Label-free, all-optical detection, imaging, and tracking of a single protein

Two-color interferometric scattering (iSCAT) microscopy reveals structural dynamics in discrete plasmonic molecules

Plasmonic molecules are discrete assemblies of noble metal nanoparticles (NPs) that are of interest as transducers in optical nanosensors. So far, NPs with diameters of ∼40 nm have been the preferred building blocks for plasmonic molecules intended as optical single molecule sensors due to difficulties associated with detecting smaller NPs through elastic scattering in conventional darkfield microscopy. Here, we apply 405 nm, 445 nm two-color interferometric scattering (iSCAT) microscopy to characterize polyethylene glycol (PEG) tethered dimers of 10 nm and 20 nm Ag NPs and their monomers. Dimers of both NP sizes can be discerned from their respective monomers through changes in the average iSCAT contrast. In the case of 20 nm Ag NPs, dimer formation induces a change in the sign of the iSCAT contrast, providing a characteristic signal for detecting binding events. 20 nm Ag NP dimers with 0.4 kDa and 3.4 kDa polyethylene glycol (PEG) spacers show iSCAT contrast distributions with significantly different averages on both wavelength channels. The iSCAT contrast measured for individual PEG-tethered 10 nm or 20 nm NP dimers as a function of time shows contrast fluctuations indicative of a rich structural dynamics in the assembled plasmonic molecules, which provides an additional metric to discern dimers from monomers and paves the path to a new class of interferometric plasmon rulers.

Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform

Label-free detection of multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. First, we characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles are required.

Label-free detection and profiling of individual solution-phase molecules

Most chemistry and biology occurs in solution, in which conformational dynamics and complexation underlie behaviour and function. Single-molecule techniques1 are uniquely suited to resolving molecular diversity and new label-free approaches are reshaping the power of single-molecule measurements. A label-free single-molecule method2-16 capable of revealing details of molecular conformation in solution17,18 would allow a new microscopic perspective of unprecedented detail. Here we use the enhanced light-molecule interactions in high-finesse fibre-based Fabry-Pérot microcavities19-21 to detect individual biomolecules as small as 1.2 kDa, a ten-amino-acid peptide, with signal-to-noise ratios (SNRs) >100, even as the molecules are unlabelled and freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of subpopulations in mixed samples. Notably, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight and composition but different conformation can also be resolved. Detection is based on the creation of a new molecular velocity filter window and a dynamic thermal priming mechanism that make use of the interplay between optical and thermal dynamics22,23 and Pound-Drever-Hall (PDH) cavity locking24 to reveal molecular motion even while suppressing environmental noise. New in vitro ways of revealing molecular conformation, diversity and dynamics can find broad potential for applications in the life and chemical sciences.

Electrophoretic Deposition Interferometric Scattering Mass Photometry

Interferometric scattering microscopy (iSCAT) has rapidly developed as a quantitative tool for the label-free detection of single macromolecules and nanoparticles. In practice, this measurement records the interferometric scattering signal of individual nanoparticles in solution as they land and stick on a coverslip, exhibiting an intensity that varies linearly with particle volume and an adsorption rate that reflects the solution-phase transport kinetics of the system. Together, such measurements provide a multidimensional gauge of the particle size and concentration in solution over time. However, the landing kinetics of particles in solution also manifest a measurement frequency limitation imposed by the slow long-range mobility of particle diffusion to the measurement interface. Here we introduce an effective means to overcome the inherent diffusion-controlled sampling limitation of spontaneous mass photometry. We term this methodology electrophoretic deposition interferometric scattering microscopy (EPD-iSCAT). This approach uses a coverslip supporting a conductive thin film of indium tin oxide (ITO). Charging this ITO film to a potential of around +1 V electrophoretically draws charged nanoparticles from solution and binds them in the focal plane of the microscope. Regulating this potential offers a direct means of controlling particle deposition. Thus, we find for a 0.1 nM solution of 50 nm polystyrene nanoparticles that the application of +1 V to an EPD-iSCAT coverslip assembly drives an electrophoretic deposition rate constant of 1.7 s-1 μm-2 nM-1. Removal of the potential causes deposition to cease. This user control of EPD-iSCAT affords a means to apply single-molecule mass photometry to monitor long-term changes in solution, owing to slow kinetic processes. In contrast with conventional coverslips chemically derivatized with charged thin films, EPD-iSCAT maintains a deposition rate that varies linearly with the bulk concentration.

Surface passivation and functionalisation for mass photometry

Interferometric scattering (iSCAT) microscopy enables the label-free observation of biomolecules. Consequently, single-particle imaging and tracking with the iSCAT-based method known as mass photometry (MP) is a growing area of study. However, establishing reliable cover glass passivation and functionalisation methods is crucial to reduce nonspecific binding and prepare surfaces for in vitro single-molecule binding experiments. Existing protocols for fluorescence microscopy can contain strongly scattering or mobile components, which make them impractical for MP-based microscopy. In this study, we characterise several different surface coatings using MP. We present approaches for cover glass passivation using 3-aminopropyltriethoxysilane (APTES) and polyethylene glycol (PEG, 2k) along with functionalisation via a maleimide-thiol linker. These coatings are compatible with water or salt buffers, and show low background scattering; thus, we are able to measure proteins as small as 60 kDa. In this technical note, we offer a surface preparation suitable for in vitro experiments with MP.

Myosin-5 varies its step length to carry cargo straight along the irregular F-actin track

Molecular motors employ chemical energy to generate unidirectional mechanical output against a track while navigating a chaotic cellular environment, potential disorder on the track, and against Brownian motion. Nevertheless, decades of nanometer-precise optical studies suggest that myosin-5a, one of the prototypical molecular motors, takes uniform steps spanning 13 subunits (36 nm) along its F-actin track. Here, we use high-resolution interferometric scattering microscopy to reveal that myosin takes strides spanning 22 to 34 actin subunits, despite walking straight along the helical actin filament. We show that cumulative angular disorder in F-actin accounts for the observed proportion of each stride length, akin to crossing a river on variably spaced stepping stones. Electron microscopy revealed the structure of the stepping molecule. Our results indicate that both motor and track are soft materials that can adapt to function in complex cellular conditions.

Label-Free Optical Imaging of Nanoscale Single Entities

The advancement of optical microscopy technologies has achieved imaging of nanoscale objects, including nanomaterials, virions, organelles, and biological molecules, at the single entity level. Recently developed plasmonic and scattering based optical microscopy technologies have enabled label-free imaging of single entities with high spatial and temporal resolutions. These label-free methods eliminate the complexity of sample labeling and minimize the perturbation of the analyte native state. Additionally, these imaging-based methods can noninvasively probe the dynamics and functions of single entities with sufficient throughput for heterogeneity analysis. This perspective will review label-free single entity imaging technologies and discuss their principles, applications, and key challenges.

Label-Free Tracking of Proteins through Plasmon-Enhanced Interference

Single unmodified biomolecules in solution can be observed and characterized by interferometric imaging approaches; however, Rayleigh scattering limits this to larger proteins (typically >30 kDa). We observe real-time image tracking of unmodified proteins down to 14 kDa using interference imaging enhanced by surface plasmons launched at an aperture in a metal film. The larger proteins show slower diffusion, quantified by tracking. When the diffusing protein is finally trapped by the nanoaperture, we perform complementary power spectral density and noise amplitude analysis, which gives information about the protein. This approach allows for rapid protein characterization with minimal sample preparation and opens the door to characterizing protein interactions in real time.

Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform

Label-free detecting multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. Herein, we first thoroughly characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles is required.

A Quantitative Description for Optical Mass Measurement of Single Biomolecules

Label-free detection of single biomolecules in solution has been achieved using a variety of experimental approaches over the past decade. Yet, our understanding of the magnitude of the optical contrast and its relationship with the underlying atomic structure as well as the achievable measurement sensitivity and precision remain poorly defined. Here, we use a Fourier optics approach combined with an atomic structure-based molecular polarizability model to simulate mass photometry experiments from first principles. We find excellent agreement between several key experimentally determined parameters such as optical contrast-to-mass conversion, achievable mass accuracy, and molecular shape and orientation dependence. This allows us to determine detection sensitivity and measurement precision mostly independent of the optical detection approach chosen, resulting in a general framework for light-based single-molecule detection and quantification.

Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform

Label-free detecting multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. Herein, we first thoroughly characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles is required.

Myosin-5 varies its steps along the irregular F-actin track

Molecular motors employ chemical energy to generate unidirectional mechanical output against a track. By contrast to the majority of macroscopic machines, they need to navigate a chaotic cellular environment, potential disorder in the track and Brownian motion. Nevertheless, decades of nanometer-precise optical studies suggest that myosin-5a, one of the prototypical molecular motors, takes uniform steps spanning 13 subunits (36 nm) along its F-actin track. Here, we use high-resolution interferometric scattering (iSCAT) microscopy to reveal that myosin takes strides spanning 22 to 34 actin subunits, despite walking straight along the helical actin filament. We show that cumulative angular disorder in F-actin accounts for the observed proportion of each stride length, akin to crossing a river on variably-spaced stepping stones. Electron microscopy revealed the structure of the stepping molecule. Our results indicate that both motor and track are soft materials that can adapt to function in complex cellular conditions.

Two-Color iSCAT Imaging of Ag Nanoparticles Resolves Size and Ambient Refractive Index Changes

The ability to discern noble metal nanoparticles (NPs) with different sizes and in ambient media with different refractive indices has important applications in imaging and sensing. Here a two-color (405 nm, 445 nm) interferometric scattering (iSCAT) detection scheme is applied to characterize the wavelength-dependent iSCAT contrast of Ag NPs with nominal diameters of 10, 20, 40, and 60 nm and to distinguish between NPs of different sizes. The iSCAT contrast also depends on the ambient refractive index and the relative iSCAT contrast on both channels revealed a spectral red-shift for 40 and 60 nm Ag NPs when the ambient refractive index was increased from n = 1.3892 to n = 1.4328. With the selected wavelength channels, the spectral resolution of the two-color imaging strategy was, however, insufficient to resolve spectral shifts induced by refractive index changes for 10 and 20 nm Ag NPs.

Enhancing Nanoparticle Detection in Interferometric Scattering (iSCAT) Microscopy Using a Mask R-CNN

Interferometric scattering microscopy (iSCAT) is a label-free optical microscopy technique that enables imaging of individual nano-objects such as nanoparticles, viruses, and proteins. Essential to this technique is the suppression of background scattering and identification of signals from nano-objects. In the presence of substrates with high roughness, scattering heterogeneities in the background, when coupled with tiny stage movements, cause features in the background to be manifested in background-suppressed iSCAT images. Traditional computer vision algorithms detect these background features as particles, limiting the accuracy of object detection in iSCAT experiments. Here, we present a pathway to improve particle detection in such situations using supervised machine learning via a mask region-based convolutional neural network (mask R-CNN). Using a model iSCAT experiment of 19.2 nm gold nanoparticles adsorbing to a rough layer-by-layer polyelectrolyte film, we develop a method to generate labeled datasets using experimental background images and simulated particle signals and train the mask R-CNN using limited computational resources via transfer learning. We then compare the performance of the mask R-CNN trained with and without inclusion of experimental backgrounds in the dataset against that of a traditional computer vision object detection algorithm, Haar-like feature detection, by analyzing data from the model experiment. Results demonstrate that including representative backgrounds in training datasets improved the mask R-CNN in differentiating between background and particle signals and elevated performance by markedly reducing false positives. The methodology for creating a labeled dataset with representative experimental backgrounds and simulated signals facilitates the application of machine learning in iSCAT experiments with strong background scattering and thus provides a useful workflow for future researchers to improve their image processing capabilities.

Axial profiling of interferometric scattering enables an accurate determination of nanoparticle size

Interferometric scattering (iSCAT) microscopy has undergone significant development in recent years. It is a promising technique for imaging and tracking nanoscopic label-free objects with nanometer localization precision. The current iSCAT-based photometry technique allows quantitative estimation for the size of a nanoparticle by measuring iSCAT contrast and has been successfully applied to nano-objects smaller than the Rayleigh scattering limit. Here we provide an alternative method that overcomes such size limitations. We take into account the axial variation of iSCAT contrast and utilize a vectorial point spread function model to uncover the position of a scattering dipole and, consequently, the size of the scatterer, which is not limited to the Rayleigh limit. We found that our technique accurately measures the size of spherical dielectric nanoparticles in a purely optical and non-contact way. We also tested fluorescent nanodiamonds (fND) and obtained a reasonable estimate for the size of fND particles. Together with fluorescence measurement from fND, we observed a correlation between the fluorescent signal and the size of fND. Our results showed that the axial pattern of iSCAT contrast provides sufficient information for the size of spherical particles. Our method enables us to measure the size of nanoparticles from tens of nanometers and beyond the Rayleigh limit with nanometer precision, making a versatile all-optical nanometric technique.

Self-supervised machine learning pushes the sensitivity limit in label-free detection of single proteins below 10 kDa

Interferometric scattering (iSCAT) microscopy is a label-free optical method capable of detecting single proteins, localizing their binding positions with nanometer precision, and measuring their mass. In the ideal case, iSCAT is limited by shot noise such that collection of more photons should extend its detection sensitivity to biomolecules of arbitrarily low mass. However, a number of technical noise sources combined with speckle-like background fluctuations have restricted the detection limit in iSCAT. Here, we show that an unsupervised machine learning isolation forest algorithm for anomaly detection pushes the mass sensitivity limit by a factor of 4 to below 10 kDa. We implement this scheme both with a user-defined feature matrix and a self-supervised FastDVDNet and validate our results with correlative fluorescence images recorded in total internal reflection mode. Our work opens the door to optical investigations of small traces of biomolecules and disease markers such as α-synuclein, chemokines and cytokines.

Simultaneous Sizing and Refractive Index Analysis of Heterogeneous Nanoparticle Suspensions

Rapid and reliable characterization of heterogeneous nanoparticle suspensions is a key technology across the nanosciences. Although approaches exist for homogeneous samples, they are often unsuitable for polydisperse suspensions, as particles of different sizes and compositions can lead to indistinguishable signals at the detector. Here, we introduce holographic nanoparticle tracking analysis, holoNTA, as a straightforward methodology that decouples size and material refractive index contributions. HoloNTA is applicable to any heterogeneous nanoparticle sample and has the sensitivity to measure the intrinsic heterogeneity of the sample. Specifically, we combined high dynamic range k-space imaging with holographic 3D single-particle tracking. This strategy enables long-term tracking by extending the imaging volume and delivers precise and accurate estimates of both scattering amplitude and diffusion coefficient of individual nanoparticles, from which particle refractive index and hydrodynamic size are determined. We specifically demonstrate, by simulations and experiments, that irrespective of localization uncertainty and size, the sizing sensitivity is improved as our extended detection volume yields considerably longer particle trajectories than previously reported by comparable technologies. As validation, we measured both homogeneous and heterogeneous suspensions of nanoparticles in the 40-250 nm size range and further monitored protein corona formation, where we identified subtle differences between the nanoparticle-protein complexes derived from avidin, bovine serum albumin, and streptavidin. We foresee that our approach will find many applications of both fundamental and applied nature where routine quantification and sizing of nanoparticles are required.

Optical Fingerprint of Flat Substrate Surface and Marker-Free Lateral Displacement Detection with Angstrom-Level Precision

We report that flat substrates such as glass coverslips with surface roughness well below 0.5 nm feature notable speckle patterns when observed with high-sensitivity interference microscopy. We uncover that these speckle patterns unambiguously originate from the subnanometer surface undulations, and develop an intuitive model to illustrate how subnanometer nonresonant dielectric features could generate pronounced interference contrast in the far field. We introduce the concept of optical fingerprint for the deterministic speckle pattern associated with a particular substrate surface area and intentionally enhance the speckle amplitudes for potential applications. We demonstrate such optical fingerprints can be leveraged for reproducible position identification and marker-free lateral displacement detection with an experimental precision of 0.22 nm. The reproducible position identification allows us to detect new nanoscopic features developed during laborious processes performed outside of the microscope. The demonstrated capability for ultrasensitive displacement detection may find applications in the semiconductor industry and superresolution optical microscopy.

Optical Detection and Imaging of Nonfluorescent Matter at the Single-Molecule/Particle Level

Since the first optical detection of single molecules in 1989, single-molecule spectroscopy has developed rapidly and been widely applied in many areas. However, the vast majority of matter is extremely inefficient at emitting photons in our physical world, which seriously limits the applications of optical methods based on photoluminescence. In addition to indirect detection by fluorescence labeling, many efforts have been made to directly image nonfluorescent matter at the single-particle or single-molecule level in different ways based on the absorption or scattering interaction between light and matter. Herein, we review five popular methods for imaging nonfluorescent particles/molecules, including dark-field microscopy (DFM), surface plasmon resonance microscopy (SPRM), surface enhanced Raman microscopy (SERM), interferometric scattering microscopy (iSCAT), and photothermal microscopy (PTM). After summarizing the principles and applications of these methods, we compare the advantages and disadvantages of each method and describe further potential development and applications.

On Some Current Challenges in High-Resolution Optical Bioimaging

In this Perspective we propose our current point of view and a suggestive roadmap on the field of high-resolution optical microscopy dedicated to bioimaging. Motivated by biological applications, researchers have indeed devised an impressive amount of strategies to address the diverse constraints of imaging and studying biological matter down to the molecular scale, making this interdisciplinary research field a vibrant forum for creativity. Throughout the discussion, we highlight several striking recent successes in this quest. We also identify some next challenges still ahead to apprehend biological questions in increasingly complex living organisms for integrative studies in a minimally invasive manner.

Multi-moded high-index contrast optical waveguide for super-contrast high-resolution label-free microscopy

The article elucidates the physical mechanism behind the generation of superior-contrast and high-resolution label-free images using an optical waveguide. Imaging is realized by employing a high index contrast multi-moded waveguide as a partially coherent light source. The modes provide near-field illumination of unlabeled samples, thereby repositioning the higher spatial frequencies of the sample into the far-field. These modes coherently scatter off the sample with different phases and are engineered to have random spatial distributions within the integration time of the camera. This mitigates the coherent speckle noise and enhances the contrast (2-10) × as opposed to other imaging techniques. Besides, the coherent scattering of the different modes gives rise to fluctuations in intensity. The technique demonstrated here is named chip-based Evanescent Light Scattering (cELS). The concepts introduced through this work are described mathematically and the high-contrast image generation process using a multi-moded waveguide as the light source is explained. The article then explores the feasibility of utilizing fluctuations in the captured images along with fluorescence-based techniques, like intensity-fluctuation algorithms, to mitigate poor-contrast and diffraction-limited resolution in the coherent imaging regime. Furthermore, a straight waveguide is demonstrated to have limited angular diversity between its multiple modes and therefore, for isotropic sample illumination, a multiple-arms waveguide geometry is used. The concepts introduced are validated experimentally via high-contrast label-free imaging of weakly scattering nanosized specimens such as extra-cellular vesicles (EVs), liposomes, nanobeads and biological cells such as fixed and live HeLa cells.

Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles

Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes.

Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel.

Progress and perspectives in single-molecule optical spectroscopy

We review some of the progress of single-molecule optical experiments in the past 20 years and propose some perspectives for the coming years. We particularly focus on methodological advances in fluorescence, super-resolution, photothermal contrast, and interferometric scattering and briefly discuss a few of the applications. These advances have enabled the exploration of new emitters and quantum optics; the chemistry and biology of complex heterogeneous systems, nanoparticles, and plasmonics; and the detection and study of non-fluorescing and non-absorbing nano-objects. We conclude by proposing some ideas for future experiments. The field will move toward more and better signals of a broader variety of objects and toward a sharper view of the surprising complexity of the nanoscale world of single (bio-)molecules, nanoparticles, and their nano-environments.

Single molecule iSCAT imaging reveals a fast, energy efficient search mode for the DNA repair protein UvrA

Exposure to UV radiation results in numerous DNA lesions, which threaten genome integrity. The nucleotide excision DNA repair pathway detects and repairs a range of such UV-induced DNA lesions. In bacteria, initial damage detection and verification is carried out by two proteins: UvrA and UvrB. Despite decades of study, the process of how these proteins locate damage remains unclear. Here we use high-speed interferometric scattering (iSCAT) microscopy, in combination with a surface-bound-DNA assay, to investigate early damage detection by UvrA. We have discovered that UvrA interacts with DNA in two phases; a slow phase (∼1.3 s^-1) that correlates with an ATP-consuming state previously identified, and a second, much faster search mode. These faster interactions persist for ∼130 ms and using ATP analogues we determine this phase does not require ATP consumption. Including this new fast-search state in a model of the DNA search process reveals that only with this state is it possible for basal levels of UvrA to explore 99% of the E. coli genome within a single division cycle. Altogether, this work uncovers the presence of a rapid, energy efficient search mechanism, which allows UvrA alone to search the entirety of the E. coli genome within a single division cycle.

The effect of stress on biophysical characteristics of misfolded protein aggregates in living Saccharomyces cerevisiae cells

Aggregation of misfolded or damaged proteins is often attributed to numerous metabolic and neurodegenerative disorders. To reveal underlying mechanisms and cellular responses, it is crucial to investigate protein aggregate dynamics in cells. Here, we used super-resolution single-molecule microscopy to obtain biophysical characteristics of individual aggregates of a model misfolded protein ∆ssCPY* labelled with GFP. We demonstrated that oxidative and hyperosmotic stress lead to increased aggregate stoichiometries but not necessarily the total number of aggregates. Moreover, our data suggest the importance of the thioredoxin peroxidase Tsa1 for the controlled sequestering and clearance of aggregates upon both conditions. Our work provides novel insights into the understanding of the cellular response to stress via revealing the dynamical properties of stress-induced protein aggregates.

Modelling of the dynamic polarizability of macromolecules for single-molecule optical biosensing

The structural dynamics of macromolecules is important for most microbiological processes, from protein folding to the origins of neurodegenerative disorders. Noninvasive measurements of these dynamics are highly challenging. Recently, optical sensors have been shown to allow noninvasive time-resolved measurements of the dynamic polarizability of single-molecules. Here we introduce a method to efficiently predict the dynamic polarizability from the atomic configuration of a given macromolecule. This provides a means to connect the measured dynamic polarizability to the underlying structure of the molecule, and therefore to connect temporal measurements to structural dynamics. To illustrate the methodology we calculate the change in polarizability as a function of time based on conformations extracted from molecular dynamics simulations and using different conformations of motor proteins solved crystalographically. This allows us to quantify the magnitude of the changes in polarizablity due to thermal and functional motions.

Tracking structural changes of protein residues by two-dimensional correlation surface-enhanced Raman spectroscopy

In-situ tracking structural changes of protein residues was developed by two-dimensional correlation surface-enhanced Raman spectroscopy (2DC-SERS). The change order of SERS fingerprints during artificial nitrification of edible bird's nest (EBN) was interpreted as the structural changes of amino acid residues. It inherently realizes reliable recognition of natural EBN and artificially dyed fakes. Both this direct structural tracking of protein residues and the indirect azo dye testing of nitrites/nitrosamines could be used as indicators for discriminating different EBN before and after the artificial dyeing. Limit of detection (LOD) for nitrite and NDMA is about 40.6 ppb and 88.1 ppb, respectively. A conceptual logical circuit of the OR gate was constructed by considering the protein structural indicator (INPUT1) and the nitrite indicator (INPUT2) as two independent inputs for automatic recognition of different EBN samples. A data-driven analog soft independent modeling (DD-SIMCA) model could quickly distinguish normal EBN from A-EBN with 98% specificity.

Voltage-gated nanofluidic devices for protein capture, concentration, and release

A nanofluidic device with spatially, non-uniformly distributed gate electrodes is reported.

Comparative Analysis of Antibodies and Heavily Glycosylated Macromolecular Immune Complexes by Size-Exclusion Chromatography Multi-Angle Light Scattering, Native Charge Detection Mass Spectrometry, and Mass Photometry

Qualitative and quantitative mass analysis of antibodies and related macromolecular immune complexes is a prerequisite for determining their identity, binding partners, stoichiometries, and affinities. A plethora of bioanalytical technologies exist to determine such characteristics, typically based on size, interaction with functionalized surfaces, light scattering, or direct mass measurements. While these methods are highly complementary, they also exhibit unique strengths and weaknesses. Here, we benchmark mass photometry (MP), a recently introduced technology for mass measurement, against native mass spectrometry (MS) and size exclusion chromatography multi-angle light scattering (SEC-MALS). We examine samples of variable complexity, namely, IgG4Δhinge dimerizing half-bodies, IgG-RGY hexamers, heterogeneously glycosylated IgG:sEGFR antibody-antigen complexes, and finally megadalton assemblies involved in complement activation. We thereby assess the ability to determine (1) binding affinities and stoichiometries, (2) accurate masses, for extensively glycosylated species, and (3) assembly pathways of large heterogeneous immune complexes. We find that MP provides a sensitive approach for characterizing antibodies and stable assemblies, with dissociation correction enabling us to expand the measurable affinity range. In terms of mass resolution and accuracy, native MS performs the best but is occasionally hampered by artifacts induced by electrospray ionization, and its resolving power diminishes when analyzing extensively glycosylated proteins. In the latter cases, MP performs well, but single-particle charge detection MS can also be useful in this respect, measuring masses of heterogeneous assemblies even more accurately. Both methods perform well compared to SEC-MALS, still being the most established method in biopharma. Together, our data highlight the complementarity of these approaches, each having its unique strengths and weaknesses.

Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins

Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.

Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin

A substantial increase in the temporal resolution of the stepping of dimeric molecular motors is possible by tracking the position of a large gold nanoparticle (GNP) attached to a labeled site on one of the heads. This technique was employed to measure the stepping trajectories of conventional kinesin (Kin1) using the time-dependent position of the GNP as a proxy. The trajectories revealed that the detached head always passes to the right of the head that is tightly bound to the microtubule (MT) during a step. In interpreting the results of such experiments, it is assumed that the GNP does not significantly alter the diffusive motion of the detached head. We used coarse-grained simulations of a system consisting of the MT-Kin1 complex with and without attached GNP to investigate how the stepping trajectories are affected. The two significant findings are: (1) The GNP does not faithfully track the position of the stepping head, and (2) the rightward bias is typically exaggerated by the GNP. Both these findings depend on the precise residue position to which the GNP is attached. Surprisingly, the stepping trajectories of kinesin are not significantly affected if, in addition to the GNP, a 1 μm diameter cargo is attached to the coiled coil. Our simulations suggest the effects of the large probe have to be considered when inferring the stepping mechanisms using GNP tracking experiments.

Anisotropic diffusion of membrane proteins at experimental timescales

Single-particle tracking (SPT) experiments of lipids and membrane proteins provide a wealth of information about the properties of biomembranes. Careful analysis of SPT trajectories can reveal deviations from ideal Brownian behavior. Among others, this includes confinement effects and anomalous diffusion, which are manifestations of both the nanoscale structure of the underlying membrane and the structure of the diffuser. With the rapid increase in temporal and spatial resolution of experimental methods, a new aspect of the motion of the particle, namely, anisotropic diffusion, might become relevant. This aspect that so far received only little attention is the anisotropy of the diffusive motion and may soon provide an additional proxy to the structure and topology of biomembranes. Unfortunately, the theoretical framework for detecting and interpreting anisotropy effects is currently scattered and incomplete. Here, we provide a computational method to evaluate the degree of anisotropy directly from molecular dynamics simulations and also point out a way to compare the obtained results with those available from SPT experiments. In order to probe the effects of anisotropic diffusion, we performed coarse-grained molecular dynamics simulations of peripheral and integral membrane proteins in flat and curved bilayers. In agreement with the theoretical basis, our computational results indicate that anisotropy can persist up to the rotational relaxation time [τ=(2D_r)^-1], after which isotropic diffusion is observed. Moreover, the underlying topology of the membrane bilayer can couple with the geometry of the particle, thus extending the spatiotemporal domain over which this type of motion can be detected.

Integrated multi-wavelength microscope combining TIRFM and IRM modalities for imaging cellulases and other processive enzymes

We describe a multimodal microscope for visualizing processive enzymes moving on immobilized substrates. The instrument combines interference reflection microscopy (IRM) with multi-wavelength total internal reflectance fluorescence microscopy (TIRFM). The microscope can localize quantum dots with a precision of 2.8 nm at 100 frames/s, and was used to image the dynamics of the cellulase, Cel7a interacting with surface-immobilized cellulose. The instrument, which was built with off-the-shelf components and is controlled by custom software, is suitable for tracking other degradative enzymes such as collagenases, as well as motor proteins moving along immobilized tracks.

A simple, switchable pili-labelling method by plasmid-based replacement of pilin

Labelling of Type IV pili (TFP) can greatly improve our understanding of the pivotal roles of TFP in a variety of bacterial activities including motility, surface sensing and DNA-uptake etc. Here we show a simple and switchable pili-labelling method by plasmid-based inducible replacement of PilA without genetic modification in bacterial genome employed by complicated methods. Using this method, we characterized pili morphology and twitching motility of Pseudomonas aeruginosa in details. More importantly, we demonstrate its application in studying the replenishment dynamics of pilin pool of P. aeruginosa.

Label-free, mass-sensitive single-molecule imaging using interferometric scattering microscopy

Single-molecule imaging has mostly been restricted to the use of fluorescence labelling as a contrast mechanism due to its superior ability to visualise molecules of interest on top of an overwhelming background of other molecules. Recently, interferometric scattering (iSCAT) microscopy has demonstrated the detection and imaging of single biomolecules based on light scattering without the need for fluorescent labels. Significant improvements in measurement sensitivity combined with a dependence of scattering signal on object size have led to the development of mass photometry, a technique that measures the mass of individual molecules and thereby determines mass distributions of biomolecule samples in solution. The experimental simplicity of mass photometry makes it a powerful tool to analyse biomolecular equilibria quantitatively with low sample consumption within minutes. When used for label-free imaging of reconstituted or cellular systems, the strict size-dependence of the iSCAT signal enables quantitative measurements of processes at size scales reaching from single-molecule observations during complex assembly up to mesoscopic dynamics of cellular components and extracellular protrusions. In this review, I would like to introduce the principles of this emerging imaging technology and discuss examples that show how mass-sensitive iSCAT can be used as a strong complement to other routine techniques in biochemistry.

Optical Biosensors for Virus Detection: Prospects for SARS-CoV-2/COVID-19

The recent pandemic of the novel coronavirus disease 2019 (COVID-19) has caused huge worldwide disruption due to the lack of available testing locations and equipment. The use of optical techniques for viral detection has flourished in the past 15 years, providing more reliable, inexpensive, and accurate detection methods. In the current minireview, optical phenomena including fluorescence, surface plasmons, surface-enhanced Raman scattering (SERS), and colorimetry are discussed in the context of detecting virus pathogens. The sensitivity of a viral detection method can be dramatically improved by using materials that exhibit surface plasmons or SERS, but often this requires advanced instrumentation for detection. Although fluorescence and colorimetry lack high sensitivity, they show promise as point-of-care diagnostics because of their relatively less complicated instrumentation, ease of use, lower costs, and the fact that they do not require nucleic acid amplification. The advantages and disadvantages of each optical detection method are presented, and prospects for applying optical biosensors in COVID-19 detection are discussed.

Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers

The quantification of membrane-associated biomolecular interactions is crucial to our understanding of various cellular processes. State-of-the-art single-molecule approaches rely largely on the addition of fluorescent labels, which complicates the quantification of the involved stoichiometries and dynamics because of low temporal resolution and the inherent limitations associated with labeling efficiency, photoblinking and photobleaching. Here, we demonstrate dynamic mass photometry, a method for label-free imaging, tracking and mass measurement of individual membrane-associated proteins diffusing on supported lipid bilayers. Application of this method to the membrane remodeling GTPase, dynamin-1, reveals heterogeneous mixtures of dimer-based oligomers, oligomer-dependent mobilities, membrane affinities and (dis)association of individual complexes. These capabilities, together with assay-based advances for studying integral membrane proteins, will enable the elucidation of biomolecular mechanisms in and on lipid bilayers.

Mass-sensitive particle tracking to elucidate the membrane-associated MinDE reaction cycle

In spite of their great importance in biology, methods providing access to spontaneous molecular interactions with and on biological membranes have been sparse. The recent advent of mass photometry to quantify mass distributions of unlabeled biomolecules landing on surfaces raised hopes that this approach could be transferred to membranes. Here, by introducing a new interferometric scattering (iSCAT) image processing and analysis strategy adapted to diffusing particles, we enable mass-sensitive particle tracking (MSPT) of single unlabeled biomolecules on a supported lipid bilayer. We applied this approach to the highly nonlinear reaction cycles underlying MinDE protein self-organization. MSPT allowed us to determine the stoichiometry and turnover of individual membrane-bound MinD/MinDE protein complexes and to quantify their size-dependent diffusion. This study demonstrates the potential of MSPT to enhance our quantitative understanding of membrane-associated biological systems.

Computational nanosensing from defocus in single particle interferometric reflectance microscopy

Single particle interferometric reflectance (SPIR) microscopy has been studied as a powerful imaging platform for label-free and highly sensitive biological nanoparticle detection and characterization. SPIR's interferometric nature yields a unique 3D defocus intensity profile of the nanoparticles over a large field of view. Here, we utilize this defocus information to recover high signal-to-noise ratio nanoparticle images with a computationally and memory efficient reconstruction framework. Our direct inversion approach recovers this image from a 3D defocus intensity stack using the vectorial-optics-based forward model developed for sub-diffraction-limited dielectric nanoparticles captured on a layered substrate. We demonstrate proof-of-concept experiments on silica beads with a 50 nm nominal diameter.

High-Precision Protein-Tracking With Interferometric Scattering Microscopy

The mobility of proteins and lipids within the cell, sculpted oftentimes by the organization of the membrane, reveals a great wealth of information on the function and interaction of these molecules as well as the membrane itself. Single particle tracking has proven to be a vital tool to study the mobility of individual molecules and unravel details of their behavior. Interferometric scattering (iSCAT) microscopy is an emerging technique well-suited for visualizing the diffusion of gold nanoparticle-labeled membrane proteins to a spatial and temporal resolution beyond the means of traditional fluorescent labels. We discuss the applicability of interferometric single particle tracking (iSPT) microscopy to investigate the minutia in the motion of a protein through measurements visualizing the mobility of the epidermal growth factor receptor in various biological scenarios on the live cell.

Single molecule mass photometry of nucleic acids

Mass photometry is a recently developed methodology capable of measuring the mass of individual proteins under solution conditions. Here, we show that this approach is equally applicable to nucleic acids, enabling their facile, rapid and accurate detection and quantification using sub-picomoles of sample. The ability to count individual molecules directly measures relative concentrations in complex mixtures without need for separation. Using a dsDNA ladder, we find a linear relationship between the number of bases per molecule and the associated imaging contrast for up to 1200 bp, enabling us to quantify dsDNA length with up to 2 bp accuracy. These results introduce mass photometry as an accurate, rapid and label-free single molecule method complementary to existing DNA characterization techniques.

3D tracking of extracellular vesicles by holographic fluorescence imaging

Fluorescence microscopy is the method of choice in biology for its molecular specificity and super-resolution capabilities. However, it is limited to a narrow z range around one observation plane. Here, we report an imaging approach that recovers the full electric field of fluorescent light with single-molecule sensitivity. We expand the principle of digital holography to fast fluorescent detection by eliminating the need for phase cycling and enable three-dimensional (3D) tracking of individual nanoparticles with an in-plane resolution of 15 nm and a z-range of 8 mm. As a proof-of-concept biological application, we image the 3D motion of extracellular vesicles (EVs) inside live cells. At short time scales (<4 s), we resolve near-isotropic 3D diffusion and directional transport. For longer lag times, we observe a transition toward anisotropic motion with the EVs being transported over long distances in the axial plane while being confined in the horizontal dimension.

More than a feeling: microscopy approaches to understanding surface-sensing mechanisms

The mechanisms by which bacteria sense and respond to surface attachment have long been a mystery. Our understanding of the structure and dynamics of bacterial appendages, notably type IV pili (T4P), provided new insights into the potential ways that bacteria sense surfaces. T4P are ubiquitous, retractable hair-like adhesins that until recently were difficult to image in the absence of fixation due to their nanoscale size. This review focuses on recent microscopy innovations used to visualize T4P in live cells to reveal the dynamics of their retraction and extension. We discuss recently proposed mechanisms by which T4P facilitate bacterial surface sensing, including the role of surface-exposed PilY1, two-component signal transduction pathways, force-induced structural modifications of the major pilin, and altered dynamics of the T4P motor complex.

Tracking Interfacial Dynamics of a Single Nanoparticle Using Plasmonic Scattering Interferometry

The ability to track interfacial dynamics of a single nanoparticle at the solution-solid interface is crucial for understanding physical, chemical, and biological processes, but it remains a challenge. Here, we demonstrated a plasmonic imaging technique that can track unlabeled nanoparticles at the solution-solid interface with high spatial and temporal resolutions. This technique is based on particle-induced interferometric scattering of a surface plasmonic wave, which results in a high vertical sensitivity. Using this ability, we tracked the trajectories of a single nanoparticle interacting with a surface, measured the hydrodynamically hindered diffusion of nanoparticles, and revealed the surface chemistry-dependent behavior of nanoparticles at the interface. The application for tracking formation of membranes from a lipid vesicle was demonstrated, indicating the potential for investigating a broad range of nano-objects at interfaces in a complex environment.

Single-Molecule Biophysical Techniques to Study Actomyosin Force Transduction

Inside the cellular environment, molecular motors can work in concert to conduct a variety of important physiological functions and processes that are vital for the survival of a cell. However, in order to decipher the mechanism of how these molecular motors work, single-molecule microscopy techniques have been popular methods to understand the molecular basis of the emerging ensemble behavior of these motor proteins.In this chapter, we discuss various single-molecule biophysical imaging techniques that have been used to expose the mechanics and kinetics of myosins. The chapter should be taken as a general overview and introductory guide to the many existing techniques; however, since other chapters will discuss some of these techniques more thoroughly, the readership should refer to those chapters for further details and discussions. In particular, we will focus on scattering-based single-molecule microscopy methods, some of which have become more popular in the recent years and around which the work in our laboratories has been centered.

Resonant scattering enhanced interferometric scattering microscopy

Interferometric scattering (iSCAT) microscopy is a powerful tool for high-sensitive label-free imaging and sensing of nano-objects with high spatial-temporal resolution. The nano-objects imaged with the current iSCAT microscopy are usually non-resonant under laser light illumination and the iSCAT signal contrast is simply proportional to the volume and weight of the objects of interest. Here in this paper, we developed a novel strategy of resonant scattering enhanced iSCAT microscopy where the imaged nanoparticles are near resonant under laser light illumination, and we demonstrated it by using gold nanorods (NRs) with tunable longitudinal surface plasmon resonances. The obtained iSCAT signal contrast shows a dramatic variation in the narrow resonance wavelength range as small as 20 nm, and this is attributed to the strong wavelength dependence of the polarizability of gold NRs under optical resonance conditions. Different factors that have contributed to the iSCAT signal are theoretically analyzed and numerically simulated, providing the basic understanding about the effect of optical resonance on the iSCAT signal of nanoparticles. Our novel work provides a promising approach toward resonant sensing, imaging, and spectroscopy of nanoscopic objects.

How Myosin 5 Walks Deduced from Single-Molecule Biophysical Approaches

Myosin 5a is a two-headed myosin that functions as a cargo transporter in cells. To accomplish this task it has evolved several unique structural and kinetic features that allow it to move processively as a single molecule along actin filaments. A plethora of biophysical techniques have been used to elucidate the detailed mechanism of its movement along actin filaments in vitro. This chapter describes how this mechanism was deduced.

Sensing Biomolecular Interactions by the Luminescence of a Planar Gold Film

We describe the operating principle and performance of a recently developed surface plasmon-enhanced optical sensor that utilizes two-photon excited luminescence of a planar gold film as the reporter signal. The sensor enables direct visualization of nanoscopic binding events near a sensing surface. Light is coupled to the Au/sample interface in an objective-based Kretschmann configuration to excite surface plasmon polariton (SPP) modes at a metal-dielectric interface. The gold luminescence induced by the confined optical field between the particle and the film is detected in the epi-direction by a far-field camera where individual binding events show up as diffraction limited bright spots against a dark background. We study the sensor's emission spectrum and the distance dependence between the target and substrate, which both suggest that the optical signal of the sensor originates from electron-hole pair excitations in the planar Au film. In addition, we show that the well-behaved pointspread function of the sensor enables a straightforward implementation of super-resolution techniques. Finally, we demonstrate the utility of the sensor for detecting DNA binding events, underlining the sensor's usefulness for label-free imaging of nanoscopic particles and biomolecular interactions.