The effects of geometry and stability of solid-state nanopores on detecting single DNA molecules

Abstract

In this work we use a combination of 3D-TEM tomography, energy filtered TEM, single molecule DNA translocation experiments, and numerical modeling to show a more precise relationship between nanopore shape and ionic conductance and show that changes in geometry while in solution can account for most deviations between predicted and measured conductance. We compare the structural stability of Ion Beam Sculpted (IBS), IBS-annealed, and TEM drilled nanopores. We demonstrate that annealing can significantly improve the stability of IBS made pores. Furthermore, the methods developed in this work can be used to predict pore conductance and current drop amplitudes of DNA translocation events for a wide variety of pore geometries. We discuss that chemical dissolution is one mechanism of the geometry change for SiNx nanopores and show that small modification in fabrication procedure can significantly increase the stability of IBS nanopores.

Surface coatings for solid-state nanopores

“…267 Specifically, SiO 2 on the nanopore walls, which originates either from membranes composed entirely of SiO 2 or from oxidation of the surface of SiN x membranes, hydrolyzes slowly to silicic acid and dissolves in the electrolyte solution during recordings. 131,268 The etch rate of SiN x or SiO 2 during nanopore experiments varies as a function of temperature, pH, salt concentration, applied voltage, nanopore shape and nanopore fabrication methods 132,267,269,270 and can sometimes be sufficiently fast to lead to a noticeable increase in conductivity through the growing pore during the experiment. The resulting uncertainty in pore diameter, shape, volume, and electric field inside the pore leads to uncertainty in quantitative resistive pulse experiments that aim to characterize translocating particles or molecules.…”

Can Nanofluidic Chemical Release Enable Fast, High Resolution Neurotransmitter-Based Neurostimulation?

“…Long-term applications will require sufficient stability of nanopores' structure and surface chemistry. Silicon nitride pores widen due to decomposition and dissolution (Rollings et al, 2015 ). In biological environments, protein adsorption presents further challenges (Yusko et al, 2011 ).…”

A tip-attached tuning fork sensor for the control of DNA translocation through a nanopore

“…The geometry and thickness of fabricated nanopores (cavities) were previously investigated in detail. 21,22 Briefly, Energy Filtered TEM (EFTEM) was used to estimate the membrane thickness profile by calculating t = λ ln (I tot /I 0 ), where t is the membrane thickness, I 0 is the energy filtered zero loss TEM image, and I tot is the unfiltered TEM image of a nanopore and its nearby area, λ is the mean free path of the beam and is a constant. The mean free path λ is calculated empirically by measuring the thickness of the same silicon nitride membrane using a standard optical reflectometer with errors of approximately 10%.…”

“…Later, a nanometer-sized pore was drilled in the cavity region with a 300 keV electron beam in transmission electron microscopy (TEM) (FEI, Titan). 22 Briefly, once the nanopore chip sample was loaded inside a high current density field emission TEM system, such as the modern FEI Tecnai or FEI Titan at the University of Arkansas, we first located the FIB milled cavity region, then we used the condensing system to converge the beam with a full width at half maximum intensity of a few nanometers. The user observed the image of the membrane until a nanopore broke through and reached the desired size.…”