Automated Fabrication of 2‐nm Solid‐State Nanopores for Nucleic Acid Analysis

Abstract

We demonstrate the automated and reproducible fabrication of sub-2-nm nanopores in 10-nm thick silicon nitride membranes, through controlled dielectric breakdown in solution. Our results reveal that under the appropriate conditions, nanopores can be fabricated with a size no larger than 2.0 ± 0.5-nm in diameter for a sample of N = 23 nanopores, with an average and standard deviation of 1.3 ± 0.6-nm. The dimensions of these nanopores are confirmed by using individual translocating DNA molecules as molecular rulers. We show that a 2.0-nm and a 2.1-nm diameter nanopore are capable of distinguishing single-stranded DNA versus double-stranded DNA, and that a 2.4-nm diameter nanopore can be used to investigate the overstretching transition in short dsDNA fragments. These results highlight the reliability and precision of the automated fabrication of nanopores via controlled dielectric breakdown, showing great promise for the manufacturing of future nanopore-based technologies.

Nanopore detection of double stranded DNA using a track-etched polycarbonate membrane

“…In addition to the The same phenomena also showed in addition to experimental studies, the entropic barrier also discussed theoretically based on different parameters such as effect of solvent, nanopore size and adsorption [51][52][53]. For our study, an entropic barrier applies to 50-bp DNA molecules to complete a translocation that a threshold voltage above 200 mV would be necessary to drive the DNA through the PC nanopore [41,54]. Figure 8A).…”

MOSAIC: A Modular Single-Molecule Analysis Interface for Decoding Multistate Nanopore Data

“…42 At an applied potential of 400 mV, the mean residence time of dsDNA in the pore is ≈440 μ s, more than an order of magnitude longer than the characteristic time constant of the system ( τ = 10 μ s; B = 100 kHz). Both algorithms produce two distinct peaks in the blockade depth histogram (〈 i 〉/〈 i 0 〉 = 0.070 ± 0.001 and 0.488 ± 0.004).…”

Interfacing solid‐state nanopores with gel media to slow DNA translocations

“…For example, modifications to solid-state nanopores have included adjusting the nanopore diameter to increase friction [58][59][60], modulating the nanopore surface charge with laser light [61], functionalizing the nanopore with hydrogen-bonding molecules [62] or coating it with a lipid bilayer [63], and altering the properties of a pH-responsive organic nanopore coating [64]. Additional methods have been proposed, including local heating of a gold layer surrounding the nanopore to stretch the DNA [65,66] and ratcheting of nucleotide strands through introduction of a third electrode [67,68].…”

“…Note that this nanopore size is chosen to ensure single-file passage of dsDNA, while at the same time avoiding translocations in the friction-dominated regime [58,60]. As shown in Figure 2.2, agarose slows down some of the DNA molecules substantially, by as much as 3 orders of magnitude (from tens of µs to tens of ms), while other DNA molecules pass through the gel with a dwell time similar to that observed in a bare nanopore of similar dimensions.…”