Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection

Ion-Solvent Interactions under Confinement Hold the Key to Tuning the DNA Translocation Speeds in Polyelectrolyte-Functionalized Nanopores

DNA sequencing and sensing using nanopore technology delves critically into the alterations in the measurable electrical signal as single-stranded DNA is drawn through a tiny passage. To make such precise measurements, however, slowing down the DNA in the tightly confined passage is a key requirement, which may be achieved by grafting the nanopore walls with a polyelectrolyte layer (PEL). This soft functional layer at the wall, under an off-design condition, however, may block the DNA passage completely, leading to the complete loss of output signal from the nanobio sensor. Whereas theoretical postulates have previously been put forward to explain the essential physics of DNA translocation in nanopores, these have turned out to be somewhat inadequate when confronted with the experimental findings on functionalized nanopores, including the prediction of the events of complete signal losses. Circumventing these constraints, herein we bring out a possible decisive role of the interplay between the inevitable variabilities in the ionic distribution along the nanopore axis due to its finite length as opposed to its idealized "infinite" limit as well as the differential permittivity of PEL and bulk solution that cannot be captured by the commonly used one-dimensional variant of the electrical double layer theory. Our analysis, for the first time, captures variations in the ionic concentration distribution across multidimensional physical space and delineates its impact on the DNA translocation characteristics that have hitherto remained unaddressed. Our results reveal possible complete blockages of DNA translocation as influenced by less-than-threshold permittivity values or greater-than-threshold grafting densities of the PEL. In addition, electrohydrodynamic blocking is witnessed due to the ion-selective nature of the nanopore at low ionic concentrations. Hence, our study establishes a functionally active regime over which the PEL layer in a finite-length nanopore facilitates controllable DNA translocation, enabling successful sequencing and sensing through the explicit modulation of translocation speed.

DNA nanostructure-assisted detection of carcinoembryonic antigen with a solid-state nanopore

In this paper, a novel detection technique for tumor marker carcinoembryonic antigen (CEA) has been developed by using a solid-state nanopore as a tool. The system utilizes the specific affinity between aptamer-modified magnetic Fe₃O₄ and CEA, rather than directly detecting the translocation of CEA through the nanopore. The aptamer-modified magnetic Fe₃O₄ was hybridized with tetrahedral DNA nanostructures (TDNs), and TDNs were released after CEA was added. We investigate the translocation behavior of individual TDNs through solid-state nanopores. The frequency of the blockage signals for TDNs is recorded for indirect detection of CEA. We realized the detection of CEA with a concentration as low as 0.1 nM and proved the specificity of the interaction between the aptamer. In addition, our designed nanopore sensing strategy can detect CEA in real samples.

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.

Solid-state nanopore: chemical modifications, interactions, and functionalities

Nanopore technology is a burgeoning detection technology for single-molecular sensing and ion rectification. Solid-state nanopores have attracted more and more attention because of their higher stability and tunability than biological nanopores. However, solid-state nanopores still suffer the drawbacks of low signal-to-noise ratio and low resolution, which hinders their practical applications. Thus, developing operatical and useful methods to overcome the shortages of solid-state nanopores is urgently needed. Here, we summarize the recent research on nanopore modification to achieve this goal. Modifying solid-state nanopores with different coating molecules can improve the selectivity, sensitivity, and stability of nanopores. The modified molecules can introduce different functions into the nanopores, greatly expanding the applications of this novel detection technology. We hope that this review of nanopore modification will provide new ideas for this field.

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.

Single-Entity Detection With TEM-Fabricated Nanopores

Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.

A solid-state nanopore-based single-molecule approach for label-free characterization of plant polysaccharides

Polysaccharides are important biomacromolecules existing in all plants, most of which are integrated into a fibrillar structure called the cell wall. In the absence of an effective methodology for polysaccharide analysis that arises from compositional heterogeneity and structural flexibility, our knowledge of cell wall architecture and function is greatly constrained. Here, we develop a single-molecule approach for identifying plant polysaccharides with acetylated modification levels. We designed a solid-state nanopore sensor supported by a free-standing SiN x membrane in fluidic cells. This device was able to detect cell wall polysaccharide xylans at concentrations as low as 5 ng/μL and discriminate xylans with hyperacetylated and unacetylated modifications. We further demonstrated the capability of this method in distinguishing arabinoxylan and glucuronoxylan in monocot and dicot plants. Combining the data for categorizing polysaccharide mixtures, our study establishes a single-molecule platform for polysaccharide analysis, opening a new avenue for understanding cell wall structures, and expanding polysaccharide applications.

Label-free single-molecule identification of telomere G-quadruplexes with a solid-state nanopore sensor

Telomere sequences can spontaneously form G-quadruplexes (G4) in the presence of some cations. In view of their relevance to genetic processes and potential as therapeutic-targets, hitherto, a wealth of conventional techniques have been reported for interrogation of G4 conformation diversity and corresponding folding kinetics, most of which are limited in precision and sensitivity. This work introduces a label-free solid-state nanopore (SSN) approach for the determination of inter-, intra- and tandem molecular G4 with distinct base permutation in various cation buffers with a tailored aperture and meanwhile captures the single-molecule G4 folding process. SSN translocation properties elucidated that both inter- and intramolecular G4 generated higher current blockage with longer duration than flexible homopolymer nucleotide, and intramolecular G4 are structurally more stable with higher event frequency and longer blockage time than intermolecular ones; base arrangement played weak role in translocation behaviors; the same sequences with one, two and three G4 skeletons displayed an increase in current blockage and a gradual extension in dwell time with the increase of molecule size recorded in the same nanopore. We observed the conformation change of single-molecule G4 which indicated the existence of folding/unfolding equilibration in nanopore, and real-time test suggested a gradual formation of G4 with time. Our results could provide a continued and improved understanding of the underlying relevance of structural stability and G4 folding process by utilizing SSN platform which exhibits strategic potential advances over the other methods with high spatial and temporal resolution.

Nanopore detection of single-molecule G-quadruplexes.

Surface coatings for solid-state nanopores

Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.

Controlled size reduction and its underlying mechanism to form solid-state nanopores via electron beam induced carbon deposition

Solid-state nanopores have drawn considerable attention for their potential applications in DNA sequencing and nanoparticle analysis. However, fabrication of nanopores, especially those of diameter below 30 nm, requires sophisticated techniques. Here, a versatile method to controllably reduce the diameter of prefabricated large-size pores down to sub-30 nm without greatly increasing the effective pore depth from the original membrane thickness is shown. This method exploits carbon deposition achieved via hydrocarbon evaporation, induced by an incident beam of electrons, and subsequent dissociation of hydrocarbon to solid carbon deposits. The carbon deposition employs a conventional scanning electron microscope equipped with direct visual feedback, along with a stable hydrocarbon source nearby the sample. This work systematically studies how electron beam accelerating voltage, imaging magnification, initial pore size and membrane composition affect the process of pore size reduction. Secondary electrons generated in the membrane material are confirmed to be the main cause of the dissociation of hydrocarbon. Thicker carbon deposited on one side than on the other of the membrane results in an asymmetric nanopore shape and a rectifying ionic transport. A physico-phenomenological model combined with Monte Carlo simulations is proposed to account for the observed carbon deposition behaviors.

Investigation of the adsorption behavior of BSA with tethered lipid layer-modified solid-state nanopores in a wide pH range

Nanopore technology was introduced for the study of the dynamic interactions between bovine serum albumin (BSA) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) phospholipids based on a modified nanopore. The results reveal that the interaction mechanism between DOPE and BSA is affected by the pH of the subphase. Far above the BSA isoelectric point (pH > 7), a weaker hydrophobic interaction and stronger electrostatic repulsion exist between the DOPE and BSA molecules. At pH = 7, the BSA structure nearly does not change, and the interaction is weak. At pH 5 and pH 6, BSA is marginally affected by the adsorption interaction, and below pH 5, the DOPE film becomes disordered, so there is a strong repulsive force interaction between the BSA and DOPE.

Label-Free Sensitive Detection of Microcystin-LR via Aptamer-Conjugated Gold Nanoparticles Based on Solid-State Nanopores

A versatile and highly sensitive strategy for nanopore detection of microcystin-LR (MC-LR) is proposed herein based on the aptamer and host-guest interactions by employing a gold nanoparticle (AuNP) probe. The aptamer of MC-LR and its complementary DNA (cDNA) are respectively immobilized on AuNPs with distinct sizes (5 nm AuNPs for the aptamer and 20 nm for the cDNA), and the constructed polymeric AuNP network via the hybridization of the aptamer and cDNA was disintegrated upon the addition of MC-LR. The specific interactions between the aptamer and MC-LR disrupt and release the cDNA-AuNPs that were then removed by centrifugation, leaving the MC-LR-aptamer-AuNP species in the supernatant for subsequent nanopore determination. By monitoring the current blockade of released MC-LR-aptamer-AuNPs using a specific tailored nanopore (10 and 20 nm in diameter, generated by current dielectric breakdown), we could deduce the presence of MC-LR, as the bulky NP network could not pass through a nanopore with a relatively smaller size. We realized the detection of MC-LR with a concentration as low as 0.1 nM; additionally, we have proved the specificity of the interaction between the aptamer and MC-LR by replacing MC-LR with other congener toxins (MC-RR and MC-YR), chlorophyll (a component abundantly coexists in water), and the mixture of the four.

Solid-State Nanopore Easy Chip Integration in a Cheap and Reusable Microfluidic Device for Ion Transport and Polymer Conformation Sensing

Solid-state nanopores have a huge potential in upcoming societal challenging applications in biotechnologies, environment, health, and energy. Nowadays, these sensors are often used within bulky fluidic devices that can cause cross-contaminations and risky nanopore chips manipulations, leading to a short experimental lifetime. We describe the easy, fast, and cheap innovative 3D-printer-helped protocol to manufacture a microfluidic device permitting the reversible integration of a silicon based chip containing a single nanopore. We show the relevance of the shape of the obtained channels thanks to finite elements simulations. We use this device to thoroughly investigate the ionic transport through the solid-state nanopore as a function of applied voltage, salt nature, and concentration. Furthermore, its reliability is proved through the characterization of a polymer-based model of protein-urea interactions on the nanometric scale thanks to a hairy nanopore.