Detection of nucleotides in hydrated ssDNA via 2D h‐BN nanopore with ionic‐liquid/salt–water interface

Abstract

Accomplishing slow translocation speed with high sensitivity has been the most critical mission for solid‐state nanopore (SSN) device to electrically detect nucleobases in ssDNA. In this study, a method to detect nucleobases of ssDNA using a 2D SSN is introduced by considerably reducing the translocation speed and effectively increasing its sensitivity. The ultra‐thin titanium dioxide coated hexagonal boron nitride nanopore was fabricated, along with an ionic‐liquid 1‐butyl‐3‐methylimidazolium hexafluorophosphate/2.0 M KCl aqueous (cis/trans) interface, for increasing both the spatial and the temporal resolutions. As the ssDNA molecules entered the nanopore, a brief surge of electrical conductivity occurred, which was followed by multiple resistive pulses from nucleobases during the translocation of ssDNA and another brief current surge flagging the exit of the molecule. The continuous detection of nucleobases using a 2D SSN device is a novel achievement: the water molecules bound to ssDNA increased the molecular conductivity and amplified electrical signals during the translocation. Along with the experiment, computational simulations using COMSOL Multiphysics are presented to explain the pivotal role of water molecules bound to ssDNA to detect nucleobases using a 2D SSN.

Nanopore Data Analysis: Baseline Construction and Abrupt Change-Based Multilevel Fitting

“…The h-BN nanopore fabrication processes are outlined in our previous work, , and the nanopores in Si x N y purchased from Norcada (NBPX5001Z-HR, nominally ∼12 nm thick) were fabricated using CDB and CT-CDB . dsDNA (10787018, Fisher Scientific) was used as supplied, and the stock solutions of hSTf (T0665, Sigma-Aldrich, USA) were prepared by dissolving the as-supplied solid in >18 MΩ cm ultra-pure water (ARS-102 Aries high-purity water systems).…”

Nanopores in Graphene and Other 2D Materials: A Decade’s Journey toward Sequencing

“…Subsequently, they were able to differentiate between all four types of 30-mer DNA homopolymers and single nucleotides by using a 2.8 nm diameter MoS 2 pore. Similarly, a viscosity gradient was proposed to considerably reduce the translocation speed of ssDNA across h -BN nanopores and, meanwhile, increase the sensitivity of nanopore detection by adding 3% of pure water to the highly viscous ionic liquids . Liang et al .…”

“…Similarly, a viscosity gradient was proposed to considerably reduce the translocation speed of ssDNA across h-BN nanopores and, meanwhile, increase the sensitivity of nanopore detection by adding 3% of pure water to the highly viscous ionic liquids. 142 Liang et al predicted via MD simulations that applying a lower voltage or decreasing pore size also resulted in slower DNA translocation through a MoS 2 pore. 143 Aside from the aforesaid general strategies, a few alternative methods possibly specific to 2D materials were also proposed for reducing DNA speed and, more importantly, moving DNA bases across the pore one base at a time.…”

Solid-State Nanopore for Molecular Detection

“…FEB/FIB is the most common technique to drill nanopore on a suspended film directly. A large variety of materials including SiN [9,30,31,[64][65][66][67][68][69][70][71][72][73], SiO 2 [80] and 2D materials [40,83,84,86,88,108] are used for the formation of nanopores in different sizes. Li et al [47] reported an ion beam sculpting technique to fabricate 1.8 nm nanopore in a free-standing SiN membrane supported on Si substrate.…”