Optical Nanopore Sensors for Quantitative Analysis

Ultrasensitive colorimetric detection of deoxynivalenol in infant milk powder based on the inhibitory effect of silver ions on the peroxidase-like activity of Ni@Pt nanoparticles

Deoxynivalenol, a hazardous mycotoxin, poses significant health risks to humans and animals, necessitating highly sensitive detection methods due to its low abundance in food. Herein, we present a colorimetric sensing strategy for deoxynivalenol detection based on the inhibitory effect of silver ions on the peroxidase-like activity of Ni@Pt nanoparticles. Silver ions adsorb onto the surface of Ni@Pt nanoparticles, blocking the active site and consequently impeding their catalytic activity. By integrating antigen-antibody interactions with the biotin-streptavidin system, a specific aptamer can be introduced to chelate silver ions, thereby modulating the activity of Ni@Pt nanoparticles for signal readout through the 3,3',5,5'-tetramethylbenzidine/hydrogen peroxide system. This method achieves a detection limit of 47.4 pg/mL, surpassing traditional enzyme-linked immunosorbent assays and rivaling the sensitivity of precision instrumental analysis. Furthermore, this colorimetric method demonstrates robust recovery and has been successfully challenged deoxynivalenol detection in infant milk powder samples, highlighting its potential for practical applications.

Designing Fluorescent Interfaces at Hotspots in a Plasmonic Nanopore for Homologous Optoelectronic Sensing

In this work, a site-selective functionalization strategy is proposed for modifying fluorescent dyes in the plasmonic nanopore, which highlights building optoelectronic dual-signal sensing interfaces at "hotspots" locations to construct multiparameter detection nanosensor. Finite-difference time-domain (FDTD) simulations confirmed the high-intensity electromagnetic field due to plasmonic nanostructure. It is demonstrated that adjusting the distance between the nanopore inner wall and fluorophore prevented the fluorescence quenching, resulting in more than a thirty fold fluorescence enhancement. Upon binding with the target analyte, the sensor produces homologous yet independent optoelectronic dual-signal responses that cross-validate one another, providing highly accurate analysis even in the presence of multiple interferences. The platform demonstrates precise, adaptable detection with linear responses to extracellular pH changes at the single-cell level, making it a versatile tool for a range of biosensing applications. By enabling the functionalization of fluorescent interfaces in the "hotspots" of metal nanopores, this interface design strategy efficiently exploits the enhancement of electromagnetic fields to achieve high-precision dual-signal measurements and greatly improves the sensitivity of biosensing applications.

Optical Nanopore Blockade Sensors for Multiplexed Detection of Proteins

Enduring challenges for quantitative analysis in nanopore sensing are the detection of low biomarker concentrations in reasonable time frames and the detection of multiple biomarkers in the same sample. Herein we report an optical blockade nanopore sensor strategy that can detect more than a protein at femtomolar concentrations in rapid time (approximately 12 min). This is done using a nanopore array functionalized with an aptamer that can bind to two different but related target proteins. The assay then monitors two different colors of fluorescent particles modified with antibodies specific to the protein of interest, as they block the nanopores using a wide-field microscope. By distinguishing specific and nonspecific blockade events for each nanoparticle based on whether they can be easily pulled out of the nanopores using an electric field, we can simultaneously quantify the concentrations of vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) down to femtomolar concentrations.

How Highly Heterogeneous Sensors with Single-Molecule Resolution can Result in Robust Continuous Monitoring Over Long Time Spans

Biomolecular sensors with single-molecule resolution are composed of multitudes of transducers that measure state changes related to single-molecular binding and unbinding events. Conventionally, signals are aggregated from many individual transducers in order to achieve sufficient statistics. However, by aggregating signals, transducer-to-transducer differences are lost and heterogeneities cannot be studied. Here, transducers with single-molecule resolution over long time spans are studied, enabling the collection of sufficient statistics from independent transducers. This allows comparisons between transducers that reveal fundamental heterogeneities in their molecular assemblies related to stochastic variations. The study is performed with biosensing by particle motion, a sensing methodology with thousands of particles that dynamically interact with a sensing surface. The signals of individual particles are studied for series of modulations of analyte concentration over 25 h. The results show large differences in individual concentration-dependent responses. Monte Carlo simulations clarify that heterogeneities can be attributed to stochastic fluctuations in the numbers of binder molecules, and that gradual changes of the response characteristics can be related to losses of molecules in the single-particle transducers. The results give insights into molecular and temporal heterogeneities of continuous transducers with single-molecule resolution and explain how sensors can be engineered to achieve robust, precise, and stable biomolecular monitoring.

Nanopore-based sensors for DNA sequencing: a review

Nanopore sensors, owing to their distinctive structural properties, can be used to detect biomolecular translocation events. These sensors operate by monitoring variations in electric current amplitude and duration, thereby enabling the calibration and distinction of various biomolecules. As a result, nanopores emerge as a potentially powerful tool in the field of deoxyribonucleic acid (DNA) sequencing. However, the interplay between testing bandwidth and noise often leads to the loss of part of the critical translocation signals, presenting a substantial challenge for the precise measurement of biomolecules. In this context, innovative detection mechanisms have been developed, including optical detection, tunneling current detection, and nanopore field-effect transistor (FET) detection. These novel detection methods are based on but beyond traditional nanopore techniques and each of them has unique advantages. Notably, nanopore FET sensors stand out for their high signal-to-noise ratio (SNR) and high bandwidth measurement capabilities, overcoming the limitations typically associated with traditional solid-state nanopore (SSN) technologies and thus paving the way for new avenues to biomolecule detection. This review begins by elucidating the fundamental detection principles, development history, applications, and fabrication methods for traditional SSNs. It then introduces three novel detection mechanisms, with a particular emphasis on nanopore FET detection. Finally, a comprehensive analysis of the advantages and challenges associated with both SSNs and nanopore FET sensors is performed, and then insights into the future development trajectories for nanopore FET sensors in DNA sequencing are provided. This review has two main purposes: firstly, to provide researchers with a preliminary understanding of advancements in the nanopore field, and secondly, to offer a comprehensive analysis of the fabrication techniques, transverse current detection principles, challenges, and future development trends in the field of nanopore FET sensors. This comprehensive analysis aims to help give researchers in-depth insights into cutting-edge advancements in the field of nanopore FET sensors.

Site-Specific Integration of Hexagonal Boron Nitride Quantum Emitters on 2D DNA Origami Nanopores

Optical emitters in hexagonal boron nitride (hBN) are promising probes for single-molecule sensing platforms. When engineered in nanoparticle form, they can be integrated as detectors in nanodevices, yet positional control at the nanoscale is lacking. Here we demonstrate the functionalization of DNA origami nanopores with optically active hBN nanoparticles (NPs) with nanometer precision. The NPs are active under three wavelengths of visible illumination and display both stable and blinking emission, enabling their accurate localization by using wide-field optical nanoscopy. Correlative opto-structural characterization reveals deterministic binding of bright, multicolor hBN NPs at the pore rim due to π-π stacking interactions at site-specific locations on the DNA origami. Our work provides a scalable, bottom-up approach toward deterministic assembly of solid-state emitters on arbitrary structural elements based on DNA origami. Such a nanoscale arrangement of optically active components can advance the development of single-molecule platforms, including optical nanopores and nanochannel sensors.

Radially distributed charging time constants at an electrode-solution interface

An electrochemically homogeneous electrode-solution interface should be understood as spatially invariant in both terms of intrinsic reactivity for the electrode side and electrical resistance mainly for the solution side. The latter remains presumably assumed in almost all cases. However, by using optical microscopy to spatially resolve the classic redox electrochemistry occurring at the whole surface of a gold macroelectrode, we discover that the electron transfer occurs always significantly sooner (by milliseconds), rather than faster in essence, at the radial coordinates closer to the electrode periphery than the very center. So is the charging process when there is no electron transfer. Based on optical measurements of the interfacial impedance, this spatially unsynchronized electron transfer is attributed to a radially non-uniform distribution of solution resistance. We accordingly manage to eliminate the heterogeneity by engineering the solution resistance distribution. The revealed spatially-dependent charging time 'constant' (to be questioned) would help paint our overall fundamental picture of electrode kinetics.

The combination of DNA nanostructures and materials for highly sensitive electrochemical detection

Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.

Nanopore Blockade Sensors for Quantitative Analysis Using an Optical Nanopore Assay

Nanopore sensing is a popular biosensing strategy that is being explored for the quantitative analysis of biomarkers. With low concentrations of analytes, nanopore sensors face challenges related to slow response times and selectivity. Here, we demonstrate an approach to rapidly detect species at ultralow concentrations using an optical nanopore blockade sensor for quantitative detection of the protein vascular endothelial growth factor (VEGF). This sensor relies on monitoring fluorescent polystyrene nanoparticles blocking nanopores in a nanopore array of 676 nanopores. The fluorescent signal is read out using a wide-field fluorescence microscope. Nonspecific blockade events are then distinguished from specific blockade events based on the ability to pull the particles out of the pore using an applied electric field. This allows the detection of VEGF at sub-picomolar concentration in less than 15 min.

Selective Single-Molecule Nanopore Detection of mpox A29 Protein Directly in Biofluids

Single-molecule antigen detection using nanopores offers a promising alternative for accurate virus testing to contain their transmission. However, the selective and efficient identification of small viral proteins directly in human biofluids remains a challenge. Here, we report a nanopore sensing strategy based on a customized DNA molecular probe that combines an aptamer and an antibody to enhance the single-molecule detection of mpox virus (MPXV) A29 protein, a small protein with an M.W. of ca. 14 kDa. The formation of the aptamer-target-antibody sandwich structures enables efficient identification of targets when translocating through the nanopore. This technique can accurately detect A29 protein with a limit of detection of ∼11 fM and can distinguish the MPXV A29 from vaccinia virus A27 protein (a difference of only four amino acids) and Varicella Zoster Virus (VZV) protein directly in biofluids. The simplicity, high selectivity, and sensitivity of this approach have the potential to contribute to the diagnosis of viruses in point-of-care settings.

Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes

We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.

Ion transport based structural description for in situ synthesized SBA-15 nanochannels in a sub-micropipette

Construction of nanoporous arrays can greatly facilitate their development in the fields of sensing, energy conversion, and nanofluidic devices. It is important to characterize the structure and understand the ion transport behaviour of a nanoporous array, especially those prepared by in situ synthesis, which are difficult to be characterized by conventional methods. Herein, an inorganic and non-crystalline mesoporous silica SBA-15 is selected as a template, where a combination (GP-SBA-15) of a sub-micropipette and SBA-15 is constructed by in situ synthesis, and the multichannel array structure of GP-SBA-15 is illustrated by its ion transport properties from current-voltage responses. Experiments of linear scan voltammetry and chronoamperometry show a rapid accumulation and slow redistribution of ions in the surface-charged nanochannels, and the high/low currents originate from the accumulation/depletion of ions in the channels. The finite element simulation is introduced to calculate the effects of surface charge and pore size on ion rectification and ion concentration distribution. In addition, the short straight channels and long bending channels present in GP-SBA-15 are demonstrated by the voltage-independent resistance pulse signals in the translocation of BSA. This study shows that electrochemical means effectively provide insight into ion transport, achieve structural description and reveal the sensing potential of GP-SBA-15.

Engineering Biological Nanopore Approaches toward Protein Sequencing

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.

Improvement of Sensitivity and Speed of Virus Sensing Technologies Using nm- and μm-Scale Components

Various viral diseases can be widespread and cause severe disruption to global society. Highly sensitive virus detection methods are needed to take effective measures to prevent the spread of viral infection. This required the development of rapid virus detection technology to detect viruses at low concentrations, even in the biological fluid of patients in the early stages of the disease or environmental samples. This review describes an overview of various virus detection technologies and then refers to typical technologies such as beads-based assay, digital assay, and pore-based sensing, which are the three modern approaches to improve the performance of viral sensing in terms of speed and sensitivity.

Low-noise and high-speed trans-impedance amplifier for nanopore sensor

The small current detection circuit is the core component of the accurate detection of the nanopore sensor. In this paper, a compact, low-noise, and high-speed trans-impedance amplifier is built for the nanopore detection system. The amplifier consists of two amplification stages. The first stage performs low-noise trans-impedance amplification by using ADA4530-1, which is a high-performance FET operational amplifier, and a high-ohm feedback resistor of 1 GΩ. The high pass shelf filter in the second stage recovers the higher frequency above the 3 dB cutoff in the first stage to extend the maximum bandwidth up to 50 kHz. The amplifier shows a low noise below sub-2 pA rms when tuned to have a bandwidth of around 5 kHz. It also guarantees a stable frequency response in the nanopore sensor.

Applications of Graphene in Five Senses, Nervous System, and Artificial Muscles

Graphene remains of great interest in biomedical applications because of biocompatibility. Diseases relating to human senses interfere with life satisfaction and happiness. Therefore, the restoration by artificial organs or sensory devices may bring a bright future by the recovery of senses in patients. In this review, we update the most recent progress in graphene based sensors for mimicking human senses such as artificial retina for image sensors, artificial eardrums, gas sensors, chemical sensors, and tactile sensors. The brain-like processors are discussed based on conventional transistors as well as memristor related neuromorphic computing. The brain-machine interface is introduced for providing a single pathway. Besides, the artificial muscles based on graphene are summarized in the means of actuators in order to react to the physical world. Future opportunities remain for elevating the performances of human-like sensors and their clinical applications.

Electronic analysis of hydrogen-bonded molecular complexes: the case of DNA sensed in a functionalized nanogap

DNA nucleotides can be interrogated by nanomaterials in order to be detected. With the aid of quantum-mechanical simulations, we unravel the intrinsic details of the electronic transport across nanoelectrodes functionalized with tiny modified diamond-like molecules. These electrodes generate a gap in which DNA nucleotides are placed and can be identified. The identification is strongly affected by the hydrogen bonding characteristics of the diamond-like particle and the nucleotides. The results point to the connection of the electronic transmission across the functionalized nanogap and the electronic and bonding characteristics of the molecular complexes within the nanogap. Specifically, our discussion focuses on the influence of the DNA dynamics on the electronic signals across the nanogap. We identify the molecular complex's details that hinder or promote the electronic transport through an analysis that moves from the bonding within the molecular complex up to the electronic current that this can accommodate. Accordingly, our work discusses pathways for analyzing hydrogen-bonded molecular complexes or molecules hydrogen-bonded to a material part having the optimization of the design of biosensing nanogaps and read-out nanopores in mind. The presented approach, though, is applicable to a wide range of applications utilizing exactly the bio/nano interface.

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.