Single-nanoparticle near-infrared surface plasmon resonance microscopy for real-time measurements of DNA hybridization adsorption

Cascaded momentum-space polarization filters enabled label-free black-field microscopy for single nanoparticles analysis

Label-free optical imaging of single-nanometer-scale matter is extremely important for a variety of biomedical, physical, and chemical investigations. One central challenge is that the background intensity is much stronger than the intensity of the scattering light from single nano-objects. Here, we propose an optical module comprising cascaded momentum-space polarization filters that can perform vector field modulation to block most of the background field and result in an almost black background; in contrast, only a small proportion of the scattering field is blocked, leading to obvious imaging contrast enhancement. This module can be installed in various optical microscopies to realize a black-field microscopy. Various single nano-objects with dimensions smaller than 20 nm appear distinctly in the black-field images. The chemical reactions occurring on single nanocrystals with edge lengths of approximately 10 nm are in situ real-time monitored by using the black-field microscopy. This label-free black-field microscopy is highly promising for a wide range of future multidisciplinary science applications.

Plasmonic Probing of Deoxyribonucleic Acid Hybridization at the Single Base Pair Resolution

Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.

Deep Learning Approach for the Localization and Analysis of Surface Plasmon Scattering

Surface plasmon resonance microscopy (SPRM) combines the principles of traditional microscopy with the versatility of surface plasmons to develop label-free imaging methods. This paper describes a proof-of-principles approach based on deep learning that utilized the Y-Net convolutional neural network model to improve the detection and analysis methodology of SPRM. A machine-learning based image analysis technique was used to provide a method for the one-shot analysis of SPRM images to estimate scattering parameters such as the scatterer location. The method was assessed by applying the approach to SPRM images and reconstructing an image from the network output for comparison with the original image. The results showed that deep learning can localize scatterers and predict other variables of scattering objects with high accuracy in a noisy environment. The results also confirmed that with a larger field of view, deep learning can be used to improve traditional SPRM such that it localizes and produces scatterer characteristics in one shot, considerably increasing the detection capabilities of SPRM.

The Employment of the Surface Plasmon Resonance (SPR) Microscopy Sensor for the Detection of Individual Extracellular Vesicles and Non-Biological Nanoparticles

A wide-field surface plasmon resonance (SPR) microscopy sensor employs the surface plasmon resonance phenomenon to detect individual biological and non-biological nanoparticles. This sensor enables the detection, sizing, and quantification of biological nanoparticles (bioNPs), such as extracellular vesicles (EVs), viruses, and virus-like particles. The selectivity of bioNP detection does not require biological particle labeling, and it is achieved via the functionalization of the gold sensor surface by target-bioNP-specific antibodies. In the current work, we demonstrate the ability of SPR microscopy sensors to detect, simultaneously, silica NPs that differ by four times in size. Employed silica particles are close in their refractive index to bioNPs. The literature reports the ability of SPR microscopy sensors to detect the binding of lymphocytes (around 10 μm objects) to the sensor surface. Taken together, our findings and the results reported in the literature indicate the power of SPR microscopy sensors to detect bioNPs that differ by at least two orders in size. Modifications of the optical sensor scheme, such as mounting a concave lens, help to achieve homogeneous illumination of a gold sensor chip surface. In the current work, we also characterize the improved magnification factor of the modified SPR instrument. We evaluate the effectiveness of the modified and the primary version of the SPR microscopy sensors in detecting EVs isolated via different approaches. In addition, we demonstrate the possibility of employing translation and rotation stepper motors for precise adjustments of the positions of sensor optical elements-prism and objective-in the primary version of the SPR microscopy sensor instrument, and we present an algorithm to establish effective sensor-actuator coupling.

Investigating the hygroscopicities of calcium and magnesium salt particles aged with SO2 using surface plasmon resonance microscopy

The hygroscopicities of calcium and magnesium salts strongly affect the environment and climate, but the aging products of these salts at high relative humidities (RHs) are still poorly understood. In this study, surface plasmon resonance microscopy (SPRM) was used to determine the hygroscopic growth factors (GFs) of Ca(NO₃)₂ and Mg(NO₃)₂ separately or mixed with galactose at different mass ratios at different RHs before and after aging. For all particles, the measured GFs showed no indication of deliquescence across the range of RHs tested, and overall hygroscopicity was clearly lower after than before aging. The Ca(NO₃)₂ and Mg(NO₃)₂ GFs at 90 % RH were 1.80 and 1.66, respectively, before aging and 1.33 and 1.42, respectively, after 4 h aging, meaning aging decreased the GFs by 26.11 % and 14.46 %, respectively. Aging decreased the hygroscopicity because insoluble or sparingly soluble substances (CaSO₃, CaSO₄, MgSO₃) formed and strongly changed the overall hygroscopicity. For bicomponent aerosols with different mass ratios, the GFs (calculated using the Zdanovskii-Stokes-Robinson method) of the other components except galactose at 90 % RH after 1 h aging were all lower, respectively, than the measured GFs of pure Ca(NO₃)₂ and Mg(NO₃)₂ after aging for 1 h, especially with the mass ratio of 1:2, their GFs have decreased by 14.63 % and 7.50 %, respectively. Subsequently, Ion chromatograms indicated that the peak area ratio of SO₄^2- to NO₃^- ratios were higher for the aged bicomponent particles than aged single-component particles, possibly because adding galactose improved the gas-liquid state stability during drying after the aging process and therefore promoted nitrate consumption and sulfate formation. The results indicated that organic components may play important roles in heterogeneous reactions between trace gases and multicomponent aerosols and should be considered in evaluating the impacts on submicron aerosol composition of high atmospheric SO₂ concentrations at high humidities.

Recent advances in surface plasmon resonance imaging and biological applications

Surface Plasmon Resonance Imaging (SPRI) is a robust technique for visualizing refractive index changes, which enables researchers to observe interactions between nanoscale objects in an imaging manner. In the past period, scholars have been attracted by the Prism-Coupled and Non-prism Coupled configurations of SPRI and have published numerous experimental results. This review describes the principle of SPRI and discusses recent developments in Prism-Coupled and Non-prism Coupled SPRI techniques in detail, respectively. And then, major advances in biological applications of SPRI are reviewed, including four sub-fields (cells, viruses, bacteria, exosomes, and biomolecules). The purpose is to briefly summarize the recent advances of SPRI and provide an outlook on the development of SPRI in various fields.

Live Cells versus Fixated Cells: Kinetic Measurements of Biomolecular Interactions with the LigandTracer Method and Surface Plasmon Resonance Microscopy

Cell-based kinetic studies of ligand or candidate drug binding to membrane proteins have produced affinity and kinetic values that are different from measurements using purified proteins. However, ligand binding to fixated cells whose membrane constituents (e.g., proteins and their glycosylated forms) are partially connected by a cross-linking reagent has not been compared to that to live cells. Under the same experimental conditions for the LigandTracer method, we measured the interactions of fluorophore-labeled lectins and antibody molecules with glycans at HFF cells and the human epithelial growth receptor 2 at SKBR3 cells, respectively. In conjunction with surface plasmon resonance microscopy, the effects of labels and cell/sub-cell heterogeneity on binding kinetics were investigated. Our results revealed that, for cell constituents whose structures and functions are not closely dependent on cell viability, the ligand binding kinetics at fixated cells is only slightly different from that at live cells. The altered kinetics is explained on the basis of a less mobile receptor confined in a local environment created by partially interconnected protein molecules. We show that cell/sub-cell heterogeneity and labels on the ligands can alter the binding reaction more significantly. Thus, fixating cells not only simplifies experimental procedures for drug screening and renders assays more robust but also provides reliable kinetic information about drug binding to cell constituents whose structures are not changed by chemical fixation.

Surface Plasmon Resonance Microscopy Based on Total Internal Reflection

Surface plasmon resonance microscopy (SPRM) has been widely employed in biological fields because of its high spatial resolution and label-free detection modality. In this study, SPRM based on total internal reflection (TIR) is studied via a home-built SPRM system, and the principle of imaging of a single nanoparticle is analyzed as well. By designing a ring filter and combining it with the deconvolution algorithm in Fourier space, the parabolic tail of the nanoparticle image is removed, in which a spatial resolution of 248 nm is obtained. In addition, we also measured the specific binding between the human IgG antigen and goat anti-human IgG antibody using the TIR-based SPRM. The experimental results have proved that the system can image sparse nanoparticles and monitor biomolecular interactions.

Microfluidically Partitioned Dual Channels for Accurate Background Subtraction in Cellular Binding Studies by Surface Plasmon Resonance Microscopy

Unlike conventional surface plasmon resonance (SPR) using an antifouling film to anchor biomolecules and a reference channel for background subtraction, SPR microscopy for single-cell analysis uses a protein- or polypeptide-modified gold substrate to immobilize cells and a cell-free area as the reference. In this work, we show that such a substrate is prone to nonspecific adsorption (NSA) of species from the cell culture media, resulting in false background signals that cannot be correctly subtracted. To obtain accurate kinetic results, we patterned a dual-channel substrate using a microfluidic device, with one channel having poly-l-lysine deposited in situ onto a preformed polyethylene glycol (PEG) self-assembled monolayer for cell immobilization and the other channel remaining as PEG-covered for reference. The two 2.0 mm-wide channels are separated by a 75 μm barrier, and parts of the channels can be readily positioned into the field of view of an SPR microscope. The use of this dual-channel substrate for background subtraction is contrasted with the conventional approach through the following binding studies: (1) wheat germ agglutinin (WGA) attachment to the N-acetyl glucosamine and N-acetyl-neuraminic acid sites of glycans on HFF cells, and (2) the S1 protein of the COVID-19 virus conjugation with angiotensin-converting enzyme 2 (ACE2) on the HEK293 cells. Both studies revealed that interferences by NSA and the surface plasmon polariton wave diffracted by cells can be excluded with the dual-channel substrate, and the much smaller refractive index changes caused by the injected solutions can be correctly subtracted. Consequently, sensorgrams with higher signal-to-noise ratios and shapes predicted by the correct binding model can be obtained with accurate kinetic and affinity parameters that are more biologically relevant. The affinity between S1 protein and ACE2 is comparable to that measured with recombinant ACE2, yet the binding kinetics is different, suggesting that the cell membrane does impose a kinetic barrier to their interaction.

Single-Particle Electrochemical Imaging Provides Insights into Silver Nanoparticle Dissolution at the Solution-Solid Interface

Dissolution of nanoparticles is an environmental interfacial process that affects the transformation of nanoparticles. Understanding the dissolution processes of nanoparticles is important to predict their fate in the aquatic environment. However, studying nanoparticle dissolution kinetics is still challenging since dissolution is usually coupled with nanoparticle aggregation. Here, we probed the dissolution process of Ag nanoparticles at the single-particle level by surface plasmon resonance microscopy. The single-particle imaging capability enabled us to classify Ag nanoparticles, measure the dissolution dynamics of single nanoparticles, and correlate the aggregation size with oxidation activity. Moreover, we studied the dual effect of natural organic matter on the dissolution of Ag nanoparticles and validated this result with real natural freshwater. Our study provides new insights into the dissolution of Ag nanoparticles, and this technique can be extended for other nanomaterials to evaluate their fate in aquatic environments.

Chemical-Based Surface Plasmon Resonance Imaging of Fingerprints

Fingerprints are extremely useful in personal identification; however, they are usually based on physical rather than chemical images because it remains a challenge to reveal a clear chemical fingerprint easily and sensitively. Herein, a surface plasmon resonance imaging (SPRi) method, combined with a chemically selective stepwise signal amplification (CS³A) strategy, is proposed to chemically image fingerprints with adjustable sensitivity and clarity. High-fidelity glucose-associated fingerprint images were obtained at five to seven cycles of CS³A based on the recognition reaction of concanavalin A (ConA) with dextran. The method is also extendable to image substances that possess and/or can be tagged with ConA- or dextran-recognizable groups. For demonstration, SPRi of carboxylic substances was conducted by amidating the carboxyl group with glucosamine to enable the ConA-based CS³A. Glucose- and carboxyl-based fingerprints were simultaneously and clearly imaged, allowing us to perform quantitative analysis of the representative of either glucose or amino acid (e.g., serine) or both. The curves measured from the standard spots were linear in the ranges of 1-4000 μM for glucose and 3.2-4000 μM for serine, with linear correlated coefficients of 0.9979 and 0.9962, respectively. It was then applied to the study of metabolic secretions in fingerprints during running exercise, yielding variation tendencies similar to those measured from sweat samples in the literature. As a noninvasive tool, the CS³A-coupled SPRi reveals both clear images of fingerprints and quantitative chemical information, and it is anticipated to become a competitive new method for chemically imaging fingerprints.

Single-Molecule Junction: A Reliable Platform for Monitoring Molecular Physical and Chemical Processes

Monitoring and manipulating the physical and chemical behavior of single molecules is an important development direction of molecular electronics that aids in understanding the molecular world at the single-molecule level. The electrical detection platform based on single-molecule junctions can monitor physical and chemical processes at the single-molecule level with a high temporal resolution, stability, and signal-to-noise ratio. Recently, the combination of single-molecule junctions with different multimodal control systems has been widely used to explore significant physical and chemical phenomena because of its powerful monitoring and control capabilities. In this review, we focus on the applications of single-molecule junctions in monitoring molecular physical and chemical processes. The methods developed for characterizing single-molecule charge transfer and spin characteristics as well as revealing the corresponding intrinsic mechanisms are introduced. Dynamic detection and regulation of single-molecule conformational isomerization, intermolecular interactions, and chemical reactions are also discussed in detail. In addition to these dynamic investigations, this review discusses the open challenges of single-molecule detection in the fields of physics and chemistry and proposes some potential applications in this field.

Detecting Pb2+by a 'turn-on' fluorescence sensor based on DNA functionalized magnetic nanocomposites

Sensitive and selective detection of the lead ion (Pb²⁺) plays an important role in terms of both human health and environmental protection, as the heavy metal is fairly ubiquitous and highly toxic. The highly stable fluorescence biosensor is composed of Fe₃O₄@TiO₂core-shell nanocomposites, functionalized with a carboxyl fluorescein labeled DNA. The morphology, physical and chemical properties of the sensing nanomaterials were studied by transmission electron microscopy, FT-IR spectroscopy (FT-IR), x-ray powder diffraction and vibrating sample magnetometer. UV-visible and fluorescence spectroscopy were used to characterize the fluorescein functionalized magnetic nanoparticles. The performance of Pb²⁺detection displayed an excellent linearity (R² = 0.995) in the range of 10^-10to 5 × 10^-9ppm with a detection limit of 10^-10ppm, based on the optimization of the fabrication process and aptamers' specification. The fluorescence biosensor has an accurate response, excellent recoveries and high adsorbent capacities. It was successfully applied for the determination of Pb²⁺in contaminated water and serum samples; the detection of limit in both media were 10^-10ppm. These features ensure the potential use of aptamer functionalized magnetic nanocomposites as a new class of non-toxic biocompatible sensors for biological and environmental applications.

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.

Engineering plasmon modes and their loss in armchair graphene nanoribbons by selected edge-extended defects

The effect of edge modification of armchair graphene nanoribbons (AGNRs) on the collective excitations are theoretically investigated. The tight-binding method is employed in conjunction with the dielectric function. Unconventional plasmon modes and their association with the flat bands of the specially designed AGNRs are thoroughly studied. We demonstrate the robust relationship between the novel collective excitations and both the type and period of the edge modification. Additionally, we reveal that the main features displayed in the (momentum, frequency)-phase diagrams for both single-particle and collective excitations of AGNRs can be efficiently tuned by edge-extended defects. Our obtained plasmon modes are found to be analogous to magnetoplasmons associated with collective excitations of Landau-quantized electrons. This work provides a unique way to engineer discrete magnetoplasmon-like modes of AGNRs in the absence of magnetic field.

Detection of Tumor DNA in Human Plasma with a Functional PLL-Based Surface Layer and Plasmonic Biosensing

Standard protocols for the analysis of circulating tumor DNA (ctDNA) include the isolation of DNA from the patient's plasma and its amplification and analysis in buffered solutions. The application of such protocols is hampered by several factors, including the complexity and time-constrained preanalytical procedures, risks for sample contamination, extended analysis time, and assay costs. A recently introduced nanoparticle-enhanced surface plasmon resonance imaging-based assay has been shown to simplify procedures for the direct detection of tumor DNA in the patient's plasma, greatly simplifying the cumbersome preanalytical phase. To further simplify the protocol, a new dual-functional low-fouling poly-l-lysine (PLL)-based surface layer has been introduced that is described herein. The new PLL-based layer includes a densely immobilized CEEEEE oligopeptide to create a charge-balanced system preventing the nonspecific adsorption of plasma components on the sensor surface. The layer also comprises sparsely attached peptide nucleic acid probes complementary to the sequence of circulating DNA, e.g., the analyte that has to be captured in the plasma from cancer patients. We thoroughly investigated the contribution of each component of the dual-functional polymer to the antifouling properties of the surface layer. The low-fouling property of the new surface layer allowed us to detect wild-type and KRAS p.G12D-mutated DNA in human plasma at the attomolar level (∼2.5 aM) and KRAS p.G13D-mutated tumor DNA in liquid biopsy from a cancer patient with almost no preanalytical treatment of the patient's plasma, no need to isolate DNA from plasma, and without PCR amplification of the target sequence.

Revealing Conformational Transition Dynamics of Photosynthetic Proteins in Single-Molecule Electrical Circuits

The function of proteins depends on their structural flexibility and conformational change. By utilizing silicon-nanowire-based single-molecule electrical circuits, here we present a label-free real-time measurement method that can directly monitor conformational changes of a photosynthetic LH1-RC complex, reaching the ultimate goal of analytic chemistry. These results manifest that the conformation of the LH1-RC complex vibrates among four conformations with strong temperature dependence. At the optimal temperature, States 2 and 3 occupy the main conformations of the LH1-RC complex, and its conformational variation mostly emerges as anharmonic vibration modes, which contributes to photon acquisition and heat transmission. The influence of light activation on occurrence percentage is observed, resulting from light-driven quivering of pigments. Therefore, this avenue proves to be an efficient platform for revealing the fundamental mechanisms of various biological processes in vitro.

A Bubble-STORM Approach for Super-Resolved Imaging of Nucleation Sites in Hydrogen Evolution Reactions

Stochastic optical reconstruction microscopy (STORM) is a powerful strategy to achieve super-resolved imaging of biological structures by virtue of the stochastic photoactivation of fluorophores and superlocalization algorithm. Herein, we report a fluorophore-free bubble-STORM approach for super-resolved imaging of nucleation sites in hydrogen evolution reactions (HER). When applying an appropriate pulse potential to the electrode, rapid electro-reduction of protons created a local oversaturation of hydrogen molecules and thus the nucleation of sparsely distributed hydrogen nanobubbles. A surface plasmon resonance microscopy was employed to monitor the process and report the localization of each nanobubble via superlocalization fitting. The withdrawal of electrode potential, or the microconvection, led to the immediate disappearance of nanobubbles and recovered the electrode surface before the next pulse. By repeating the procedures for thousands of cycles, one was able to reconstruct a map of nucleation sites with a spatial resolution beyond the optical diffraction limit. This approach does not require a model fluorogenic reaction or fluorescent labeling to the nanobubbles, thus revealing the intrinsic nucleation sites in the natural states. Our results further indicated the fast growth, coalescence, and detachment behaviors of nanobubbles on a time scale of sub-milliseconds, underscoring the significance of high temporal resolution for studying nanobubble nucleation.

Complex Resonant Scattering Behavior in the Surface Plasmon Resonance Imaging Microscopy of Single Gold Nanorods

Diffraction patterns observed in surface plasmon resonance imaging (SPRI) microscopy measurements of single gold nanorods (AuNRs) exhibit a complex behavior at wavelengths near the longitudinal plasmonic resonance band. SPRI microscopy measurements at 814 nm from AuNRs in three samples with resonance extinction maxima at 670, 816, and 980 nm reveal a variety of diffraction patterns with central peaks that are either positive, negative, or biphasic. A unitless ratio parameter M_R (-1 ≤ M_R ≤ 1) is created to describe the distribution of diffraction patterns. A purely negative (M_R = -1) central peak is observed for 30%, 57%, and 98% of the diffraction patterns in the 670, 816, and 980 nm samples, respectively. These results along with a theoretical modeling of the diffraction patterns with an anisotropic complex scattering coefficient suggests that this behavior only occurs for AuNRs when the laser wavelength used in SPRI experiments is shorter than the AuNR plasmonic resonance maxima, that is, in the anomalous dispersion region.

Individual Plasmonic Nanoprobes for Biosensing and Bioimaging: Recent Advances and Perspectives

With the advent of nanofabrication techniques, plasmonic nanoparticles (PNPs) have been widely applied in various research fields ranging from photocatalysis to chemical and bio-sensing. PNPs efficiently convert chemical or physical stimuli in their local environment into optical signals. PNPs also have excellent properties, including good biocompatibility, large surfaces for the attachment of biomolecules, tunable optical properties, strong and stable scattering light, and good conductivity. Thus, single optical biosensors with plasmonic properties enable a broad range of uses of optical imaging techniques in biological sensing and imaging with high spatial and temporal resolution. This work provides a comprehensive overview on the optical properties of single PNPs, the description of five types of commonly used optical imaging techniques, including surface plasmon resonance (SPR) microscopy, surface-enhanced Raman scattering (SERS) technique, differential interference contrast (DIC) microscopy, total internal reflection scattering (TIRS) microscopy, and dark-field microscopy (DFM) technique, with an emphasis on their single plasmonic nanoprobes and mechanisms for applications in biological imaging and sensing, as well as the challenges and future trends of these fields.

Identification of Small-Molecule Regulators of Testicular Receptor 4 via a Drug Repurposing Screening

The testicular receptor 4 (TR4) is a nuclear receptor implicated in multiple pathological processes, including cancer development, chemotherapy, and radiotherapy resistance. However, no effective TR4 small-molecule regulator is available to date. Here, we assessed a physical-interaction-based surface plasmon resonance imaging assay for discovery of TR4 regulators. We screened 1018 FDA-approved drugs and obtained 126 drugs with K _D values below 10^-6 M. The dual-luciferase-based biological assay verified four activatory compounds and two inhibitory compounds against TR4. Among them, nilotinib exhibited the most potent inhibitor, with an EC₅₀ of 1.05 μM, while genistein represented the most potent activator, with an EC₅₀ of 2.42 μM. Both drugs were predicted to bind in the ligand binding pocket of TR4. The circular dichroism spectroscopic assay revealed differed conformation changes upon nilotinib or genistein binding. These results established our combined physical and biological approaches as a highly effective way to identify and develop new TR4 regulators.

High-performance imaging of cell-substrate contacts using refractive index quantification microscopy

Non-invasive imaging of living cells is an advanced technique that is widely used in the life sciences and medical research. We demonstrate a refractive index quantification microscopy (RIQM) that enables label-free studies of glioma cell-substrate contacts involving cell adhesion molecules and the extracellular matrix. This microscopy takes advantage of the smallest available spot created when an azimuthally polarized perfect optical vortex beam (POV) is tightly focused with a first-order spiral phase, which results in a relatively high imaging resolution among biosensors. A high refractive index (RI) resolution enables the RI distribution within neuronal cells to be monitored. The microscopy shows excellent capability for recognizing cellular structures and activities, demonstrating great potential in biological sensing and live-cell kinetic imaging.

Critical Review: digital resolution biomolecular sensing for diagnostics and life science research

One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.

Real-Time Measurement of the Hygroscopic Growth Dynamics of Single Aerosol Nanoparticles with Bloch Surface Wave Microscopy

The growth in aerosol particles caused by water uptake during increasing ambient relative humidity alters the physical and chemical properties of aerosols, which then affects public health, atmospheric chemistry, and the Earth's climate. The temporal resolution and sensitivity of current techniques are not sufficient to measure the growth dynamics of single aerosol nanoparticles. Additionally, the specific time required for phase transition from solid to aqueous has not been measured. Here, we describe a label-free photonic microscope that uses the Bloch surface waves as the illumination source for imaging and sensing to provide real-time measurements of the hygroscopic growth dynamics of a single aerosol (diameter <100 nm) containing the main components of air pollution. This specific time can be measured for both pure and mixed aerosols, showing that organics will delay the phase transition. This photonic microscope can be extended to investigate physicochemical reactions of various aerosols, and then knowing this specific time will be favorable for understanding the reaction kinetics among single aerosols and the surrounding medium.

Transmission enhanced SPR nano-microscope

We propose a transmission enhanced surface plasmon resonance nano-microscope. The nano-microscope is prepared at the cone-frustum-shaped annular-core fiber (ACF) end by mechanical polishing at the end of the ACF, and the gold film deposition on this end surface through magnetron sputtering technology obtains an excited surface plasmon resonance (SPR) that can direct to the center along the radial direction of the fiber. The cone-frustum-shaped ACF end surface is taken as a stage, and with the advantage of the SPR resonance enhancement effect, the ordinary microscope can realize nano-imaging. The imaging experiment results of 300nm polystyrene nano-spheres show that this auxiliary microscopic imaging technology can break through the diffraction limit and can eliminate the smear image caused by the surface plasmon wave (SPW) illumination in a single direction.

Phase imaging of transition from classical to quantum plasmonic couplings between a metal nanoparticle and a metal surface

When a metal nanoparticle is brought near to a metal surface within electron tunneling distance (∼1 nm), classical electromagnetic coupling between the nanoparticle and the metal is expected to transition to quantum coupling. We show that this transition can be observed as a drastic phase change in the surface plasmon resonance (SPR) images of the gold nanoparticles. We study the transition by controlling the distance between the nanoparticles and electrode surface, modeling the impact of the transition on the SPR image in terms of a phase shift and demonstrating detection of microRNA based on the transition from classical to quantum coupling. The work shows that the quantum coupling can be directly visualized in SPR, and the extremely sensitive dependence of the transition on distance leads to a biosensing principle with SPR.

Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays

The ability to detect low concentrations of analytes and in particular low-abundance biomarkers is of fundamental importance, e.g., for early-stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single-molecule bioaffinity assays. While many review articles have highlighted the potentials of single-molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real-world applications as one should expect. This Review provides a theoretical background on single-molecule-or better digital-assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single-molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.

Surface Plasmon Resonance Microscopy: From Single-Molecule Sensing to Single-Cell Imaging

Surface plasmon resonance microscopy (SPRM) is a versatile platform for chemical and biological sensing and imaging. Great progress in exploring its applications, ranging from single-molecule sensing to single-cell imaging, has been made. In this Minireview, we introduce the principles and instrumentation of SPRM. We also summarize the broad and exciting applications of SPRM to the analysis of single entities. Finally, we discuss the challenges and limitations associated with SPRM and potential solutions.

Single-Molecule Electrical Detection: A Promising Route toward the Fundamental Limits of Chemistry and Life Science

The ultimate limit of analytical chemistry is single-molecule detection, which allows one to visualize the dynamic processes of chemical/biological interactions with single-molecule or single-event sensitivity and hence enables the study of stochastic fluctuations under equilibrium conditions and the observation of time trajectories and reaction pathways of individual species in nonequilibrated systems. In addition, such studies may also allow the direct observation of novel microscopic quantum effects and fundamental discoveries of underlying molecular mechanisms in organic reactions and biological processes that are not accessible in ensemble experiments, thus providing unique opportunities to solve the key problems of physical, chemical, and life sciences. Consequently, the field of single-molecule detection has received considerable attention and has witnessed tremendous advances in different directions in combination with other disciplines. This Account describes our ongoing work on the development of groundbreaking methods (termed "single-molecule electrical approaches") of translating the detailed processes of chemical reactions or biological functions into detectable electrical signals at the single-event level on the platform of single-molecule electronic devices, with a particular focus on graphene-molecule-graphene single-molecule junctions (GMG-SMJs) and silicon-nanowire-based single-molecule electrical nanocircuits. These nanocircuit-based architectures are complementary to conventional optical or mechanical techniques but exhibit obvious advantages such as the absence of problems associated with bleaching and fluorescent labeling. Dash-line lithography (DLL) is an efficient lithographic method of cutting graphene and forming carboxylic-acid-functionalized nanogapped graphene point contact arrays developed to address the formidable challenges of molecular device fabrication difficulty and poor stability. Molecules of interest terminated by amines on both ends can be covalently sandwiched between graphene point contacts to create high-throughput robust GMG-SMJs containing only one molecule as the conductive element. In conjunction with the ease of device fabrication and device stability, this feature distinguishes GMG-SMJs as a new testbed platform for single-molecule analysis characterized by high temporal resolution and superior signal-to-noise ratios. By exploiting the DLL method, we have fabricated molecular devices that are sensitive to external stimuli and are capable of transducing chemical/biochemical events into electrical signals at the single-molecule level, with notable examples including host-guest interaction, hydrogen bond dynamics, DNA intercalation, photoinduced conformational transition, carbocation formation, nucleophilic addition, and stereoelectronic effect. In addition to GMG-SMJs and considering compatibility with the silicon-based industry, we have also developed a reliable method of point-functionalizing silicon-nanowire-based nanotransistors to afford single-molecule electrical nanocircuits. This approach proved to be a robust platform for single-molecule electrical analysis capable of probing fast dynamic processes such as single-protein detection, DNA hybridization/polymorphism, and motor rotation dynamics. The above systematic investigations emphasize the importance and unique advantages of universal single-molecule electrical approaches for realizing direct, label-free, real-time electrical measurements of reaction dynamics with single-event sensitivity. These approaches promise a fascinating mainstream platform to explore the dynamics of stochastic processes in chemical/biological systems as well as gain information in fields ranging from reaction chemistry for elucidating the intrinsic mechanisms to genomics or proteomics for accurate molecular and even point-of-care clinical diagnoses.

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.

Determining the Subnanometer Thickness of the Water-Depletion Layer at the Interface between Water and the Hydrophobic Substrate

Surface plasmon resonance (SPR) is one of the most popular and powerful techniques for label-free detecting and quantitatively analyzing the interfacial refractive index (RI). So far, most of the SPR measurements are mainly applied to detect the relative change of RI upon biological and chemical events occurring at the interface, while the determinations on the absolute value of RI remains challenging. However, the absolute value of RI has become increasingly urgent in some cases, such as the existence and physical properties of the water depletion layer (WDL). WDL refers to a subnanometer-thick layer with reduced density between water and the hydrophobic substrate. The detailed explanations of how water meets hydrophobic surface have been studied by several kinds of techniques for decades but it remains under debate. In this work, we successfully established a method to measure the absolute RI at a gold-liquid interface by surface plasmon resonance microscopy (SPRM) and 2D Fourier transformation image processing and further applied this method to study the existence and physical nature of WDL. It was found that a 0.6 nm thick WDL existed at the interface of water and the hydrophobic substrate, leading to a reduced refractive index of 1.3295 ± 0.0006 compared with the standard value of 1.3325. Our results further indicated that the WDL consisted of a uniform layer rather than numerous isolated surface nanobubbles that distributed at the interface with high density.

Plasmonic coloration of silver nanodome arrays for a smartphone-based plasmonic biosensor

In this study, the utility of plasmonic coloration on silver nanodome arrays for sensitive and quantitative detection of biomolecules using a smartphone-based sensor is proposed. In particular, a quantitative analysis of DNA hybridization was achieved using the hue angle in the HSV color space obtained from a photograph of a sensing spot taken using a smartphone camera. Silver and gold nanodome arrays consisting of a polystyrene bead layer covered with a thin metal film can be created over a large area by a bottom-up fabrication process. The metal nanodome arrays exhibited unique colorations which can be tuned by the dome diameter ϕ, metal species, and refractive index of the surrounding medium. The measurement of the bulk refractive index sensitivity revealed that the Ag nanodome with ϕ = 500 nm can provide the highest sensitivity of up to 588 nm per refractive index unit. The detection of DNA hybridization was performed by using a bimetallic nanodome consisting of silver and thin gold overlayers and DNA modified gold nanoparticles (AuNPs) for enhancing the sensor signals. Upon the immobilization of AuNPs, the Ag nanodome (ϕ = 200 nm) exhibited a large shift in the resonance wavelength accompanied by a dramatic change in coloration. The analysis of detection sensitivity of DNA hybridization using a model system revealed that colorimetric detection based on hue can be used for the quantitative detection of biomolecules in the same manner as the spectroscopic method with a few pM level of detectable concentration.

Deep Learning Approach for Enhanced Detection of Surface Plasmon Scattering

A deep learning approach has been taken to improve detection characteristics of surface plasmon microscopy (SPM) of light scattering. Deep learning based on the convolutional neural network algorithm was used to estimate the effect of scattering parameters, mainly the number of scatterers. The improvement was assessed on a quantitative basis by applying the approach to SPM images formed by coherent interference of scatterers. It was found that deep learning significantly improves the accuracy over conventional detection: the enhancement in the accuracy was shown to be significantly higher by almost 6 times and useful for scattering by polydisperse mixtures. This suggests that deep learning can be used to find scattering objects effectively in the noisy environment. Furthermore, deep learning can be extended directly to label-free molecular detection assays and provide considerably improved detection in imaging and microscopy techniques.

Measuring the activation energy barrier for the nucleation of single nanosized vapor bubbles

Heterogeneous bubble nucleation is one of the most fundamental interfacial processes that has received broad interest from diverse fields of physics and chemistry. While most studies focused on large microbubbles, here we employed a surface plasmon resonance microscopy to measure the nucleation rate constant and activation energy barrier of single nanosized embryo vapor bubbles upon heating a flat gold film with a focused laser beam. Image analysis allowed for simultaneously determining the local temperature and local nucleation rate constant from the same batch of optical images. By analyzing the dependence of nucleation rate constant on temperature, we were able to calculate the local activation energy barrier within a submicrometer spot. Scanning the substrate further led to a nucleation rate map with a spatial resolution of 100 nm, which revealed no correlation with the local roughness. These results indicate that facet structure and surface chemistry, rather than geometrical roughness, regulated the activation energy barrier for heterogeneous nucleation of embryo nanobubbles.

Label-Free Optical Imaging of the Dynamic Stick-Slip and Migration of Single Sub-100-nm Surface Nanobubbles: A Superlocalization Approach

The past decade has witnessed theoretical and experimental debates on the extraordinary long lifetime and low contact angle of surface nanobubbles. While several kinds of imaging techniques have provided promising evidence on the lifetime and gaseous nature of single surface nanobubble, each of them suffered from its own limitations before a consensus can be reached. In the present work, we employ a recently developed surface plasmon resonance microscopy (SPRM) to nonintrusively visualize single sub-100-nm surface nanobubble without labeling for the first time. The quantitative dependence between optical signal and nanobubble volume allows for resolving the dissolution kinetics, which is a key for understanding the lifetime. A superlocalization method is further introduced to monitor the trajectory of its mass center during dissolution, which uncovers the stick-slip behavior in the early stage and the migration behavior in the late stage. The label-free, nonintrusive, quantitative and sensitive features of SPRM and the potential compatibility with atomic force microscopy shed new light on the long-standing puzzle behind surface nanobubbles.

Tracking the rotation of single CdS nanorods during photocatalysis with surface plasmon resonance microscopy

Rotational dynamics of anisotropic nanomaterials reveals and regulates their behaviors and functions in diverse fields ranging from nanomotors, biomechanics, and enzymatic catalysis to microrheology. An optical imaging technique that is suitable for all kinds of anisotropic nanoobjects, regardless of its inherent optical property, is thus highly desirable and it is yet to be demonstrated. In the present work, by taking a nonfluorescent and nonplasmonic CdS nanorod as an example, we demonstrate the capability of a recently developed surface plasmon resonance microscopy for determining the orientation of single anisotropic nanomaterials with arbitrary chemical composition and morphology.

While rotational dynamics of anisotropic nanoobjects has often been limited in plasmonic and fluorescent nanomaterials, here we demonstrate the capability of a surface plasmon resonance microscopy (SPRM) to determine the orientation of all kinds of anisotropic nanomaterials. By taking CdS nanorods as an example, it was found that two-dimensional Fourier transform of the asymmetrical wave-like SPRM image resulted in a peak in its angular spectrum in k space. Consistency between the peak angle and the geometrical orientation of the nanorod was validated by both in situ scanning electron microscope characterizations and theoretical calculations. Real-time monitoring of the rotational dynamics of single CdS nanorods further revealed the accelerated rotation under appropriate reaction conditions for photocatalyzed hydrogen generation. The driving force was attributed to the asymmetric production of hydrogen molecules as a result of inhomogeneous distribution of reactive sites within the nanorod. The present work not only builds the experimental and theoretical connections between the orientation of anisotropic nanomaterials and its SPRM images; the general suitability of SPRM also sheds light on broad types of nonfluorescent and nonplasmonic anisotropic nanoobjects from semiconductors to bacteria and viruses.

Label-free surface-sensitive photonic microscopy with high spatial resolution using azimuthal rotation illumination

Surface plasmon resonance microscopy (SPRM) with single-direction illumination is a powerful platform for biomedical imaging because of its wide-field, label-free, and high-surface-sensitivity imaging capabilities. However, two disadvantages prevent wider use of SPRM. The first is its poor spatial resolution that can be as large as several micrometers. The second is that SPRM requires use of metal films as sample substrates; this introduces working wavelength limitations. In addition, cell culture growth on metal films is not as universally available as growth on dielectric substrates. Here we show that use of azimuthal rotation illumination allows SPRM spatial resolution to be enhanced by up to an order of magnitude. The metal film can also be replaced by a dielectric multilayer and then a different label-free surface-sensitive photonic microscopy is developed, which has more choices in terms of the working wavelength, polarization, and imaging section, and will bring opportunities for applications in biology.

Beating the reaction limits of biosensor sensitivity with dynamic tracking of single binding events

The clinical need for ultrasensitive molecular analysis has motivated the development of several endpoint-assay technologies capable of single-molecule readout. These endpoint assays are now primarily limited by the affinity and specificity of the molecular-recognition agents for the analyte of interest. In contrast, a kinetic assay with single-molecule readout could distinguish between low-abundance, high-affinity (specific analyte) and high-abundance, low-affinity (nonspecific background) binding by measuring the duration of individual binding events at equilibrium. Here, we describe such a kinetic assay, in which individual binding events are detected and monitored during sample incubation. This method uses plasmonic gold nanorods and interferometric reflectance imaging to detect thousands of individual binding events across a multiplex solid-phase sensor with a large area approaching that of leading bead-based endpoint-assay technologies. A dynamic tracking procedure is used to measure the duration of each event. From this, the total rates of binding and debinding as well as the distribution of binding-event durations are determined. We observe a limit of detection of 19 fM for a proof-of-concept synthetic DNA analyte in a 12-plex assay format.

Total Internal Reflection-Based Extinction Spectroscopy of Single Nanoparticles

Herein we report a reflection-mode total internal reflection microscopy (TIRM) to measure the extinction spectrum of individual dielectric, plasmonic, or light-absorbing nanoparticles, and to differentiate absorption and scattering components from the total optical output. These capabilities were enabled via illuminating the sample with evanescent wave of which the lightpath length was comparable with the size of single nanoparticles, leading to a dramatically improved reflectance change (ΔI/I₀ ) up to tens of percent. It was further found that scattering and absorption of light contributed to bright and dark centroids, respectively, in the optical patterns of single nanoparticles, allowing to distinguish scattering and absorption components from the extinction spectrum by the use of an appropriate image processing method. In addition, wide-field feature of TIRM enabled the studies on tens of nanoparticles simultaneously with gentle illumination.

Absolute Analysis of Nanoparticle Suspension with Surface Plasmon Microscopy

The recently developed surface plasmon microscopy of single nanoparticles offers a powerful tool for monitoring particle transfer from bulk solution to the adsorbing surface. In the present work, the possibility of absolute analysis of suspension, based on particle transfer observation, was examined. A model based on particle diffusion in a laminar flow, which allows analytical solution of mass transport equation, was considered. It was demonstrated that direct determination of particle concentration, based on counting the particles that bind to the sensor surface, is possible. The model contains only independent, easy to determine parameters: flow cell geometry, flow rate, particle size, and liquid viscosity. For applicability of the model, particles should be irreversibly bound when touching the sensor surface. It was demonstrated that the required "perfect binding" is provided in certain electrolyte concentration range because even particles oppositely charged to the surface do not bind in pure water. If the binding probability is less than 100%, "absoluteness" of the method is not violated. It will require the extension of the transport model with the sticking coefficient, which can be also measured by the surface plasmon microscopy directly. The present work shows the feasibility of the absolute analysis. It demonstrates the great potential of the method toward the comprehensive nanoparticle analytics and investigation of binding processes.

Point Spread Function of Objective-Based Surface Plasmon Resonance Microscopy

Objective-based surface plasmon resonance microscopy (SPRM) is a novel optical imaging technique that can map the spatial distribution of a local refractive index based on propagating surface plasmon polaritons (SPPs). Different from some other optical microscopy that shows a dot-like point spread function (PSF), a nanosized object appears as a wave-like pattern containing parabolic tails in SPRM. The geometrical complexity of the wave-like pattern hampered the quantitative interpretation of the PSF of SPRM. Previous studies have shown that two adjacent rings were obtained in the frequency domain by applying a two-dimensional Fourier transform to such patterns. In the present work, a ring-fitting method was developed to extract geometrical features out of the dual rings and to connect these features with several experimental parameters. It was found that the radius of ring equaled to the wavevector of SPPs. Its orientation revealed the propagation direction of SPPs. The coordinate distance of the center of ring gave the parallel component of the wavevector of the incident light, which was regulated by the incident angle. The ring-broadening factor reflected the propagation length of SPPs in a reciprocal relationship. Systematical and quantitative interpretations in the frequency domain not only advanced the basic understanding on the PSF of SPRM but also opened up the possibility to utilize these frequency-domain features for detection and sensing purposes in future.

Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology's Achilles' heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ("digital") regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique's simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.

Particle sensing with confined optical field enhanced fluorescence emission (Cofefe)

We describe the development and performance of a new type of optical sensor suitable for registering the binding/dissociation of nanoscopic particles near a gold sensing surface. The method shares similarities with surface plasmon resonance microscopy but uses a completely different optical signature for reading out binding events. This new optical read-out mechanism, which we call confined optical field enhanced fluorescence emission (Cofefe), uses pulsed surface plasmon polariton fields at the gold/liquid interface that give rise to confined optical fields upon binding of the target particle to the gold surface. The confined near-fields are sufficient to induce two-photon absorption in the gold sensor surface near the binding site. Subsequent radiative recombination of the electron-hole pairs in the gold produces fluorescence emission, which can be captured by a camera in the far-field. Bound nanoparticles show up as bright confined spots against a dark background on the camera. We show that the Cofefe sensor is capable of detecting gold and silicon nanoparticles, as well as polymer nanospheres and sub-μm lipid droplets in a label-free manner with average illumination powers of less than 10 μW/μm2.