Nanopore-based sensing devices and applications to genome sequencing: a brief history and the missing pieces

Detection of Biomolecules Using Solid-State Nanopores Fabricated by Controlled Dielectric Breakdown

Nanopore sensor technology is widely used in biomolecular detection due to its advantages of low cost and easy operation. In a variety of nanopore manufacturing methods, controlled dielectric breakdown has the advantages of a simple manufacturing process and low cost under the premise of ensuring detection performance. In this paper, we have made enhancements to the applied pulses in controlled dielectric breakdown and utilized the improved dielectric breakdown technique to fabricate silicon nitride nanopores with diameters of 5 to 15 nm. Our improved fabrication method offers the advantage of precise control over the nanopore diameter (±0.4 nm) and enhances the symmetry of the nanopore. After fabrication, we performed electrical characterization on the nanopores, and the IV characteristics exhibited high linearity. Subsequently, we conducted detection experiments for DNA and protein using the prepared nanopores to assess the detection performance of the nanopores fabricated using our method. In addition, we also give a physical model of molecule translocation through the nanopores to give a reasonable explanation of the data processing results.

Recent advances in nanopore-based analysis for carbohydrates and glycoconjugates

Saccharides are not only the basic constituents and nutrients of living organisms, but also participate in various life activities, and play important roles in cell recognition, immune regulation, development, cancer, etc. The analysis of carbohydrates and glycoconjugates is a necessary means to study their transformations and physiological roles in living organisms. Existing detection techniques can hardly meet the requirements for the analysis of carbohydrates and glycoconjugates in complex matrices as they are expensive, involve complex derivatization, and are time-consuming. Nanopore sensing technology, which is amplification-free and label-free, and is a high-throughput process, provides a new solution for the identification and sequencing of carbohydrates and glycoconjugates. This review highlights recent advances in novel nanopore-based single-molecule sensing technologies for the detection of carbohydrates and glycoconjugates and discusses the advantages and challenges of nanopore sensing technologies. Finally, current issues and future perspectives are discussed with the aim of improving the performance of nanopores in complex media diagnostic applications, as well as providing a new direction for the quantification of glycan chains and the study of glycan chain properties and functions.

A Nanopore Based Molnupiravir Sensor

Nucleoside analogues are reagents that resemble the structure of natural nucleosides and are widely applied in antiviral and anticancer therapy. Molnupiravir, a recently reported nucleoside analogue drug, has shown its inhibitory effect against SARS-CoV-2. Rapid tracing of molnupiravir and its metabolites is important in the evaluation of its pharmacology effect, but direct sensing of molnupiravir as a single molecule has not been reported to date. Here, we demonstrate a nanopore-based sensor with which direct sensing of molnupiravir and its two major metabolites β-d-N4-hydroxycytidine and its triphosphate can be achieved simultaneously. In conjunction with a custom machine learning algorithm, an accuracy of 92% was achieved. This sensing strategy may be useful in the current pandemic and is in principle suitable for other nucleoside analogue drugs.

Advances in nucleic acid amplification techniques (NAATs): COVID-19 point-of-care diagnostics as an example

Achieving superhigh sensitivity is the ultimate goal for bio-detection in modern analytical science and life science. Among variable signal amplification strategies, nucleic acid amplification technologies are revolutionizing the field of bio-detection, providing greater possibilities in novel diagnosis achieving high efficiency, specificity, and cost-effectiveness. Nucleic acid amplification techniques (NAATs), such as Polymerase Chain Reaction (PCR), Rolling Circle Amplification (RCA), Loop-Mediated Isothermal Amplification (LAMP), Recombinase Polymerase Amplification (RPA), CRISPR-related amplification, and others are dominating methods employed in research and clinical settings. They each provide distinctively unique features that can offer desirable performance in terms of sensitivity, specificity, simplicity, stability, and cost. NAATs are in unmet demand in molecular diagnosis, especially in point-of-care scenario. This review will discuss the principles and recent advancements of each NAAT, respectively, revealing their strengths and challenges in achieving rapid and accurate bio-detection with a focus on point-of-care diagnosis. Furthermore, this review will explore the application of each of the technologies through the contemporary COVID-19 pandemic, analyzing their ability in point-of-care diagnosis of the COVID-19 with high sensitivity to emphasize significance of developing NAATs based methods in battling COVID-19. Finally, advantages and potentials of each NAAT in enhancements of sensitivity and specificity in bio-detection from bench side to the bedside will be discussed, aiming for full exploitation of capability of each NAAT. This review will provide novel aspects in the selection and combination of usages of various NAATs based on their distinctive characteristics and limitations. A possible advancing direction of future accurate POCT is also proposed.

SERS Detection of Nucleobases in Single Silver Plasmonic Nanopores

Conventional ion current-based nanopore techniques that identify single molecules are hampered by limitations of providing only the ionic current information. Here, we introduce a silver nanotriangle-based nanopore (diameter < 50 nm) system for detecting molecule translocation using surface-enhanced Raman scattering. Rhodamine 6G is used as a model molecule to study the effect of an electric field (-1 V) on the mass transport. The four DNA bases also show significantly different SERS signals when they are transported into the plasmonic nanopore. The observations suggest that in the electric field, analyte molecules are driven into the nanopipette through the hot spot of the silver nanopore. The plasmonic nanopore shows great potential as a highly sensitive SERS platform for detecting molecule transport and paves the way for single molecule probing.

Retarded Translocation of Nucleic Acids through α-Hemolysin Nanopore in the Presence of a Calcium Flux

Electrophysiological measurement of molecular translocation through a nanopore is the fundamental basis of nanopore sensing. Free translocation of nucleic acids however is normally so fast that the identities of the compounds are not clearly resolvable. Inspired by recent progress in fluorescence imaging based nanopore sensing, we found that during electrophysiology measurements, translocation of nucleic acids is also retarded whenever a calcium flux around the pore vicinity is established. The residence time of nucleic acids has been extended to tens of milliseconds, a result of the strong coupling between nucleic acids and free calcium ions. The methodology presented here is applicable to both DNAs and RNAs and is able to clearly discriminate between different RNA homopolymers. This offers new insights for calcium imaging based nanopore sensing and suggests a new strategy of electrophysiology-based nanopore sensing aimed at a retarded motion of nucleic acids.

Electrode-free nanopore sensing by DiffusiOptoPhysiology

A wide variety of single molecules can be identified by nanopore sensing. However, all reported nanopore sensing applications result from the same measurement configuration adapted from electrophysiology. Although urgently needed in commercial nanopore sequencing, parallel electrophysiology recording is limited in its cost and its throughput due to the introduced complexities from electronic integration. We present the first electrode-free nanopore sensing method defined as DiffusiOptoPhysiology (DOP), in which single-molecule events are monitored optically without any electrical connections. Single-molecule sensing of small molecules, macromolecules, and biomacromolecules was subsequently demonstrated. As a further extension, a fingertip-sized, multiplexed chip with single-molecule sensing capabilities has been introduced, which suggests a new concept of clinical diagnosis using disposable nanopore sensors. DOP, which is universally compatible with all types of channels and a variety of fluorescence imaging platforms, may benefit diverse areas such as nanopore sequencing, drug screening, and channel protein investigations.

Direct sequencing of 2'-deoxy-2'-fluoroarabinonucleic acid (FANA) using nanopore-induced phase-shift sequencing (NIPSS)

2'-deoxy-2'-fluoroarabinonucleic acid (FANA), which is one type of xeno-nucleic acid (XNA), has been intensively studied in molecular medicine and synthetic biology because of its superior gene-silencing and catalytic activities. Although urgently required, FANA cannot be directly sequenced by any existing platform. Nanopore sequencing, which identifies a single molecule analyte directly from its physical and chemical properties, shows promise for direct XNA sequencing. As a proof of concept, different FANA homopolymers show well-distinguished pore blockage signals in a Mycobacterium smegmatis porin A (MspA) nanopore. By ligating FANA with a DNA drive-strand, direct FANA sequencing has been demonstrated using phi29 DNA polymerase by Nanopore-Induced Phase Shift Sequencing (NIPSS). When bound with an FANA template, the phi29 DNA polymerase shows unexpected reverse transcriptase activity when monitored in a single molecule assay. Following further investigations into the ensemble, phi29 DNA polymerase is shown to be a previously unknown reverse transcriptase for FANA that operates at room temperature, and is potentially ideal for nanopore sequencing. These results represent the first direct sequencing of a sugar-modified XNA and suggest that phi29 DNA polymerase could act as a promising enzyme for sustained sequencing of a wide variety of XNAs.

Osmosis-Driven Motion-Type Modulation of Biological Nanopores for Parallel Optical Nucleic Acid Sensing

Recent developments in nanopore sequencing have inspired new concepts in precision medicine but limited in throughput. By optically encoding calcium flux from an array of nanopores, parallel measurements from hundreds of nanopores were reported, while lateral drifts of biological nanopores set obstacles for signal processing. In this paper, optical single-channel recording (oSCR) serves to track nanopores with high precision and a general principle of nanopore motion kinetics is quantitatively investigated. By finely adjusting the osmosis-oriented interactions between the lipid/substrate interfaces, motions of nanopores could be controllably restricted. Improved signal-to-noise ratio is observed from motion-restricted nanopores, which is experimentally demonstrated. To systematically evaluate oSCR with asymmetric salt concentrations, a finite element method simulation is established. oSCR with an array of immobilized nanopores suggests new strategies for sequencing DNA by microscopic imaging in high throughput and is widely applicable to the investigation of other transmembrane proteins.

High-throughput optical sensing of nucleic acids in a nanopore array

Protein nanopores such as α-haemolysin and Mycobacterium smegmatis porin A (MspA) can be used to sequence long strands of DNA at low cost. To provide high-speed sequencing, large arrays of nanopores are required, but current nanopore sequencing methods rely on ionic current measurements from individually addressed pores and such methods are likely to prove difficult to scale up. Here we show that, by optically encoding the ionic flux through protein nanopores, the discrimination of nucleic acid sequences and the detection of sequence-specific nucleic acid hybridization events can be parallelized. We make optical recordings at a density of ∼10(4) nanopores per mm(2) in a single droplet interface bilayer. Nanopore blockades can discriminate between DNAs with sub-picoampere equivalent resolution, and specific miRNA sequences can be identified by differences in unzipping kinetics. By creating an array of 2,500 bilayers with a micropatterned hydrogel chip, we are also able to load different samples into specific bilayers suitable for high-throughput nanopore recording.