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 .
“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
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
“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.