DNA Translocation in Nanometer Thick Silicon Nanopores

Abstract

Solid-state nanopores are single-molecule sensors that detect changes in ionic conductance (ΔG) when individual molecules pass through them. Producing high signal-to-noise ratio for the measurement of molecular structure in applications such as DNA sequencing requires low noise and large ΔG. The latter is achieved by reducing the nanopore diameter and membrane thickness. While the minimum diameter is limited by the molecule size, the membrane thickness is constrained by material properties. We use molecular dynamics simulations to determine the theoretical thickness limit of amorphous Si membranes to be ∼1 nm, and we designed an electron-irradiation-based thinning method to reach that limit and drill nanopores in the thinned regions. Double-stranded DNA translocations through these nanopores (down to 1.4 nm in thickness and 2.5 nm in diameter) provide the intrinsic ionic conductance detection limit in Si-based nanopores. In this regime, where the access resistance is comparable to the nanopore resistance, we observe the appearance of two conductance levels during molecule translocation. Considering the overall performance of Si-based nanopores, our work highlights their potential as a leading material for sequencing applications.

Measurement of DNA Translocation Dynamics in a Solid-State Nanopore at 100 ns Temporal Resolution

“…(c) Bright-field TEM image of nanopores made in STEM-thinned membranes. 29 Circles indicating diameters of 1.7 nm, 2.0 nm, and 2.6 nm are shown in overlay with corresponding nanopores. (d) Simplified electrical schematic illustrating the various capacitances and noise sources that determine high-frequency noise behavior.…”

“…Silicon nitride nanopores in this work were thinned to an absolute thickness of less than 4 nm, 29 allowing for blockade current signals ΔI , as high as 30 nA in 3M KCl at 900 mV bias. The ΔI of a nanopore is maximized for small nanopore thickness, and can be estimated by the equation, $$\mathrm{normal\Delta }I=\sigma V_{\mathit{\text{bias}}}true({true[\frac{4h_{\mathit{\text{eff}}}}{\pi d^2}+\frac{1}{d}true]}^{-1}-{true[\frac{4h_{\mathit{\text{eff}}}}{\pi d_{\mathit{\text{eff}}}^2}+\frac{1}{d_{\text{italiceff}}}true]}^{-1}true)$$ where V bias is the applied transmembrane voltage, σ is the solution conductivity, h eff is the effective membrane thickness, d is the nanopore diameter, and d eff is a reduced effective diameter of the nanopores in the presence of DNA defined as $d_{\mathit{\text{eff}}}=\sqrt{d^2-d_{dna}^2}$, where d dna is the cross-sectional width of ssDNA.…”

“…29 STEM thinning uses electron irradiation with rastering of the electron probe of a JEOL 2010F S/TEM over a defined area of silicon nitride. This causes the sputtering of silicon and nitrogen atoms 31 with the final membrane consisting of amorphous silicon, due to the higher rate of sputtering of nitrogen.…”

“…This causes the sputtering of silicon and nitrogen atoms 31 with the final membrane consisting of amorphous silicon, due to the higher rate of sputtering of nitrogen. 29 A two-step process is used, with an initial thinning of a 65 nm × 65 nm region of 50-nm thick freestanding silicon nitride membrane to 10 nm amorphous silicon by using a 2.5 nm probe size, with membrane thickness controlled by quantifying the mass loss using electron-energy loss spectroscopy (EELS) (see Supplementary Information). A second thinning in a smaller 25 nm × 25 nm region is made using a 0.5-nm spot size, bringing the membrane thickness down from 10 nm to less than 4 nm.…”

Nanopore Sensing

“…Drndić and co-workers have developed an electron-irradiation-based thinning method of SiN x membranes. 58 In this method, the target membrane area is raster-scanned with the electron beam from a scanning transmission electron microscope (STEM), and real-time acquisition of both a high-angle annular dark-field (HAADF) STEM image and an energy electron-loss spectrum (EELS) of the same area is achieved. By monitoring and quantifying the mass loss with the HAADF STEM images and EELS, the film thickness can be controlled.…”