Kinked nanopores enable easier DNA sequencing

13 August 2010

A new technique for slowing down the passage of DNA through nanopores by putting a kink in them will enable better DNA sequencing.

Nanopores are tiny tunnels sculpted from silicon dioxide that are slightly wider than a molecule of DNA. They are used as sensors to detect and characterize DNA, RNA and proteins as they pass through the tunnels. But these materials shoot through so rapidly that sequencing the DNA is a problem.

A team led by Sandia National Laboratories in the US has used self-assembly techniques to fabricate kinked nanopores. Combined with atomic-layer deposition to modify the chemical characteristics of the nanopores, they achieved a fivefold slowdown in the voltage-driven translocation speeds critically needed in DNA sequencing. The research was reported in the August 2010 issue of Nature Materials [1].

“By control of pore size, length, shape and composition,” says lead researcher Jeff Brinker, “we capture the main functional behaviours of protein pores in our solid-state nanopore system.” The importance of a fivefold slowdown in this kind of work, Brinker says, is large.

Also of note is the technique’s capability to separate single- and double-stranded DNA in an array format. “There are promising DNA sequencing technologies that require this,” says Brinker.

The idea of using synthetic solid-state nanopores as single-molecule sensors for detection and characterization of DNA and its sister materials is currently under intensive investigation by researchers around the world. The thrust was inspired by the exquisite selectivity and flux demonstrated by natural biological channels. Researchers hope to emulate these behaviours by creating more robust synthetic materials more readily integrated into practical devices.

Current procedures align the formation of nominally cylindrical or conical pores at right angles to a membrane surface. These are less capable of significantly slowing the passage of DNA than the kinked nanopores.

“We had a pretty simple idea,” Brinker says. “We use the self-assembly approaches we pioneered to make ultrathin membranes with ordered arrays of about 3-nanometer diameter pores. We then further tune the pore size via an atomic-layer deposition process we invented. This allows us to control the pore diameter and surface chemistry at the subnanometer scale. Compared to other solid state nanopores developed to date, our system combines finer control of pore size with the development of a kinked pore pathway. In combination, these allow slowing down the DNA velocity.”


1. DNA translocation through an array of kinked nanopores. Zhu Chen, Yingbing Jiang, Darren R. Dunphy, David P. Adams, Carter Hodges, Nanguo Liu, Nan Zhang, George Xomeritakis, Xiaozhong Jin, N. R. Aluru, Steven J. Gaik, Hugh W. Hillhouse & C. Jeffrey Brinker. Nature Materials, August 2010, Volume 9 No 8, 667-675. doi:10.1038/nmat2805


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