Electrophoretic Transport of Single-Stranded DNA through a Two Dimensional Nanopore Patterned on an In-Plane Heterostructure

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.

Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials

Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.

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.

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.

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.

Single nucleobase identification for transversally-confined ssDNA using longitudinal ionic currents

High-fidelity DNA sequencing using solid-state nanopores remains a big challenge, partly due to difficulties related to efficient molecular capture and subsequent control of the dwell time. To help address these issues, here we propose a sequencing platform consisting of stacked two-dimensional materials with tailored structures containing a funnel-shaped step defect and a nanopore drilled inside the nanochannel. Our all-atom molecular dynamics (MD) simulations showed that, assisted by the step defect, single-stranded DNA (ssDNA) can be transported to the nanopore in a deterministic way by pulsed transversal electric fields. Furthermore, different types of DNA bases can reside in the pore for a sufficiently long time which can be successfully differentiated by longitudinal ionic currents. By using the decoupled driving forces for ssDNA transport and ionic current measurements, this approach holds potential for high-fidelity DNA sequencing.

Superlattice in a Ru Superstructure for Enhancing Hydrogen Evolution

Superlattices are attracting extensive attention due to their unique properties. Nevertheless, the observations of superlattices are limited to those layered structures with weak interlayered interactions, and the effect of the superlattice in metal-based nanostructures on catalysis is unexplored yet. We here report a facile wet-chemical method for synthesizing two-dimensional Ru multilayered nanosheets (Ru MNSs) with a superlattice. Characterizations reveal that the superlattice is formed by stacking Ru layers with twisted angles from 2° to 30°. Owing to the strong synergy between the adjacent layers, Ru MNSs can serve as an efficient catalyst for the alkaline hydrogen evolution reaction (HER). Theoretical calculations reveal that the superlattice can induce the strain effect, which leads to lattice contraction and weak *H adsorption ability, as a result of improved HER performance. This work sheds new light on the utilization of the superlattice on enhancing catalysis in metal-based materials.

When graphene meets white graphene - recent advances in the construction of graphene and h-BN heterostructures

2D heterostructures have very recently witnessed a boom in scientific and technological activities owing to the customized spatial orientation and tailored physical properties. A large amount of 2D heterostructures have been constructed on the basis of the combination of mechanical exfoliation and located transfer method, opening wide possibilities for designing novel hybrid systems with tuned structures, properties, and applications. Among the as-developed 2D heterostructures, in-plane graphene and h-BN heterostructures have drawn the most attention in the past few decades. The controllable synthesis, the investigation of properties, and the expansion of applications have been widely explored. Herein, the fabrication of graphene and h-BN heterostructures is mainly focused on. Then, the spatial configurations for the heterostructures are systematically probed to identify the highly related unique features. Moreover, as a most promising approach for the scaled production of 2D materials, the in situ CVD fabrication of the heterostructures is summarized, demonstrating a significant potential in the controllability of size, morphology, and quality. Further, the recent applications of the 2D heterostructures are discussed. Finally, the concerns and challenges are fully elucidated and a bright future has been envisioned.

Exploring an In-Plane Graphene and Hexagonal Boron Nitride Array for Separation of Single Nucleotides

Regular nanofluidic sieving structures are emerging as rapid and compatible on-chip techniques for biomolecular separation. Although the current nanofluidic sieving devices, mostly based on three-dimensional nanostructures, have achieved a separation resolution of ∼20 nm, it is still far away from single-nucleotide resolution. Using all-atom molecular dynamics simulations, here we demonstrate a two-dimensional (2D) nanofluidic sieve consisting of an in-plane graphene (GRA)/hexagonal boron nitride (h-BN) nanoarray, which enables ultrahigh resolution in the successful separation of four types of single nucleotides. The alternating GRA and h-BN stripes can create size-dependent energy barriers for adsorbed nucleotides, which provide a strong modulation for their mobility, thus causing distinct band separations on the 2D surface. We further show that this 2D sieve is particularly sensitive when the sample dimensions are within the range from a half period to one period of the nanoarray. This 2D sieving structure may shed light on the development of lab-on-a-chip sequencing in the future.

Interface chemistry of two-dimensional heterostructures - fundamentals to applications

Two-dimensional heterostructures (2D HSs) have emerged as a new class of materials where dissimilar 2D materials are combined to synergise their advantages and alleviate shortcomings. Such a combination of dissimilar components into 2D HSs offers fascinating properties and intriguing functionalities attributed to the newly formed heterointerface of constituent components. Understanding the nature of the surface and the complex heterointerface of HSs at the atomic level is crucial for realising the desired properties, designing innovative 2D HSs, and ultimately unlocking their full potential for practical applications. Therefore, this review provides the recent progress in the field of 2D HSs with a focus on the discussion of the fundamentals and the chemistry of heterointerfaces based on van der Waals (vdW) and covalent interactions. It also explains the challenges associated with the scalable synthesis and introduces possible methodologies to produce large quantities with good control over the heterointerface. Subsequently, it highlights the specialised characterisation techniques to reveal the heterointerface formation, chemistry and nature. Afterwards, we give an overview of the role of 2D HSs in various emerging applications, particularly in high-power batteries, bifunctional catalysts, electronics, and sensors. In the end, we present conclusions with the possible solutions to the associated challenges with the heterointerfaces and potential opportunities that can be adopted for innovative applications.