Surface modification of solid-state nanopores for sticky-free translocation of single-stranded DNA

Impact of Translocation Dynamics and Bandwidth on the Readout of DNA Structural Barcodes with Membrane-Based Solid-State Nanopores

Recent advances in nanopore technology have promoted significant progress in single-molecule detection and analysis. In particular, membrane-based solid-state nanopores show promise as highly scalable readout platforms. This study explores the detection performance of this class of nanopores, with a focus on their application in molecular sensing schemes using DNA structural barcodes. The barcode structures, here specifically a series of dumbbell-shaped hairpins, encode information in a dumbbell-bit, which modulates the nanopore ionic current during translocation for readout. Our experiments evaluate the detection capabilities of membrane-based solid-state nanopores with a diameter of ∼15 nm. We investigate the detection success rates of individual dumbbell-bits with lengths ranging from 5 dumbbells (∼35 nm) to 29 dumbbells (∼195 nm) and with varying transmembrane potential. Longer dumbbell-bits exhibit a quasi-constant detection rate, whereas shorter bits show a significant decrease in the detection rate with increasing voltage. The observed dependencies are shown to be due to the increasing translocation velocity with voltage, in combination with the temporal resolution limit of the measurement system. Moreover, we show that a local increase of the effective charge at the dumbbell-bits leads to a proportionally increased local translocation velocity. This local velocity increase further degrades the detection success rate for dumbbell-bits. The findings in this study enhance our understanding of the fundamental limitations and capabilities of nanopore technology in high-throughput biosensing applications and have important implications for the design and optimization of future molecular assays and solid-state nanopore readout platforms.

Non-sticky SiNx nanonets for single protein denaturation analysis

Proteins play crucial roles in nearly all biological activities, with their functional structures deriving from stable folded conformations. Protein denaturation, induced by chemical and physical agents, is a complex process where proteins lose their stable structures, thereby impairing their biological functions. Characterizing protein denaturation at the single-molecule level remains a significant challenge. In this study, we developed non-adhesive silicon nitride nanonets coated with polyethylene glycol to capture individual proteins. We utilized these nanonets to investigate the denaturation of ovalbumin induced by guanidine hydrochloride (Gdn-HCl) and lead chloride. The entire denaturation and renaturation processes of a single ovalbumin molecule were monitored via ionic current measurements through the nanonets. These non-sticky nanonets offer a versatile tool for real-time studies of structural changes during protein denaturation.

Graphene or MoS2 nanopores: pore adhesion and protein linearization

Nanopores drilled in materials can electrophoretically drive charged biomolecules to enable their detection. Here, we explore and compare two-dimensional nanopores, graphene and MoS2, in order to unravel their advantages and disadvantages with regard to protein detection. We tuned the protein translocation and its dynamics by the choice and concentration of the surrounding solvent. For this, we used a typical monovalent salt solution, as well as a molecular solution. We assessed, with the aid of atomistic simulations, the efficiency of both nanopores in threading the protein on the basis of measurable ionic current signals. In the case of graphene, the protein adheres on the graphene surface, hindering the translocation under physiological conditions. This stickiness is resolved with the addition of a denaturant by the formation of a hydrophilic cationic layer on the pore surface and the protein can thread the pore in a linearized configuration. On the other hand, the MoS2 nanopores can thread the protein also in a physiological solution, leading to longer passage times, while the degree of protein linearization is lower than in the case of graphene in a molecular solution. We analyze the differences between the two nanopore materials on the basis of the complex molecular interactions between all components, the material, the target protein, and the solvent. We discuss the relevance of the results with respect to controlling the protein dynamics and enhancing the read-out ionic signals in view of an efficient detection of proteins through 2D nanopores.

Light-Driven Ionic and Molecular Transport through Atomically Thin Single Nanopores in MoS2/WS2 Heterobilayers

Nanofluidic ionic and molecular transport through atomically thin nanopore membranes attracts broad research interest from both scientific and industrial communities for environmental, healthcare, and energy-related technologies. To mimic the biological ion pumping functions, recently, light-induced and quantum effect-facilitated charge separation in heterogeneous 2D-material assemblies is proposed as the fourth type of driving force to achieve active and noninvasive transport of ionic species through synthetic membrane materials. However, to date, engineering versatile van der Waals heterostructures into 2D nanopore membranes remains largely unexplored. Herein, we fabricate single nanopores in heterobilayer transition metal dichalcogenide membranes with helium ion beam irradiation and demonstrate the light-driven ionic transport and molecular translocation phenomena through the atomically thin nanopores. Experimental and simulation results further elucidate the driving mechanism as the photoinduced near-pore electric potential difference due to type II band alignment of the semiconducting WS2 and MoS2 monolayers. The strength of the photoinduced localized electric field near the pore region can be approximately 1.5 times stronger than that of its counterpart under the conventional voltage-driven mode. Consequently, the light-driven mode offers better spatial resolution for single-molecule detection. Light-driven ionic and molecular transport through nanopores in van der Waals heterojunction membranes anticipates transformative working principles for next-generation biomolecular sequencing and gives rise to fascinating opportunities for light-to-chemical energy harvesting nanosystems.

Oligonucleotide Discrimination Enabled by Tannic Acid-Coordinated Film-Coated Solid-State Nanopores

Discrimination of nucleotides serves as the basis for DNA sequencing using solid-state nanopores. However, the translocation of DNA is usually too fast to be detected, not to mention nucleotide discrimination. Here, we utilized polyphenolic TA and Fe³⁺, an attractive metal-organic thin film, and achieved a fast and robust surface coating for silicon nitride nanopores. The hydrophilic coating layer can greatly reduce the low-frequency noise of an original unstable nanopore, and the nanopore size can be finely tuned in situ at the nanoscale by simply adjusting the relative ratio of Fe³⁺ and TA monomers. Moreover, the hydrogen bonding interaction formed between the hydroxyl groups provided by TA and the phosphate groups of DNAs significantly increases the residence time of a short double-strand (100 bp) DNA. More importantly, we take advantage of the different strengths of hydrogen bonding interactions between the hydroxyl groups provided by TA and the analytes to discriminate between two oligonucleotide samples (oligodeoxycytidine and oligodeoxyadenosine) with similar sizes and lengths, of which the current signal patterns are significantly different using the coated nanopore. The results shed light on expanding the biochemical functionality of surface coatings on solid-state nanopores for future biomedical applications.

Molecular Dynamics Simulation of a Single Carbon Chain through an Asymmetric Double-Layer Graphene Nanopore for Prolonging the Translocation Time

In recent years, sensing technology based on nanopores has become one of the trustworthy options for characterization and even identification of a single biomolecule. In nanopore based DNA sequencing technology, the DNA strand in the electrolyte solution passes through the nanopore under an applied bias electric field. Commonly, the ionic current signals carrying the sequence information are difficult to detect effectively due to the fast translocation speed of the DNA strand, so that slowing down the translocation speed is expected to make the signals easier to distinguish and improve the sequencing accuracy. Modifying the nanopore structure is one of the effective methods. Through all-atom molecular dynamics simulations, we designed an asymmetric double-layer graphene nanopore structure to regulate the translocation speed of a single carbon chain. The structure consists of two nanopores with different sizes located on two layers. The simulation results indicate that the asymmetric nanopore structure will affect the chain's translocation speed and the ionic current value. When the single carbon chain passes from the smaller pore to the larger pore, the translocation time is significantly prolonged, which is about three times as long as the chain passing from the larger pore to the smaller pore. These results provide a new idea for designing more accurate and effective single-molecule solid-state nanopore sensors.

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.

Four Aspects about Solid-State Nanopores for Protein Sensing: Fabrication, Sensitivity, Selectivity, and Durability

Solid-state nanopores are a mimic of innate biological nanopores embedded on lipid membranes. They are fabricated on thin suspended layers of synthetic materials that provide superior thermal, mechanical, chemical stability, and geometry flexibility. As their counterpart biological nanopores reach the goal of DNA sequencing and become commercial, solid-state nanopores thrive in aspects of protein sensing and have become an important research component for clinical diagnostic technologies. This review focuses on resistive pulse sensing modes, which are versatile for low-cost, portable sensing devices and summarizes four main aspects toward commercially available resistive pulse-based protein sensing techniques using solid-state nanopores. In each aspect of fabrication, sensitivity, selectivity, and durability, brief fundamentals are introduced and the challenges and improvements are discussed. The rapid advance of a practical technique requires greater multidisciplinary cooperation. The review aims at clarifying existing obstacles in solid-state nanopore based protein sensing, intriguing readers with existing solutions and finally encouraging multidisciplinary researchers to advance the development of this promising protein sensing methodology.

Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores

Biological nanopores are emerging as powerful tools for single-molecule analysis and sequencing. Here, we engineered the two-component pleurotolysin (PlyAB) toxin to assemble into 7.2 × 10.5 nm cylindrical nanopores with a low level of electrical noise in lipid bilayers, and we addressed the nanofluidic properties of the nanopore by continuum simulations. Surprisingly, proteins such as human albumin (66.5 kDa) and human transferrin (76-81 kDa) did not enter the nanopore. We found that the precise engineering of the inner surface charge of the PlyAB induced electro-osmotic vortices that allowed the electrophoretic capture of the proteins. Once inside the nanopore, two human plasma proteins could be distinguished by the characteristics of their current blockades. This fundamental understanding of the nanofluidic properties of nanopores provides a practical method to promote the capture and analysis of folded proteins by nanopores.

Surface modification of solid-state nanopore by plasma-polymerized chemical vapor deposition of poly(ethylene glycol) for stable device operation

Biopolymer adsorption onto a membrane is a significant issue in the reliability of solid-state nanopore devices, since it degrades the device performance or promotes device failure. In this work, a poly(ethylene glycol) (PEG) layer was coated on a silicon nitride (SiN_x) membrane by plasma-polymerized vapor deposition to inhibit biopolymer adsorption. From optical observations, the deposited PEG layer demonstrated increased hydrophilicity and anti-adsorption property compared to the SiN_x surface. Electrical properties of the PEG/SiN_x nanopore were characterized, showing Ohmic behavior and a 6.3 times higher flicker noise power due to the flexible conformation of PEG in water. Antifouling performance of each surface was analyzed by measuring the average time from voltage bias to the first adsorption during DNA translocation experiments, where the modified surface enabled two times prolonged device operation. The time to adsorption was dependent on the applied voltage, implying adsorption probability was dominated by the electrophoretic DNA approach to the nanopore. DNA translocation behaviors on each surface were identified from translocation signals, as the PEG layer promoted unfolded and fast movement of DNA through the nanopore. This work successfully analyzed the effect of the PEG layer on DNA adsorption and translocation in solid-state nanopore experiments.

Application of Solid-State Nanopore in Protein Detection

A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.

Estimation of Shape, Volume, and Dipole Moment of Individual Proteins Freely Transiting a Synthetic Nanopore

This paper demonstrates that high-bandwidth current recordings in combination with low-noise silicon nitride nanopores make it possible to determine the molecular volume, approximate shape, and dipole moment of single native proteins in solution without the need for labeling, tethering, or other chemical modifications of these proteins. The analysis is based on current modulations caused by the translation and rotation of single proteins through a uniform electric field inside of a nanopore. We applied this technique to nine proteins and show that the measured protein parameters agree well with reference values but only if the nanopore walls were coated with a nonstick fluid lipid bilayer. One potential challenge with this approach is that an untethered protein is able to diffuse laterally while transiting a nanopore, which generates increasingly asymmetric disruptions in the electric field as it approaches the nanopore walls. These "off-axis" effects add an additional noise-like element to the electrical recordings, which can be exacerbated by nonspecific interactions with pore walls that are not coated by a fluid lipid bilayer. We performed finite element simulations to quantify the influence of these effects on subsequent analyses. Examining the size, approximate shape, and dipole moment of unperturbed, native proteins in aqueous solution on a single-molecule level in real time while they translocate through a nanopore may enable applications such as identifying or characterizing proteins in a mixture, or monitoring the assembly or disassembly of transient protein complexes based on their shape, volume, or dipole moment.

Fabrication and Applications of Solid-State Nanopores

Nanopores fabricated from synthetic materials (solid-state nanopores), platforms for characterizing biological molecules, have been widely studied among researchers. Compared with biological nanopores, solid-state nanopores are mechanically robust and durable with a tunable pore size and geometry. Solid-state nanopores with sizes as small as 1.3 nm have been fabricated in various films using engraving techniques, such as focused ion beam (FIB) and focused electron beam (FEB) drilling methods. With the demand of massively parallel sensing, many scalable fabrication strategies have been proposed. In this review, typical fabrication technologies for solid-state nanopores reported to date are summarized, with the advantages and limitations of each technology discussed in detail. Advanced shrinking strategies to prepare nanopores with desired shapes and sizes down to sub-1 nm are concluded. Finally, applications of solid-state nanopores in DNA sequencing, single molecule detection, ion-selective transport, and nanopatterning are outlined.

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

In this work, we demonstrate a chemical modification approach, by means of covalent-bonding amphoteric poly-l-lysine (PLL) on the interior nanopore surface, which could intensively protect the pore from etching when exposed in the electrolyte under various pH conditions (from pH 4 to 12). Nanopore was generated via simple current dielectric breakdown methodology, covalent modification was performed in three steps, and the functional nanopore was fully characterized in terms of chemical structure, hydrophilicity, and surface morphology. I-V curves were recorded under a broad range of pH stimuli to evaluate the stability of the chemical bonding layer; the plotted curves demonstrated that nanopore with a covalent bonding layer has good pH tolerance and showed apparent reversibility. In addition, we have also measured the conductance of modified nanopore with varied KCl concentration (from 0.1 mM to 1 M) at different pH conditions (pHs 5, 7, 9, and 11). The results suggested that the surface charge density does not fluctuate with variation in salt concentration, which inferred that the SiN _x nanopore was fully covered by PLL. Moreover, the PLL functionalized nanopore has realized the detection of single-stranded DNA homopolymer translocation under bias voltage of 500 mV, and the 20 nt homopolymers could be evidently differentiated in terms of the current amplitude and dwell time at pHs 5, 8, and 11.

Intrinsic and membrane-facilitated α-synuclein oligomerization revealed by label-free detection through solid-state nanopores

α-Synuclein (α-Syn) is an abundant cytosolic protein involved in the release of neurotransmitters in presynaptic terminal and its aberrant aggregation is found to be associated with Parkinson’s disease. Recent study suggests that the oligomers formed at the initial oligomerization stage may be the root cause of cytotoxicity. While characterizing this stage is challenging due to the inherent difficulties in studying heterogeneous and transient systems by conventional biochemical technology. Here we use solid-state nanopores to study the time-dependent kinetics of α-Syn oligomerization through a label-free and single molecule approach. A tween 20 coating method is developed to inhibit non-specific adsorption between α-Syn and nanopore surface to ensure successful and continuous detection of α-Syn translocation. We identify four types of oligomers formed in oligomerization stage and find an underlying consumption mechanism that the formation of large oligomers consumes small oligomers. Furthermore, the effect of lipid membrane on oligomerization of α-Syn is also investigated and the results show that 1,2-dioleoyl-sn-glycero-3-[phospho-L-serine] (DOPS) small unilamellar vesicles (SUVs) dramatically enhances the aggregation rate of α-Syn while do not alter the aggregation pathway.