Identification of single nucleotides in MoS2 nanopores

Abstract: Ultrathin membranes have drawn much attention due to their unprecedented spatial resolution for DNA nanopore sequencing. However, the high translocation velocity (3000-50000 nt/ms) of DNA molecules moving across such membranes limits their usability. To this end, we have introduced a viscosity gradient system based on room-temperature ionic liquids (RTILs) to control the dynamics of DNA translocation through a nanometer-size pore fabricated in an atomically thin MoS2 membrane. This allows us for the first time to statistically identify all four types of nucleotides with solid state nanopores. Nucleotides are identified according to the current signatures recorded during their transient residence in the narrow orifice of the atomically thin MoS2 nanopore. In this novel architecture that exploits high viscosity of RTIL, we demonstrate single-nucleotide translocation velocity that is an optimal speed (1-50 nt/ms) for DNA sequencing, while keeping the signal to noise ratio (SNR) higher than 10. Our findings pave the way for future low-cost and rapid DNA sequencing using solid-state nanopores.

• The paper demonstrates a novel RTIL-based viscosity gradient approach to slow down DNA translocation for effective single nucleotide identification.
• The methodology optimizes translocation speeds to 1–50 nt/ms while achieving a high signal-to-noise ratio (>10) for accurate nucleotide discrimination.
• The study integrates advanced material science and fluid dynamics to present a scalable, robust solid-state alternative for low-cost DNA sequencing.

Identification of Single Nucleotides in MoS Nanopores

The study presented in this paper investigates the potential for single nucleotide identification using molybdenum disulfide (MoS₂) nanopores, leveraging room-temperature ionic liquids (RTILs) to modulate DNA translocation dynamics. This research addresses a fundamental challenge in nanopore sequencing: the rapid translocation velocity of DNA which hinders effective sequencing accuracy. The utilization of an RTIL-based viscosity gradient system marks a significant advancement in controlling the translocation velocity, thereby enhancing the sequencing capabilities with solid-state nanopores.

The methodology centers around a novel architecture involving the use of ultra-thin MoS₂ membranes. These membranes are adapted to a viscosity gradient environment, facilitating the reduction of DNA translocation speed from previously excessive rates (3000-50000 nt/ms) to an optimal sequencing range (1-50 nt/ms). Notably, the study achieves a signal-to-noise ratio (SNR) exceeding 10, which is crucial for accurate single-nucleotide discrimination.

Key findings of this study include the successful and statistically robust identification of all four nucleotides (adenine, thymine, cytosine, guanine) based on distinct ionic current signatures as they transit the MoS₂ nanopore. The researchers recorded discernible current drops for each nucleotide type, demonstrating the potential for applying solid-state nanopores in low-cost, rapid DNA sequencing applications.

The combination of MoS₂ nanopores with viscosity gradient techniques achieved using RTILs addresses several limitations of traditional nanopore technologies, such as the need for biochemical reagents in biological nanopores and the fragility of these biological sensors. The implementation of solid-state nanopores not only broadens the operational fluid conditions but also increases device robustness and scalability, offering a feasible alternative for genomic sequencing applications.

From a theoretical standpoint, the study contributes significantly by solving the Poisson–Nernst–Planck (PNP) equations, thus providing a detailed numerical simulation of ionic transport under the viscosity gradient. This simulation aligns well with empirical data, confirming the validity of the approach and providing insights into the molecular dynamics as influenced by the inhomogeneous solution phase.

Practically, the implications of this research are profound, offering a pathway towards enhancing current nanopore sequencing technologies through improved temporal resolution and signal fidelity. The strategy outlined sets the stage for subsequent integration with electronic detection schemes like transverse current detection modalities, which could potentially facilitate multiplexing and further cost reductions in sequencing technologies.

Future research could explore the integration of electronic detection methods with the RTIL system to enhance sequencing throughput and accuracy. Exploring the scalable production of MoS₂ nanopores and their application in various liquid conditions could solidify this approach as a cornerstone technique for high-performance sequencing technologies. Implementing these findings could lead to substantial advancements in the field of genomic sequencing, particularly in terms of cost-effectiveness and accessibility.

This paper demonstrates a clear pathway for enhancing nanopore sequencing through innovative engineering solutions in material science and fluid dynamics, potentially revolutionizing approaches to genetic analysis and diagnostics. The advancement underscores how cross-disciplinary approaches can yield transformative results in DNA sequencing technologies.