlook on exciting new research directions to which quantitative super-resolution microscopy might be applied.

Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens

Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems¹. However, optimal performance is usually reached using laser-based systems (for example, confocal microscopy), restricting its broad applicability in clinical pathology, as most centres have access only to light-emitting diode (LED)-based widefield systems. As a possible alternative, a computational method for image resolution enhancement, namely, super-resolution radial fluctuations (SRRF)^2,3, has recently been developed. However, this method has not been explored in pathology specimens to date, because on its own, it does not achieve sufficient resolution for routine clinical use. Here, we report expansion-enhanced super-resolution radial fluctuations (ExSRRF), a simple, robust, scalable and accessible workflow that provides a resolution of up to 25 nm using LED-based widefield microscopy. ExSRRF enables molecular profiling of subcellular structures from archival formalin-fixed paraffin-embedded tissues in complex clinical and experimental specimens, including ischaemic, degenerative, neoplastic, genetic and immune-mediated disorders. Furthermore, as examples of its potential application to experimental and clinical pathology, we show that ExSRRF can be used to identify and quantify classical features of endoplasmic reticulum stress in the murine ischaemic kidney and diagnostic ultrastructural features in human kidney biopsies.

DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging

Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.

Towards Unbiased Fluorophore Counting in Superresolution Fluorescence Microscopy

With the advent of fluorescence superresolution microscopy, nano-sized structures can be imaged with a previously unprecedented accuracy. Therefore, it is rapidly gaining importance as an analytical tool in the life sciences and beyond. However, the images obtained so far lack an absolute scale in terms of fluorophore numbers. Here, we use, for the first time, a detailed statistical model of the temporal imaging process which relies on a hidden Markov model operating on two timescales. This allows us to extract this information from the raw data without additional calibration measurements. We show this on the basis of added data from experiments on single Alexa 647 molecules as well as GSDIM/dSTORM measurements on DNA origami structures with a known number of labeling positions.

Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology

Since its inception nearly 40 years ago [Kallenbach, et al., Nature, 1983, 305, 829; N. C. Seeman, J. Theoretical Biology, 1982, 99, 237], Nucleic Acid Nanotechnology (NAN) has matured and is beginning to find commercial applications. For the last 20 years, it has been suggested that NAN might be an effective replacement for parts of the semiconductor lithography or protein engineering workflows. However, in that time, these incumbent technologies have made significant advances, and our understanding of NAN's strengths and weaknesses has progressed, suggesting that the greatest opportunities in fact lie elsewhere. Given the commitment of resources necessary to bring new technologies to the market and the desire to use those resources as wisely as possible, we conduct a critical examination of where NAN may benefit from, and provide benefit to, adjacent technologies and compete least with market incumbents. While the accuracy of our conclusions may be limited by our ability to extrapolate from the current state of NAN to its future commercial success, we conclude that the next promising direction is to create a bridge between biology and semiconductor technology. We also hope to stimulate a robust conversation around this technology's capabilities with the goal of building consensus on those research and development efforts that would advance NAN to the greatest effect in real-world applications.

Single-molecule counting applied to the study of GPCR oligomerization

Single-molecule counting techniques enable a precise determination of the intracellular abundance and stoichiometry of proteins and macromolecular complexes. These details are often challenging to quantitatively assess yet are essential for our understanding of cellular function. Consider G-protein-coupled receptors-an expansive class of transmembrane signaling proteins that participate in many vital physiological functions making them a popular target for drug development. While early evidence for the role of oligomerization in receptor signaling came from ensemble biochemical and biophysical assays, innovations in single-molecule measurements are now driving a paradigm shift in our understanding of its relevance. Here, we review recent developments in single-molecule counting with a focus on photobleaching step counting and the emerging technique of quantitative single-molecule localization microscopy-with a particular emphasis on the potential for these techniques to advance our understanding of the role of oligomerization in G-protein-coupled receptor signaling.

Single molecule DNA origami nanoarrays with controlled protein orientation

The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.

ATP-Responsive Strand Displacement Coupling with DNA Origami/AuNPs Strategy for the Determination of Microcystin-LR Using Surface-Enhanced Raman Spectroscopy

The DNA origami-mediated self-assembly strategy has emerged as a powerful tool in surface-enhanced Raman spectroscopy (SERS). However, these self-assembly approaches typically do not possess high detection specificity. Herein, a novel strategy based on adenosine triphosphate (ATP)-responsive strand displacement (ARSD) coupling with DNA origami/AuNPs for SERS analysis of microcystin-LR (MC-LR) is presented. In the presence of MC-LR and ATP molecules, nucleic acid sensing structures fabricated with anti-MC-LR aptamer (T1) and ATP aptamer (T2) were triggered to release the remaining ATP. In addition, DNA origami-assisted assembly results in the formation of homogeneous plasmonic nanostructures for Raman enhancement via strong plasmonic coupling. After the binding in the gaps of functionalized DNA origami/AuNPs, the Raman shift of the ATP molecules becomes detectable, leading to increased SERS intensity in 734 cm^-1. A linear response to MC-LR was obtained in the concentration range of 1.56-50 μg·L^-1, and the limit of detection (LOD) was 0.29 μg·L^-1. Combined with the solid-phase extraction sample pretreatment for extraction and 10-fold concentration, this proposed method was successfully used to detect MC-LR type in real lake-water samples with good recoveries of 98.4-116% and relative standard deviations of 1.9-6.7%. Furthermore, for the detection of MC-LR in contaminated lake-water samples, the results of the developed method and ultrahigh-performance liquid chromatography-tandem mass spectrometry were found to be in agreement with relative errors between -12 and 2.4%. The proposed strategy provides a sensitive recognition and signal amplification platform for trace MC-LR analysis as well as innovative nucleic acid sensing structures for toxin analysis more generally.

Salt-induced conformational switching of a flat rectangular DNA origami structure

A rectangular DNA origami structure is one of the most studied and often used motif for applications in DNA nanotechnology. Here, we present two assays to study structural changes in DNA nanostructures and reveal a reversible rolling-up of the rectangular DNA origami structure induced by bivalent cations such as magnesium or calcium. First, we applied one-color and two-color superresolution DNA-PAINT with protruding strands along the long edges of the DNA origami rectangle. At increasing salt concentration, a single line instead of two lines is observed as a first indicator of rolling-up. Two-color measurements also revealed different conformations with parallel and angled edges. Second, we placed a gold nanoparticle and a dye molecule at different positions on the DNA origami structure. Distance dependent fluorescence quenching by the nanoparticle reports on dynamic transitions as well as it provides evidence that the rolling-up occurs preferentially along the diagonal of the DNA origami rectangle. The results will be helpful to test DNA structural models and the assays presented will be useful to study further structural transitions in DNA nanotechnology.

Dipole-spread-function engineering for simultaneously measuring the 3D orientations and 3D positions of fluorescent molecules

Interactions between biomolecules are characterized by both where they occur and how they are organized, e.g., the alignment of lipid molecules to form a membrane. However, spatial and angular information are mixed within the image of a fluorescent molecule-the microscope's dipole-spread function (DSF). We demonstrate the pixOL algorithm for simultaneously optimizing all pixels within a phase mask to produce an engineered Green's tensor-the dipole extension of point-spread function engineering. The pixOL DSF achieves optimal precision for measuring simultaneously the 3D orientation and 3D location of a single molecule, i.e., 4.1° orientation, 0.44 sr wobble angle, 23.2 nm lateral localization, and 19.5 nm axial localization precisions in simulations over a 700-nm depth range using 2500 detected photons. The pixOL microscope accurately and precisely resolves the 3D positions and 3D orientations of Nile red within a spherical supported lipid bilayer, resolving both membrane defects and differences in cholesterol concentration in 6 dimensions.

DNA Origami Calibrators for Counting Fluorophores on Single Particles by Flow Cytometry

Flow cytometry (FCM) is a high-throughput fluorescence-based technique for multiparameter analysis of individual particles, including cells and nanoparticles. Currently, however, FCM does in many cases not permit proper counting of fluorophore-tagged markers on individual particles, due to a lack of tools for translating FCM output intensities into accurate numbers of fluorophores. This lack hinders derivation of detailed biologic information and comparison of data between experiments with FCM. To address this technological void, the authors here use DNA nanotechnology to design and construct barrel-shaped DNA-origami nanobeads for fluorescence/antigen quantification in FCM. Each bead contains a specific number of calibrator fluorophores and a fluorescent trigger domain with an alternative fluorophore for proper detection in FCM. Using electron microscopy, single-particle fluorescence microscopy, and FCM, the design of each particle is verified. To validate that the DNA bead-based FCM calibration enabled the authors to determine the number of antigens on a biological particle, the uniform and well-characterized murine leukemia virus (MLV) is studied. 48 ± 11 envelope surface protein (Env) trimers per MLV is obtained, which is consistent with reported numbers that relied on low-throughput imaging. Thus, the authors' DNA-beads should accelerate quantitative studies of the biology of individual particles with FCM.

Standardizing resolution definition in scanning helium microscopy

Resolution is a key parameter for microscopy, but methods for standardizing its definition are often poorly defined. For a developing technique such as scanning helium microscopy, it is critical that a consensus-based protocol for determining instrument resolution is prepared as a written standard to allow both comparable quantitative measurements of surface topography and direct comparisons between different instruments. In this paper we assess a range of quantitative methods for determining instrument resolution and determine their relative merits when applied to the specific case of the scanning helium microscope (SHeM). Consequently, we present a preliminary protocol for measuring the resolution in scanning helium microscopy based upon utilizing appropriate test samples with sets of slits of well-defined dimensions to establish the quantitative resolution of any similar instrument.

Fluorescence nanoscopy at the sub-10 nm scale

Fluorescence nanoscopy represented a breakthrough for the life sciences as it delivers 20-30 nm resolution using far-field fluorescence microscopes. This resolution limit is not fundamental but imposed by the limited photostability of fluorophores under ambient conditions. This has motivated the development of a second generation of fluorescence nanoscopy methods that aim to deliver sub-10 nm resolution, reaching the typical size of structural proteins and thus providing true molecular resolution. In this review, we present common fundamental aspects of these nanoscopies, discuss the key experimental factors that are necessary to fully exploit their capabilities, and discuss their current and future challenges.

Photobleaching step analysis for robust determination of protein complex stoichiometries

The counting of discrete photobleaching steps in fluorescence microscopy is ideally suited to study protein complex stoichiometry in situ. The counting range of photobleaching step analysis has been significantly improved with more-sophisticated algorithms for step detection, albeit at an increasing computational cost and with the necessity for high-quality data. Here, we address concerns regarding robustness, automation, and experimental validation, optimizing both data acquisition and analysis. To make full use of the potential of photobleaching step analysis, we evaluate various labeling strategies with respect to their molecular brightness, photostability, and photoblinking. The developed analysis algorithm focuses on automation and computational efficiency. Moreover, we validate the developed methods with experimental data acquired on DNA origami labeled with defined fluorophore numbers, demonstrating counting of up to 35 fluorophores. Finally, we show the power of the combination of optimized trace acquisition and automated data analysis by counting labeled nucleoporin 107 in nuclear pore complexes of intact U2OS cells. The successful in situ application promotes this framework as a new resource enabling cell biologists to robustly determine the stoichiometries of molecular assemblies at the single-molecule level in an automated manner.

Extending the Capabilities of Molecular Force Sensors via DNA Nanotechnology

At the nanoscale, pushing, pulling, and shearing forces drive biochemical processes in development and remodeling as well as in wound healing and disease progression. Research in the field of mechanobiology investigates not only how these loads affect biochemical signaling pathways but also how signaling pathways respond to local loading by triggering mechanical changes such as regional stiffening of a tissue. This feedback between mechanical and biochemical signaling is increasingly recognized as fundamental in embryonic development, tissue morphogenesis, cell signaling, and disease pathogenesis. Historically, the interdisciplinary field of mechanobiology has been driven by the development of technologies for measuring and manipulating cellular and molecular forces, with each new tool enabling vast new lines of inquiry. In this review, we discuss recent advances in the manufacturing and capabilities of molecular-scale force and strain sensors. We also demonstrate how DNA nanotechnology has been critical to the enhancement of existing techniques and to the development of unique capabilities for future mechanosensor assembly. DNA is a responsive and programmable building material for sensor fabrication. It enables the systematic interrogation of molecular biomechanics with forces at the 1- to 200-pN scale that are needed to elucidate the fundamental means by which cells and proteins transduce mechanical signals.

2D DNA nanoporous scaffold promotes osteogenic differentiation of pre-osteoblasts

Biofunctional materials with nanomechanical parameters similar to bone tissue may promote the adherence, migration, proliferation, and differentiation of pre-osteoblasts. In this study, deoxyribonucleic acid (DNA) nanoporous scaffold (DNA-NPS) was synthesized by the polymerization of rectangular and double-crossover (DX) DNA tiles. The diagonally precise polymerization of nanometer-sized DNA tiles (A + B) through sticky end cohesion gave rise to a micrometer-sized porous giant-sheet material. The synthesized DNA-NPS exhibited a uniformly distributed porosity with a size of 25 ± 20 nm. The morphology, dimensions, sectional profiles, 2-dimensional (2D) layer height, texture, topology, pore size, and mechanical parameters of DNA-NPS have been characterized by atomic force microscopy (AFM). The size and zeta potential of DNA-NPS have been characterized by the zeta sizer. Cell biocompatibility, proliferation, and apoptosis have been evaluated by flow cytometry. The AFM results confirmed that the fabricated DNA-NPS was interconnected and uniformly porous, with a surface roughness of 0.125 ± 0.08035 nm. The elastic modulus of the DNA-NPS was 22.45 ± 8.65 GPa, which was comparable to that of native bone tissue. DNA-NPS facilitated pre-osteoblast adhesion, proliferation, and osteogenic differentiation. These findings indicated the potential of 2D DNA-NPS in promoting bone tissue regeneration.

Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility

Dynein, a dimeric motor protein, moves along microtubules through adenosine 5′-triphosphate- and thermal-driven motions of two large ring domains (AAA rings) and small microtubule-binding domains (MTBDs) separated by a long coiled-coil. Previous single-molecule studies have tracked the positions of the AAA rings during motility, but not the MTBDs. Here, we tracked the relative positions of both MTBDs and one AAA ring by three-color, nanometer-resolution imaging. The observation of both MTBDs provided a direct measurement of how dynein steps on the tubulin subunits, and the simultaneous observation of three fiducial markers revealed extraordinary flexibility and previously unknown conformational states of the motor during motility. The techniques presented here can be used to explore conformational dynamics of many other macromolecular complexes.

The motor protein dynein undergoes coordinated conformational changes of its domains during motility along microtubules. Previous single-molecule studies analyzed the motion of the AAA rings of the dynein homodimer, but not the distal microtubule-binding domains (MTBDs) that step along the track. Here, we simultaneously tracked with nanometer precision two MTBDs and one AAA ring of a single dynein as it underwent hundreds of steps using three-color imaging. We show that the AAA ring and the MTBDs do not always step simultaneously and can take differently sized steps. This variability in the movement between the AAA ring and MTBDs results in an unexpectedly large number of conformational states of dynein during motility. Extracting data on conformational transition biases, we could accurately model dynein stepping in silico. Our results reveal that the flexibility between major dynein domains is critical for dynein motility.

3D test sample for the calibration and quality control of stimulated emission depletion (STED) and confocal microscopes

Multiple samples are required to monitor and optimize the quality and reliability of quantitative measurements of stimulated emission depletion (STED) and confocal microscopes. Here, we present a single sample to calibrate these microscopes, align their laser beams and measure their point spread function (PSF) in 3D. The sample is composed of a refractive index matched colloidal crystal of silica beads with fluorescent and gold cores. The microscopes can be calibrated in three dimensions using the periodicity of the crystal; the alignment of the laser beams can be checked using the reflection of the gold cores; and the PSF can be measured at multiple positions and depths using the fluorescent cores. It is demonstrated how this sample can be used to visualize and improve the quality of STED and confocal microscopy images. The sample is adjustable to meet the requirements of different NA objectives and microscopy techniques and additionally can be used to evaluate refractive index mismatches as a function of depth quantitatively.

Optical and Topological Characterization of Hexagonal DNA Origami Nanotags

DNA origami can be applied as a "ruler" for nanoscale calibration or super-resolution fluorescence microscopy with an ideal structure for defining fluorophore arrangement, allowing the distance between fluorophores to be precisely controlled at the nanometer scale. DNA origami can also be used as a nanotag with arbitrary programmable shapes for topological identification. In this paper, we formed a hexagonal origami structure embedded with three different fluorescent dyes on the surface. The distance between each fluorescent block was ~120 nm, which is below the diffraction limit of light, allowing for its application as a nano-ruler for super-resolution fluorescence microscopy. The outside edge of the hexagonal structure was redesigned to form three different substructures as topological labels. Atomic and scanning force microscopy demonstrated consistency of the nanoscale distance between morphological and fluorescent labels. Therefore, this fluorophore-embedded hexagonal origami platform can be used as a dual nano-ruler for both optical and topological calibration.

Super-resolution STED microscopy in live brain tissue

STED microscopy is one of several fluorescence microscopy techniques that permit imaging at higher spatial resolution than what the diffraction-limit of light dictates. STED imaging is unique among these super-resolution modalities in being a beam-scanning microscopy technique based on confocal or 2-photon imaging, which provides the advantage of superior optical sectioning in thick samples. Compared to the other super-resolution techniques that are based on widefield microscopy, this makes STED particularly suited for imaging inside live brain tissue, such as in slices or in vivo. Notably, the 50 nm resolution provided by STED microscopy enables analysis of neural morphologies that conventional confocal and 2-photon microscopy approaches cannot resolve, including all-important synaptic structures. Over the course of the last 20 years, STED microscopy has undergone extensive developments towards ever more versatile use, and has facilitated remarkable neurophysiological discoveries. The technique is still not widely adopted for live tissue imaging, even though one of its particular strengths is exactly in resolving the nanoscale dynamics of synaptic structures in brain tissue, as well as in addressing the complex morphologies of glial cells, and revealing the intricate structure of the brain extracellular space. Not least, live tissue STED microscopy has so far hardly been applied in settings of pathophysiology, though also here it shows great promise for providing new insights. This review outlines the technical advantages of STED microscopy for imaging in live brain tissue, and highlights key neurobiological findings brought about by the technique.

Pitfalls and opportunities in quantitative fluorescence-based nanomedicine studies - A commentary

Fluorescence-based techniques are prevalent in studies of nanomedicine-targeting to cells and tissues. However, fluorescence-based studies are rarely quantitative, thus prohibiting direct comparisons of nanomedicine-performance across studies. With this Commentary, we aim to provoke critical thinking about experimental design by treating some often-overlooked pitfalls in 'quantitative' fluorescence-based experimentation. Focusing on fluorescence-labeled nanoparticles, we cover mechanisms like solvent-interactions and fluorophore-dissociation, which disqualify the assumption that 'a higher fluorescence readout' translates directly to 'a better targeting efficacy'. With departure in recent literature, we propose guidelines for circumventing these pitfalls in studies of tissue-accumulation and cell-uptake, thus covering fluorescence-based techniques like bulk solution fluorescence measurements, fluorescence microscopy, flow cytometry, and infrared fluorescence imaging. With this, we hope to lay a foundation for more 'quantitative thinking' during experimental design, enabling (for example) the estimation and reporting of actual numbers of fluorescent nanoparticles accumulated in cells and organs.

An update on molecular counting in fluorescence microscopy

Quantitative assessment of protein complexes, such as receptor clusters in the context of cellular signalling, has become a pressing objective in cell biology. The advancements in the field of single molecule fluorescence microscopy have led to different approaches for counting protein copy numbers in various cellular structures. This has resulted in an increasing interest in robust calibration protocols addressing photophysical properties of fluorescent labels and the effect of labelling efficiencies. Here, we want to give an update on recent methods for protein counting with a focus on novel calibration protocols. In this context, we discuss different types of calibration samples and identify some of the challenges arising in molecular counting experiments. Some recently published applications offer potential approaches to tackle these challenges.

Picosecond time-resolved photon antibunching measures nanoscale exciton motion and the true number of chromophores

The particle-like nature of light becomes evident in the photon statistics of fluorescence from single quantum systems as photon antibunching. In multichromophoric systems, exciton diffusion and subsequent annihilation occurs. These processes also yield photon antibunching but cannot be interpreted reliably. Here we develop picosecond time-resolved antibunching to identify and decode such processes. We use this method to measure the true number of chromophores on well-defined multichromophoric DNA-origami structures, and precisely determine the distance-dependent rates of annihilation between excitons. Further, this allows us to measure exciton diffusion in mesoscopic H- and J-type conjugated-polymer aggregates. We distinguish between one-dimensional intra-chain and three-dimensional inter-chain exciton diffusion at different times after excitation and determine the disorder-dependent diffusion lengths. Our method provides a powerful lens through which excitons can be studied at the single-particle level, enabling the rational design of improved excitonic probes such as ultra-bright fluorescent nanoparticles and materials for optoelectronic devices.

Self-Regeneration and Self-Healing in DNA Origami Nanostructures

DNA nanotechnology and advances in the DNA origami technique have enabled facile design and synthesis of complex and functional nanostructures. Molecular devices are, however, prone to rapid functional and structural degradation due to the high proportion of surface atoms at the nanoscale and due to complex working environments. Besides stabilizing mechanisms, approaches for the self-repair of functional molecular devices are desirable. Here we exploit the self-assembly and reconfigurability of DNA origami nanostructures to induce the self-repair of defects of photoinduced and enzymatic damage. We provide examples of repair in DNA nanostructures showing the difference between unspecific self-regeneration and damage specific self-healing mechanisms. Using DNA origami nanorulers studied by atomic force and superresolution DNA PAINT microscopy, quantitative preservation of fluorescence properties is demonstrated with direct potential for improving nanoscale calibration samples.

Programmable DNA Nanodevices for Applications in Neuroscience

The broad area of neuroscience has witnessed an increasing exploitation of a variety of synthetic biomaterials with controlled nanosized features. Different bionanomaterials offer very peculiar physicochemical and biochemcial properties contributing to the development of novel imaging devices toward imaging the brain, or as smartly functionalized scaffolds, or diverse tools contributing toward a better understanding of nervous tissue and its functions. DNA nanotechnology-based devices and scaffolds have emerged as ideal materials for cellular and tissue engineering due to their very biocompatible properties, robust adaptation with diverse biological systems, and biosafety in terms of reduced immune response triggering. Here we present technologies with respect to DNA nanodevices that are designed to better interact with nervous systems like neural cells, advanced molecular imaging technologies for imaging brain, biomaterials in neural regeneration, neuroprotection, and targeted delivery of drugs and small molecules across the blood-brain barrier. Along with comments regarding the progress of DNA nanotechnology in neuroscience, we also present a perspective on challenges and opportunities for applying DNA nanotechnology in applications pertaining to neurosciences.

Self-assembled, Programmable DNA Nanodevices for Biological and Biomedical Applications

The broad field of structural DNA nanotechnology has diverged into various areas of applications ranging from computing, photonics, synthetic biology, and biosensing to in-vivo bioimaging and therapeutic delivery, to name but a few. Though the field began to exploit DNA to build various nanoscale architectures, it has now taken a new path to diverge from structural DNA nanotechnology to functional or applied DNA nanotechnology. More recently a third sub-branch has emerged-biologically oriented DNA nanotechnology, which seeks to explore the functionalities of combinatorial DNA devices in various biological systems. In this review, we summarize the key developments in DNA nanotechnology revealing a current trend that merges the functionality of DNA devices with the specificity of biomolecules to access a range of functions in biological systems. This review seeks to provide a perspective on the evolution and biological applications of DNA nanotechnology, where the integration of DNA structures with biomolecules can now uncover phenomena of interest to biologists and biomedical scientists. Finally, we conclude with the challenges, limitations, and perspectives of DNA nanodevices in fundamental and applied research.

DNA nanotechnology-empowered nanoscopic imaging of biomolecules

DNA nanotechnology has led to the rise of DNA nanostructures, which possess programmable shapes and are capable of organizing different functional molecules and materials. A variety of DNA nanostructure-based imaging probes have been developed.

Nuclease resistance of DNA nanostructures

DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

Biology demonstrates how a near infinite array of complex systems and structures at many scales can originate from the self-assembly of component parts on the nanoscale. But to fully exploit the benefits of self-assembly for nanotechnology, a crucial challenge remains: How do we rationally encode well-defined global architectures in subunits that are much smaller than their assemblies? Strain accumulation via geometric frustration is one mechanism that has been used to explain the self-assembly of global architectures in diverse and complex systems a posteriori. Here we take the next step and use strain accumulation as a rational design principle to control the length distributions of self-assembling polymers. We use the DNA origami method to design and synthesize a molecular subunit known as the PolyBrick, which perturbs its shape in response to local interactions via flexible allosteric blocking domains. These perturbations accumulate at the ends of polymers during growth, until the deformation becomes incompatible with further extension. We demonstrate that the key thermodynamic factors for controlling length distributions are the intersubunit binding free energy and the fundamental strain free energy, both which can be rationally encoded in a PolyBrick subunit. While passive polymerization yields geometrical distributions, which have the highest statistical length uncertainty for a given mean, the PolyBrick yields polymers that approach Gaussian length distributions whose variance is entirely determined by the strain free energy. We also show how strain accumulation can in principle yield length distributions that become tighter with increasing subunit affinity and approach distributions with uniform polymer lengths. Finally, coarse-grained molecular dynamics and Monte Carlo simulations delineate and quantify the dominant forces influencing strain accumulation in a molecular system. This study constitutes a fundamental investigation of the use of strain accumulation as a rational design principle in molecular self-assembly.

DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells

Fluorescence microscopy has been one of the most discovery-rich methods in biology. In the digital age, the discipline is becoming increasingly quantitative. Virtually all biological laboratories have access to fluorescence microscopes, but abilities to quantify biomolecule copy numbers are limited by the complexity and sophistication associated with current quantification methods. Here, we present DNA-origami-based fluorescence brightness standards for counting 5-300 copies of proteins in bacterial and mammalian cells, tagged with fluorescent proteins or membrane-permeable organic dyes. Compared to conventional quantification techniques, our brightness standards are robust, straightforward to use, and compatible with nearly all fluorescence imaging applications, thereby providing a practical and versatile tool to quantify biomolecules via fluorescence microscopy.

The applications of functionalized DNA nanostructures in bioimaging and cancer therapy

Deoxyribonucleic acid (DNA) is a molecular carrier of genetic information that can be fabricated into functional nanomaterials in biochemistry and engineering fields. Those DNA nanostructures, synthesized via Watson-Crick base pairing, show a wide range of attributes along with excellent applicability, precise programmability, and extremely low cytotoxicity in vitro and in vivo. In this review, the applications of functionalized DNA nanostructures in bioimaging and tumor therapy are summarized. We focused on approaches involving DNA origami nanostructures due to their widespread use in previous and current reports. Non-DNA origami nanostructures such as DNA tetrahedrons are also covered. Finally, the remaining challenges and perspectives regarding DNA nanostructures in the biomedical arena are discussed.

Label as you fold: methyltransferase-assisted functionalization of DNA nanostructures

Non-DNA labels are key components for the construction of functional DNA nanostructures. Here, we present a method to graft covalent labels onto DNA origami nanostructures in an enzymatic one-pot reaction. The DNA methyltransferase M.TaqI labels the DNA nanostructures with azide groups, which serve as universal attachment points via click chemistry. Direct labeling with fluorescent dyes is also demonstrated. The procedure yields structures with high fluorescence intensities and narrow intensity distributions. In combination with UV crosslinking it enables the creation of temperature-stable, intense fluorescent beacons.