Aleksandra Radenovic, director of Engineering’s Nanoscale Biology Laboratory, has worked for several years to improve nanopore technology, which involves passing molecules such as DNA through small holes (Researchers control individual molecules for precise detection) in the membrane to measure current ions. Scientists can determine the nucleotide sequence of DNA – which encodes genetic information – by measuring how each individual disrupts the current as it passes.
Currently, the passage of molecules through the nanopore and the time of their analysis is affected by random physical forces, and the rapid movement of molecules makes it difficult to reach the limit of analysis. Radenovic has used optical tweezers and viscous liquids to solve these problems before. Now, a collaboration with Georg Fantner and his colleagues at EPFL‘s Laboratory of Bio- and Nano-Instrumentation has produced the breakthrough he was looking for – with results that can go beyond DNA.
“We have combined the sensitivity of nanopores with the precision of ion conductance microscopy (SICM), allowing us to lock in molecules at different locations and control their speed. This excellent control can help fill big gaps on the pitch,” said Radenovic.
The researchers made this observation using a modern ion conductance scanning microscope, which was recently developed at the Bio and Nano-Instrumentation Laboratory. The new method was recently published in Nature Nanotechnology.
The accuracy of the search has improved by two orders of magnitude
Excellent collaboration between laboratories was facilitated by doctoral student Samuel Leitão. His research focuses on SICM, which uses a difference in ion current passing through a probe to produce high-resolution 3D image data. For his PhD, Leitão developed and applied SICM technology to visualize cellular structures at the nanoscale, using glass nanopores as probes. In this new work, the team applied the precision of the SICM probe to move particles through the nanopore, instead of allowing them to diffuse randomly.
Called scanning ion conductance spectroscopy (SICS), the new material accelerates through the nanopore, making it possible to take thousands of readings of a single molecule, and even from different in molecules. The ability to control the transport threshold and average multiple readings of a single molecule led to an increase in the signal-to-noise ratio of two orders of magnitude compared to conventional methods.
“The most exciting thing is that this detection capability in SICS can be transferred to other solid and biological nanopore systems, which can improve the analytical tools and processing methods,” says Leitao. Fantner used the example of a car to sum up the idea of the approach: “Imagine that you are standing in front of the window and watching the car come.
It is easier to read their license plate numbers if the cars slow down more often and pass,” he said. “We can also decide if we want to measure 1,000 different molecules each time or the same molecule 1,000 times, which is really a paradigm shift in the field.”
This brevity and flexibility means that this method can be applied to molecules beyond DNA, such as blocks of proteins called peptides, which can help improve proteomics and biomedical and clinical research.
“Finding a solution for the structure of peptides has been a great challenge due to the complexity of their ‘license’, which consists of 20 letters (amino acids) as opposed to four nucleotides of DNA.”, Radenovic explains. “For me, the most exciting hope is that this new control can open a simpler way for peptide systems.”
Source: EPFL
