Monitoring of an ATP-binding aptamer and its conformational changes using an α-hemolysin nanopore

pH-Stimulated Response Gating for Mimic Cytochrome C Transport on Biomimetic Asymmetric Nanochannels

Proteins are vital components in cells, biological tissues, and organs, playing a pivotal role in growth and developmental processes in living organisms. Cytochrome C (Cyt C) is a class of heme proteins found in almost all life and is involved in cellular energy metabolic processes such as respiration, mainly as electron carriers or terminal reductases. It binds cardiolipin in the inner mitochondrial membrane, leading to apoptosis. It is a challenge to design a simple and effective artificial system to mimic the complex Cyt C biological transport process. In this paper, an asymmetric biomimetic pH-driven protein gate is described by introducing arginine (Arg) at one end of an hourglass-shaped nanochannel. The nanochannel shows a sensitive protonation-driven protein gate that can be "off" at pH = 7 and "on" at pH = 2. Further studies show that differences in the binding of Arg and Cyt C at different levels of protonation lead to different switching behaviors within the nanochannels, which in turn lead to different surface charges within the nanochannels. It can be used for detecting Cyt C and as an excellent and robust gate for developing integrated circuits and nanoelectronic logic devices.

An aptamer-assisted nanopore strategy with a salt gradient for direct protein sensing

Nanopore sensing is at the forefront of the technological revolution of the protein research field and has been widely used in molecular diagnosis and molecular dynamics, as well as for various sequencing applications. However, direct protein sensing with biological nanopores is still challenging owing to the large molecular size. Here, we propose an aptamer-assisted nanopore strategy for direct protein sensing and demonstrate its proof-of-concept utilities by experiments with SARS-Cov-2 nucleocapsid protein (NP), the most abundantly expressed viral protein, that is widely used in clinical diagnosis for COVID-19. NP binds with an oligonucleotide-tailed aptamer to form a protein-DNA complex which induces a discriminative two-level pattern of current blockades. We reveal the potential molecular interaction mechanism for the characteristic blockades and identify the salt gradient condition as the dominant factor of the phenomenon. Furthermore, we achieve a high sensitivity of 10 pM for NP detection within one hour and make a preliminary exploration on clinical diagnosis. This work promises a new platform for rapid and label-free protein detection.

The application of single molecule nanopore sensing for quantitative analysis

Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.

Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method

A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.

Biomimetic Molecular Clamp Nanopores for Simultaneous Quantifications of NAD+ and NADH

NADH/NAD⁺ is pivotal to fundamental biochemistry research and molecular diagnosis, but recognition and detection for them are a big challenge at the single-molecule level. Inspired by the biological system, here, we designed and synthesized a biomimetic NAD⁺/NADH molecular clamp (MC), octakis-(6-amino-6-deoxy)-γ-cyclomaltooctaose, and harbored in the engineered α-HL(M113R)₇ nanopore, forming a novel single-molecule biosensor. The single-molecule measurement possesses high selectivity and a high signal-to-noise ratio, allowing to simultaneously recognize and detect for sensing NADH/NAD⁺ and their transformations.

Tertiary RNA Folding-Targeted Drug Screening Strategy Using a Protein Nanopore

Bacterial riboswitch RNAs are attractive targets for novel antibiotics against antibiotic-resistant superbacteria. Their binding to cognate metabolites is essential for the regulation of bacterial gene expression. Despite the importance of RNAs as therapeutic targets, the development of RNA-targeted, small-molecule drugs is limited by current biophysical methods. Here, we monitored the specific interaction between the adenine-sensing riboswitch aptamer domain (ARS) and adenine at the single-molecule level using α-hemolysin (αHL) nanopores. During adenine-induced tertiary folding, adenine-bound ARS intermediates exhibited characteristic nanopore events, including a two-level ionic current blockade and a ∼ 5.6-fold longer dwell time than that of free RNA. In a proof-of-concept experiment, tertiary RNA folding-targeted drug screening was performed using a protein nanopore, which resulted in the discovery of three new ARS-targeting hit compounds from a natural compound library. Taken together, these results reveal that αHL nanopores are a valuable platform for ultrasensitive, label-free, and single-molecule-based drug screening against therapeutic RNA targets.

Biological Nanopores: Engineering on Demand

Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.

Sensing with Nanopores and Aptamers: A Way Forward

In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.

Engineering bio-mimicking functional vesicles with multiple compartments for quantifying molecular transport

Controlled design of giant unilamellar vesicles under defined conditions has vast applications in the field of membrane and synthetic biology. Here, we bio-engineer bacterial-membrane mimicking models of controlled size under defined salt conditions over a range of pH. A complex bacterial lipid extract is used for construction of physiologically relevant Gram-negative membrane mimicking vesicles whereas a ternary mixture of charged lipids (DOPG, cardiolipin and lysyl-PG) is used for building Gram-positive bacterial-membrane vesicles. Furthermore, we construct stable multi-compartment biomimicking vesicles using the gel-assisted swelling method. Importantly, we validate the bio-application of the bacterial vesicle models by quantifying diffusion of chemically synthetic amphoteric antibiotics. The transport rate is pH-responsive and depends on the lipid composition, based on which a permeation model is proposed. The permeability properties of antimicrobial peptides reveal pH dependent pore-forming activity in the model vesicles. Finally, we demonstrate the functionality of the vesicles by quantifying the uptake of membrane-impermeable molecules facilitated by embedded pore-forming proteins. We suggest that the bacterial vesicle models developed here can be used to understand fundamental biological processes like the peptide assembly mechanism or bacterial cell division and will have a multitude of applications in the bottom-up assembly of a protocell.

Giant vesicle functional models mimicking a bacterial membrane under physiological conditions are constructed.

Rapid quantification of prion proteins using resistive pulse sensing

Prion diseases are a group of fatal transmissible neurological conditions caused by the change in conformation of intrinsic cellular prion protein (PrP^C). We present a rapid assay using aptamers and resistive pulse sensing, RPS, to extract and quantify PrP^C from complex sample matrices. We functionalise the surface of superparamagnetic beads, SPBs, with a DNA aptamer. First SPB's termed P-beads, are used to pre-concentrate the analyte from a large sample volume. The PrP^C protein is then eluted from the P-beads before aptamer modified sensing beads, S-beads, are added. The velocity of the S-beads through the nanopore reveals the concentration of the PrP^C protein. The process is done in under an hour and allows the detection of picomol's of protein.

Simultaneous High-Resolution Detection of Bioenergetic Molecules using Biomimetic-Receptor Nanopore

A novel artificial receptor, heptakis-[6-deoxy-6-(2-hydroxy-3-trimethylammonion-propyl) amino]-beta-cyclomaltoheptaose, with similar functions of mitochondrial ADP/ATP carrier protein, was synthesized and harbored in the engineered α-HL (M113R)₇ nanopore, forming a single-molecule biosensor for sensing bioenergetic molecules and their transformations. The strategy significantly elevates both selectivity and signal-to-noise, which enables simultaneous recognition and detection of ATP, ADP, and AMP by real-time single-molecule measurement.

Nanopore-Based Confined Spaces for Single-Molecular Analysis

The field of nanopore sensing at the single-molecular level is in a "boom" period. Such nanopores, which are either composed of biological materials or are fabricated from solid-state substrates, offer a unique confined space that is compatible with the single-molecular scale. Under the influence of an electrical field, such single-biomolecular interfaces can read single-molecular information and, if appropriately fine-tuned, each molecule plays its individual ionic rhythm to compose a "molecular symphony". Over the past few decades, many research groups have worked on nanopore-based single-molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore-based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.

Label-Free Detection of DNA Mutations by Nanopore Analysis

Cancers are caused by mutations to genes that regulate cell normal functions. The capability to rapid and reliable detection of specific target gene variations can facilitate early disease detection and diagnosis and also enables personalized treatment of cancer. Most of the currently available methods for DNA mutation detection are time-consuming and/or require the use of labels or sophisticated instruments. In this work, we reported a label-free enzymatic reaction-based nanopore sensing strategy to detect DNA mutations, including base substitution, deletion, and insertion. The method was rapid and highly sensitive with a detection limit of 4.8 nM in a 10 min electrical recording. Furthermore, the nanopore assay could differentiate among perfect match, one mismatch, and two mismatches. In addition, simulated serum samples were successfully analyzed. Our developed nanopore-based DNA mutation detection strategy should find useful application in genetic diagnosis.

Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis

Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.

Measuring a frequency spectrum for single-molecule interactions with a confined nanopore

The time-domain nanopore signal is preciously converted into energy–frequency–time spectra with high frequency resolution and high time resolution using the Hilbert–Huang transform for revealing the detail behaviours of single-molecule weak interactions.

Adaption of a Solid-State Nanopore to Homogeneous DNA Organization Verification and Label-Free Molecular Analysis without Covalent Modification

Recent advances have shown increasing designs of nucleic acid organizations via controlling the thermodynamics and kinetics of oligonucleotides. Nevertheless, deeper understanding and further applications of these DNA nanotechnologies are majorly hampered by the lack of effective analytical methodologies that are competent enough to investigate them. To deliver a potential solution, here we developed an innovative exploration that employed the emerging nanopore technique to characterize DNA organization at the single-molecule level and in completely homogeneous condition without covalent modification. With the help of counting and profiling the translocation-induced current drop of a DNA assembly structure passing through a conical glass nanopore (CGN), we have directly verified the formation of the individual double-helix concatemer generated from our model, hybridization chain reaction (HCR). Due to the ultrasensitivity of the nanopore technology, those concatemers that were difficult to observe on a conventional electrophoresis image were brought to light. The translocation duration time also provided the approximate length and folding information for the concatemers. These advantages were proven also applicable to structures with more sophisticated folding behaviors. Eventually, when coupling with an upstream reaction, CGN was further turned to a universal detector that was capable of even detecting other nucleic acid organization behaviors as well as targets that were unable to generate huge products. All of these results are expected to promote deeper study and applications of the nanopore technique in the field of nucleic acid nanotechnology.

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.

Peptide-Mediated Nanopore Detection of Uranyl Ions in Aqueous Media

Uranium is one of the most common radioactive contaminants in the environment. As a major nuclear material in production, environmental samples (like soil and groundwater) can provide signatures on uranium production activity inside the facility. Thus, developing a new and portable analytical technology for uranium in aqueous media is significant not only for environmental monitoring, but also for nonproliferation. In this work, a label-free method for the detection of uranyl (UO₂²⁺) ions is developed by monitoring the translocation of a peptide probe in a nanopore. Based on the difference in the number of peptide events in the absence and presence of uranyl ions, nanomolar concentration of UO₂²⁺ ions could be detected in minutes. The method is highly selective; micromolar concentrations of Cd²⁺, Cu²⁺, Zn²⁺, Ni²⁺, Pb²⁺, Hg²⁺, Th⁴⁺, Mg²⁺, and Ca²⁺ would not interfere with the detection of UO₂²⁺ ions. In addition, simulated water samples were successfully analyzed.

Label-Free Nanopore Biosensor for Rapid and Highly Sensitive Cocaine Detection in Complex Biological Fluids

Detection of very low amounts of illicit drugs such as cocaine in clinical fluids like serum continues to be important for many areas in the fight against drug trafficking. Herein, we constructed a label-free nanopore biosensor for rapid and highly sensitive detection of cocaine in human serum and saliva samples based on target-induced strand release strategy. In this bioassay, an aptamer for cocaine was prehybridized with a short complementary DNA. Owing to cocaine specific binding with aptamer, the short DNA strand was displaced from aptamer and translocation of this output DNA through α-hemolysin nanopore generated distinct spike-like current blockages. When plotted in double-logarithmic scale, a linear relationship between target cocaine concentration and output DNA event frequency was obtained in a wide concentration range from 50 nM to 100 μM of cocaine, with the limit of detection down to 50 nM. In addition, this aptamer-based sensor method was successfully applied for cocaine detection in complex biological fluids like human saliva and serum samples with great selectivity. Simple preparation, low cost, rapid, label-free, and real sample detection are the motivating factors for practical application of the proposed biosensor.

Single molecule based SNP detection using designed DNA carriers and solid-state nanopores

A novel nanopore-DNA carrier method is demonstrated for SNP detection and following DNA strand displacement kinetics at the single molecule level.

Bioinspired Assemblies and Plasmonic Interfaces for Electrochemical Biosensing

Electrochemical biosensing represents a collection of techniques that may be utilized for capture and detection of biomolecules in both simple and complex media. While the instrumentation and technological aspects play important roles in detection capabilities, the interfacial design aspects are of equal importance, and often, those inspired by nature produce the best results. This review highlights recent material designs, recognition schemes, and method developments as they relate to targeted electrochemical analysis for biological systems. This includes the design of electrodes functionalized with peptides, proteins, nucleic acids, and lipid membranes, along with nanoparticle mediated signal amplification mechanisms. The topic of hyphenated surface plasmon resonance assays is also discussed, as this technique may be performed concurrently with complementary and/or confirmatory measurements. Together, smart materials and experimental designs will continue to pave the way for complete biomolecular analyses of complex and technically challenging systems.

A highly versatile platform based on geometrically well-defined 3D DNA nanostructures for selective recognition and positioning of multiplex targets

We develop a versatile recognition system based on 3D triangular-shaped DNA nanotubes by integrating three different aptamer sequences along the three edges. This would allow multiple binding activities to be combined into a single system. The versatility of this nanotube platform can also provide a framework for spatial orientation and positioning of different aptamer-binding ligands in a 'pea-pod' architecture.

Nanopore-Based Selective Discrimination of MicroRNAs with Single-Nucleotide Difference Using Locked Nucleic Acid-Modified Probes

The accurate discrimination of microRNAs (miRNAs) with highly similar sequences would greatly facilitate the screening and early diagnosis of diseases. In the present work, a locked nucleic acid (LNA)-modified probe was designed and used for α-hemolysin (α-HL) nanopore to selectively and specifically identify miRNAs. The hybridization of the LNA probe with the target miRNAs generated unique long-lived signals in the nanopore thus facilitated an accurate discrimination of miRNAs with similar sequences, even a single-nucleotide difference. Furthermore, the developed nanopore-based analysis with LNA probe could selectively detect target miRNAs in a natural serum background. This selective and sensitive approach may be highly valuable in the detection of clinically relevant biomarkers in complex samples.

Alkyl detection facilitated by a DNA conjugate with an α-hemolysin nanopore

A novel α-hemolysin nanopore (α-HL) based strategy for the detection of an alkyl linker at the single-molecule level.

A conformation and charge co-modulated ultrasensitive biomimetic ion channel

For the first time, an ultrasensitive nanopore-based sensor that co-modulated simultaneously by conformation and charge has been developed for the detection of ATP.

Single-molecule analysis of the self-assembly process facilitated by host–guest interactions

The self-assembly process operated by para-sulfonatocalix[6]arenes and methyl viologen was analyzed at the single-molecule level through an α-hemolysin nanopore.

Enhanced resolution of low molecular weight poly(ethylene glycol) in nanopore analysis

A design with conjugation of DNA hairpin structure to the poly(ethylene glycol) molecule was presented to enhance the temporal resolution of low molecular weight poly(ethylene glycol) in nanopore studies. By the virtue of this design, detection of an individual PEG with molecular weight as low as 140 Da was achieved at the single-molecule level in solution, which provides a novel strategy for characterization of an individual small molecule within a nanopore. Furthermore, we found that the current duration time of poly(ethylene glycol) was scaled with the relative molecular weight, which has a potential application in single-molecule detection.

Single molecule analysis by biological nanopore sensors

Nanopore sensors provide a highly innovative technique for a rapid and label-free single molecule analysis, which holds a great potential in routing applications. Biological nanopores have been used as ultra-sensitive sensors over a wide range of single molecule analysis including DNA sequencing, disease diagnosis, drug screening, environment monitoring and the construction of molecule machines. This mini review will focus on the current strategies for the identification and characterization of an individual analyte, especially based on our recent achievements in biological nanopore biosensors.