MoS2 Nanopores Research Articles

Single-layer MoS2 solid-state nanopores for coarse-grained sequencing of proteins

Proteins are essential biological molecules to use as biomarkers for early disease diagnosis. Therefore, their detection is crucial. In recent years, protein sequencing has become one of the most promising techniques. In particular, solid-state nanopores (SSNs) are powerful platforms for single biological molecule sensing without any labeling and with high sensitivity. Atomically thin two-dimensional (2D) materials with nanometer-sized pores, such as single-layer MoS2, represent the ideal SSN because of their ultimate thinness. Despite the benefits they offer, their use for protein sequencing applications remains very challenging since the fast translocation speed provides a short observation time per single molecule. In this work, we performed extensive molecular dynamics simulations of the translocation of the 20 proteinogenic amino acids through single-layer MoS2 nanopores. From ionic current traces, we characterized peptide-induced blockade levels of current and duration for each of the 20 natural amino acids. Using clustering techniques, we demonstrate that positively and negatively charged amino acids present singular fingerprints and can be visually distinguished from neutral amino acids. Furthermore, we demonstrate that this information would be sufficient to identify proteins using the coarse-grained sequencing technique made of only three amino acid categories depending on their charge. Therefore, single-layer MoS2 nanopores have great potential as sensors for the identification of biomarkers.

Interaction between peptides and an MoS2 monolayer containing a nanopore: First-principles calculations

• The reaction between small peptide molecules and the MoS2 nanopore are explored: • Serine and Glycylglycine don't have any bonding and interaction with MoS2/NP. Each plays the role of a passer in the system. • Two dipeptides, Aspartame and Carnosine, and the tripeptide Glutathione react with Mo and S atoms surrounding the hole and form stable compounds. First-principles density functional theory (DFT) is employed to explore the interaction between a peptide molecule and two-dimensional (2-D) monolayer of molybdenum disulfide (MoS 2 ) containing a nanopore. A variety of monopeptides, dipeptides and also a tripeptide are individually positioned in the hole of a MoS 2 layer and the overall electronic structure calculated. The results indicate that bonding occurs between some molecules and the hole edge. The outcome of reaction can be predicted through the potential energy surface. These results strongly suggest that 2-D MoS 2 nanopores have a wide range of biological applications and deserve further exploitation by experiment.

Pore Diameter and Chemistry Modulated Flexible Ion Selectivity through a Single-Layer MoS2 Nanopore

Nanoporous membranes based on 2D materials are promising as the most efficient technologies for practical engineering applications such as seawater desalination, ion sieving, and gas separation. In this work, we utilize various nanopores in molybdenum disulfide (MoS2) membranes to enable flexible ion selectivity that is tuned efficiently by adjusting pore diameter and surface chemistry. We theoretically uncover the molecular mechanisms that lead to MoS2 nanopores with varied diameters and pore atom chemistry exhibiting distinctly different ion selectivity. MoS2 nanopores with S atoms at the nanopore boundary facilitate K+ ion translocation and rejection of Cl– ions. MoS2 nanopores with Mo atoms at the nanopore boundary permit Cl– ion translocation and reject K+ ions. The average flow velocity of K+ ions in the MoS2 nanopore with S atoms at the nanopore boundary is larger than that of Cl– ions in the MoS2 nanopore with Mo atoms at the nanopore boundary. This phenomenon is attributed to the totally different ion transport mechanisms modulated by the nanopore boundary atoms. This work provides new insights into designing multifunctional membranes on a single 2D material membrane with flexible and optimal ion selectivity toward broad applications.

MoS2 nanopore identifies single amino acids with sub-1 Dalton resolution

The sequencing of single protein molecules using nanopores is faced with a huge challenge due to the lack of resolution needed to resolve single amino acids. Here we report the direct experimental identification of single amino acids in nanopores. With atomically engineered regions of sensitivity comparable to the size of single amino acids, MoS2 nanopores provide a sub-1 Dalton resolution for discriminating the chemical group difference of single amino acids, including recognizing the amino acid isomers. This ultra-confined nanopore system is further used to detect the phosphorylation of individual amino acids, demonstrating its capability for reading post-translational modifications. Our study suggests that a sub-nanometer engineered pore has the potential to be applied in future chemical recognition and de novo protein sequencing at the single-molecule level.

Role of Chemical Etching in the Nucleation of Nanopores in 2D MoS2: Insights from First-Principles Calculations

Nanoscale devices made using two-dimensional (2D) materials, including transition-metal dichalcogenides (TMDs) such as molybdenum disulfide (MoS2), are currently being explored for various applications, e.g., optoelectronic devices, water desalination membranes, and DNA sequencing. In such applications, defects and nanopores play a key role in modulating the 2D material’s physicochemical properties, e.g., the band gap, chemical reactivity, catalytic activity, and molecular/ionic permeation rate. However, there exists a lack of a fundamental understanding of nanopore formation in TMDs, especially MoS2. In this work, we elucidate the mechanism of nanopore formation in 2D MoS2 using an extensive set of first-principles density functional theory (DFT) calculations. We calculate the energies of etching of atoms using DFT and use Marcus theory for atom-transfer reactions to convert the energies to activation barriers. We postulate the role of silicon as an etchant and show that the MoS6 vacancy can be a potential nucleation site for the growth of nanopores in MoS2. By fitting our kinetic predictions to experimental microscopy data on the formation time of a MoS6 vacancy, we show that the intrinsic barrier for the etching of atoms in MoS2, as described by Marcus theory, is 0.228 eV in the presence of silicon atoms. We find that the slowest step in the formation of the MoS6 vacancy is the step leading from a S5 vacancy to a S6 vacancy, with an activation barrier of ∼0.85 eV. This allows atoms to be etched at close to room-temperature conditions (27 °C) under the action of an electron beam that can move around the silicon etchant atoms. Using this new understanding of the nanopore formation process, researchers will be able to accurately model the controlled fabrication of nanopores in 2D MoS2.

High durability and stability of 2D nanofluidic devices for long-term single-molecule sensing

Nanopores in two-dimensional (2D) membranes hold immense potential in single-molecule sensing, osmotic power generation, and information storage. Recent advances in 2D nanopores, especially on single-layer MoS2, focus on the scalable growth and manufacturing of nanopore devices. However, there still remains a bottleneck in controlling the nanopore stability in atomically thin membranes. Here, we evaluate the major factors responsible for the instability of the monolayer MoS2 nanopores. We identify chemical oxidation and delamination of monolayers from their underlying substrates as the major reasons for the instability of MoS2 nanopores. Surface modification of the substrate and reducing the oxygen from the measurement solution improves nanopore stability and dramatically increases their shelf-life. Understanding nanopore growth and stability can provide insights into controlling the pore size, shape and can enable long-term measurements with a high signal-to-noise ratio and engineering durable nanopore devices.

Ionic Liquid Decelerates Single-Stranded DNA Transport through Molybdenum Disulfide Nanopores.

Nanopores in two-dimensional (2D) materials have emerged to offer in principle necessary spatial resolution for high-throughput DNA sequencing. However, their fidelity is severely limited by the fast DNA translocation. A recent experiment indicates that introducing ionic liquids could slow down DNA translocation in a MoS2 nanopore. However, the corresponding in-depth molecular mechanism underlying the experimental findings is not fully understood, which is crucial for the future improvement of rational DNA translocation control. Here, we computationally investigate and then experimentally identify the effect of BmimCl ionic liquid on the retardation of ssDNA translocation through a single-layer MoS2 nanopore. Our all-atom molecular dynamics simulations demonstrate that the strong interaction between Bmim+ and ssDNA offers a considerable dragging force to decelerate the electrophoretic motion of ssDNA in the BmimCl solution. Moreover, we show that Bmim+ ions exhibit preferential binding on the sulfur edges of the nanopore. These Bmim+ in the pore region can not only act as a steric blockage but also form π-π stackings with nucleobases, which provide a further restriction on the ssDNA motion. Therefore, our molecular dynamics simulation investigations deepen the understanding of the critical role of ionic liquid in DNA translocation through a nanopore from a molecular landscape, which may benefit practical implementations of ionic liquids in nanopore sequencing.

Ultrasensitive and Selective Field-Effect Transistor-Based Biosensor Created by Rings of MoS2 Nanopores.

The ubiquitous field-effect transistor (FET) is widely used in modern digital integrated circuits, computers, communications, sensors, and other applications. However, reliable biological FET (bio-FET) is not available in real life due to the rigorous requirement for highly sensitive and selective bio-FET fabrication, which remains a challenging task. Here, we report an ultrasensitive and selective bio-FET created by the nanorings of molybdenum disulfide (MoS2) nanopores inspired by nuclear pore complexes. We characterize the nanoring of MoS2 nanopores by scanning transmission electron microscopy, Raman, and X-ray photoelectron spectroscopy spectra. After fabricating MoS2 nanopore rings-based bio-FET, we confirm edge-selective functionalization by the gold nanoparticle tethering test and the change of electrical signal of the bio-FET. Ultrahigh sensitivity of the MoS2 nanopore edge rings-based bio-FET (limit of detection of 1 ag/mL) and high selectivity are accomplished by effective coupling of the aptamers on the nanorings of the MoS2 nanopore edge for cortisol detection. We believe that MoS2 nanopore edge rings-based bio-FET would provide platforms for everyday biosensors with ultrahigh sensitivity and selectivity.

Electronic structure of molecular hydrogen in MoS2 nanopores

Atom controlled sub-nanometer MoS2 pores have been recently fabricated with promising applications, such gas sensing, hydrogen storage and DNA translocation. In this work we carried out first-principles calculations of hydrogen adsorption in tiny MoS2 nanopores. Some of the pores show metallic behaviour whereas others have a sizeable band gap. Whereas adsorption of molecular hydrogen on bare pores are dominated by physisorption, adsorption in the nanopores show chemisorption behaviour with high selectivity depending on the pore inner termination. Finally, we show that functionalization with copper atoms leads to does not improve dignificantly the adsorption energies of selected pores.

Molecular dynamics simulation on DNA translocating through MoS2 nanopores with various structures

The emergence of MoS2 nanopores has provided a new avenue for high performance DNA sequencing, which is critical for modern chemical/biological research and applications. Herein, molecular dynamics simulations were performed to design a conceptual device to sequence DNA with MoS2 nanopores of different structures (e.g., pore rim contained Mo atoms only, S atoms only, or both Mo and S atoms), where various unfolded single-stranded DNAs (ssDNAs) translocated through the nanopores driven by transmembrane bias; the sequence content was identified by the associating ionic current. All ssDNAs adsorbed onto the MoS2 surface and translocated through the nanopores by transmembrane electric field in a stepwise manner, where the pause between two permeation events was long enough for the DNA fragments in the nanopore to produce well-defined ionic blockage current to deduce the DNA’sbase sequence. The transmembrane bias and DNA-MoS2 interaction could regulate the speed of the translocation process. Furthermore, the structure (atom constitution of the nanopore rim) of the nanopore considerably regulated both the translocate process and the ionic current. Thus, MoS2 nanopores could be employed to sequence DNA with the flexibility to regulate the translocation process and ionic current to yield the optimal sequencing performance.

Correction: Single nucleotide detection using bilayer MoS2 nanopores with high efficiency

Correction for ‘Single nucleotide detection using bilayer MoS2 nanopores with high efficiency’ by Payel Sen et al., RSC Adv., 2021, 11, 6114–6123. DOI: 10.1039/D0RA10222A.

Single nucleotide detection using bilayer MoS2 nanopores with high efficiency.

Single nucleotide detection is important for early detection of diseases and for DNA sequencing. Monolayer (ML) MoS2 nanopores have been used to identify and distinguish single nucleotides with good signal-to-noise ratio in the recent past. Here, we use a bilayer (BL) MoS2 nanopore (∼1.3 nm thick) to detect distinct single nucleotides with high spatial resolution and longer dwell time. In this study, the performance of similar sized (<3 nm) ML and BL MoS2 nanopores for detection of a single nucleotide has been compared. Both single nucleotide and single stranded DNA translocations through them are studied. For single nucleotide detection, we observe that BL MoS2 nanopores demonstrate twice the dwell time as compared to ML MoS2 nanopores with 95% confidence. Single nucleotide detection rate for BL MoS2 nanopores (50–60 nucleotides per s) is five-fold higher as compared to ML MoS2 nanopores (10–15 nucleotides per s) in 10 pM analyte concentration. For single stranded DNA, we observe 89% (for 60 DNA molecules detected) single nucleotide detection efficiency with BL MoS2 nanopores as compared to 85% for ML MoS2. The DNA sequencing efficiency through BL MoS2 nanopores is also found to be 8–10% better than through ML MoS2 nanopores, irrespective of DNA sequencing orientation. Thus, owing to improved analyte/nanopore charge interaction BL MoS2 nanopores can be used for single nucleotide detection with high resolution due to longer dwell time, detection rate and efficiency. This study demonstrates the improved ability of BL MoS2 nanopores in sequencing DNA with 8–10% higher efficiency, two-times temporally resolved single-nucleotide current signatures and five-times higher detection rate, compared to ML MoS2 nanopores.

Nanopore Confinement for Single‐Molecule Measurement of Proteins

Nanopore Confinement for Single‐Molecule Measurement of Proteins

Interaction dynamics and site-specific electronic recognition of DNA-nicks with 2D solid-state nanopores

Single-stranded breaks in the DNA backbone caused by many endogenous and exogenous agents often lead to double-stranded breaks that are known causes of chromosomal instabilities leading to copious diseases. We describe a label-free detection technique using two-dimensional (2D) solid-state nanopore field-effect transistors (FETs) to sense and map site-specific nicks in the DNA backbone. We use all-atom molecular dynamics simulations coupled with electronic transport modeling to illustrate the 2D membrane device capability to sense minute structural changes of any translocating biomolecules via their in-plane electronic sheet current signatures, whereas Van der Waals analyses explain the distinct hydrophobic interactions between various DNA-nick types with graphene and MoS2 nanopore membranes. Specifically, we describe the atypical unzipping behavior of DNA strands caused by the biomolecule sticking at nicked site in the graphene nanopore, under the influence of voltage-specific translocations.

Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS2 Nanopore.

Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS2 membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS2 nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.

Wafer‐Scale Fabrication of Nanopore Devices for Single‐Molecule DNA Biosensing using MoS2

AbstractAtomically thin (2D) nanoporous membranes are an excellent platform for a broad scope of academic research. Their thickness and intrinsic ion selectivity (demonstrated for example in molybdenum disulfide‐MoS2) make them particularly attractive for single‐molecule biosensing experiments and osmotic energy harvesting membranes. Currently, one of the major challenges associated with the research progress and industrial development of 2D nanopore membrane devices is small‐scale thin‐film growth and small‐area transfer methods. To address these issues, a large‐area protocol including a wafer‐scale monolayer MoS2 synthesis, Si/SiNx substrate fabrication and wafer‐scale material transfer are demonstrated. First, the 7.62 cm wafer‐scale MOCVD growth yielding homogenous monolayer MoS2 films are introduced. Second, a large number of devices are fabricated in one batch by employing the wafer‐scale thin‐film transfer method with high transfer efficiency (&gt;70% device yield). The growth, the transfer quality and cleanliness are investigated using transmission electron microscopy, atomic force microscopy and Raman spectroscopy. Finally, the applicability and robustness of the large‐area protocol is demonstrated by performing a set of double‐stranded DNA translocation experiments through as‐fabricated MoS2 nanopore devices. It is believed that the shown approach will pave the way toward wafer‐scale, high‐throughput use of 2D nanopores in various applications.

Unbalanced Ion Flushing Effect in MoS2 Nanopore Biosensors

In MoS2 nanopores, in addition to the widely measured ionic current signal to detect DNA nucleotides or epigenetic malformations, recent efforts have focused on the use of the transverse electronic current along the membrane for biomolecules sensing. This approach provides larger current magnitude and allows detection at the observed DNA translocation speed in the solid-state nanopore, which are crucial for accurate biomolecule sensing and faster DNA sequencing. As of today, no existing model is able to relate the variations of the transverse current to the interaction between ions, biomolecules and the MoS2 membrane. In this presentation, we report a comprehensive transport model based on the Poisson-Boltzmann transport formalism that considers the effect of biomolecules, electrolyte, and ion screening on conducting carriers along a MoS2 membrane. By accounting for membrane geometry and material properties used in recent experiment, we are able to extract the different electrical contributions to the transverse current variation during a DNA translocation event. In particular, we show that the major contribution to the electrical signal is caused by an unbalanced-ion-flushing effect that arises when the ion double-layer around the nanopore edge is swept out of the pore by the biomolecule translocation. By optimizing the MoS2 membrane geometry and nanopore size, we predict higher sensitivity to detect the translocation event in the corresponding transverse current signal. Thus,the identification of the unbalanced ion effect on the transverse electronic current foresees a critical new direction to improving the signal-to-noise ratio in solid-state nanopore sensing device.

Salt parameterization can drastically affect the results from classical atomistic simulations of water desalination by MoS2 nanopores.

Water scarcity is a reality in our world, and scenarios predicted by leading scientists in this area indicate that it will worsen in the next decades. However, new technologies based on low-cost seawater desalination can prevent the worst scenarios, providing fresh water for humanity. With this goal, membranes based on nanoporous materials have been suggested in recent years. One of the materials suggested is MoS2, and classical Molecular Dynamics (MD) simulation is one of the most powerful tools to explore these nanomaterials. However, distinct force fields employed in MD simulations are parameterized based on distinct experimental quantities. In this paper, we compare two models of salt that were built based on distinct properties of water-salt mixtures. One model fits the hydration free energy and lattice properties, and the second fits the crystal density and the density and the dielectric constant of water and salt mixtures. To compare the models, MD simulations for salty water flow through nanopores of two sizes were used - one pore big enough to accommodate hydrated ions, and one smaller in which the ion has to dehydrate to enter - and two rigid water models from the TIP4P family - TIP4P/2005 and TIP4P/ε. Our results indicate that the water permeability and salt rejection by the membrane are more influenced by the salt model than by the water model, especially for the narrow pore. In fact, completely distinct mechanisms were observed, and they are related to the characteristics employed in the ion model parameterization. The results show that not only can the water model influence the outcomes, but the ion model plays a crucial role when the pore is small enough.

Nanopore sensing of single-biomolecules: a new procedure to identify protein sequence motifs from molecular dynamics.

Solid-state nanopores have emerged as one of the most versatile tools for single-biomolecule detection and characterization. Nanopore sensing is based on the measurement of variations in ionic current as charged biomolecules immersed in an electrolyte translocate through nanometer-sized channels, in response to an external voltage applied across the membrane. The passage of a biomolecule through a pore yields information about its structure and chemical properties, as demonstrated experimentally with sub-microsecond temporal resolution. However, extracting the sequence of a biomolecule without the information about its position remains challenging due to the fact there is a large variability of sensing events recorded. In this paper, we performed microsecond time scale all-atom non-equilibrium Molecular Dynamics (MD) simulations of peptide translocation (motifs of alpha-synuclein, associated with Parkinson's disease) through single-layer MoS2 nanopores. First, we present an analysis based on the current threshold to extract and characterize meaningful sensing events from ionic current time series computed from MD. Second, a mechanism of translocation is established, for which side chains of each amino acid are oriented parallel to the electric field when they are translocating through the pore and perpendicular otherwise. Third, a new procedure based on the permutation entropy (PE) algorithm is detailed to identify protein sequence motifs related to ionic current drop speed. PE is a technique used to quantify the complexity of a given time series and it allows the detection of regular patterns. Here, PE patterns were associated with protein sequence motifs composed of 1, 2 or 3 amino acids. Finally, we demonstrate that this very promising procedure allows the detection of biological mutations and could be tested experimentally, despite the fact that reconstructing the sequence information remains unachievable at this time.

Experimental study of protein translocation through MoS2 nanopores

This experimental work studies the translocation of bovine serum albumin (BSA) proteins through MoS2 nanopores. A simple method of device fabrication is developed based on dry-transfer of exfoliated MoS2 membranes and subsequent TEM drilling, yielding MoS2 nanopores of a few monolayers thick and diameters as small as ∼11 nm. The current-voltage relation and low-frequency current noise of the devices are characterized. Typical BSA translocation signals that possibly correspond to various orientations are observed in the MoS2 devices, exhibiting enhanced amplitude and similar characteristics when compared to those from a silicon nitride (SiNx) control. Furthermore, the statistical data of the signal amplitude and dwell time at various biases are analyzed. These results show opportunities of single-molecular protein analysis using MoS2 nanopores.