Interfacing solid-state nanopores with gel media to slow DNA translocations.

We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude.

Kinetics of nanopore fabrication during controlled breakdown of dielectric membranes in solution.

Nanopore fabrication by controlled breakdown (CBD) overcomes many of the challenges of traditional nanofabrication techniques, by reliably forming solid-state nanopores sub-2 nm in size in a low-cost and scalable way for nucleic acid analysis applications. Herein, the breakdown kinetics of thin dielectric membranes immersed in a liquid environment are investigated in order to gain deeper insights into the mechanism of solid-state nanopore formation by high electric fields. For various fabrication conditions, we demonstrate that nanopore fabrication time is Weibull-distributed, in support of the hypothesis that the fabrication mechanism is a stochastic process governed by the probability of forming a connected path across the membrane (i.

Nanopore fabrication by controlled dielectric breakdown.

Nanofabrication techniques for achieving dimensional control at the nanometer scale are generally equipment-intensive and time-consuming. The use of energetic beams of electrons or ions has placed the fabrication of nanopores in thin solid-state membranes within reach of some academic laboratories, yet these tools are not accessible to many researchers and are poorly suited for mass-production. Here we describe a fast and simple approach for fabricating a single nanopore down to 2-nm in size with sub-nm precision, directly in solution, by controlling dielectric breakdown at the nanoscale.

Automated fabrication of 2-nm solid-state nanopores for nucleic acid analysis.

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.

Fine-tuning the size and minimizing the noise of solid-state nanopores.

Solid-state nanopores have emerged as a versatile tool for the characterization of single biomolecules such as nucleic acids and proteins. However, the creation of a nanopore in a thin insulating membrane remains challenging. Fabrication methods involving specialized focused electron beam systems can produce well-defined nanopores, but yield of reliable and low-noise nanopores in commercially available membranes remains low and size control is nontrivial.

Precise control of the size and noise of solid-state nanopores using high electric fields.

We present a methodology for preparing silicon nitride nanopores that provides in situ control of size with sub-nanometer precision while simultaneously reducing electrical noise by up to three orders of magnitude through the cyclic application of high electric fields in an aqueous environment. Over 90% of nanopores treated with this technique display desirable noise characteristics and readily exhibit translocation of double-stranded DNA molecules. Furthermore, previously used nanopores with degraded electrical properties can be rejuvenated and used for further single-molecule experiments.