Untangling DNA: Researchers filter the entropy out of nanopore measurements

Posted on Thursday, December 7, 2017

A new revolutionary nanodevice could be a huge step towards personalized medicine – for which truly affordable diagnostic technologies for rapidly and accurately detecting disease biomarkers, at the point of care, are needed.

One thousand times smaller than the diameter of a human hair, a nanopore is a tiny hole that holds huge potential to revolutionize personalized diagnostic medicine. Nanopores can electrically detect single biological molecules like proteins or DNA with exacting precision, and hold the promise of helping to create a new era in the life sciences and medicine where technologies that combine greater sensitivity, speed and point-of-care decentralization will be essential.

However, the potential of nanopore devices for sequencing, genome mapping, and barcoded biomarker detection is currently hindered by the tendency of DNA molecules to get coiled up into a ball before they reach the nanopore. This has the unfortunate effect of producing a cacophony of complicated signals as molecules pass through the nanopore and, without a way to filter the noise from the wide possibility of available molecular conformations, makes it exceedingly difficult to extract useful and precise information. 

Vincent Tabard-Cossa and Kyle Briggs standing in front of the device they created

Researchers at the University of Ottawa, in collaboration with the University of Rochester, have developed a game-changer for nanopore sensing. They have found a clever way to fabricate a nanodevice which overcomes this fundamental problem. Together, they have created a unique two-membrane nanodevice which ‘untangles’ DNA molecules by forcing them to stretch out between two pores, thus filtering the confounding contributions of DNA entropy out of their nanopore signals.

“The nanofiltered nanopore device we created, with essentially two pores in series, reveals fundamental physics of polymer translocation previously hidden in the noise,” says University of Ottawa graduate student Kyle Briggs, first author of the work which will be described in an article published in Nano Letters . “Our work will allow for much more precise measurements of single DNA molecules, enabling important healthcare applications to be developed, such as helping to more accurately detect disease biomarkers.”

Despite being hinted at in theory and simulation work, the link between the possible configurations of each molecule and the way they pass through the pore has eluded experimental verification for years, and was only recently made possible by a ground-breaking innovation at the same lab – a revolutionary nanofabrication technique called Controlled Breakdown, or CBD.

“Nanopores are traditionally made by drilling with beams of high-energy electrons or ions. But this line of sight approach cannot practically be used on a two-membrane structure, since the presence of the second membrane would interfere with the drilling process,” explains Vincent Tabard-Cossa, who heads the T.-Cossa LAB located in the Center for Interdisciplinary Nanophysics at the University of Ottawa, where Briggs and other researchers are pushing to develop and translate such discoveries into new tools for the life and health sciences.

“CBD fabricates the sensing nanopore by essentially causing a nano-scale spark to perforate a thin membrane,” he explains. “Since it is possible to precisely control which layer of the device this happens to without needing line-of-sight access to the pore fabrication site, it is now possible to fabricate a nanopore within an embedded structure using nothing more than a couple of 9V batteries in place of the million-dollar electron microscope that was used before.”

The nanodevice that the team of reseachers created

Created in collaboration PhD student Greg Madejski in the lab of James McGrath, from the University of Rochester, the resulting novel device is comprised of three ultrathin layers: a nanoporous silicon nitride membrane which serves as a pre-filter, a biosensor membrane with a single nanopore, and a spacer layer that separates these by only 200 nm. The arrangement creates a nanocavity between the membranes filled with less than a femtoliter of fluid—or about a million times smaller than the tiniest drops of rain. The principle of operation of the device is shown in this video.The group of Hendrick de Haan at the University of Ontario Institute of Technology also provided coarse grained simulation results to support the interpretation of the experimental results.

Other groups have failed at fabricating two-pores in series devices using conventional nanofabrication techniques. The University of Ottawa’s revolutionary CBD nanofabrication technique used to make the sensing nanopore (the single hole in the lower membrane), combined with the ultra-thin nanoporous membrane (the nanofilter on top) developed at the University of Rochester, was key to being able to fabricate such a complex nanodevice with relative ease and high yield.

 “There is a big need to fabricate tiny holes on the cheap, especially if nanopore technologies are going to disrupt the field of molecular diagnostics,” explains Briggs. “With CBD, we’ve demonstrated the only commercially viable method of precisely fabricating solid-state nanopores.”

 “Together with techniques for controlling the motion of DNA, as shown in this work, our lab is tackling two of the most pressing issues on the path to realizing the full potential of solid-state nanopore sensing.”

Media inquiries

Karyne Vienneau
Media Relations Officer
University of Ottawa

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