Voltage-Driven Translocation of DNA through a High Throughput Conical Solid-State Nanopore

Abstract

Nanopores have become an important tool for molecule detection at single molecular level. With the development of fabrication technology, synthesized solid-state membranes are promising candidate substrates in respect of their exceptional robustness and controllable size and shape. Here, a 30–60 (tip-base) nm conical nanopore fabricated in 100 nm thick silicon nitride (Si3N4) membrane by focused ion beam (FIB) has been employed for the analysis of λ-DNA translocations at different voltage biases from 200 to 450 mV. The distributions of translocation time and current blockage, as well as the events frequencies as a function of voltage are investigated. Similar to previously published work, the presence and configurations of λ-DNA molecules are characterized, also, we find that greater applied voltages markedly increase the events rate, and stretch the coiled λ-DNA molecules into linear form. However, compared to 6–30 nm ultrathin solid-state nanopores, a threshold voltage of 181 mV is found to be necessary to drive DNA molecules through the nanopore due to conical shape and length of the pore. The speed is slowed down ∼5 times, while the capture radius is ∼2 fold larger. The results show that the large nanopore in thick membrane with an improved stability and throughput also has the ability to detect the molecules at a single molecular level, as well as slows down the velocity of molecules passing through the pore. This work will provide more motivations for the development of nanopores as a Multi-functional sensor for a wide range of biopolymers and nano materials.

A nanopore machine promotes the vectorial transport of DNA across membranes

“…The threading of ssDNA or dsDNA into biological nanopores is often observed above a threshold potential333435363738 (Supplementary Fig. S3) that can be tuned by altering the charge distribution of the lumen of the pore or by changing the ionic strength of the solution2739.…”

Slowing DNA Transport Using Graphene–DNA Interactions

“…Various methods have been suggested in solid-state nanopores to slow DNA translocation speed including the use of stick-slip interactions by using dielectric materials with high surface charge density like Al 2 O 3 and HfO 2 . [28,29] Other proposed techniques include the use of different ionic solutions such as LiCl, [30] increasing solution viscosity with glycerol, [31] optoelectronic control, [32] fluidic gating, [33] reducing nanopore diameter, [34] use of pressure gradients, [35] thicker membranes, [36] and temporary hydrogen bonding. [37] Recently, the potential for DNA–graphene hydrophobic interactions to induce ssDNA translocations in single-nucleotide steps was discussed.…”

Slowing Down DNA Translocation through Solid-State Nanopores by Edge-Field Leakage

“…We observed an average translocation time ~ 125 ms for 22 nt ssDNA in Al2O3-coated PET nanopores (half cone angle ~ 9 ± 2 o , diameter 8 nm, applied voltage 400mV). Due to confinement effects and electrostatic interactions, translocation times of DNA molecules (and other small molecules) through small-diameter (and/or charged) nanopores are well-modeled as activated processes [52][53][54][55] . As the electric field 0 pulls the stalled DNA into the pore with a force 0 , where is the effective charge of the molecule, translocation times decrease exponentially with the field in such activated entries, reducing the barrier by a factor ΔG~∫ 0 0 associated to the work done by the applied field to move the DNA molecule a distance 53,54 .…”

“…Due to confinement effects and electrostatic interactions, translocation times of DNA molecules (and other small molecules) through small-diameter (and/or charged) nanopores are well-modeled as activated processes [52][53][54][55] . As the electric field 0 pulls the stalled DNA into the pore with a force 0 , where is the effective charge of the molecule, translocation times decrease exponentially with the field in such activated entries, reducing the barrier by a factor ΔG~∫ 0 0 associated to the work done by the applied field to move the DNA molecule a distance 53,54 . Translocation times can then be estimated through 0 −∆ / , where τ0 is the zero-field translocation time, kB is Boltzmann constant, and T is the temperature of the system [52][53][54] .…”