Detecting the translocation of DNA through a nanopore using graphene nanoribbons

Solid-state nanopores can act as single-molecule sensors and could potentially be used to rapidly sequence DNA molecules. However, nanopores are typically fabricated in insulating membranes that are as thick as 15 bases, which makes it difficult for the devices to read individual bases. Graphene is only 0.335 nm thick (equivalent to the spacing between two bases in a DNA chain) and could therefore provide a suitable membrane for sequencing applications. Here, we show that a solid-state nanopore can be integrated with a graphene nanoribbon transistor to create a sensor for DNA translocation. As DNA molecules move through the pore, the device can simultaneously measure drops in ionic current and changes in local voltage in the transistor, which can both be used to detect the molecules. We examine the correlation between these two signals and use the ionic current measurements as a real-time control of the graphene-based sensing device.

Fabrication and practical applications of molybdenum disulfide nanopores

Jiandong Feng, Michael Graf, Martina Lihter, Ke Liu, Aleksandra Radenovic, Mukeshchand Thakur

Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin membranes have the advantage of providing relatively high ionic currents at very small pore sizes. This increases the signal generated during translocation of biomolecules and improves the nanopores’ efficiency when used for desalination or reverse electrodialysis applications. The atomic thickness of MoS2 nanopores approaches the inter-base distance of DNA, creating a potential candidate for DNA sequencing. In terms of geometry, MoS2 nanopores have a well-defined vertical profile due to their atomic thickness, which eliminates any unwanted effects associated with uneven pore profiles observed in other materials. This protocol details all the necessary procedures for the fabrication of solid-state devices. We discuss different methods for transfer of monolayer MoS2, different approaches for the creation of nanopores, their applicability in detecting DNA translocations and the analysis of translocation data through open-source programming packages. We present anticipated results through the application of our nanopores in DNA translocations and osmotic power generation. The procedure comprises four parts: fabrication of devices (2–3 d), transfer of MoS2 and cleaning procedure (24 h), the creation of nanopores within MoS2 (30 min) and performing DNA translocations (2–3 h). We anticipate that our protocol will enable large-scale manufacturing of single-molecule-analysis devices as well as next-generation DNA sequencing.

2019

2D nanopores: fabrication, energy harvesting and field-effect sensing

Michael Graf

Solid-state nanopores are man-made, nano-sized openings in membranes separating two chambers containing an electrolyte solution. When applying an electric field across the membrane, the nanopore provides the only path for mobile ions to pass from one side of the membrane to the other. This current of ions is highly dependent on the pore size, membrane thickness, and surface charge. Small modulations in the system can lead to a large current modulation. We take advantage of this by translocating biomolecules through the nanopore. Typically, molecules such as DNA have an intrinsic charge in solution and will be attracted by the electric field generated around the nanopore. If the size of the pore allows it, they will thread into the pore and translocate to the opposite chamber. Generally, the thinner the membrane, the more ion current is generated and therefore the larger is the recorded signal. The isolation of mono-atomic crystals of carbon, also known as graphene, at the beginning of the 21st century, sparked much interest in using 2D materials for nanopore sensors. The thickness of these materials is approaching the distance between two bases in a DNA molecule, which raised the hopes of sequencing DNA when it passes through the orifice. First, I will introduce the reader to 2D nanopores made in MoS2. In the last few years, I gained a lot of insights into 2D-nanopore fabrication. Therefore, I will first detail how MoS2-nanopore devices can be fabricated reliably and I will discuss potential pitfalls that researchers might encounter when manufacturing these devices. We realized that nanopores in atomically thin MoS2 not only provide a system with low resistance to ionic current but also exhibit excellent ion-selectivity. Therefore, we developed an energy-harvesting system based on the osmotic pressure generated when concentration gradients are applied across the membrane. Converting this osmotic energy through reverse-electrodialysis relies on ion-selective membranes. By exploiting the photo-excitability of MoS2 membranes, I will show that we can raise the ion selectivity of the membrane by a factor of 5 while staying at a neutral pH and conclude that the observed effect is due to a change in the surface charge caused by light-induced charge generation. Although ionic sensing with nanopores allows the precise measurements of single molecules, the spatial resolution in ionic sensing is limited by the access resistance. This limitation can potentially be overcome by an alternative sensing scheme independent from the ionic current. I will present a supplementary sensing scheme taking advantage of the semiconducting properties of MoS2. I fabricated freestanding nanoribbons of monolayer MoS2 in which a nanopore is drilled. The nanoribbons are then contacted through metal leads, which allow measuring the current through the material itself. The ionic current and the transverse current are recorded simultaneously and show correlated current modulations when DNA molecules translocate through the nanopore. The precise sensing mechanism of these devices is currently not well understood but is believed to originate from the charged molecules themselves or from local potential changes near the nanopore. I will discuss the challenges in fabricating such devices and propose possible explanations for the observed current traces.

EPFL2019

Fabrication of solid-state Nanopores for DNA analysis

Maïté Volatier

One of revolutionary technologies to sequence single molecules, such as DNA, is using nanopore devices. A single-channel with nanometer-scale aperture allows an extremely rapid electric analysis of such single molecules. The objective of this work is to fabricate nanopores into robust, solid-state membranes to achieve better performances. The technological challenge is in the small required dimension of the nanopore, around 50-100 nm in diameter and depth. To reach this objective, we used two different techniques: the ion track technique and a microfabrication method associated with Focused Ion Beam (FIB). A literature review has been done on the ion track technique. Threshold values of the ion track formation have been found for different insulator materials (polymers, SiO2, SiN). We did experiments with the linear accelerator UNILAC (Universal Linear Accelerator) at the GSI (Darmstadt, Germany) where we irradiated our samples with heavy gold ions (11.4 MeV/nucleon). On very thin membranes, we expect that a direct perforation would occur, and we chose SiN membranes and SU-8 thin films as samples. However, the experiment of ion bombardment was not possible to be done early enough, thus TEM analysis have not been done yet. If the direct perforation by ion bombardment is not possible, a chemical etching step would be necessary. About the microfabrication method associated with Focused Ion Beam (FIB) perforation, we did experiments at the Center of Micro Nano Technology (CMI) in EPFL. First trial with FIB was done on SiN membranes. In order to obtain required aperture size, reduction of membrane thickness before perforation by FIB was attempted, but this process was difficult to be achieved because of charging. To overcome this dimension limitation we chose a silicon membrane. With silicon membranes, oxidation would be performed after perforation by FIB, since channel opening will be reduced by SiO2 growth. Moreover, this oxide layer allows a functionalisation of the inner surface of the nanopore by silane chemistry. That should improve the resolution of DNA analysis. Though the aperture size reduction by oxidation has not been done yet, refining and perforation by FIB will be done according to this idea. We should reach ca. 100 nm-aperture size. Even if validation measurements are not easy, our specifications should be reached with the oxidation. More experiments and analysis have to be performed for further improvement.