Porous Zero-Mode Waveguides for Picogram-Level DNA Capture

Our plain-English summary of Porous Zero-Mode Waveguides for Picogram-Level DNA Capture, by V. Jadhav, D.P. Hoogerheide, J. Korlach, et al (Nano Letters, 2019).

The study

• Authors: V. Jadhav, D.P. Hoogerheide, J. Korlach, M. Wanunu
• Journal: Nano Letters
• Published: 2019;19(2):921-929
• Cited by: 19 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

We have recently shown that nanopore zero-mode waveguides are effective tools for capturing picogram levels of long DNA fragments for single-molecule DNA sequencing. Despite these key advantages, the manufacturing of large arrays is not practical due to the need for serial nanopore fabrication. To overcome this challenge, we have developed an approach for the wafer-scale fabrication of waveguide arrays on low-cost porous membranes, which are deposited using molecular-layer deposition. The membrane at each waveguide base contains a network of serpentine pores that allows for efficient electrophoretic DNA capture at picogram levels while eliminating the need for prohibitive serial pore milling. Here, we show that the loading efficiency of these porous waveguides is up to 2 orders of magnitude greater than their nanopore predecessors. This new device facilitates the scaling-up of the process, greatly reducing the cost and effort of manufacturing. Furthermore, the porous zero-mode waveguides can be used for applications that benefit from low-input single-molecule real-time sequencing.

In plain English

This article is not about asbestos or human health. It is a laboratory engineering study of a device used in DNA sequencing. The authors built very small wells, called zero-mode waveguides, on a thin porous aluminum oxide-based film called alucone. Earlier versions needed a tiny hole, a nanopore, made one at a time under each well, which the authors described as prohibitively expensive and impractical for large arrays. Neutron measurements found the film's water-accessible porosity to be 28%. With no voltage applied, almost no dye-labeled DNA was drawn into the wells. With voltage applied, DNA was drawn in and held. The authors tested DNA lengths from 500 base pairs to 48 kilobase pairs at 200 mV. They reported capture rates at least 1 order of magnitude higher (2 for shorter molecules) than data they had previously reported for their nanopore-based devices. Steady capture lasted more than 8 hours. The authors cautioned that the opposite length trends seen in the two devices may be somewhat skewed by how each device holds DNA. The authors concluded that the porous devices allow efficient loading from small input quantities and low-cost fabrication at the wafer scale.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: laboratory device-fabrication and experimental study (nanotechnology); not a medical or epidemiological study
• Who was studied: No people or animals; the study used fabricated porous zero-mode waveguide chips (for example a 21 × 8 array) and dye-labeled DNA fragments from 500 bp to 48 kbp
• Exposure: Not applicable: no asbestos or other human exposure was studied. The experimental condition was an applied voltage (70 mV and 200 mV) used to draw DNA into the devices.
• Main results:
  • The water-accessible porosity of the alucone film measured by neutron reflectometry was 28%
  • In the porous waveguides, no activity was seen without voltage, although DNA capture was observed over time in a few waveguides; applying 70 mV drew individual DNA molecules into the waveguides
  • Porous waveguides showed at least 1 order of magnitude (2 for shorter molecules) higher capture rate than the authors' previously reported nanopore waveguides, across all DNA lengths tested
  • Steady DNA capture was observed for more than 8 hours
  • Average conductance of the porous waveguide chip after the experiment was 0.20 ± 0.09 μS/μm2
• The authors' conclusion: The authors concluded that they had demonstrated second-generation waveguide devices with a porous membrane at the base of each well that load single molecules efficiently from small input quantities, are stable for more than 1 day, and can be fabricated at low cost at the wafer scale
• Limitations the authors state:
  • The authors stated that the opposite DNA-length trends seen in the nanopore and porous devices may be somewhat skewed because the two devices handle captured DNA differently
  • The authors stated that the nonlinear current-voltage curve above 100 mV suggests concentration polarization, which limits ion transport at higher voltages

Topics

The National Library of Medicine indexes this study under subjects our site covers: Chrysotile.

Medical terms in this study, explained in our Lexicon: Deposition, Serpentine Group.

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