By combining nanopore technology with scanning ion conductance microscopy for the first time, EPFL researchers have achieved near-perfect control over the manipulation of individual molecules, allowing them to be identified and characterized with unprecedented precision. Credit: Samuel Leitão / EPFL
Aleksandra
Radenovic, head of the Laboratory of Nanoscale Biology in the School of
Engineering, has worked for years to improve nanopore technology, which
involves passing a molecule like DNA through a tiny pore in a membrane to
measure an ionic current. Scientists can determine DNA's sequence of
nucleotides—which encodes genetic information—by analyzing how each one
perturbs this current as it passes through. The research has been published in Nature Nanotechnology.
Currently, the passage of molecules
through a nanopore and the timing of their analysis are influenced
by random physical forces, and the rapid movement of molecules makes achieving
high analytical accuracy challenging. Radenovic has previously addressed these
issues with optical tweezers and viscous
liquids. Now, a
collaboration with Georg Fantner and his team in the Laboratory for Bio- and
Nano-Instrumentation at EPFL has yielded the advancement she's been looking
for—with results that could go far beyond DNA.
"We have combined the sensitivity
of nanopores with the precision of scanning ion conductance microscopy (SICM),
allowing us to lock onto specific molecules and locations and control how fast
they move. This exquisite control could help fill a big gap in the field,"
Radenovic says. The researchers achieved this control using a repurposed
state-of-the-art scanning ion conductance microscope, recently developed at the
Lab for Bio- and Nano-Instrumentation.
By combining nanopore technology with scanning
ion conductance microscopy for the first time, EPFL researchers have achieved
near-perfect control over the manipulation of individual molecules, allowing
them to be identified and characterized with unprecedented precision. Credit:
Samuel Leitão / EPFL
Improving sensing precision by two orders of magnitude
The serendipitous collaboration
between the labs was catalyzed by Ph.D. student Samuel Leitão. His research
focuses on SICM, in which variations in the ionic current flowing through a
probe tip are used to produce high-resolution 3D image data. For his Ph.D.,
Leitão developed and applied SICM technology to the imaging of nanoscale
cell structures, using a glass nanopore as the probe. In this new work, the team applied a
SICM probe's precision to moving molecules through a nanopore, rather than
letting them diffuse through randomly.
Dubbed scanning ion conductance
spectroscopy (SICS), the innovation slows molecule transit through the
nanopore, allowing thousands of consecutive readings to be taken of the same
molecule, and even of different locations on the molecule. The ability to
control transit speed and average multiple readings of the same molecule has
resulted in an increase in signal-to-noise ratio of two orders of magnitude
compared to conventional methods.
"What's particularly exciting
is that this increased detection capability with SICS may be transferable to
other solid-state and biological nanopore methods, which could significantly
improve diagnostic and sequencing applications," Leitão says.
Fantner summarizes the logic of the
approach with an automotive analogy: "Imagine you are watching cars drive
back and forth as you stand in front of a window. It's a lot easier to read
their license plate numbers if the cars slow down and drive by
repeatedly," he says. "We also get to decide if we want to measure
1,000 different molecules each one time or the same molecule 1,000 times, which
represents a real paradigm shift in the field."
This precision and versatility mean
that the approach could be applied to molecules beyond DNA, such as protein building blocks
called peptides, which could help advance proteomics as well as biomedical
and clinical research.
"Finding a solution for sequencing peptides has been a significant challenge due to the complexity of their 'license plates,' which are made up of 20 characters (amino acids) as opposed to DNA's four nucleotides," says Radenovic. "For me, the most exciting hope is that this new control might open an easier path ahead to peptide sequencing."
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