Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection

Photothermophoretic Splitting of Gold Nanoparticles for Plasmonic Nanopores and Nanonets Sensing

Optical processing of single plasmonic nanoparticles reinvents the way of high-density information storage, high-performance sensing, and high-definition displays. However, such laser-fabricated nanoplasmonics with well-defined hot spots remain elusive due to the diffraction limit of light. Here we show Au nanoparticle (NP) decorated nanopores can be facilely generated with photothermal splitting of single Au NPs embedded in a silica matrix. The extremely high local temperature induced by plasmonic heating renders gradients of the temperature and surface tension around the Au NP, which drives the nanoscale thermophoretic and Marangoni flow of molten Au/silica. As a result, a nanopore decorated with fragmented Au NPs is formed in the silica film, which presents much stronger surface-enhanced Raman scattering as compared to a single Au NP due to the emergence of hot spots. This strategy can be used to generate plasmonic nanopores of various sizes in the silicon nitride (SiNx) films, which further transforms into nanonets at ambient conditions via light-induced reconstruction of silicon nitride membrane. These nanonets can serve as a robust platform for single particle trapping and analysis.

Emerging Data Processing Methods for Single-Entity Electrochemistry

Single-entity electrochemistry is a powerful tool that enables the study of electrochemical processes at interfaces and provides insights into the intrinsic chemical and structural heterogeneities of individual entities. Signal processing is a critical aspect of single-entity electrochemical measurements and can be used for data recognition, classification, and interpretation. In this review, we summarize the recent five-year advances in signal processing techniques for single-entity electrochemistry and highlight their importance in obtaining high-quality data and extracting effective features from electrochemical signals, which are generally applicable in single-entity electrochemistry. Moreover, we shed light on electrochemical noise analysis to obtain single-molecule frequency fingerprint spectra that can provide rich information about the ion networks at the interface. By incorporating advanced data analysis tools and artificial intelligence algorithms, single-entity electrochemical measurements would revolutionize the field of single-entity analysis, leading to new fundamental discoveries.

Effect of nanoporous membranes thickness in electrochemical biosensing performance: application for the detection of a wound infection biomarker

Introduction: Nanoporous alumina membranes present a honeycomb-like structure characterized by two main parameters involved in their performance in electrochemical immunosening: pore diameter and pore thickness. Although this first one has been deeply studied, the effect of pore thickness in electrochemical-based nanopore immunosensors has been less taken into consideration. Methods: In this work, the influence of the thickness of nanoporous membranes in the steric blockage is studied for the first time, through the formation of an immunocomplex in their inner walls. Finally, the optimal nanoporous membranes were applied to the detection of catalase, an enzyme related with chronic wound infection and healing. Results: Nanoporous alumina membranes with a fixed pore diameter (60 nm) and variable pore thicknesses (40, 60, 100 μm) have been constructed and evaluated as immunosensing platform for protein detection. Our results show that membranes with a thickness of 40 μm provide a higher sensitivity and lower limit-of-detection (LOD) compared to thicker membranes. This performance is even improved when compared to commercial membranes (with 20 nm pore diameter and 60 μm pore thickness), when applied for human IgG as model analyte. A label-free immunosensor using a monoclonal antibody against anti-catalase was also constructed, allowing the detection of catalase in the range of 50-500 ng/mL and with a LOD of 1.5 ng/mL. The viability of the constructed sensor in real samples was also tested by spiking artificial wound infection solutions, providing recovery values of 110% and 118%. Discussion: The results obtained in this work evidence the key relevance of the nanochannel thickness in the biosensing performance. Such findings will illuminate nanoporous membrane biosensing research, considering thickness as a relevant parameter in electrochemical-based nanoporous membrane sensors.

Unleashing the potential of tungsten disulfide: Current trends in biosensing and nanomedicine applications

The discovery of graphene ignites a great deal of interest in the research and advancement of two-dimensional (2D) layered materials. Within it, semiconducting transition metal dichalcogenides (TMDCs) are highly regarded due to their exceptional electrical and optoelectronic properties. Tungsten disulfide (WS2) is a TMDC with intriguing properties, such as biocompatibility, tunable bandgap, and outstanding photoelectric characteristics. These features make it a potential candidate for chemical sensing, biosensing, and tumor therapy. Despite the numerous reviews on the synthesis and application of TMDCs in the biomedical field, no comprehensive study still summarizes and unifies the research trends of WS2 from synthesis to biomedical applications. Therefore, this review aims to present a complete and thorough analysis of the current research trends in WS2 across several biomedical domains, including biosensing and nanomedicine, covering antibacterial applications, tissue engineering, drug delivery, and anticancer treatments. Finally, this review also discusses the potential opportunities and obstacles associated with WS2 to deliver a new outlook for advancing its progress in biomedical research.

Solid-State Nanopores for Biomolecular Analysis and Detection

Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.

A molecularly imprinted sensor for single-molecule detection of pesticide metabolite at the amol/L level sensitized by water-soluble luminol derivative encapsulated liposome via click reaction

A novel luminol derivative, 4-[(1,4-dioxo-1,2,3,4-tetrahydrophthalazin-5-yl)amino]-4-oxobut-2-enoic acid (ALD) with electrochemiluminescence intensity and stability characteristics similar to luminol, but higher solubility in near neutral solution, was designed and synthesized in this study. Using this derivative, a molecular imprinted electrochemiluminescence sensor (MIECLS) was prepared for the sensitive and selective determination of 2-amino-5-mercapto-1,3,4-thiadiazole (AMT), a metabolite of bismerthiazol, thiediazole copper, thiazole zinc, and other pesticides. The ALD probes encapsulated in liposomes are immobilized on the molecularly imprinted film by light-triggered click reaction, and the concurrent release of multiple probes allows for highly sensitive detection. In the AMT concentration range of 1.00 × 10-18 - 5.00 × 10-13 mol/L, the relation between ECL response and log AMT concentration is linear. With a detection limit of 5.25 × 10-19 mol/L (about 4 - 6 molecules in 10 μL of the sample), the sensor allows for high sensitivity analysis of ultra-trace amounts of small organic compounds. In general, the ECL-based single-molecule detection technique proposed herein might be a promising alternative to fluorescence single-molecule detection.

Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks

DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.

Nanofluidic Aptamer Nanoarray to Enable Stochastic Capture of Single Proteins at Normal Concentrations

Single-molecule experiments allow understanding of the diversity, stochasticity, and heterogeneity of molecular behaviors and properties hidden by conventional ensemble-averaged measurements. They hence have great importance and significant impacts in a wide range of fields. Despite significant advances in single-molecule experiments at ultralow concentrations, the capture of single molecules in solution at normal concentrations within natural biomolecular processes remains a formidable challenge. Here, a high-density, well-defined nanofluidic aptamer nanoarray (NANa) formed via site-specific self-assembly of well-designed aptamer molecules in nanochannels with nano-in-nano gold nanopatterns is presented. The nanofluidic aptamer nanoarray exhibits a high capability to specifically capture target proteins (e.g., platelet-derived growth factor BB; PDGF-BB) to form uniform protein nanoarrays under optimized nanofluidic conditions. Owing to these fundamental features, the nanofluidic aptamer nanoarray enables the stochastic capture of single PDGF-BB molecules at a normal concentration from a sample with an ultrasmall volume equivalent to a single cell by following Poisson statistics, forming a readily addressable single-protein nanoarray. This approach offers a methodology and device to surpass both the concentration and volume limits of single-protein capture in most conventional methodologies of single-molecule experiments, thus opening an avenue to explore the behavior of individual biomolecules in a manner close to their natural forms, which remains largely unexplored to date.

Plasmonic Nanostructure Biosensors: A Review

Plasmonic nanostructure biosensors based on metal are a powerful tool in the biosensing field. Surface plasmon resonance (SPR) can be classified into localized surface plasmon resonance (LSPR) and propagating surface plasmon polariton (PSPP), based on the transmission mode. Initially, the physical principles of LSPR and PSPP are elaborated. In what follows, the recent development of the biosensors related to SPR principle is summarized. For clarity, they are categorized into three groups according to the sensing principle: (i) inherent resonance-based biosensors, which are sensitive to the refractive index changes of the surroundings; (ii) plasmon nanoruler biosensors in which the distances of the nanostructure can be changed by biomolecules at the nanoscale; and (iii) surface-enhanced Raman scattering biosensors in which the nanostructure serves as an amplifier for Raman scattering signals. Moreover, the advanced application of single-molecule detection is discussed in terms of metal nanoparticle and nanopore structures. The review concludes by providing perspectives on the future development of plasmonic nanostructure biosensors.

Adaptive time modulation technique for multiplexed on-chip particle detection across scales

Integrated optofluidic biosensors have demonstrated ultrasensitivity down to single particle detection and attomolar target concentrations. However, a wide dynamic range is highly desirable in practice and can usually only be achieved by using multiple detection modalities or sacrificing linearity. Here, we demonstrate an analysis technique that uses temporal excitation at two different time scales to simultaneously enable digital and analog detection of fluorescent targets. We demonstrated the seamless detection of nanobeads across eight orders of magnitude from attomolar to nanomolar concentration. Furthermore, a combination of spectrally varying modulation frequencies and a closed-loop feedback system that provides rapid adjustment of excitation laser powers enables multiplex analysis in the presence of vastly different concentrations. We demonstrated this ability to detect across scales via an analysis of a mixture of fluorescent nanobeads at femtomolar and picomolar concentrations. This technique advances the performance and versatility of integrated biosensors, especially toward point-of-use applications.

Optical Manipulation Heats up: Present and Future of Optothermal Manipulation

Optothermal manipulation is a versatile technique that combines optical and thermal forces to control synthetic micro-/nanoparticles and biological entities. This emerging technique overcomes the limitations of traditional optical tweezers, including high laser power, photon and thermal damage to fragile objects, and the requirement of refractive-index contrast between target objects and the surrounding solvents. In this perspective, we discuss how the rich opto-thermo-fluidic multiphysics leads to a variety of working mechanisms and modes of optothermal manipulation in both liquid and solid media, underpinning a broad range of applications in biology, nanotechnology, and robotics. Moreover, we highlight current experimental and modeling challenges in the pursuit of optothermal manipulation and propose future directions and solutions to the challenges.

Single-Molecule Electrical and Spectroscopic Profiling Protein Allostery Using a Gold Plasmonic Nanopore

Direct structural and dynamic characterization of protein conformers in solution is highly desirable but currently impractical. Herein, we developed a single molecule gold plasmonic nanopore system for observation of protein allostery, enabling us to monitor translocation dynamics and conformation transition of proteins by ion current detection and SERS spectrum measurement, respectively. Allosteric transition of calmodulin (CaM) was elaborately probed by the nanopore system. Two conformers of CaM were well-resolved at a single-molecule level using both the ion current blockage signal and the SERS spectra. The collected SERS spectra provided structural evidence to confirm the interaction between CaM and the gold plasmonic nanopore, which was responsible for the different translocation behaviors of the two conformers. SERS spectra revealed the amino acid residues involved in the conformational change of CaM upon calcium binding. The results demonstrated that the excellent spectral characterization furnishes a single-molecule nanopore technique with an advanced capability of direct structure analysis.

Raman spectroscopy of optical-trapped single particle using bull's eye nanostructure

Surface-enhanced Raman spectroscopy (SERS) has enabled single nanoparticle Raman sensing with abundant applications in analytical chemistry, biomaterials, and environmental monitoring. Genuine single particle Raman sensing requires a cumbersome technique, such as atomic force microscopy (AFM) based tip-enhanced Raman spectroscopy; SERS-based single particle Raman sensing still collects an ensemble signal that samples, in principle, a number of particles. Here, we develop in situ Raman-coupled optical tweezers, based on a hybrid nanostructure consisting of a single bowtie aperture surrounded by bull's eye rings, to trap and excite a rhodamine-6G-dye-doped polystyrene sphere. We simulated a platform to ensure sufficient enhancement capability for both optical trapping and SERS of a single nanoparticle. Experiments with well-designed controls clearly attribute the Raman signal origin to a single 15-nm particle trapped at the center of a nanohole, and they also clarified the trapping and Raman enhancement role of the bull's eye rings. We claim Raman sensing of a smallest optically trapped particle.

Double-sided plasmonic metasurface for simultaneous biomolecular separation and SERS detection

Porous membrane-based nanofiltration separation of small biomolecules is a widely used biotechnology for which size-based selectivity is a critical parameter of technological relevance. Efficient determination of size selectivity calls for an advanced detection method capable of performing sensitive, rapid, and on-membrane examination. Surface-enhanced Raman spectroscopy (SERS) is such a detection method that has been widely recognized as an ultrasensitive technique for trace-level detection with sensitivity down to the single-molecule level. In this work, we for the first time develop a double-sided hierarchical porous membrane-like plasmonic metasurface to realize high-selectivity bimolecular separation and simultaneous ultrasensitive SERS detection. This highly flexible device, consisting of subwavelength nanocone pairs surrounded by randomly orientated sub-5 nm nanogrooves, was prepared by combining customized "top-down" fabrication of conical nanopores in an ion-track registered polycarbonate membrane and self-assembly of nanogrooves on the membrane surface through physical vapor deposition. The unique tip-to-tip oriented conical nanopores in the device enables excellent size-based molecular selectivity; the hierarchical groove-pore structure supports a peculiar cascaded electromagnetic near-field enhancement mechanism, endowing the device with SERS-based molecular detection of ultrahigh sensitivity, uniformity, repeatability, and polarization independence. With such dual structural merits and performance enhancement, we demonstrate effective nanofiltration separation of small-sized adenine from big-sized ss-DNA and synergistic SERS determination of their species. We experimentally demonstrate an ultrasensitive detection of 4-mercaptopyridine down to 10 pM. Together with its unparalleled mechanical flexibility, this double-side-responsive plasmonic metasurface membrane can find great potential in real-world molecular filtration and detection under extremely complex working conditions.

Plasmonic Biosensors with Nanostructure for Healthcare Monitoring and Diseases Diagnosis

Nanophotonics has been widely utilized in enhanced molecularspectroscopy or mediated chemical reaction, which has major applications in the field of enhancing sensing and enables opportunities in developing healthcare monitoring. This review presents an updated overview of the recent exciting advances of plasmonic biosensors in the healthcare area. Manufacturing, enhancements and applications of plasmonic biosensors are discussed, with particular focus on nanolisted main preparation methods of various nanostructures, such as chemical synthesis, lithography, nanosphere lithography, nanoimprint lithography, etc., and describing their respective advances and challenges from practical applications of plasmon biosensors. Based on these sensing structures, different types of plasmonic biosensors are summarized regarding detecting cancer biomarkers, body fluid, temperature, gas and COVID-19. Last, the existing challenges and prospects of plasmonic biosensors combined with machine learning, mega data analysis and prediction are surveyed.

Pore performance: artificial nanoscale constructs that mimic the biomolecular transport of the nuclear pore complex

The nuclear pore complex is a nanoscale assembly that achieves shuttle-cargo transport of biomolecules: a certain cargo molecule can only pass the barrier if it is attached to a shuttle molecule. In this review we summarize the most important efforts aiming to reproduce this feature in artificial settings. This can be achieved by solid state nanopores that have been functionalized with the most important proteins found in the biological system. Alternatively, the nanopores are chemically modified with synthetic polymers. However, only a few studies have demonstrated a shuttle-cargo transport mechanism and due to cargo leakage, the selectivity is not comparable to that of the biological system. Other recent approaches are based on DNA origami, though biomolecule transport has not yet been studied with these. The highest selectivity has been achieved with macroscopic gels, but they are yet to be scaled down to nano-dimensions. It is concluded that although several interesting studies exist, we are still far from achieving selective and efficient artificial shuttle-cargo transport of biomolecules. Besides being of fundamental interest, such a system could be potentially useful in bioanalytical devices.

Materials Perspectives of Integrated Plasmonic Biosensors

With the growing need for portable, compact, low-cost, and efficient biosensors, plasmonic materials hold the promise to meet this need owing to their label-free sensitivity and deep light-matter interaction that can go beyond the diffraction limit of light. In this review, we shed light on the main physical aspects of plasmonic interactions, highlight mainstream and future plasmonic materials including their merits and shortcomings, describe the backbone substrates for building plasmonic biosensors, and conclude with a brief discussion of the factors affecting plasmonic biosensing mechanisms. To do so, we first observe that 2D materials such as graphene and transition metal dichalcogenides play a major role in enhancing the sensitivity of nanoparticle-based plasmonic biosensors. Then, we identify that titanium nitride is a promising candidate for integrated applications with performance comparable to that of gold. Our study highlights the emerging role of polymer substrates in the design of future wearable and point-of-care devices. Finally, we summarize some technical and economic challenges that should be addressed for the mass adoption of plasmonic biosensors. We believe this review will be a guide in advancing the implementation of plasmonics-based integrated biosensors.

Which 2D Material is Better for DNA Detection: Graphene, MoS2, or MXene?

Despite much research on characterizing 2D materials for DNA detection with nanopore technology, a thorough comparison between the performance of different 2D materials is currently lacking. In this work, using extensive molecular dynamics simulations, we compare nanoporous graphene, MoS₂ and titanium carbide MXene (Ti₃C₂) for their DNA detection performance and sensitivity. The ionic current and residence time of DNA are characterized in each nanoporous materials by performing hundreds of simulations. We devised two statistical measures including the Kolmogorov-Smirnov test and the absolute pairwise difference to compare the performance of nanopores. We found that graphene nanopore is the most sensitive membrane for distinguishing DNA bases. The MoS₂ is capable of distinguishing the A and T bases from the C and G bases better than graphene and MXene. Physisorption and the orientation of DNA in nanopores are further investigated to provide molecular insight into the performance characteristics of different nanopores.

Biosensors and Drug Delivery in Oncotheranostics Using Inorganic Synthetic and Biogenic Magnetic Nanoparticles

Magnetic nanocarriers have attracted attention in translational oncology due to their ability to be employed both for tumor diagnostics and therapy. This review summarizes data on applications of synthetic and biogenic magnetic nanoparticles (MNPs) in oncological theranostics and related areas. The basics of both types of MNPs including synthesis approaches, structure, and physicochemical properties are discussed. The properties of synthetic MNPs and biogenic MNPs are compared with regard to their antitumor therapeutic efficiency, diagnostic potential, biocompatibility, and cellular toxicity. The comparative analysis demonstrates that both synthetic and biogenic MNPs could be efficiently used for cancer theranostics, including biosensorics and drug delivery. At the same time, reduced toxicity of biogenic particles was noted, which makes them advantageous for in vivo applications, such as drug delivery, or MRI imaging of tumors. Adaptability to surface modification based on natural biochemical processes is also noted, as well as good compatibility with tumor cells and proliferation in them. Advances in the bionanotechnology field should lead to the implementation of MNPs in clinical trials.

Localized Nanopore Fabrication via Controlled Breakdown

Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.

Single-Molecule Surface-Enhanced Raman Spectroscopy

Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) has the potential to detect single molecules in a non-invasive, label-free manner with high-throughput. SM-SERS can detect chemical information of single molecules without statistical averaging and has wide application in chemical analysis, nanoelectronics, biochemical sensing, etc. Recently, a series of unprecedented advances have been realized in science and application by SM-SERS, which has attracted the interest of various fields. In this review, we first elucidate the key concepts of SM-SERS, including enhancement factor (EF), spectral fluctuation, and experimental evidence of single-molecule events. Next, we systematically discuss advanced implementations of SM-SERS, including substrates with ultra-high EF and reproducibility, strategies to improve the probability of molecules being localized in hotspots, and nonmetallic and hybrid substrates. Then, several examples for the application of SM-SERS are proposed, including catalysis, nanoelectronics, and sensing. Finally, we summarize the challenges and future of SM-SERS. We hope this literature review will inspire the interest of researchers in more fields.

Optical Quantification by Nanopores of Viruses, Extracellular Vesicles, and Nanoparticles

Nanopores combined with optical approaches can be used to detect viral particles. In this work, we demonstrate the ability of hydrodynamical driving and optical sensing to identify and quantify viral particles in a biological sample. We have developed a simple and rapid method which requires only fluorescent labeling of the particles and can therefore be applied to a wide range of virus type. The system operates in real time and at the single particle level while providing a low error on concentration (4%) and a low limit of detection of 10⁵ particles/mL for an acquisition time of 60 s with the ability to increase the acquisition time to achieve a lower limit.

Single molecule detection; from microscopy to sensors

Single molecule detection is necessary to find out physical, chemical properties and their mechanism involved in the normal functioning of body cells. In this way, they can provide a new direction to the healthcare system. Various techniques have been developed and employed for their successful detection. Herein, we have emphasized various traditional methods as well as biosensing technology which offer single molecule sensitivity. The various methods including plasmonic resonance, nanopores, whispering gallery mode, Simoa assay and recognition tunneling are discussed in the initial part which has been followed by a discussion about biosensor-based detection. Plasmonic, SERS, CRISPR/Cas, and other types of biosensors are focused in this review and found to be highly sensitive for single molecule detection. This review provides an overview of progression in different techniques employed for single molecule detection.

Directivity-Enhanced Detection of a Single Nanoparticle Using a Plasmonic Slot Antenna

In situ refractive index sensors integrated with nanoaperture-based optical tweezers possess stable and sensitive responsivity to single nanoparticles. In most existing works, detection events are only identified using the total light intensity with directivity information ignored, leading to a low signal-to-noise ratio. Here, we propose to detect an optically trapped 20 nm silica particle by monitoring directivity of a plasmonic antenna. The main and secondary radiation lobes of the antenna reverse upon trapping because the particle-induced perturbation negates the relative phase between two antenna elements, leading to a significant change of the antenna front-to-back ratio. As a result, we obtain a signal-to-noise ratio of 20, with an order-of-magnitude improvement as compared to the intensity-only detection scheme.

Visualized SERS Imaging of Single Molecule by Ag/Black Phosphorus Nanosheets

Ag/BP-NS exhibit remarkable surface-enhanced Raman scattering performance with single-molecule detection ability. This remarkable enhancement can be attributed to the synergistic resonance enhancement of R6G molecular resonance, photo-induced charge transfer resonance and electromagnetic resonance. A new polarization-mapping method was proposed, which can quickly screen out single-molecule signals and prove that the obtained spectra are emitted by single molecule. The recognition of different tumor exosomes can be realized combining the method of machine learning.

ABSTRACT

Single-molecule detection and imaging are of great value in chemical analysis, biomarker identification and other trace detection fields. However, the localization and visualization of single molecule are still quite a challenge. Here, we report a special-engineered nanostructure of Ag nanoparticles embedded in multi-layer black phosphorus nanosheets (Ag/BP-NS) synthesized by a unique photoreduction method as a surface-enhanced Raman scattering (SERS) sensor. Such a SERS substrate features the lowest detection limit of 10^–20 mol L⁻¹ for R6G, which is due to the three synergistic resonance enhancement of molecular resonance, photo-induced charge transfer resonance and electromagnetic resonance. We propose a polarization-mapping strategy to realize the detection and visualization of single molecule. In addition, combined with machine learning, Ag/BP-NS substrates are capable of recognition of different tumor exosomes, which is meaningful for monitoring and early warning of the cancer. This work provides a reliable strategy for the detection of single molecule and a potential candidate for the practical bio-application of SERS technology. [Image: see text]

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40820-022-00803-x.

Electrically Controlled Enrichment of Analyte for Ultrasensitive SERS-Based Plasmonic Sensors

Recently, sensors using surface-enhanced Raman scattering (SERS) detectors combined with superhydrophobic/superhydrophilic analyte concentration systems showed the ability to reach detection limits below the femto-molar level. However, a further increase in the sensitivity of these sensors is limited by the impossibility of the concentration systems to deposit the analyte on an area of less than 0.01 mm². This article proposes a fundamentally new approach to the analyte enrichment, based on the effect of non-uniform electrostatic field on the evaporating droplet. This approach, combined with the optimized geometry of a superhydrophobic/superhydrophilic concentration system allows more than a six-fold reduction of the deposition area. Potentially, this makes it possible to improve the detection limit of the plasmonic sensors by the same factor, bringing it down to the attomolar level.

Optical Nanopore Sensors for Quantitative Analysis

Nanopore sensors have received significant interest for the detection of clinically important biomarkers with single-molecule resolution. These sensors typically operate by detecting changes in the ionic current through a nanopore due to the translocation of an analyte. Recently, there has been interest in developing optical readout strategies for nanopore sensors for quantitative analysis. This is because they can utilize wide-field microscopy to independently monitor many nanopores within a high-density array. This significantly increases the amount of statistics that can be obtained, thus enabling the analysis of analytes present at ultralow concentrations. Here, we review the use of optical nanopore sensing strategies for quantitative analysis. We discuss optical nanopore sensing assays that have been developed to detect clinically relevant biomarkers, the potential for multiplexing such measurements, and techniques to fabricate high density arrays of nanopores with a view toward the use of these devices for clinical applications.

Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity

Detection of molecular interactions is the foundation for many important biotechnology applications in society and industry, such as drug discovery, diagnostics, and DNA sequencing. This report describes a broadly applicable platform for detecting molecular interactions at the single-molecule scale, in real-time, label-free, and potentially highly multiplexable fashion, using single-molecule sensors on a highly scalable semiconductor sensor array chip. Such chips are both practically manufacturable in the near term, and have a durable long-term scaling roadmap, thus providing an ideal way to bring the power of modern chip technology to the broad area of biosensing. This work also realizes a 50-year-old scientific vision of integrating single molecules into electronic chips to achieve the ultimate miniaturization of electronics.

For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.

Plasmon-enhanced fluorimetric and colorimetric dual sensor based on fluorescein/Ag nanoprisms for sensitive determination of mancozeb

A plasmon-enhanced fluorimetric and colorimetric dual sensor was designed to detect mancozeb based on fluorescein (as a fluorimetric reporter) and AgNPRs (as a fluorescence enhancer and colorimetric reporter). The sensing mechanism was based on the shape transformation of AgNPRs due to etching and anti-etching effect of S₂O₃^2- and mancozeb. We observed that AgNPRs enhanced the fluorescence intensity of fluorescein around 4-fold. By adding S₂O₃^2-_, the AgNPR florescence enhancement effect decreased, also SPR peak of AgNPRs blue-shifted and the solution color altered from blue to purple. The fluorescein fluorescence intensity and AgNPR's SPR peak position restored in the presence of mancozeb due to its protecting effect on AgNPRs. The restored fluorescence intensity and the SPR wavelength shift were proportional to the mancozeb concentration at the range of 0.005-0.1 and 0.005-0.075 mg/L, respectively. The developed sensor was successfully applied to measure mancozeb in fruit juice samples.

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to experimental limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with experimental measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, associated with the collective contribution from "substrate-receptor-analyte" conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomolecules onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomolecule-surface complex formation as a whole.

Exploring near-field sensing efficiency of complementary plasmonic metasurfaces for immunodetection of tumor markers

Plasmonic metasurface biosensors have great potential on label-free high-throughput clinical detection of human tumor markers. In the past decades, nanopillar and nanohole metasurfaces have become the common choices for plasmonic biosensing, because they typically enable universal simple large-area nanopatterns via a low-cost reproducible fabrication manner. The two kinds of metasurfaces have the complementary shapes and are used to be assumed as the same type of two-dimensional plasmonic nanograting for biosensing. Up to date, there is still a lack of comparison study on their biosensing performance, which is critical to guide their better applications on tumor marker detection. In this study, we compare the bulk/surface refractive index and sensitivity of plasmonic nanopillar (PNP) and plasmonic nanohole (PNH) metasurfaces in order to evaluate their biosensing capabilities. The sensing physics about their space near-field utilization is systematically revealed. The PNH metasurface demonstrates a higher biomolecule sensitivity versus the complementary PNP metasurface, and its limit of detection for bovine serum albumin reaches ∼0.078 ng/mL, which implies a greater potential of detecting cancer biomarkers. We further adopt the PNH metasurfaces for immunoassay of three typical tumor markers by testing clinical human serum samples. The results imply that the immunodetection of alpha-fetoprotein has the most optimal sensing efficiency with the lowest detection concentration (<5 IU/mL), which is much lower than its clinical diagnosis threshold of ∼16.5 IU/mL for medical examination. Our work has not only illuminated the distinct biosensing properties of complementary metasurfaces, but also provided a promising way to boost plasmonic biosensing for point-of-care testing.

Self-Induced Back-Action Actuated Nanopore Electrophoresis (SANE) Sensor for Label-Free Detection of Cancer Immunotherapy-Relevant Antibody-Ligand Interactions

We fabricated a novel single molecule nanosensor by integrating a solid-state nanopore and a double nanohole nanoaperture. The nanosensor employs Self-Induced Back-Action (SIBA) for optical trapping and enables SIBA-Actuated Nanopore Electrophoresis (SANE) for concurrent acquisition of bimodal optical and electrical signatures of molecular interactions. This work describes how to fabricate and use the SANE sensor to quantify antibody-ligand interactions. We describe how to analyze the bimodal optical-electrical data to improve upon the discrimination of antibody and ligand versus bound complex compared to electrical measurements alone. Example results for specific interaction detection are described for T-cell receptor-like antibodies (TCRmAbs) engineered to target peptide-presenting Major Histocompatibility Complex (pMHC) ligands, representing a model of target ligands presented on the surface of cancer cells. We also describe how to analyze the bimodal optical-electrical data to discriminate between specific and non-specific interactions between antibodies and ligands. Example results for non-specific interactions are shown for cancer-irrelevant TCRmAbs targeting the same pMHCs, as a control. These example results demonstrate the utility of the SANE sensor as a potential screening tool for ligand targets in cancer immunotherapy, though we believe that its potential uses are much broader.

Bio-inspired Track-Etched Polymeric Nanochannels: Steady-State Biosensors for Detection of Analytes

Bio-inspired polymeric nanochannel (also referred as nanopore)-based biosensors have attracted considerable attention on account of their controllable channel size and shape, multi-functional surface chemistry, unique ionic transport properties, and good robustness for applications. There are already very informative reviews on the latest developments in solid-state artificial nanochannel-based biosensors, however, which concentrated on the resistive-pulse sensing-based sensors for practical applications. The steady-state sensing-based nanochannel biosensors, in principle, have significant advantages over their counterparts in term of high sensitivity, fast response, target analytes with no size limit, and extensive suitable range. Furthermore, among the diverse materials, nanochannels based on polymeric materials perform outstandingly, due to flexible fabrication and wide application. This compressive Review summarizes the recent advances in bio-inspired polymeric nanochannels as sensing platforms for detection of important analytes in living organisms, to meet the high demand for high-performance biosensors for analysis of target analytes, and the potential for development of smart sensing devices. In the future, research efforts can be focused on transport mechanisms in the field of steady-state or resistive-pulse nanochannel-based sensors and on developing precisely size-controlled, robust, miniature and reusable, multi-functional, and high-throughput biosensors for practical applications. Future efforts should aim at a deeper understanding of the principles at the molecular level and incorporating these diverse pore architectures into homogeneous and defect-free multi-channel membrane systems. With the rapid advancement of nanoscience and biotechnology, we believe that many more achievements in nanochannel-based biosensors could be achieved in the near future, serving people in a better way.

Macromolecule sensing and tumor biomarker detection by harnessing terminal size and hydrophobicity of viral DNA packaging motor channels into membranes and flow cells

Biological nanopores for single-pore sensing have the advantage of size homogeneity, structural reproducibility, and channel amenability. In order to translate this to clinical applications, the functional biological nanopore must be inserted into a stable system for high-throughput analysis. Here we report factors that control the rate of pore insertion into polymer membrane and analyte translocation through the channel of viral DNA packaging motors of Phi29, T3 and T7. The hydrophobicity of aminol or carboxyl terminals and their relation to the analyte translocation were investigated. It was found that both the size and the hydrophobicity of the pore terminus are critical factors for direct membrane insertion. An N-terminus or C-terminus hydrophobic mutation is crucial for governing insertion orientation and subsequent macromolecule translocation due to the one-way traffic property. The N- or C-modification led to two different modes of application. The C-terminal insertion permits translocation of analytes such as peptides to enter the channel through the N terminus, while N-terminus insertion prevents translocation but offers the measurement of gating as a sensing parameter, thus generating a tool for detection of markers. A urokinase-type Plasminogen Activator Receptor (uPAR) binding peptide was fused into the C-terminal of Phi29 nanopore to serve as a probe for uPAR protein detection. The uPAR has proven to be a predictive biomarker in several types of cancer, including breast cancer. With an N-terminal insertion, the binding of the uPAR antigen to individual peptide probe induced discretive steps of current reduction due to the induction of channel gating. The distinctive current signatures enabled us to distinguish uPAR positive and negative tumor cell lines. This finding provides a theoretical basis for a robust biological nanopore sensing system for high-throughput macromolecular sensing and tumor biomarker detection.

Optical trapping assisted label-free and amplification-free detection of SARS-CoV-2 RNAs with an optofluidic nanopore sensor

Ultrasensitive, versatile sensors for molecular biomarkers are a critical component of disease diagnostics and personalized medicine as the COVID-19 pandemic has revealed in dramatic fashion. Integrated electrical nanopore sensors can fill this need via label-free, direct detection of individual biomolecules, but a fully functional device for clinical sample analysis has yet to be developed. Here, we report amplification-free detection of SARS-CoV-2 RNAs with single molecule sensitivity from clinical nasopharyngeal swab samples on an electro-optofluidic chip. The device relies on optically assisted delivery of target carrying microbeads to the nanopore for single RNA detection after release. A sensing rate enhancement of over 2,000x with favorable scaling towards lower concentrations is demonstrated. The combination of target specificity, chip-scale integration and rapid detection ensures the practicality of this approach for COVID-19 diagnosis over the entire clinically relevant concentration range from 10⁴-10⁹ copies/mL.

Nanoplatforms for Sepsis Management: Rapid Detection/Warning, Pathogen Elimination and Restoring Immune Homeostasis

Sepsis, a highly life-threatening organ dysfunction caused by uncontrollable immune responses to infection, is a leading contributor to mortality in intensive care units. Sepsis-related deaths have been reported to account for 19.7% of all global deaths. However, no effective and specific therapeutic for clinical sepsis management is available due to the complex pathogenesis. Concurrently eliminating infections and restoring immune homeostasis are regarded as the core strategies to manage sepsis. Sophisticated nanoplatforms guided by supramolecular and medicinal chemistry, targeting infection and/or imbalanced immune responses, have emerged as potent tools to combat sepsis by supporting more accurate diagnosis and precision treatment. Nanoplatforms can overcome the barriers faced by clinical strategies, including delayed diagnosis, drug resistance and incapacity to manage immune disorders. Here, we present a comprehensive review highlighting the pathogenetic characteristics of sepsis and future therapeutic concepts, summarizing the progress of these well-designed nanoplatforms in sepsis management and discussing the ongoing challenges and perspectives regarding future potential therapies. Based on these state-of-the-art studies, this review will advance multidisciplinary collaboration and drive clinical translation to remedy sepsis.

Nanopore sensors for viral particle quantification: current progress and future prospects

Rapid, inexpensive, and laboratory-free diagnostic of viral pathogens is highly critical in controlling viral pandemics. In recent years, nanopore-based sensors have been employed to detect, identify, and classify virus particles. By tracing ionic current containing target molecules across nano-scale pores, nanopore sensors can recognize the target molecules at the single-molecule level. In the case of viruses, they enable discrimination of individual viruses and obtaining important information on the physical and chemical properties of viral particles. Despite classical benchtop virus detection methods, such as amplification techniques (e.g., PCR) or immunological assays (e.g., ELISA), that are mainly laboratory-based, expensive and time-consuming, nanopore-based sensing methods can enable low-cost and real-time point-of-care (PoC) and point-of-need (PoN) monitoring of target viruses. This review discusses the limitations of classical virus detection methods in PoN virus monitoring and then provides a comprehensive overview of nanopore sensing technology and its emerging applications in quantifying virus particles and classifying virus sub-types. Afterward, it discusses the recent progress in the field of nanopore sensing, including integrating nanopore sensors with microfabrication technology, microfluidics and artificial intelligence, which have been demonstrated to be promising in developing the next generation of low-cost and portable biosensors for the sensitive recognition of viruses and emerging pathogens.

Spatiotemporally Controlled DNA Nanoclamps: Single-Molecule Imaging of Receptor Protein Oligomerization

Cell membrane surface receptor proteins play an important role in cellular biological processes. There are numerous methods to detect receptors, yet developing an artificially controlled and specific detection and treatment strategy remains a challenge. Herein, we develop such a strategy based on upconversion nanoparticles (UCNPs) loaded DNA probes that enable two-color ratiometric imaging excitated by a 980 nm laser. The light response controllable signal opening strategy avoids waste during probe transportation and improves sensitivity. Thereby the number of receptors on individual DU145 cell membranes is counted by single-molecule detection. Due to the different expression of specific receptor proteins, the number of single fluorescent dots counted can be used as a basis for distinguishing DU145 from other cells. This work is highly controllable to increase sensitivity, providing a platform for cancer diagnosis and treatment.

Understanding Electrical Conduction and Nanopore Formation During Controlled Breakdown

Controlled breakdown has recently emerged as a highly appealing technique to fabricate solid-state nanopores for a wide range of biosensing applications. This technique relies on applying an electric field of approximately 0.4-1 V nm^-1 across the membrane to induce a current, and eventually, breakdown of the dielectric. Although previous studies have performed controlled breakdown under a range of different conditions, the mechanism of conduction and breakdown has not been fully explored. Here, electrical conduction and nanopore formation in SiN_x membranes during controlled breakdown is studied. It is demonstrated that for Si-rich SiN_x , oxidation reactions that occur at the membrane-electrolyte interface limit conduction across the dielectric. However, for stoichiometric Si₃ N₄ the effect of oxidation reactions becomes relatively small and conduction is predominately limited by charge transport across the dielectric. Several important implications resulting from understanding this process are provided which will aid in further developing controlled breakdown in the coming years, particularly for extending this technique to integrate nanopores with on-chip nanostructures.

Probing Multidimensional Structural Information of Single Molecules Transporting through a Sub-10 nm Conical Plasmonic Nanopore by SERS

Probing the orientation and oxygenation state of single molecules (SMs) is of great importance for understanding the advanced structure of individual molecules. Here, we manipulate molecules transporting through the hot spot of a sub-10 nm conical gold nanopore and acquire the multidimensional structural information of the SMs by surface enhanced Raman scattering (SERS) detection. The sub-10 nm size and conical shape of the plasmonic nanopore guarantee its high detection sensitivity. SERS spectra show a high correlation with the orientations of small-sized single rhodamine 6G (R6G) during transport. Meanwhile, SERS spectra of a single hemoglobin (Hb) reveal both the vertical/parallel orientations of the porphyrin ring and oxygenated/deoxygenated states of Hb. The present study provides a new strategy for bridging the primary sequence and the advanced structure of SMs.

Recent advances in integrated solid-state nanopore sensors

The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.