Sensing with Nanopores and Aptamers: A Way Forward

Quantum plasmonics pushes chiral sensing limit to single molecules: a paradigm for chiral biodetections

Chiral sensing of single molecules is vital for the understanding of chirality and their applications in biomedicine. However, current technologies face severe limitations in achieving single-molecule sensitivity. Here we overcome these limitations by designing a tunable chiral supramolecular plasmonic system made of helical oligoamide sequences (OS) and nanoparticle-on-mirror (NPoM) resonator, which works across the classical and quantum regimes. Our design enhances the chiral sensitivity in the quantum tunnelling regime despite of the reduced local E-field, which is due to the strong Coulomb interactions between the chiral OSs and the achiral NPoMs and the additional enhancement from tunnelling electrons. A minimum of four molecules per single-Au particle can be detected, which allows for the detection of an enantiomeric excess within a monolayer, manifesting great potential for the chiral sensing of single molecules.

Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity

The ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited in achieving this goal. Here, we establish a method for long-range, single-molecule reading of intact protein strands on a commercial nanopore sensor array. By using the ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieve single-amino acid level sensitivity, enabling sequencing of combinations of amino acid substitutions across long protein strands. For greater sequencing accuracy, we demonstrate the ability to reread individual protein molecules, spanning hundreds of amino acids in length, multiple times, and explore the potential for high accuracy protein barcode sequencing. Further, we develop a biophysical model that can simulate raw nanopore signals a priori, based on amino acid volume and charge, enhancing the interpretation of raw signal data. Finally, we apply these methods to examine intact, folded protein domains for complete end-to-end analysis. These results provide proof-of-concept for a platform that has the potential to identify and characterize full-length proteoforms at single-molecule resolution.

Aptamers: Features, Synthesis and Applications

Aptamers have become a topic of interest among the researchers and scientists since they not only possess all of the benefits of antibodies but also possess special qualities including heat stability, low cost, and limitless uses⋅ Here we give a review about the features, applications, and challenges of aptamers and also how they are beneficial over the antibodies for biomedical applications. Their unique features make aptamers a prominent tool in therapeutics, diagnostics, biosensors and targeted drug delivery. In conclusion, aptamers represent exciting materials for a variety of applications and can be modified to improve their properties and to extend their applications in biomedical field.

Identifying residues in unfolded whole proteins with a nanopore: a theoretical model based on linear inequalities

A theoretical model is proposed for the identification of individual amino acids (AAs) in an unfolded whole protein's primary sequence. It is based in part on a recent report (Nat. Biotech. 41, 1130-1139, 2023) that describes the unfolding and translocation of whole proteins at constant speed through a biological nanopore (alpha-Hemolysin) of length 5 nm with a residue dwell time inside the pore of ~10 μs. Here current blockade levels in the pore due to the translocating protein are assumed to be measured with a limited precision of 70 nm3 and a bandwidth of 20 KHz for measurement with a low-bandwidth detector. Exclusion volumes in two pores of slightly different lengths are used as a computational proxy for the blockade signal; subsequence exclusion volume differences along the protein sequence are computed from the sampled translocation signals in the two pores relatively shifted multiple times. These are then converted into a system of linear inequalities that can be solved with linear programming and related methods; residues are coarsely identified as belonging to one of 4 subsets of the 20 standard AAs. To obtain the exact identity of a residue an artifice analogous to the use of base-specific tags for DNA sequencing with a nanopore (PNAS 113, 5233-5238, 2016) is used. Conjugates that add volume are attached to a given AA type, this biases the set of inequalities toward the volume of the conjugated AA, from this biased set the position of occurrence of every residue of the AA type in the whole sequence is extracted. By applying this step separately to each of the 20 standard AAs the full sequence can be obtained. The procedure is illustrated with a protein in the human proteome (Uniprot id UP000005640_9606).

Recent Advances in Nanopore Technology for Copper Detection and Their Potential Applications

Recently, nanopore technology has emerged as a promising technique for the rapid, sensitive, and selective detection of various analytes. In particular, the use of nanopores for the detection of copper ions has attracted considerable attention due to their high sensitivity and selectivity. This review discusses the principles of nanopore technology and its advantages over conventional techniques for copper detection. It covers the different types of nanopores used for copper detection, including biological and synthetic nanopores, and the various mechanisms used to detect copper ions. Furthermore, this review provides an overview of the recent advancements in nanopore technology for copper detection, including the development of new nanopore materials, improvements in signal amplification, and the integration of nanopore technology with other analytical methods for enhanced detection sensitivity and accuracy. Finally, we summarize the extensive applications, current challenges, and future perspectives of using nanopore technology for copper detection, highlighting the need for further research in the field to optimize the performance and applicability of the technique.

A binary/digital approach to amino acid identification and its application to peptide sequencing and protein identification

A binary/digital method is proposed in theory for the identification of single amino acids (AAs) in the bulk or with a few molecules from a single binary measurement. Combined with Edman degradation (or other cleaving method), it can be used to sequence a peptide or identify the parent protein from a partial sequence. The approach is centered on the superspecificity property of transfer RNAs (tRNAs). Markedly different from conventional and recent single molecule (SM) sequencing methods based on analog measurements, it changes the analytical question 'Which AA is it?' to the much simpler one 'Is there an AA in the detection space?'. Each of 20 terminal residues cleaved from 20 copies of a peptide enters a different cavity with a unique tRNA; tRNA charging (or binding with AA) occurs only in the cavity with the cognate AA. The bound AA or the AA separated from the tRNA is detected with a single binary measurement; its identity is known from the position of the single high bit in the resulting 20-bit output. Alternatively, a 20-stage pipeline can be used with sparse samples. Detection of the bound AA can be done optically by tagging the AAs with a fluorescent dye, or of the freed AA electrically with a nanopore. Necessary conditions for accurate AA identification are satisfied in principle; related computations and simulation results are presented. A modified version that can be used for de novo sequencing in parallel of large numbers of peptides immobilized on a glass slide with the tRNAs carrying a fluorescent tag is also proposed. Both methods can be used for protein identification from partial sequences containing 2 or 3 AA types by using only the corresponding tRNAs. Experiments may be performed to validate them, followed by translation into practice with existing technology; potential implementation issues are discussed. Binary/digital amino acid identification for peptide sequencing.

SELEX: Critical factors and optimization strategies for successful aptamer selection

Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.

Nanopore-based aptasensor for label-free and sensitive vanillin determination in food samples

Dielectric breakdown technique was utlised to fabricate 5-6 nm nanopores for vanillin detection in various food samples. A highly selective aptamer (Van_74) with high binding affinity towards vanillin was used as capture probe. Under optimal conditions, aptamer/vanillin complex translocation induced deeper events than the bare aptamer. As a result, the proposed nanopore aptasensor exhibits a linear range from 0.5 to 5 nM (R² = 0.972) and a low detection limit of 500 pM, which is significantly better than conventional platforms. Furthermore, our aptasensor showed excellent immunity against different interferons and was used to detect vanillin in different food samples. The food sample measurements were confirmed with an additional UV-Vis assay, the results of the two techniques were statistically evaluated and showed no statistically significant difference. Hence, this work represents a proof-of-concept involving the design and testing of aptamer/nanopore sensors for small molecules detection, which plays a critical role in food safety.

Smart Approach for the Design of Highly Selective Aptamer-Based Biosensors

Aptamers are chemically synthesized single-stranded DNA or RNA oligonucleotides widely used nowadays in sensors and nanoscale devices as highly sensitive biorecognition elements. With proper design, aptamers are able to bind to a specific target molecule with high selectivity. To date, the systematic evolution of ligands by exponential enrichment (SELEX) process is employed to isolate aptamers. Nevertheless, this method requires complex and time-consuming procedures. In silico methods comprising machine learning models have been recently proposed to reduce the time and cost of aptamer design. In this work, we present a new in silico approach allowing the generation of highly sensitive and selective RNA aptamers towards a specific target, here represented by ammonium dissolved in water. By using machine learning and bioinformatics tools, a rational design of aptamers is demonstrated. This “smart” SELEX method is experimentally proved by choosing the best five aptamer candidates obtained from the design process and applying them as functional elements in an electrochemical sensor to detect, as the target molecule, ammonium at different concentrations. We observed that the use of five different aptamers leads to a significant difference in the sensor’s response. This can be explained by considering the aptamers’ conformational change due to their interaction with the target molecule. We studied these conformational changes using a molecular dynamics simulation and suggested a possible explanation of the experimental observations. Finally, electrochemical measurements exposing the same sensors to different molecules were used to confirm the high selectivity of the designed aptamers. The proposed in silico SELEX approach can potentially reduce the cost and the time needed to identify the aptamers and potentially be applied to any target molecule.

Atomistic Simulation of Molecules Interacting with Biological Nanopores: From Current Understanding to Future Directions

Biological nanopores have been at the focus of numerous studies due to their role in many biological processes as well as their (prospective) technological applications. Among many other topics, recent studies on nanopores have addressed two key areas: antibiotic permeation through bacterial channels and sensing of analytes. Although the two areas are quite far apart in terms of their objectives, in both cases atomistic simulations attempt to understand the solute dynamics and the solute-protein interactions within the channel lumen. While decades of studies on various channels have culminated in an improved understanding of the key molecular factors and led to practical applications in some cases, successful utilization is limited. In this Perspective we summarize recent progress in understanding key issues in molecular simulations of antibiotic translocation and in the development of nanopore sensors. Moreover, we comment on possible advancements in computational algorithms that can potentially resolve some of the issues.

Capture and translocation of a rod-like molecule by a nanopore: orientation, charge distribution and hydrodynamics

We investigate the translocation of rods with different charge distributions using hybrid Langevin dynamics and lattice Boltzmann (LD-LB) simulations. Electrostatic interactions are added to the system using the P³M algorithm to model the electrohydrodynamic interactions (EHI). We first examine the free-solution electrophoretic properties of rods with various charge distributions. Our translocation simulation results suggest that the order parameter is asymmetric during the capture and escape processes despite the symmetric electric field lines, while the impacts of the charge distribution on rod orientation are more significant during the capture process. The capture/threading/escape times are under the combined effects of charge screening, rod orientation, and charge distributions. We also show that the mean capture time of a rod is shorter when it is launched near the wall because rods tend to align along the wall and hence with the local field lines. Remarkably, the orientational capture radius we proposed previously for uniformly charged rods is still valid in the presence of EHI.

Detection of small-sized DNA fragments in a glassy nanopore by utilization of CRISPR-Cas12a as a converter system

The fabrication of nanopores with a matched pore size, and the existence of multiple interferents make the reproducible detection of small-sized molecules by means of solid-state nanopores still challenging. A useful method to solve these problems is based on the detection of large DNA nanostructures related to the existence of small-sized targets. In particular, a DNA tetrahedron with a well-defined 3D nanostructure is the ideal candidate for use as a signal transducer. Here, we demonstrate the detection of an L1-encoding gene of HPV18 as a test DNA target sequence in a reaction buffer solution, where long single-stranded DNA linking DNA tetrahedra onto the surface of the magnetic beads is cleaved by a target DNA-activated CRISPR-cas12 system. The DNA tetrahedra are subsequently released and can be detected by the current pulse in a glassy nanopore. This approach has several advantages: (1) one signal transducer can be used to detect different targets; (2) a glassy nanopore with a pore size much larger than the target DNA fragment can boost the tolerance of the contaminants and interferents which often degrade the performance of a nanopore sensor.

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.

Simulation Study of Chain-like Body Translocation through Conical Pores in Thick Membranes

Artificial membranes with conical pores and controllable thickness reveal ionic-transport capabilities that are superior compared with those offered by cylindrical pores. By simulating the translocation of an abstract chain-like body through a conical pore in a membrane with a variable thickness, we formulate a statistical model of the translocation time τ. Our rough model encodes the biochemical details of a given real chain-like molecule as evolving sequences of the allowed chain-like body’s conformations. In our simulation experiments, we focus primarily on pore geometry and kinetic aspects of the translocation process. We study the impact of the membrane thickness L, and both conical-pore diameters ϕcis,ϕtrans on the probability distribution of τ. We have found that for all considered simulation setups, the randomness of τ is accurately described by the family of Moyal distributions while its expected value τ is proportional to Lξ, with ξ being dependent on ϕcis,ϕtrans.

Current pulse signature of native kanamycin aptamer and its implication for molecular interactions on a single protein nanopore sensing interface

Due to the pore size limitation of single α-hemolysin (α-HL) nanopore sensing interface, ssDNA with secondary conformations can only pass through the nanopore after unzipping as linear ssDNA. For hairpin DNA, a tail with 15-50 bases was usually added to the stem terminal (5' or 3') to facilitate the capture rate and unzipping process, and the typical translocation signal behaves as a square wave with a short dip at the end of the pulse. In this work, the pulse signal of native kanamycin aptamer, a hairpin DNA without the added long tail, was investigated with the single nanopore sensing interface, and different current pulse pattern was observed. The pulse signal exhibited two precise current levels with significantly extended duration of the second, and both duration of the two levels correlate to the interaction of the aptamer to kanamycin. Moreover, the pulse signal not only reveals the selectivity of the aptamer to its target, but also sensitive to the loop sequence change of the aptamer. This work shows that a single nanopore sensing interface could be used as a unique alternative means for interaction investigation of hairpin DNA aptamer without labeling or adding the extra-long tail.

Bioinspired Solid-State Nanochannel Sensors: From Ionic Current Signals, Current, and Fluorescence Dual Signals to Faraday Current Signals

Inspired from bioprotein channels of living organisms, constructing "abiotic" analogues, solid-state nanochannels, to achieve "smart" sensing towards various targets, is highly seductive. When encountered with certain stimuli, dynamic switch of terminal modified probes in terms of surface charge, conformation, fluorescence property, electric potential as well as wettability can be monitored via transmembrane ionic current, fluorescence intensity, faraday current signals of nanochannels and so on. Herein, the modification methodologies of nanochannels and targets-detecting application are summarized in ions, small molecules, as well as biomolecules, and systematically reviewed are the nanochannel-based detection means including 1) by transmembrane current signals; 2) by the coordination of current- and fluorescence-dual signals; 3) by faraday current signals from nanochannel-based electrode. The coordination of current and fluorescence dual signals offers great benefits for synchronous temporal and spatial monitoring. Faraday signals enable the nanoelectrode to monitor both redox and non-redox components. Notably, by incorporation with confined effect of tip region of a needle-like nanopipette, glorious in-vivo monitoring is conferred on the nanopipette detector at high temporal-spatial resolution. In addition, some outlooks for future application in reliable practical samples analysis and leading research endeavors in the related fantastic fields are provided.

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.

Advanced materials-integrated electrochemical sensors as promising medical diagnostics tools: A review

Electrochemical sensors have increasingly been linked with terms as modern biomedically effective highly selective and sensitive devices, wearable and wireless technology, portable electronics, smart textiles, energy storage, communication and user-friendly operating systems. The work brings the overview of the current advanced materials and their application strategies for improving performance, miniaturization and portability of sensing devices. It provides the extensive information on recently developed (bio)sensing platforms based on voltammetric, amperometric, potentiometric and impedimetric detection modes including portable, non-invasive, wireless, and self-driven miniaturized devices for monitoring human and animal health. Diagnostics of selected free radical precursors, low molecular biomarkers, nucleic acids and protein-based biomarkers, bacteria and viruses of today's interest is demonstrated.