Self-Limited Formation of Bowl-Shaped Nanopores for Directional DNA Translocation

Abstract

Solid-state nanopores of on-demand dimensions and shape can facilitate desired sensor functions. However, reproducible fabrication of arrayed nanopores of predefined dimensions remains challenging despite numerous techniques explored. Here, bowl-shaped nanopores combining properties of ultrathin membrane and tapering geometry are manufactured using a self-limiting process developed on the basis of standard silicon technology. The upper opening of the bowl-nanopores is 60–120 nm in diameter, and the bottom orifice reaches sub-5 nm. Current–voltage characteristics of the fabricated bowl-nanopores display insignificant rectification indicating weak ionic selectivity, in accordance to numerical simulations showing minor differences in electric field and ionic velocity upon the reversal of bias voltages. Simulations reveal, concomitantly, high-momentum electroosmotic flow downward along the concave nanopore sidewall. Collisions between the left and right tributaries over the bottom orifice drive the electroosmotic flow both up into the nanopore and down out of the nanopore through the orifice. The resultant asymmetry in electrophoretic–electroosmotic force is considered the cause responsible for the experimentally observed strong directionality in λ-DNA translocation with larger amplitude, longer duration, and higher frequencies for the downward movements from the upper opening than the upward ones from the orifice. Thus, the resourceful silicon nanofabrication technology is shown to enable nanopore designs toward enriching sensor applications.

Plasmonic Photochemistry as a Tool to Prepare Metallic Nanopores with Controlled Diameter for Optimized Detection of Single Entities

“…Bowl-shaped nanopores have been recently reported using more complex fabrication procedures, but still demonstrating improved performance in single-molecule translocation and detection. [54] Similar simulations for nanopores with additional Au deposition are reported in Figures S14, S15 and Note S11 (Supporting Information), which reveal a maximum intensity enhancement I/I 0 up to 150 at 610 nm excitation wavelength. The broad response of the Au nanopore in the visible spectral range suggests its potential use in enhanced spectroscopies.…”

A Generalized Transformer-Based Pulse Detection Algorithm

“…Higher voltage offers larger capture area, thereby yielding higher frequency . The observed constant duration of streptavidin translocation at the bias voltages used is attributed to the limited bandwidth of signal acquisition in our experiment; it is readily conceivable that a high translocating speed of small molecules such as protein can lead to a sharp and featureless spike. , The duration does not display a monotonous trend in the DNA translocation data, which may result from complicated interactions between long and densely-charged DNA and nanopore. , The traditional method in which different multiples of noise level are utilized as thresholds for spike detection yields diversified results on both frequency and duration (SI, Figure S15). In sharp contrast, physics-plausible, stable, and consistent trends are obtained by PETR based on the same experimental data (SI).…”

“… 44 , 45 The duration does not display a monotonous trend in the DNA translocation data, which may result from complicated interactions between long and densely-charged DNA and nanopore. 44 , 46 The traditional method in which different multiples of noise level are utilized as thresholds for spike detection yields diversified results on both frequency and duration (SI, Figure S15 ). In sharp contrast, physics-plausible, stable, and consistent trends are obtained by PETR based on the same experimental data (SI).…”

Effects of off-axis translocation through nanopores on the determination of shape and volume estimates for individual particles

“…The Poisson-Nernst-Planck (PNP) equations are commonly used to express the flow of ionic current through a nanopore [29,[32][33][34][35][36][37][38]. The Poisson function describes the distribution of potentials, Φ, in an electrolyte solution containing ionic species, i (K + or Cl − , in this case), at concentration c i and charge z i…”