New Nanopore Method Achieves Near-Perfect Control of Individual DNA Molecules


Aleksandra Radenovic, head of the Laboratory of Nanoscale Biology in the School of Engineering, has been working for years to improve nanopore technology, which involves passing molecules such as DNA through tiny pores in membranes to measure ionic currents. Scientists can determine the nucleotide sequence of DNA – which encodes genetic information – by analyzing how each nucleotide disrupts this current as it passes through it. This research has been published today in Nature Nanotechnology.

Currently, the trajectory of molecules through the nanopores and their analysis time are affected by random physical forces, and the fast movement of molecules makes achieving high analytical accuracy a challenge. Radenovic has previously overcome this problem with optical tweezers and viscous liquids. Now, a collaboration with Georg Fantner and his team at the Laboratory for Bio- and Nano-Instrumentation at EPFL has produced the advancement he was looking for – with results that go far beyond DNA.

“We have combined the sensitivity of nanopores with the scanning precision of ion conductance microscopy (SICM), allowing us to lock onto specific molecules and locations and control how fast they move. This incredible control can help fill big gaps on the pitch.” Radenovic said. The researchers achieved this control using a state-of-the-art scanning ion conductance microscope, recently developed in the Lab for Bio and Nano Instruments.

Increases Sensing Precision by Two Orders of Magnitude

The serendipitous collaboration between the laboratories was catalyzed by PhD student Samuel Leitão. His research focuses on SICM, in which variations in ionic current flowing through a probe tip are used to generate high-resolution 3D image data. For his PhD, Leitão developed and applied SICM technology to imaging nanoscale cell structures, using glass nanopores as probes. In this new work, the team applied the precision of the SICM probe to move molecules through the nanopores, rather than allowing them to scatter randomly.

Dubbed scanning ion conductance spectroscopy (SICS), the innovation slows the transit of molecules through the nanopores, allowing thousands of consecutive readings to be taken of the same molecule, and even from different locations on the molecule. The ability to control the transit speed and average multiple reads of the same molecule has resulted in a two-fold increase in signal-to-noise ratio compared to conventional methods.

“What’s really exciting is that this increased detection capability with SICS is transferable to other solid nanopore methods and biologics, which could significantly improve diagnostic and sequencing applications,” said the pig.

Fantner summarizes the logic of the approach with an automotive analogy: “Imagine watching the car go back and forth as you stand in front of the window. It’s much easier to read the license plate number if the car slows down and accelerates repeatedly,” he says. “We also had to decide whether we wanted to measure 1,000 different molecules each time or the same molecule 1,000 times, which is a real paradigm shift in the field.”

This precision and versatility mean that the approach can be applied to molecules beyond DNA, such as the building blocks of proteins called peptides, which can help advance proteomics as well as biomedical and clinical research.

“Finding solutions to sequence peptides has been a significant challenge due to the complexity of their “licence plates”, which consist of 20 characters (amino acids) as opposed to four nucleotides of DNA,” Radenovic said. “For me, the most exciting hope is that this new control could pave an easier path to peptide sequencing.”



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