Spontaneous DNA translocation through a van der Waals heterostructure nanopore for single-molecule detection

Precision Basecalling of Single DNA Nucleotide from Overlapped Transmission Readouts with Machine Learning Aided Solid-State Nanogap

DNA sequencing with the quantum tunneling technique heralds a paradigm shift in genetic analysis, promising rapid and accurate identification for diverging applications ranging from personalized medicine to security issues. However, the widespread distribution of molecular conductance, conduction orbital alignment for resonant transport, and decoding crisscrossing conductance signals of isomorphic nucleotides have been persistent experimental hurdles for swift and precise identification. Herein, we have reported a machine learning (ML)-driven quantum tunneling study with solid-state model nanogap to determine nucleotides at single-base resolution. The optimized ML basecaller has demonstrated a high predictive basecalling accuracy of all four nucleotides from seven distinct data pools, each containing complex transmission readouts of their different dynamic conformations. ML classification of quaternary, ternary, and binary nucleotide combinations is also performed with high precision, sensitivity, and F1 score. ML explainability unravels the evidence of how extracted normalized features within overlapped nucleotide signals contribute to classification improvement. Moreover, electronic fingerprints, conductance sensitivity, and current readout analysis of nucleotides have promised practical applicability with significant sensitivity and distinguishability. Through this ML approach, our study pushes the boundaries of quantum sequencing by highlighting the effectiveness of single nucleotide basecalling with promising implications for advancing genomics and molecular diagnostics.

Confined Transport Behavior of Biomolecules within Tilted Nanopores

The transport behavior of biomolecules at the confined nanoscale is very different from that of the bulk state. Numerous disease diagnostics and targeted drug treatments are performed based on nanochannels in cells. The specific structure and shape of nanochannels play an important role in the behavior and efficiency of substance transport. In this paper, we fabricated nanopores with different tilt angles and the same diameters using focused ion beam. The capture frequency and the blocking current amplitude of λ-DNA within large-angle nanopores decrease obviously, suggesting an increase in the energy barrier of large-angle nanopores and the fact that they stretch biomolecules to thinness. Most importantly, large-angle nanopores slow down λ-DNA transport by 2-4 times. MD simulations find that the sloped electroosmotic flow inside the tilted nanopores is the main factor contributing to the transport phenomena. The increase in the capture time of biomolecules by nanopores assists in obtaining more biological information from the current trajectories. Our study provides a new understanding of substance transport in specially shaped nanopores, which can be instrumental in providing fresh inspiration and approaches to the biomedical field.

Theoretical study of protein adsorption on graphene/h-BN heterostructures

The biological characteristics of planar heterojunction nanomaterials and their interactions with biomolecules are crucial for the potential application of these materials in the biomedical field. This study employed molecular dynamics (MD) simulations to investigate the interactions between proteins with distinct secondary structures (a single α-helix representing the minimal oligomeric domain protein, a single β-sheet representing the WW structural domain of the Yap65 protein, and a mixed α/β structure representing the BBA protein) and a planar two-dimensional heterojunction (a GRA/h-BN heterojunction consisting of a graphene nanoplate (GRA) and a hexagonal boron nitride nanoplate (h-BN)). The results indicate that all three kinds of protein can be quickly and stably adsorbed on the GRA/h-BN heterojunction due to the strong van der Waals interaction, regardless of their respective types, structures and initial orientations. Moreover, the proteins exhibit a pronounced binding preference for the hBN region of the GRA/h-BN heterojunction. Upon adsorption, the α-helix structure of the minimal oligomeric domain protein experiences partial or complete denaturation. Conversely, while the secondary structure of the single β-sheet and mixed α/β structure (BBA protein) undergoes slight changes (focus on the coil and turn regions), the main α-helix and β-sheet structures remain intact. The initial orientation significantly impacts the degree of protein adsorption and its position on the GRA/h-BN heterojunction. However, regardless of the initial orientation, proteins can ultimately be adsorbed onto the GRA/h-BN heterojunction. Furthermore, the initial orientation has a minor influence on the structural changes of proteins. Significantly, the combination of different secondary structures helps mitigate the denaturation of a single α-helix structure to some extent. Overall, the adsorption of proteins on GRA/h-BN is primarily driven by van der Waals and hydrophobic interactions. Proteins with β-sheet or mixed structures exhibit stronger biocompatibility on the GRA/h-BN heterojunction. Our research elucidated the biological characteristics of GRA/h-BN heterojunction nanomaterials and their interactions with proteins possessing diverse secondary structures. It offers a theoretical foundation for considering heterojunction nanomaterials as promising candidates for biomedical applications.

Deciphering DNA nucleotide sequences and their rotation dynamics with interpretable machine learning integrated C3N nanopores

A solid-state nanopore combined with the quantum transport method has garnered substantial attention and intrigue for DNA sequencing due to its potential for providing rapid and accurate sequencing results, which could have numerous applications in disease diagnosis and personalized medicine. However, the intricate and multifaceted nature of the experimental protocol poses a formidable challenge in attaining precise single nucleotide analysis. Here, we report a machine learning (ML) framework combined with the quantum transport method to accelerate high-throughput single nucleotide recognition with C3N nanopores. The optimized eXtreme Gradient Boosting Regression (XGBR) algorithm has predicted the fingerprint transmission of each unknown nucleotide and their rotation dynamics with root mean square error scores as low as 0.07. Interpretability of ML black box models with the game theory-based SHapley Additive exPlanation method has provided a quasi-explanation for the model working principle and the complex relationship between electrode-nucleotide coupling and transmission. Moreover, a comprehensive ML classification of nucleotides based on binary, ternary, and quaternary combinations shows maximum accuracy and F1 scores of 100%. The results suggest that ML in tandem with a nanopore device can potentially alleviate the experimental hurdles associated with quantum tunneling and facilitate fast and high-precision DNA sequencing.

Two Detection Modes of Nanoslit Sensing Based on Planar Heterostructure of Graphene/Hexagonal Boron Nitride

Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the y and z directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.

Electric Field-Controlled Peptide Self-Assembly through Funnel-Shaped Two-Dimensional Nanopores

Self-assembly of biomolecules is critical for the realization of biological functions. Thus, the precise control of self-assembly has great significance in the design of biochips and biomedical agents. In this report, we design a Y-shaped funnel on a two-dimensional (2D) heterostructure, called 2D funnel, based on monolayered polyaniline carbon nitride (C₃N) and boron carbide (BC₃), and study its application in the self-assembly state regulation of the peptide oligomer, using Aβ_16-21 as the representative model. Structurally, the 2D funnel is composed of three regions: channel area, triangle area, and barrier area. The channel and triangle areas show higher binding affinity to the peptide than that of the barrier area, which leads to the confinement of the peptide in the 2D funnel. Our results show that when an external electric field is applied along the 2D funnel, the oligomer is driven to migrate across the funnel. Its trajectory is confined inside the narrow channel area, which effectively causes peptide dissociation into the individual peptide chains. Then, when the external electric field is turned off, the separated peptide chains spontaneously assemble in the triangle area and tend to reunite. Our present findings propose a novel heterostructure platform, which enables the manipulation of the self-assembly state of peptides by switching the electric field, which could guide the design and fabrication of nanodevices for sensing and sequencing applications.

Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes

Two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.

Fabrication of Nanopore in MoS2-Graphene vdW Heterostructure by Ion Beam Irradiation and the Mechanical Performance

Nanopore structure presents great application potential especially in the area of biosensing. The two-dimensional (2D) vdW heterostructure nanopore shows unique features, while research around its fabrication is very limited. This paper proposes for the first time the use of ion beam irradiation for creating nanopore structure in 2D vdW graphene-MoS2 heterostructures. The formation process of the heterostructure nanopore is discussed first. Then, the influence of ion irradiation parameters (ion energy and ion dose) is illustrated, based on which the optimal irradiation parameters are derived. In particular, the effect of stacking order of the heterostructure 2D layers on the induced phenomena and optimal parameters are taken into consideration. Finally, uniaxial tensile tests are conducted by taking the effect of irradiation parameters, nanopore size and stacking order into account to demonstrate the mechanical performance of the heterostructure for use under a loading condition. The results would be meaningful for expanding the applications of heterostructure nanopore structure, and can arouse more research interest in this area.