Solid-State Quad-Nanopore Array for High-Resolution Single-Molecule Analysis and Discrimination

Single-molecule resolution of macromolecules with nanopore devices

Nanopore-based electrical detection technology holds single-molecule resolution and combines the advantages of high sensitivity, high throughput, rapid analysis, and label-free detection. It is widely applied in the determination of organic and biological macromolecules, small molecules, and nanomaterials, as well as in nucleic acid and protein sequencing. There are a wide variety of organic polymers and biopolymers, and their chemical structures, and conformation in solution directly affect their ensemble properties. Currently, there is limited approach available for the analysis of single-molecule conformation and self-assembled topologies of polymers, dendrimers and biopolymers. Nanopore single-molecule platform offers unique advantages over other sensing technologies, particularly in molecular size differentiation of macromolecules and complex conformation analysis. In this review, the classification of nanopore devices, including solid-state nanopores (SSNs), biological nanopores, and hybrid nanopores is introduced. The recent developments and applications of nanopore devices are summarized, with a focus on the applications of nanopore platform in the resolution of the structures of synthetic polymer, including dendritic, star-shaped, block copolymers, as well as biopolymers, including polysaccharides, nucleic acids and proteins. The future prospects of nanopore sensing technique are ultimately discussed.

Quad-Nanopore Array Enables High-Resolution Identification of Four Single-Stranded DNA Homopolymers

The solid-state nanopore technique holds the potential to develop mechanically stable and miniaturized DNA sequencing devices. However, the limited temporal resolution due to the high electric field inside the nanopore and the lack of an effective speed control strategy have hindered the realization of sequencing. Here, we reported a quad-array (four nanopores milled with ∼30 nm interpore spacing as a detection unit) that induced a redistribution of the electric field inside and outside the nanopore array and offered high-resolution discrimination of four ssDNA homopolymer types. We demonstrated that the quad-nanopore array well resolved the translocation events of polyA25 and had a length resolution of 20 nt. The molecular dynamic simulation confirmed the slowed-down translocations and superior performance of a quad-nanopore array. We found that the nanopore array configuration induced a direct reduction of the electric field inside the nanopore as well as an increase in the electrical field outside the nanopore due to electric field crosstalk. This dual benefit not only reduced the large driving force on DNA but also facilitated molecule capture through nanopores, therefore decreasing the voltage thresholds. Finally, the successful discrimination of four ssDNA homopolymer types (polyA25, polyT25, polyC25, and polyG10) was achieved using a voltage as low as 30 mV with a translocation speed of 8 μs/nt. These findings provide insights into nanopore arrays for discriminating short single-stranded nucleotides with high resolution and demonstrate promising potential for developing DNA sequencers that utilize nanopore arrays as sensing units.

Advances and Challenges in Solid-State Nanopores for DNA Sequencing

Solid-state nanopore sensing, a state-of-the-art technology for single-molecule detection, has rapidly advanced in recent years and demonstrates significant potential in DNA sequencing. This technology determines the nucleotide sequences by analyzing the electrical or optical signal variations that occur when DNA molecules pass through the nanopore. It offers notable advantages, including high-throughput, single-molecule detection, real-time monitoring, and the elimination of the need for polymerase chain reaction (PCR) amplification, thereby presenting broad application prospects in areas such as the diagnosis and treatment of genetic diseases. This paper reviews the solid-state nanopore DNA sequencing technology by discussing advancements in nanopore types, preparation techniques, and sequencing detection methods. It examines various nanopore materials, including silicon-based materials and two-dimensional (2D) materials, as well as preparation techniques such as transmission electron microscopy (TEM), focused ion beam (FIB) etching, and controlled breakdown (CBD). Additionally, it elucidates sequencing detection mechanisms, including ion-current blockade, transverse-current detection, and optical detection. However, this technology faces numerous challenges in its implementation and future commercialization. For instance, limited spatial resolution hampers single-base identification; the rapid translocation speed of DNA impacts time resolution; and various types of noise significantly disrupt detection signals. In response, researchers have proposed several solutions, including local thinning of the film, adjustment of surface charges, and optimization of detection materials and structures. With interdisciplinary integration and technological innovation, solid-state nanopore DNA sequencing technology is expected to make breakthroughs, bringing transformations to life sciences research and medical diagnosis.

Sub-5 nm Silicon Nanopore Sensors: Scalable Fabrication via Self-Limiting Metal-Assisted Chemical Etching

Solid-state nanopores offer unique possibilities for biomolecule sensing; however, scalable production of sub-5 nm pores with precise diameter control remains a manufacturing challenge. In this work, we developed a scalable method to fabricate sub-5 nm nanopores in silicon (Si) nanomembranes through metal-assisted chemical etching (MACE) using gold nanoparticles. Notably, we present a previously unreported self-limiting effect that enables sub-5 nm nanopore formation from both 10 and 40 nm nanoparticles in the 12 nm thick monocrystalline device layer of a silicon-on-insulator substrate. This effect reveals distinctive etching dynamics in ultrathin Si nanomembranes, enabling precise control over nanopore dimensions. The resulting nanopore sensor, suspended over self-aligned spheroidal oxide undercuts with diameters of just a few hundred nanometers, exhibited low electrical noise and high stability due to encapsulation within dielectric layers. In DNA translocation experiments, our nanopore platform could distinguish folded and unfolded DNA conformations and maintained stable baseline conductance for up to 6 h, demonstrating both sensitivity and robustness. Our scalable nanopore fabrication method is compatible with wafer-level and batch processing and holds promise for advancing biomolecular sensing and analysis.

The Research Progress of Single-Molecule Sequencing and Its Significance in Nucleic Acid Metrology

Single-molecule sequencing technology, a novel method for gene sequencing, utilizes nano-sized materials to detect electrical and fluorescent signals. Compared to traditional Sanger sequencing and next-generation sequencing technologies, it offers significant advantages, including ultra-long read lengths, rapid sequencing, and the absence of amplification steps, making it widely applicable across various fields. By examining the development and components of single-molecule sequencing technology, it becomes clear that its unique characteristics provide new opportunities for advancing metrological traceability. Notably, its direct detection capabilities offer a novel approach to nucleic acid metrology. This paper provides a detailed overview of library construction, signal generation and detection, and data analysis methods in single-molecule sequencing and discusses its implications for nucleic acid metrology.

Nucleic Acid-Based Biological Nanopore Sensing Strategies for Tumor Marker Detection

Cancer, which is characterized by high mortality rates, poses a significant threat to global human health. Early diagnosis is of paramount importance in managing cancer, and tumor markers have emerged as crucial indicators for achieving this goal. The advent of precision medicine has further emphasized the need for the effective detection of these markers. However, traditional detection methods are hampered by numerous limitations. In recent years, nanopore technology has emerged as a promising alternative, due to its unique physical and chemical properties, which facilitate rapid, label-free, and amplification-free detection. This Review focuses on the direct detection of tumor markers through nucleic acid analysis and indirect detection mediated by nucleic acids and facilitated by biological nanopores. Furthermore, it also discusses the challenges and prospects of applying biological nanopore sensing technology in early cancer diagnosis, underscoring its potential to revolutionize tumor marker detection.

Sequence-Dependent Single-Molecule DNA Sensing Using Covalent Organic Framework Nanopores

Enzyme-free single-molecule sequencing has the potential to significantly expand the application of nanopore technology to DNA, proteins, and saccharides. Despite their advantages over biological nanopores and natural suitability for enzyme-free single-molecule sequencing, conventional solid-state nanopores have not yet achieved single-molecule DNA sequencing. The biggest challenge for the accuracy of single-molecule sequencing using solid-state nanopores lies in the precise control of the pore size and conformity. In this study, we fabricated nanopore devices by covering the tip of a quartz nanopipette with ultrathin two-dimensional (2D) covalent organic framework (COF) nanosheets (pore size ≈ 1.1 nm). The size of the periodically arranged nanopores in COF is comparable to that of protein nanopores, and the structure of each COF nanopore is consistent at the atomic scale. The COF nanopore device could roughly distinguish dAMP, dCMP, dGMP, and dTMP. Furthermore, a certain percentage of the current blockades originating from 150 nucleotides model DNA molecules (13.5% for dA50dC50dA50 and 11.1% for dC50dA50dC50) show distinct DNA sequence-specific concave and convex resistive current patterns. The finite element simulation confirmed that the current blockade pattern of a DNA molecule passing through a COF nanopore is dependent on the relative location of the nanopore with respect to the wall of the nanopipette. Our study is a significant step toward single-molecule DNA sequencing by solid-state nanopores.

Enhanced Nanoparticle Sensing in a Highly Viscous Nanopore

Slowing down translocation dynamics is a crucial challenge in nanopore sensing of small molecules and particles. Here, it is reported on nanoparticle motion-mediated local viscosity enhancement of water-organic mixtures in a nanofluidic channel that enables slow translocation speed, enhanced capture efficiency, and improved signal-to-noise ratio by transmembrane voltage control. It is found that higher detection rates of nanoparticles under larger electrophoretic voltage in the highly viscous solvents. Meanwhile, the strongly pulled particles distort the liquid in the pore at high shear rates over 103 s-1 which leads to a counterintuitive phenomenon of slower translocation speed under higher voltage via the induced dilatant viscosity behavior. This mechanism is demonstrated as feasible with a variety of organic molecules, including glycerol, xanthan gum, and polyethylene glycol. The present findings can be useful in resistive pulse analyses of nanoscale objects such as viruses and proteins by allowing a simple and effective way for translocation slowdown, improved detection throughput, and enhanced signal-to-noise ratio.

Stimuli-Responsive Ion Transport Regulation in Nanochannels by Adhesion-Induced Functionalization of Macroscopic Outer Surface

Responsive regulation of ion transport through nanochannels is crucial in the design of smart nanofluidic devices for sequencing, sensing, and water-energy nexus. Functionalization of the inner wall of the nanochannel enhances interaction with ions and fluid but restricts versatile chemical approaches and accurate characterizations of fluidic interfaces. Herein, we reveal a responsive regulating mechanism of ion transport through nanochannels by polydopamine (PDA)-induced functionalization on the macroscopic outer surface of nanochannels. Responsive molecules were codeposited with PDA on the outer surface of nanochannels and formed a valve of nanometer thickness to manually manipulate ion transport by changing its gap spacing, surface charge, and wettability under external stimulus. The response ratio can be up to 100-fold by maximizing the proportion of responsive molecules on the outer surface. Laminating the codepositions of different responsive molecules with PDA on the channel's outer surface produces multiple responses. A nearly universal adhesion of PDA with responsive molecules on the open outer surface induces nanochannels responsive to different external stimuli with variable response ratios and arbitrary combinations. The results challenge the primary role of functionalization on the nanoconfined interface of nanofluidics and open opportunities for developing new-style nanofluidic devices through the functionalization of macroscopic interface.

Selective Capture and Manipulation of DNA through Double Charged Nanopores

In the past few decades, nanometer-scale pores have been employed as powerful tools for sensing biological molecules. Owing to its unique structure and properties, solid-state nanopores provide interesting opportunities for the development of DNA sequencing technology. Controlling DNA translocation in nanopores is an important means of improving the accuracy of sequencing. Here we present a proof of principle study of accelerating DNA captured across targeted graphene nanopores using surface charge density and find the intrinsic mechanism of the combination of electroosmotic flow induced by charges of nanopore and electrostatic attraction/repulsion between the nanopore and ssDNA. The theoretical study performed here provides a new means for controlling DNA transport dynamics and makes better and cheaper application of graphene in molecular sequencing.

Nanopore sensitization based on a double loop hybridization chain reaction and G-quadruplex

The widespread implementation of solid-state nanopores faces challenges such as lower resolution and increased electrical noise when compared to biological nanopores. Incorporating specific nucleic acid reactions can enhance resolution. In this study, we've developed a nucleic acid amplifier to enhance the sensitivity of solid-state nanopores, utilizing a G-rich sequence and hybridization chain reaction. This amplifier improves target concentration and volume amplification, showing promise in nanopore sensitivity tests.

Ion Transport in Multi-Nanochannels Regulated by pH and Ion Concentration

Nanochannels are a powerful technique for detecting a wide range of biomolecules without labeling. The ion transport phenomena in nanochannel arrays differ from those in single nanochannels and are caused by interchannel communication. This study uses a fully coupled Poisson-Nernst-Planck (PNP) and Navier-Stokes model to investigate ion transport in nanochannel arrays. Instead of being set at a constant value, the surface charge density used in this study is established by the protonation and deprotonation of the silanol groups that are present on the walls of the silicon-based nanochannels. The surface charge density of the nanochannel walls varies with the number of nanochannels, the channel lateral distance, and the background solution properties, which consequently influence the ionic concentration distribution, flow velocity, and electric field strength. For example, in different numbers of nanochannel systems, the ion concentration in nanochannels is not much different, but it is different in reservoirs, especially near the openings of nanochannels. The number of nanochannels and the distance between nanochannels can also affect the formation of electro-convective vortex zones under certain conditions. These findings can aid in optimizing the nanochannel array design by regulating the number and distance of nanochannels and facilitating the construction of solid-state nanochannel arrays with any desired nanochannel dimensions.

Direct and Continuous Monitoring of Multicomponent Antibiotic Gentamicin in Blood at Single-Molecule Resolution

Point-of-care monitoring of small molecules in biofluids is crucial for clinical diagnosis and treatment. However, the inherent low degree of recognition of small molecules and the complex composition of biofluids present significant obstacles for current detection technologies. Although nanopore sensing excels in the analysis of small molecules, the direct detection of small molecules in complex biofluids remains a challenge. In this study, we present a method for sensing the small molecule drug gentamicin in whole blood based on the mechanosensitive channel of small conductance in Pseudomonas aeruginosa (PaMscS) nanopore. PaMscS can directly detect gentamicin and distinguish its main components with only a monomethyl difference. The 'molecular sieve' structure of PaMscS enables the direct measurement of gentamicin in human whole blood within 10 min. Furthermore, a continuous monitoring device constructed based on PaMscS achieved continuous monitoring of gentamicin in live rats for approximately 2.5 h without blood consumption, while the drug components can be analyzed in situ. This approach enables rapid and convenient drug monitoring with single-molecule level resolution, which can significantly lower the threshold for drug concentration monitoring and promote more efficient drug use. Moreover, this work also lays the foundation for the future development of continuous monitoring technology with single-molecule level resolution in the living body.