Which 2D Material is Better for DNA Detection: Graphene, MoS2, or MXene?

Automated-Screening Oriented Electric Sensing of Vitamin B1 Using a Machine Learning Aided Solid-State Nanopore

Micronutrient detection and identification at the single-molecule level are paramount for both clinical and home diagnostics. Analytical tools such as high-performance liquid chromatography and liquid chromatography-tandem mass spectrometry have been widely used but include a high instrument cost and prolonged analysis time. Here, as a model system, by merging nanopore signatures with machine learning algorithms, we propose an automated electric sensing strategy to identify vitamin B1 and its phosphorylated derivatives with good accuracy. Further, the relationship between vitamin B1 dynamics and nanopore signatures is examined. To understand the machine-decision-making process, Shapley additive explanations are made. Using a machine learning aided solid-state nanopore, we pave the way for next-generation micronutrient detection.

Sequence-Dependent Slowdown of DNA Translocation Using Transmembrane RNA-DNA Interactions in MoS2 Nanopore

The emergence of nanopores in two-dimensional (2D) nanomaterials offers an attractive solid-state platform for high-throughput and low-cost DNA sequencing. However, several challenges remain to be addressed before their wide application, including the too-fast DNA translocation speed (compared to state-of-the-art single nucleoside detection techniques) and too large noise/signal ratios due to DNA fluctuations inside the nanopores. Here, we use molecular dynamics (MD) simulations to demonstrate the feasibility of utilizing RNA-DNA interactions in modulating DNA translocations in 2D MoS2 nanopores. By constructing a transmembrane-RNA-oligonucleotide-decorated nanopore (TOD nanopore), we find that the translocation speed of DNA can be significantly slowed in a sequence-dependent manner, with up to 160-fold deceleration compared with the naked control. The strong interactions between the translocating DNA and the first and second guanines of transmembrane RNAs are thought to play a key role in regulating the translocation process. Moreover, the observed suppression of base conformational fluctuations within the TOD nanopore can further improve the single nucleotide detecting resolution. Therefore, our investigations demonstrate that the proposed TOD nanopore can be a potential candidate for enhanced DNA sequencing with solid-state nanopores.

Two-Dimensional Material-Based Nanofluidic Devices and Their Applications

Nanofluidics is an interdisciplinary field of study that bridges hydrodynamics, statistical physics, chemistry, materials science, biology, and other fields to investigate the transport of fluids and ions on the nanometric scale. The progress in this field, however, has been constrained by challenges in fabricating nanofluidic devices suitable for systematic investigations. Recent advances in two-dimensional (2D) materials have revolutionized the development of nanofluids. Their ultrathin structure and photothermoelectric response make it possible to achieve the scale control, friction limitation, and regulatory response, all of which are challenging to achieve with traditional solid materials. In this review, we provide a comprehensive overview of the preparation methods and corresponding structures of three types of 2D material-based nanofluidic devices, including nanopores, nanochannels, and membranes. We highlight their applications and recent advances in exploring physical mechanisms, detecting biomolecules (DNA, protein), developing iontronics devices, improving ion/gas selectivity, and generating osmotic energy. We discuss the challenges facing 2D material-based nanofluidic devices and the prospects for future advancements in this field.

Nanopore-based sensors for DNA sequencing: a review

Nanopore sensors, owing to their distinctive structural properties, can be used to detect biomolecular translocation events. These sensors operate by monitoring variations in electric current amplitude and duration, thereby enabling the calibration and distinction of various biomolecules. As a result, nanopores emerge as a potentially powerful tool in the field of deoxyribonucleic acid (DNA) sequencing. However, the interplay between testing bandwidth and noise often leads to the loss of part of the critical translocation signals, presenting a substantial challenge for the precise measurement of biomolecules. In this context, innovative detection mechanisms have been developed, including optical detection, tunneling current detection, and nanopore field-effect transistor (FET) detection. These novel detection methods are based on but beyond traditional nanopore techniques and each of them has unique advantages. Notably, nanopore FET sensors stand out for their high signal-to-noise ratio (SNR) and high bandwidth measurement capabilities, overcoming the limitations typically associated with traditional solid-state nanopore (SSN) technologies and thus paving the way for new avenues to biomolecule detection. This review begins by elucidating the fundamental detection principles, development history, applications, and fabrication methods for traditional SSNs. It then introduces three novel detection mechanisms, with a particular emphasis on nanopore FET detection. Finally, a comprehensive analysis of the advantages and challenges associated with both SSNs and nanopore FET sensors is performed, and then insights into the future development trajectories for nanopore FET sensors in DNA sequencing are provided. This review has two main purposes: firstly, to provide researchers with a preliminary understanding of advancements in the nanopore field, and secondly, to offer a comprehensive analysis of the fabrication techniques, transverse current detection principles, challenges, and future development trends in the field of nanopore FET sensors. This comprehensive analysis aims to help give researchers in-depth insights into cutting-edge advancements in the field of nanopore FET sensors.

Advancement of Next-Generation DNA Sequencing through Ionic Blockade and Transverse Tunneling Current Methods

DNA sequencing is transforming the field of medical diagnostics and personalized medicine development by providing a pool of genetic information. Recent advancements have propelled solid-state material-based sequencing into the forefront as a promising next-generation sequencing (NGS) technology, offering amplification-free, cost-effective, and high-throughput DNA analysis. Consequently, a comprehensive framework for diverse sequencing methodologies and a cross-sectional understanding with meticulous documentation of the latest advancements is of timely need. This review explores a broad spectrum of progress and accomplishments in the field of DNA sequencing, focusing mainly on electrical detection methods. The review delves deep into both the theoretical and experimental demonstrations of the ionic blockade and transverse tunneling current methods across a broad range of device architectures, nanopore, nanogap, nanochannel, and hybrid/heterostructures. Additionally, various aspects of each architecture are explored along with their strengths and weaknesses, scrutinizing their potential applications for ultrafast DNA sequencing. Finally, an overview of existing challenges and future directions is provided to expedite the emergence of high-precision and ultrafast DNA sequencing with ionic and transverse current approaches.

Mixed-Dimensional Integration of 3D-on-2D Heterostructures for Advanced Electronics

Two-dimensional (2D) materials have garnered significant attention due to their exceptional properties requisite for next-generation electronics, including ultrahigh carrier mobility, superior mechanical flexibility, and unusual optical characteristics. Despite their great potential, one of the major technical difficulties toward lab-to-fab transition exists in the seamless integration of 2D materials with classic material systems, typically composed of three-dimensional (3D) materials. Owing to the self-passivated nature of 2D surfaces, it is particularly challenging to achieve well-defined interfaces when forming 3D materials on 2D materials (3D-on-2D) heterostructures. Here, we comprehensively review recent progress in 3D-on-2D incorporation strategies, ranging from direct-growth- to layer-transfer-based approaches and from non-epitaxial to epitaxial integration methods. Their technological advances and obstacles are rigorously discussed to explore optimal, yet viable, integration strategies of 3D-on-2D heterostructures. We conclude with an outlook on mixed-dimensional integration processes, identifying key challenges in state-of-the-art technology and suggesting potential opportunities for future innovation.

The Role of MXene Surface Terminations on Peptide Transportation in Nanopore Sensing

Nanopores with two-dimensional materials have various advantages in sensing, but the fast translocation of molecules hinders their scale-up applications. In this work, we investigate the influence of -F, -O, and -OH surface terminations on the translocation of peptides through MXene nanopores. We find that the longest dwell time always occurs when peptides pass through the Ti3C2O2 nanopores. This elongated dwell time is induced by the strongest interaction between peptides and the Ti3C2O2 membrane, in which the van der Waals interactions dominate. Compared to the other two MXene nanopores, the braking effect is indicated during the whole translocation process, which evidence the advantage of Ti3C2O2 in nanopore sensing. Our work demonstrates that membrane surface chemistry has a great influence on the translocation of peptides, which can be introduced in the design of nanopores for a better performance.

Label-Free Imaging of DNA Interactions with 2D Materials

Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.

Exploring the non-monotonic DNA capture behavior in a charged graphene nanopore

Nanopore-based biomolecule detection has emerged as a promising and sought-after innovation, offering high throughput, rapidity, label-free analysis, and cost-effectiveness, with potential applications in personalized medicine. However, achieving efficient and tunable biomolecule capture into the nanopore remains a significant challenge. In this study, we employ all-atom molecular dynamics simulations to investigate the capture of double-stranded DNA (dsDNA) molecules into graphene nanopores with varying positive charges. We discover a non-monotonic relationship between the DNA capture rate and the charge of the graphene nanopore. Specifically, the capture rate initially decreases and then increases with an increase in nanopore charge. This behavior is primarily attributed to differences in the electrophoretic force, rather than the influence of electroosmosis or counterions. Furthermore, we also observe this non-monotonic trend in various ionic solutions, but not in ionless solutions. Our findings shed light on the design of novel DNA sequencing devices, offering valuable insights into enhancing biomolecule capture rates in nanopore-based sensing platforms.

Adsorption of DNA nucleobases on single-layer Ti3C2 MXene and graphene: vdW-corrected DFT and NEGF studies

We investigated the interaction of DNA nucleobases [adenine (A), guanine (G), thymine (T), and cytosine (C)] with single-layer Ti3C2 MXene using Van der Waals (vdW)-corrected density functional theory and non-equilibrium Green's function methods. All calculations were benchmarked against graphene. We showed that depending on the initial vertical height of a nucleobase above the Ti3C2 surface, two interaction mechanisms are possible, namely, physisorption and chemisorption. For graphene, DNA nucleobases always physisorbed onto the graphene surface irrespective of the initial vertical height of the nucleobase above the graphene sheet. The PBE+vdW binding energies for graphene are high (0.55-0.74 eV) and follow the order G > A > T > C, with adsorption heights in the range of 3.16-3.22 Å, indicating strong physisorption. For Ti3C2, the PBE+vdW binding energies are relatively weaker (0.16-0.20 eV) and follow the order A > G = T > C, with adsorption heights in the range of 5.51-5.60 Å, indicating weak physisorption. The binding energies for chemisorption follow the order G > A > T > C, which is the same order for physisorption. The binding energy values (5.3-7.5 eV) indicate very strong chemisorption (∼40 times larger than the physisorption binding energies). Furthermore, our band structure and electronic transport analysis showed that for physisorption, there is neither significant variation in the band structure nor modulation in the transmission function and device density of states. The relatively weak physisorption and strong chemisorption show that Ti3C2 might not be capable of identifying DNA nucleobases using the physisorption method.

Unlocking the Power of Nanopores: Recent Advances in Biosensing Applications and Analog Front-End

The biomedical field has always fostered innovation and the development of various new technologies. Beginning in the last century, demand for picoampere-level current detection in biomedicine has increased, leading to continuous breakthroughs in biosensor technology. Among emerging biomedical sensing technologies, nanopore sensing has shown great potential. This paper reviews nanopore sensing applications, such as chiral molecules, DNA sequencing, and protein sequencing. However, the ionic current for different molecules differs significantly, and the detection bandwidths vary as well. Therefore, this article focuses on current sensing circuits, and introduces the latest design schemes and circuit structures of different feedback components of transimpedance amplifiers mainly used in nanopore DNA sequencing.

Development of an Artificially Intelligent Nanopore for High-Throughput DNA Sequencing with a Machine-Learning-Aided Quantum-Tunneling Approach

Solid-state nanopore-based single-molecule DNA sequencing with quantum tunneling technology poses formidable challenges to achieve long-read sequencing and high-throughput analysis. Here, we propose a method for developing an artificially intelligent (AI) nanopore that does not require extraction of the signature transmission function for each nucleotide of the whole DNA strand by integrating supervised machine learning (ML) and transverse quantum transport technology with a graphene nanopore. The optimized ML model can predict the transmission function of all other nucleotides after training with data sets of all the orientations of any nucleotide inside the nanopore with a root-mean-square error (RMSE) of as low as 0.062. Further, up to 96.01% accuracy is achieved in classifying the unlabeled nucleotides with their transmission readouts. We envision that an AI nanopore can alleviate the experimental challenges of the quantum-tunneling method and pave the way for rapid and high-precision DNA sequencing by predicting their signature transmission functions.

Integrated Approach from Sample-to-Answer for Grapevine Varietal Identification on a Portable Graphene Sensor Chip

Identifying grape varieties in wine, related products, and raw materials is of great interest for enology and to ensure its authenticity. However, these matrices' complexity and low DNA content make this analysis particularly challenging. Integrating DNA analysis with 2D materials, such as graphene, offers an advantageous pathway toward ultrasensitive DNA detection. Here, we show that monolayer graphene provides an optimal test bed for nucleic acid detection with single-base resolution. Graphene's ultrathinness creates a large surface area with quantum confinement in the perpendicular direction that, upon functionalization, provides multiple sites for DNA immobilization and efficient detection. Its highly conjugated electronic structure, high carrier mobility, zero-energy band gap with the associated gating effect, and chemical inertness explain graphene's superior performance. For the first time, we present a DNA-based analytic tool for grapevine varietal discrimination using an integrated portable biosensor based on a monolayer graphene field-effect transistor array. The system comprises a wafer-scale fabricated graphene chip operated under liquid gating and connected to a miniaturized electronic readout. The platform can distinguish closely related grapevine varieties, thanks to specific DNA probes immobilized on the sensor, demonstrating high specificity even for discriminating single-nucleotide polymorphisms, which is hard to achieve with a classical end-point polymerase chain reaction or quantitative polymerase chain reaction. The sensor was operated in ultralow DNA concentrations, with a dynamic range of 1 aM to 0.1 nM and an attomolar detection limit of ∼0.19 aM. The reported biosensor provides a promising way toward developing decentralized analytical tools for tracking wine authenticity at different points of the food value chain, enabling data transmission and contributing to the digitalization of the agro-food industry.