Designed protein pores as components for biosensors

Identification of phoxim and omethoate using α-hemolysin nanopore and aptamers

Contamination with pesticides has inflicted substantial harm on human health; therefore, developing rapid, ultra-sensitive, and non-labelling simultaneous detection methods for multiple pesticides is necessary. In this study, we demonstrated that α-hemolysin (α-HL) nanopore sensor can detect and discriminate organophosphorus pesticides of phoxim and omethoate in a single nanopore without requiring labels of the probes or purification of the pesticides in real samples. Aptamers specifically recognise and bind pesticides to obtain pesticide-aptamer complexes that produce characteristic current signals while passing through the nanopore. Phoxim and omethoate were accurately distinguished by a portable instrument within minutes, and their detection sensitivity was up to the femtomole level, whether detected alone or simultaneously. The detection limits of phoxim and omethoate were 8.13 × 10-16 M and 4.16 × 10-15 M. The recoveries of phoxim and omethoate from pear, tomato, and cucumber samples were 82.0-107.0 % and 81.9-118.3 % respectively, with coefficient of variable below 8.0 %.

Electrochemical kinetic fingerprinting of single-molecule coordinations in confined nanopores

Metal centers are essential for enzyme catalysis, stabilizing the active site, facilitating electron transfer, and maintaining the structure through coordination with amino acids. In this study, K238H-AeL nanopores with histidine sites were designed as single-molecule reactors for the measurement of single-molecule coordination reactions. The coordination mechanism of Au(III) with histidine and glutamate in biological nanopore confined space was explored. Specifically, Au(III) interacts with the nitrogen (N) atom in the histidine imidazole ring of the K238H-AeL nanopore and the oxygen (O) atom in glutamate to form a stable K238H-Au-Cl2 complex. The formation mechanism of this complex was further validated through single-molecule nanopore analysis, mass spectrometry, and molecular dynamics simulations. Introducing histidine and negative charge amino acids with carboxyl group into different positions within the nanopore revealed that the formation of the histidine-Au coordination bond in the confined space requires a suitable distance between the ligand and the central metal atom. By analyzing the association and dissociation rates of the single Au(III) ion under the applied voltages, it was found that a confined nanopore increased the bonding rate constant of Au(III)-histidine coordination reactions by around 10-100 times compared to that in the bulk solution and the optimal voltage for single-molecule. Therefore, nanopore techniques for tracking single-molecule reactions could offer valuable insights into designing metalloenzymes in metal-catalyzed organic reactions.

Repurposing an antimicrobial peptide for the development of a dual ion channel/molecular receptor-like platform for metal ion detection

The presence of non-essential metals in the environment as contaminants is prone to cause hazardous health problems following accumulation in the human body and the ensuing toxic effects. This calls for continuous discovery and innovation in the realm of developing easy-to-operate, cheap and sensitive sensors. Herein, we describe the proof of concept approach for designing a molecular receptor-like, chimeric sensor based on the pore-forming peptide alamethicin (Alm), tethered via a linker with an ultrashort peptide nucleic acid (PNA) moiety, capable of generating functional ion channel oligomers in planar lipid membranes. The working principle of the sensor exploits the ability of Hg2+ ions to complex mismatching thymine-thymine sequences between the PNA receptor moiety on Alm oligomers and free, thymine-based, single-stranded DNAs (ssDNAs) in solution, thus creating a stable base pair at the oligomer entrance. This generates a transducing mechanism which converts the metal ion complexation into a specific electrical signature of the self-assembled Alm oligomers, enabling selective Hg2+ ion detection. The platform is programmable, whereby the simple exchange of the PNA sequence and its ssDNA counterpart in solution rendered the system selective for Cu2+ ion detection. With further optimization, the presented solution has the potential to translate into miniaturized, cost-effective biosensors suitable for the real-time, label-free and continuous detection of metal ions or other biomolecules.

Exploring ssDNA translocation through α-hemolysin using coarse-grained steered molecular dynamics

Protein nanopores have proven to be effective for single-molecule studies, particularly for single-stranded DNA (ssDNA) translocation. Previous experiments demonstrated their ability to distinguish differences in purine and pyrimidine bases and in the orientation of the ssDNA molecule inside nanopores. Unfortunately, the microscopic details of ssDNA translocation over experimental time scales, which are not accessible through all-atom molecular dynamics (MD), have yet to be examined. However, coarse-grained (CG) MD simulations enable systems to be simulated over longer characteristic times closer to experiments than all-atom MD. This paper studies ssDNA translocation through α-hemolysin nanopores exploiting steered MD using the MARTINI CG force field. The impacts of the sequence length, orientation inside the nanopore and DNA charges on translocation dynamics as well as the conformational dynamics of ssDNA during the translocation are explored. Our results highlight the efficacy of CG molecular dynamics in capturing the experimental properties of ssDNA translocation, including a wide distribution in translocation times per base. In particular, the phosphate charges of the DNA molecule are crucial in the translocation dynamics and impact the translocation rate. Additionally, the influence of the ssDNA molecule orientation on the translocation rate is explained by the conformational differences of ssDNA inside the nanopore during its translocation. Our study emphasizes the significance of obtaining sufficient statistics via CG MD, which can elucidate the great variety of translocation processes.

Nanopore analysis of salvianolic acids in herbal medicines

Natural herbs, which contain pharmacologically active compounds, have been used historically as medicines. Conventionally, the analysis of chemical components in herbal medicines requires time-consuming sample separation and state-of-the-art analytical instruments. Nanopore, a versatile single molecule sensor, might be suitable to identify bioactive compounds in natural herbs. Here, a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore is used as a sensor for herbal medicines. A variety of bioactive compounds based on salvianolic acids, including caffeic acid, protocatechuic acid, protocatechualdehyde, salvianic acid A, rosmarinic acid, lithospermic acid, salvianolic acid A and salvianolic acid B are identified. Using a custom machine learning algorithm, analyte identification is performed with an accuracy of 99.0%. This sensing principle is further used with natural herbs such as Salvia miltiorrhiza, Rosemary and Prunella vulgaris. No complex sample separation or purification is required and the sensing device is highly portable.

Nanopore analysis of cis-diols in fruits

Natural fruits contain a large variety of cis-diols. However, due to the lack of a high-resolution sensor that can simultaneously identify all cis-diols without a need of complex sample pretreatment, direct and rapid analysis of fruits in a hand-held device has never been previously reported. Nanopore, a versatile single molecule sensor, can be specially engineered to perform this task. A hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore modified with a sole phenylboronic acid (PBA) adapter is prepared. This engineered MspA accurately recognizes 1,2-diphenols, alditols, α-hydroxy acids and saccharides in prune, grape, lemon, different varieties of kiwifruits and commercial juice products. Assisted with a custom machine learning program, an accuracy of 99.3% is reported and the sample pretreatment is significantly simplified. Enantiomers such as DL-malic acids can also be directly identified, enabling sensing of synthetic food additives. Though demonstrated with fruits, these results suggest wide applications of nanopore in food and drug administration uses.

Protein engineering of pores for separation, sensing, and sequencing

Proteins are critical to cellular function and survival. They are complex molecules with precise structures and chemistries, which allow them to serve diverse functions for maintaining overall cell homeostasis. Since the discovery of the first enzyme in 1833, a gamut of advanced experimental and computational tools has been developed and deployed for understanding protein structure and function. Recent studies have demonstrated the ability to redesign/alter natural proteins for applications in industrial processes of interest and to make customized, novel synthetic proteins in the laboratory through protein engineering. We comprehensively review the successes in engineering pore-forming proteins and correlate the amino acid-level biochemistry of different pore modification strategies to the intended applications limited to nucleotide/peptide sequencing, single-molecule sensing, and precise molecular separations.

Stochastic Sensing of Dynamic Interactions and Chemical Reactions with Nanopores/Nanochannels

Nanopore sensing technology is an emerging analysis method with the advantages of simple operation, high sensitivity, fast output and being label free, and it is widely used in protein analysis, gene sequencing, biomarker detection, and other fields. The confined space of the nanopore provides a place for dynamic interactions and chemical reactions between substances. The use of nanopore sensing technology to track these processes in real time is helpful to understand the interaction/reaction mechanism at the single-molecule level. According to nanopore materials, we summarize the development of biological nanopores and solid-state nanopores/nanochannels in the stochastic sensing of dynamic interactions and chemical reactions. The goal of this paper is to stimulate the interest of researchers and promote the development of this field.

Quantitative Microscopic Observation of Base-Ligand Interactions via Hydrogen Bonds by Single-Molecule Counting

Chemical properties have been based on statistical averages since the introduction of Avogadro's number. The lack of suitable methods for counting identified single molecules has posed challenges to counting statistics. The selectivity, affinity, and mode of hydrogen bonding between base and small molecules that make up DNA, which is vital for living organisms, have not yet been revealed at the single molecule level. Here, we show the quantitation of the above-mentioned parameters via single-molecule counting based on the combination of single-molecule electrical measurements and AI. The binding selectivity values of five ligands to four different base molecules were evaluated quantitatively by determining the ratio of the number of aggregates in a solution mixture of base molecules and a ligand. In addition, we show the ligand dependence of the mode and number of microscopic hydrogen bonds via single-molecule counting and quantum chemical calculations.

Advances of nanopore-based sensing techniques for contaminants evaluation of food and agricultural products

Food safety assurance systems are becoming more stringent in response to the growing food safety problems. Rapid, sensitive, and reliable detection technology is a prerequisite for the establishment of food safety assurance systems. Nanopore technology has been taken as one of the emerging technology capable of dealing with the detection of harmful contaminants as efficiently as possible due to the advantage of label-free, high-throughput, amplification-free, and rapid detection features. Start with the history of nanopore techniques, this review introduced the underlying knowledge of detection mechanism of nanopore-based sensing techniques. Meanwhile, sensing interfaces for the construction of nanopore sensors are comprehensively summarized. Moreover, this review covers the current advances of nanopore techniques in the application of food safety screening. Currently, the establishment of nanopore sensing devices is mainly based on the blocking current phenomenon. Sensing interfaces including biological nanopores, solid-state nanopores, DNA origami, and de novo designed nanopores can be used in the manufacture of sensing devices. Food harmful substances, including heavy metals, veterinary drugs, pesticide residues, food toxins, and other harmful substances can be quickly determined by nanopore-based sensors. Moreover, the combination of nanopore techniques with advanced materials has become one of the most effective methods to improve sensing properties.

Nanopore Sensing Technique for Studying the Hofmeister Effect

The nanopore sensing technique is an emerging method of detecting single molecules, and extensive research has gone into various fields, including nanopore sequencing and other applications of single-molecule studies. Recently, several researchers have explored the specific ion effects in nanopore channels, enabling a unique understanding of the Hofmeister effect at the single-molecule level. Herein, the recent advances of using nanopore sensing techniques are reviewed to study the Hofmeister effect and the physicochemical mechanism of this process is attempted. The challenges and goals are also discussed for the future in this field.

Chemistry solutions to facilitate nanopore detection and analysis

Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.

Functional Nanopore Screen: A Versatile High-Throughput Assay to Study and Engineer Protein Nanopores in Escherichia coli

Nanopores comprise a versatile class of membrane proteins that carry out a range of key physiological functions and are increasingly developed for different biotechnological applications. Yet, a capacity to study and engineer protein nanopores by combinatorial means has so far been hampered by a lack of suitable assays that combine sufficient experimental resolution with throughput. Addressing this technological gap, the functional nanopore (FuN) screen now provides a quantitative and dynamic readout of nanopore assembly and function in the context of the inner membrane of Escherichia coli. The assay is based on genetically encoded fluorescent protein sensors that resolve the nanopore-dependent influx of Ca²⁺ across the inner membrane of E. coli. Illustrating its versatile capacity, the FuN screen is first applied to dissect the molecular features that underlie the assembly and stability of nanopores formed by the S²¹68 holin. In a subsequent step, nanopores are engineered by recombining the transmembrane module of S²¹68 with different ring-shaped oligomeric protein structures that feature defined hexa-, hepta-, and octameric geometries. Library screening highlights substantial plasticity in the ability of the S²¹68 transmembrane module to oligomerize in alternative geometries, while the functional properties of the resultant nanopores can be fine-tuned through the identity of the connecting linkers. Overall, the FuN screen is anticipated to facilitate both fundamental studies and complex nanopore engineering endeavors with many potential applications in biomedicine, biotechnology, and synthetic biology.

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.

Spiers Memorial Lecture. Next generation nanoelectrochemistry: the fundamental advances needed for applications

Nanoelectrochemistry, where electrochemical processes are controlled and investigated with nanoscale resolution, is gaining more and more attention because of the many potential applications in energy and sensing and the fact that there is much to learn about fundamental electrochemical processes when we explore them at the nanoscale. The development of instrumental methods that can explore the heterogeneity of electrochemistry occurring across an electrode surface, monitoring single molecules or many single nanoparticles on a surface simultaneously, have been pivotal in giving us new insights into nanoscale electrochemistry. Equally important has been the ability to synthesise or fabricate nanoscale entities with a high degree of control that allows us to develop nanoscale devices. Central to the latter has been the incredible advances in nanomaterial synthesis where electrode materials with atomic control over electrochemically active sites can be achieved. After introducing nanoelectrochemistry, this paper focuses on recent developments in two major application areas of nanoelectrochemistry; electrocatalysis and using single entities in sensing. Discussion of the developments in these two application fields highlights some of the advances in the fundamental understanding of nanoelectrochemical systems really driving these applications forward. Looking into our nanocrystal ball, this paper then highlights: the need to understand the impact of nanoconfinement on electrochemical processes, the need to measure many single entities, the need to develop more sophisticated ways of treating the potentially large data sets from measuring such many single entities, the need for more new methods for characterising nanoelectrochemical systems as they operate and the need for material synthesis to become more reproducible as well as possess more nanoscale control.

Biological nanopores for sensing applications

Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapter-assisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.

Recent Progress on Single-Molecule Detection Technologies for Food Safety

Rapid and sensitive detection technologies for food contaminants play vital roles in food safety. Due to the complexity of the food matrix and the trace amount distribution, traditional methods often suffer from unsatisfying accuracy, sensitivity, or specificity. In past decades, single-molecule detection (SMD) has emerged as a way to realize the rapid and ultrasensitive measurement with low sample consumption, showing a great potential in food contaminants detection. For instance, based on the nanopore technique, simple and effective methods for single-molecule analysis of food contaminants have been developed. To our knowledge, there has been a rare review that focuses on SMD techniques for food safety. The present review attempts to cover some typical SMD methods in food safety, including electrochemistry, optical spectrum, and atom force microscopy. Then, recent applications of these techniques for detecting food contaminants such as biotoxins, pesticides, heavy metals, and illegal additives are reviewed. Finally, existing research challenges and future trends of SMD in food safety are also tentatively proposed.

A Lipid-Based Droplet Processor for Parallel Chemical Signals

A key goal of bottom-up synthetic biology is to construct cell- and tissue-like structures. Underpinning cellular life is the ability to process several external chemical signals, often in parallel. Until now, cell- and tissue-like structures have been constructed with no more than one signaling pathway. Many pathways rely on signal transport across membranes using protein nanopores. However, such systems currently suffer from the slow transport of molecules. We have optimized the application of these nanopores to permit fast molecular transport, which has allowed us to construct a processor for parallel chemical signals from the bottom up in a modular fashion. The processor comprises three aqueous droplet compartments connected by lipid bilayers and operates in an aqueous environment. It can receive two chemical signals from the external environment, process them orthogonally, and then produce a distinct output for each signal. It is suitable for both sensing and enzymatic processing of environmental signals, with fluorescence and molecular outputs. In the future, such processors could serve as smart drug delivery vehicles or as modules within synthetic tissues to control their behavior in response to external chemical signals.

The expanding toolbox to study the LRRC8-formed volume-regulated anion channel VRAC

The volume-regulated anion channel (VRAC) is activated upon cell swelling and facilitates the passive movement of anions across the plasma membrane in cells. VRAC function underlies many critical homeostatic processes in vertebrate cells. Among them are the regulation of cell volume and membrane potential, glutamate release and apoptosis. VRAC is also permeable for organic osmolytes and metabolites including some anti-cancer drugs and antibiotics. Therefore, a fundamental understanding of VRAC's structure-function relationships, its physiological roles, its utility for therapy of diseases, and the development of compounds modulating its activity are important research frontiers. Here, we describe approaches that have been applied to study VRAC since it was first described more than 30 years ago, providing an overview of the recent methodological progress. The diverse applications reflecting a compromise between the physiological situation, biochemical definition, and biophysical resolution range from the study of VRAC activity using a classic electrophysiology approach, to the measurement of osmolytes transport by various means and the investigation of its activation using a novel biophysical approach based on fluorescence resonance energy transfer.

Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era

The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-read), PacBio (long-read), and Oxford Nanopore (long-read) are the most popular sequencing technologies. Unlike PacBio or the popular short-read sequencers before it, which, as examples of the second or so-called Next-Generation Sequencing platforms, need to synthesize when sequencing, nanopore technology directly sequences native DNA and RNA molecules. Nanopore sequencing, therefore, avoids converting mRNA into cDNA molecules, which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases. In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology, we focus on their development and application achievements, discussing their challenges and future perspective. We also address the problems researchers may encounter applying these approaches in their research topics, and how to resolve them.

Programmable nano-reactors for stochastic sensing

Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, "programmable nano-reactors for stochastic sensing" (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.

Nanopore sensing: A physical-chemical approach

Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.

Influence of Substrate Hydrophilicity on Structural Properties of Supported Lipid Systems on Graphene, Graphene Oxides, and Silica

Pristine graphene, a range of graphene oxides, and silica substrates were used to investigate the effect of surface hydrophilicity on supported lipid bilayers by means of all-atom molecular dynamics simulations. Supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers were found in close-contact conformations with hydrophilic substrates with as low as 5% oxidation level, while self-assembled monolayers occur on pure hydrophobic graphene only. Lipids and water at the surface undergo large redistribution to maintain the stability of the supported bilayers. Deposition of bicelles on increasingly hydrophilic substrates shows the continuous process of reshaping of the supported system and makes intermediate stages between self-assembled monolayers and supported bilayers. The bilayer thickness changes with hydrophilicity in a complex manner, while the number of water molecules per lipid in the hydration layer increases together with hydrophilicity.

Rapid and multiplex preparation of engineered Mycobacterium smegmatis porin A (MspA) nanopores for single molecule sensing and sequencing

Acknowledging its unique conical lumen structure, Mycobacterium smegmatis porin A (MspA) was the first type of nanopore that has successfully sequenced DNA. Recent developments of nanopore single molecule chemistry have also suggested MspA to be an optimum single molecule reactor. However, further investigations with this approach require heavy mutagenesis which is labor intensive and requires high end instruments for purifications. We here demonstrate an efficient and economic protocol which performs rapid and multiplex preparation of a variety of MspA mutants. The prepared MspA mutants were demonstrated in operations such as nanopore insertion, sequencing, optical single channel recording (oSCR), nanopore single molecule chemistry and nanopore rectification. The performance is no different from that of pores however prepared by other means. The time of all human operations and the cost for a single batch of preparation have been minimized to 40 min and 0.4$, respectively. This method is extremely useful in the screening of new MspA mutants, which has an urgent requirement in further investigations of new MspA nanoreactors. Its low cost and simplicity also enable efficient preparations of MspA nanopores for both industrial manufacturing and academic research.

Mapping Potential Engineering Sites of Mycobacterium smegmatis porin A (MspA) to Form a Nanoreactor

Protein nanopores can be engineered as nanoreactors to investigate single-molecule chemical reactions. Recent studies have demonstrated that Mycobacterium smegmatis porin A (MspA) nanopore is a superior engineering template acknowledging its geometrical advantages. However, reported engineering of MspA to form a nanoreactor has focused only on site 91 and mapping of other engineering sites have never been performed before. By taking tetrachloraurate(III) ([AuCl₄]^-) as a model reactant, potential engineering sites within the pore constriction of MspA have been thoroughly investigated. It is discovered that the produced event amplitude is inversely correlated to the cross-sectional diameter of the pore constriction size at the engineering site, providing evidence that site 91 is actually already the optimum place to introduce the chemical reactivity. Other unavailable engineering sites, which either significantly interfere with the pore assembly or produce reactive sites facing to the pore's exterior instead of to the pore lumen, were also spotted and discussed. All results demonstrated above have provided a complete map of engineering sites within the constriction area of MspA and may be beneficial as a reference in future engineering of corresponding nanoreactors.

Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications

Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.

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.

A Single-Molecule Observation of Dichloroaurate(I) Binding to an Engineered Mycobacterium smegmatis porin A (MspA) Nanopore

Gold(I) compounds are known to bind sulfur-containing proteins, forming the basis in the design of gold(I)-based drugs. However, the intrinsic molecular mechanism of the chemical reaction is easily hidden when monitored in ensemble. We have previously demonstrated that Mycobacterium smegmatis porin A (MspA) can be engineered (MspA-M) to contain a specialized nanoreactor to probe chemical reactions involving tetrachloroaurate(III). Here, we provide further investigations of coordination interactions between dichloroaurate(I) and MspA-M. Gold compounds of different coordination geometry and valence states are as well probed and evaluated, demonstrating the generality of MspA-M. With single-molecule evidence, MspA-M demonstrates a preference for dichloroaurate(I) than tetrachloroaurate(III), an observation in a single molecule that has never been reported. By counting the maximum number of simultaneous ion bindings, the narrowly confined pore restriction also efficiently distinguishes dichloroaurate(I) and tetrachloroaurate(III) according to their differences in geometry or size. The above demonstration complemented a previous study by demonstrating other possible gold-based single-molecule chemical reactions observable by MspA. These observations bring insights in the understanding of gold-based coordination chemistry in a nanoscale.

Single molecule mass photometry of nucleic acids

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

Nanopore detection of metal ions: Current status and future directions

In this review, we highlight recent research efforts that aimed at developing nanopore sensors for detection of metal ions, which play a crucial role in environmental safety and human health. Protein pores use three stochastic sensing-based strategies for metal ion detection. The first strategy is to construct engineered nanopores with metal ion binding sites, so that the interaction between the target analytes and the nanopore can slow the movement of metal ions in the nano-channel. Second, large molecules such as nucleic acids and especially peptides could be utilized as external selective molecular probes to detect metal ions based on the conformational change of the ligand molecules induced by the metal ion-ligand chelation / coordination interaction. Third, enzymatic reactions can also be used as an alternative to the molecule probe strategy in the situation that a sensitive and selective probe molecule for the target analyte is difficult to obtain. On the other hand, by taking advantage of steady-state analysis, synthetic nanopores mainly use two strategies (modification and modification-free) to detect metals. Given the advantages of high sensitivity & selectivity, and label-free detection, nanopore-based metal ion sensors should find useful application in many fields, including environmental monitoring, medical diagnosis, and so on.

Evaluating the sensing performance of nanopore blockade sensors: A case study of prostate-specific antigen assay

The detection principle of nanopore sensors relies on measuring changes in electrical signal as analyte molecules translocate through a nanoscale pore. There are two challenges with this experimental construct when using nanopores for quantitative sensing with low detection limits in complex samples. The first is getting the analyte to the nanopore in a reasonable time frame and the second is other species in the sample also translocating through the nanopore and generating erroneous signals. We have developed a nanopore blockade sensor that alleviates the limitations of diffusion-limited mass transport and non-specific signals. Antibody-modified magnetic nanoparticles are utilized to deliver analytes of interest extracted from sample to an array of antibody-modified nanopores under a controlled electromagnet, resulting in long-term nanopore blocking events due to the formation of sandwiched immunocomplexes. Herein, this study reports on understanding some of important parameters in determining the performance of nanopore blockade sensing system, where prostate-specific antigen (PSA) is used as a model analyte. We describe the characterization of nanopore blockade sensing of PSA by (1) tuning on/off the electromagnet, (2) varying nanopore number in a nanopore chip, and (3) deploying the sensor in human plasma. Results show that magnetophoresis effectively facilitates active delivery and selective sensing of PSA to the nanopore. Nanopore chips with a larger number of nanopores are shown to receive more nanopore blockades for a given concentration of analyte. Furthermore, identifiable blockade events accounted for successful detection of PSA in plasma, indicate the high specificity of the sensing system.

Layer-by-layer modification effects on a nanopore's inner surface of polycarbonate track-etched membranes

The control of the morphology, as well as the physical and chemical properties, of nanopores is a key issue for many applications. Reducing pore size is important in nanopore-based sensing applications as it helps to increase sensitivity. Changes of other physical properties such as surface net charge can also modify transport selectivity of the pores. We have studied how polyelectrolyte layer-by-layer (LBL) surface modification can be used to change the characteristics of nanoporous membranes. Studies were performed with a custom made three-dimensional multilayer microfluidic device able to fit membrane samples. The device allowed us to efficiently control LBL film deposition over blank low-cost commercially available polycarbonate track-etched (PCTE) membranes. We have demonstrated pore diameter reduction and deposition of the layers inside the pores through confocal and SEM images. Posterior impedance measurement studies served to evaluate experimentally the effect of the LBL deposition on the net inner nanopore surface charge and diameter. Measurements using direct current (DC) and alternative current (AC) voltages have demonstrated contrasted behaviors depending on the number and parity of deposited opposite charge layers. PCTE membranes are originally negatively charged and results evidenced higher impedance increases for paired charge LBL depositions. Impedance decreased when an unpaired positive layer was added. These results showed a different influence on the overall ion motility due to the effect of different surface charges. Results have been fit into a model that suggested a strong dependence of nanopores' impedance module to surface charge on conductive buffers, such as Phosphate Buffer Saline (PBS), even on relatively large nanopores. In AC significant differences between paired and unpaired charged LBL depositions tended to disappear as the total number of layers increased.

The control of the morphology, as well as the physical and chemical properties, of nanopores is a key issue for many applications.

Controlled deprotection and release of a small molecule from a compartmented synthetic tissue module

Synthetic tissues built from communicating aqueous droplets offer potential applications in biotechnology, however, controlled release of their contents has not been achieved. Here we construct two-droplet synthetic tissue modules that function in an aqueous environment. One droplet contains a cell-free protein synthesis system and a prodrug-activating enzyme and the other a small-molecule prodrug analog. When a Zn2+-sensitive protein pore is made in the first droplet, it allows the prodrug to migrate from the second droplet and become activated by the enzyme. With Zn2+ in the external medium, the activated molecule is retained in the module until it is released on-demand by a divalent cation chelator. The module is constructed in such a manner that one or more, potentially with different properties, might be incorporated into extended synthetic tissues, including patterned materials generated by 3D-printing. Such modules will thereby increase the sophistication of synthetic tissues for applications including controlled multidrug delivery.

Giant single molecule chemistry events observed from a tetrachloroaurate(III) embedded Mycobacterium smegmatis porin A nanopore

Biological nanopores are capable of resolving small analytes down to a monoatomic ion. In this research, tetrachloroaurate(III), a polyatomic ion, is discovered to bind to the methionine residue (M113) of a wild-type α-hemolysin by reversible Au(III)-thioether coordination. However, the cylindrical pore geometry of α-hemolysin generates shallow ionic binding events (~5–6 pA) and may have introduced other undesired interactions. Inspired by nanopore sequencing, a Mycobacterium smegmatis porin A (MspA) nanopore, which possesses a conical pore geometry, is mutated to bind tetrachloroaurate(III). Subsequently, further amplified blockage events (up to ~55 pA) are observed, which report the largest single ion binding event from a nanopore measurement. By taking the embedded Au(III) as an atomic bridge, the MspA nanopore is enabled to discriminate between different biothiols from single molecule readouts. These phenomena suggest that MspA is advantageous for single molecule chemistry investigations and has applications as a hybrid biological nanopore with atomic adaptors.

Engineered biological nanopores enable observation of single molecule chemistry events; however a cylindrical pore geometry can have undesired effects. The authors report a conical biological pore which was embedded with tetrachloroaurate(III) to allow for discrimination between different biothiols.

Single molecule observation of hard-soft-acid-base (HSAB) interaction in engineered Mycobacterium smegmatis porin A (MspA) nanopores

In the formation of coordination interactions between metal ions and amino acids in natural metalloproteins, the bound metal ion is critical either for the stabilization of the protein structure or as an enzyme co-factor. Though extremely small in size, metal ions, when bound to the restricted environment of an engineered biological nanopore, result in detectable perturbations during single channel recordings. All reported work of this kind was performed with engineered α-hemolysin nanopores and the observed events appear to be extremely small in amplitude (∼1–3 pA). We speculate that the cylindrical pore restriction of α-hemolysin may not be optimal for probing extremely small analytes. Mycobacterium smegmatis porin A (MspA), a conical shaped nanopore, was engineered to interact with Ca²⁺, Mn²⁺, Co²⁺, Ni²⁺, Zn²⁺, Pb²⁺ and Cd²⁺ and a systematically larger event amplitude (up to 10 pA) was observed. The measured rate constant suggests that the coordination of a single ion with an amino acid follows hard–soft-acid–base theory, which has never been systematically validated in the case of a single molecule. By adjusting the measurement pH from 6.8 to 8.0, the duration of a single ion binding event could be modified with a ∼46-fold time extension. The phenomena reported suggest MspA to be a superior engineering template for probing a variety of extremely small analytes, such as monatomic and polyatomic ions, small molecules or chemical intermediates, and the principle of hard–soft-acid–base interaction may be instructive in the pore design.

The principle of hard–soft-acid–base (HSAB) theory was first validated in single molecule by measurements with engineered Mycobacterium smegmatis porin A (MspA) nanopore reactors.

Enzymatic reaction-based nanopore detection of zinc ions

We report a label-free nanopore sensor for the detection of Zn2+ ions. By taking advantage of the cleavage of a substrate peptide by zinc-dependent enzymes, nanomolar concentrations of Zn2+ ions could be detected within minutes. Furthermore, structurally similar transition metals such as Ni2+, Co2+, Hg2+, Cu2+, and Cd2+ did not interfere with their detection. The enzymatic reaction-based nanopore sensing strategy developed in this work may find potential applications in environmental monitoring and medical diagnosis.

Self-Assembled Polymeric Membranes and Nanoassemblies on Surfaces: Preparation, Characterization, and Current Applications

Biomembranes play a crucial role in a multitude of biological processes, where high selectivity and efficiency are key points in the reaction course. The outstanding performance of biological membranes is based on the coupling between the membrane and biomolecules, such as membrane proteins. Polymer-based membranes and assemblies represent a great alternative to lipid ones, as their presence not only dramatically increases the mechanical stability of such systems, but also opens the scope to a broad range of chemical functionalities, which can be fine-tuned to selectively combine with a specific biomolecule. Tethering the membranes or nanoassemblies on a solid support opens the way to a class of functional surfaces finding application as sensors, biocomputing systems, molecular recognition, and filtration membranes. Herein, the design, physical assembly, and biomolecule attachment/insertion on/within solid-supported polymeric membranes and nanoassemblies are presented in detail with relevant examples. Furthermore, the models and applications for these materials are highlighted with the recent advances in each field.

Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-inspired lipid monolayers

In the context of sensing and characterizing single proteins with synthetic nanopores, lipid bilayer coatings provide at least four benefits: first, they minimize unwanted protein adhesion to the pore walls by exposing a zwitterionic, fluid surface. Second, they can slow down protein translocation and rotation by the opportunity to tether proteins with a lipid anchor to the fluid bilayer coating. Third, they provide the possibility to impart analyte specificity by including lipid anchors with a specific receptor or ligand in the coating. Fourth, they offer a method for tuning nanopore diameters by choice of the length of the lipid's acyl chains. The work presented here compares four properties of various lipid compositions with regard to their suitability as nanopore coatings for protein sensing experiments: (1) electrical noise during current recordings through solid-state nanopores before and after lipid coating, (2) long-term stability of the recorded current baseline and, by inference, of the coating, (3) viscosity of the coating as quantified by the lateral diffusion coefficient of lipids in the coating, and (4) the success rate of generating a suitable coating for quantitative nanopore-based resistive pulse recordings. We surveyed lipid coatings prepared from bolaamphiphilic, monolayer-forming lipids inspired by extremophile archaea and compared them to typical bilayer-forming phosphatidylcholine lipids containing various fractions of curvature-inducing lipids or cholesterol. We found that coatings from archaea-inspired lipids provide several advantages compared to conventional phospholipids; the stable, low noise baseline qualities and high viscosity make these membranes especially suitable for analysis that estimates physical protein parameters such as the net charge of proteins as they enable translocation events with sufficiently long duration to time-resolve dwell time distributions completely. The work presented here reveals that the ease or difficulty of coating a nanopore with lipid membranes did not depend significantly on the composition of the lipid mixture, but rather on the geometry and surface chemistry of the nanopore in the solid state substrate. In particular, annealing substrates containing the nanopore increased the success rate of generating stable lipid coatings.

Biomimetic hybrid membranes: incorporation of transport proteins/peptides into polymer supports

Molecular sensing, water purification and desalination, drug delivery, and DNA sequencing are some striking applications of biomimetic hybrid membranes. These devices take advantage of biomolecules, which have gained excellence in their specificity and efficiency during billions of years, and of artificial materials that load the purified biological molecules and provide technological properties, such as robustness, scalability, and suitable nanofeatures to confine the biomolecules. Recent methodological advances allow more precise control of polymer membranes that support the biomacromolecules, and are expected to improve the design of the next generation of membranes as well as their applicability. In the first section of this review we explain the biological relevance of membranes, membrane proteins, and the classification used for the latter. After this, we critically analyse the different approaches employed for the production of highly selective hybrid membranes, focusing on novel materials made of self-assembled block copolymers and nanostructured polymers. Finally, a summary of the advantages and disadvantages of the different methodologies is presented and the main characteristics of biomimetic hybrid membranes are highlighted.

Investigation of compacted DNA structures induced by Na+ and K+ monovalent cations using biological nanopores

In aqueous solutions, an elongated, negatively charged DNA chain can quickly change its conformation into a compacted globule in the presence of positively charged molecules, or cations. This well-known process, called DNA compaction, is a method with great potential for gene therapy and delivery. Experimental conditions to induce these compacted DNA structures are often limited to the use of common compacting agents, such as cationic surfactants, polymers, and multivalent cations. In this study, we show that in highly concentrated buffers of 1 M monovalent cation solutions at pH 7.2 and 10, biological nanopores allow real-time sensing of individual compacted structures induced by K⁺ and Na⁺, the most abundant monovalent cations in human bodies. Herein, we studied the ratio between compacted and linear structures for 15-mer single-stranded DNA molecules containing only cytosine nucleotides, optimizing the probability of linear DNA chains being compacted. Since the binding affinity of each nucleotide to cation is different, the ability of the DNA strand to fold into a compacted structure greatly depends on the type of cations and nucleotides present. Our experimental results compare favorably with findings from previous molecular dynamics simulations for the DNA compacting potential of K⁺ and Na⁺ monovalent cations. We estimate that the majority of single-stranded DNA molecules in our experiment are compacted. From the current traces of nanopores, the ratio of compacted DNA to linear DNA molecules is approximately 30 : 1 and 15 : 1, at a pH of 7.2 and 10, respectively. Our comparative studies reveal that Na⁺ monovalent cations have a greater potential of compacting the 15C-ssDNA than K⁺ cations.

Challenges and Solutions in Developing Ultrasensitive Biosensors

This Perspective focuses on the latest strategies and challenges for the development of bioanalytical sensors with sub-picomolar detection limits. Achieving sub-picomolar detection limits has three major challenges: (1) assay sensitivity, (2) response time, and (3) selectivity (including limiting background signals). Each of these challenges is discussed, along with how nanomaterials provide the solutions. One strategy to gain greater sensitivity involves confining the sensing volume to the nanoscale, as used in nanopore- or nanoparticle-based sensors, because nanoparticles are ubiquitous in amplification. Methods to improve response time typically focus on obtaining an intimate mixture between the sensor and the sample either by extending the length scale of nanoscale sensors using nanostructuring or by dispersing magnetic nanoparticles through the sample to capture the analyte. Loading nanoparticles with many biorecognition species is one solution to help address the challenge of selectivity. Many examples in this Perspective explore the detection of prostate-specific antigen which enables a comparison between strategies. Finally, exciting future opportunities in developing single-molecule sensors and the requirements to go even lower in concentration are explored.

Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging

Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.

Sequencing of semiflexible polymers of varying bending rigidity using patterned pores

We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and depends strongly on the interplay of polymer stiffness and pore-polymer interactions. For heterogeneous polymers with periodically varying stiffness along their lengths, we find that variation of the block size of the sequences and the orientation results in large variations in the translocation time distributions. We show how this fact may be utilized to develop an effective sequencing strategy. This strategy involving multiple pores with patterned surface energetics can predict heteropolymer sequences having different bending rigidity to a high degree of accuracy.

Single-molecule nanopore enzymology

Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here, we describe the approaches and challenges in nanopore enzymology.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.

Determining the Physical Properties of Molecules with Nanometer-Scale Pores

Nanometer-scale pores have been developed for the detection, characterization, and quantification of a wide range of analytes (e.g., ions, polymers, proteins, anthrax toxins, neurotransmitters, and synthetic nanoparticles) and for DNA sequencing. We describe the key requirements that made this method possible and how the technique evolved. Finally, we show that, despite sound theoretical work, which advanced both the conceptual framework and quantitative capability of the method, there are still unresolved questions that need to be addressed to further improve the technique.