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Belgian Nanoelectronics Firm Imec Developing Solid State Nanopore Technology for DNA Analysis

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SAN FRANCISCO (GenomeWeb) – Imec, a nanoelectronics and digital technology company based in Belgium, is harnessing its expertise in semiconductor manufacturing in order to move into the solid-state nanopore single-molecule sensing and DNA sequencing field.

At last week's Advances in Genome Biology and Technology meeting in Marco Island, Florida, Pol Van Dorpe, a principal member of the technical staff at Imec, described in a presentation and subsequent interview the technology the company has been developing, which combines a silicon wafer with an array of nanoslits with Raman spectroscopy to identify single molecules.

The Imec team and its collaborators at the Catholic University of Leuven also described its technology in an article in Nature Communications last year.

Imec's focus is on microchip development, and it has applied its expertise to the life sciences field, working with companies to help develop technologies such as microfluidics and PCR on a chip. It worked with Pacific Biosciences, for instance, to design its SMRT chip for the Sequel instrument. The company, however, also has its own R&D division, one focus of which has been the development of nanopore-related technologies.

Van Dorpe said that aside from the Raman spectroscopy-based nanoslit technology, the firm is working on other nanopore technologies, including one that would couple micro transistors with a nanopore for DNA sequencing.

He was quick to note that the spectroscopy detection method is not yet a sequencing technology but added that it could eventually get there. However, the main issue that is not solved is the ability to control translocation of a DNA molecule through the pore. "We don't have the enzymatic approaches," he said, which Oxford Nanopore Technologies, for example, employs to slow down DNA traveling through its pore. Van Dorpe added that if Imec were to commercialize the technology, it would most likely be through a partnership with a company with expertise in proteins and enzymatic processes.

Overall, controlling DNA translocation has continued to hamper development of solid-state nanopores as DNA tends to fly through the pore too fast to be detected.

Van Dorpe said one nearer-term application would be to detect epigenetic DNA modifications, since a methylated molecule would have a different signature than a non-methylated one. In addition, he said, the company would also look to use the technology for single-molecule sensing, for things like protein detection, for instance.

While most nanopore detection methods rely on electronic readouts, he said, Imec is developing an optical approach, making use of Raman spectroscopy to read molecules directly.

Standard Raman spectroscopy relies on identifying molecules through detecting differences in vibrations of the molecule when it is hit with a laser.

However, standard Raman spectroscopy is "too weak for single-molecule resolution," so the researchers instead turned to surface-enhanced Raman spectroscopy, or SERS. To enable SERS, the researchers relied on Imec's expertise in nanoscale microfluidics and fabrication to design a chip with nanoslits, rather than pores, that are less than 10 nanometers wide and around 1 micron long. The nanoslits concentrate the light, creating a hotspot within the slit, to yield single-molecule resolution SERS.

To test its ability to detect DNA molecules, the researchers first created a SERS library of nucleotides by measuring the resulting signal from a high concentration nucleotides of each type, confirming that the different nucleotides can be distinguished by their signal.

To further demonstrate that the technique had single-molecule sensitivity, Van Dorpe said the researchers relied on a bi-analyte strategy, where they analyzed two molecules with distinct Raman spectra but that are chemically similar. The team detected distinct spectra elicited from the two molecules, verifying that the signal detected was indeed a single-molecule signal.

Then, to see whether the device could measure bases within a strand of DNA, the researchers created a poly-A oligonucleotide with a cytosine and guanine at the end.

"There's a clear appearance of peaks attributable to the adjacent C and G bases at different moments in time," Van Dorpe said. 

The team plans to continue to develop the technology, he said, but will likely develop it as a sensing device rather than a sequencing instrument, with possible applications for "direct fingerprinting of epigenetic modification."

To enable sequencing, "there's still quite a bit of work remaining," Van Dorpe said, noting that the challenges include figuring out how to control the DNA through the nanoslits, so that individual bases can be read, and designing the system to spatially overlap the hotspot and nanoslit.

"We brought it to this level to see who's interested in the technique," Van Dorpe said, and "to see what's the best way to take it forward."

He also noted that Imec is continuing to work on other solid-state nanopore technologies. For example, researchers have designed nanoscale transistors that could be coupled with nanopores to amplify the signal of DNA translocating through a pore, which could potentially eliminate the need for enzymes to slow the DNA down. "We hope to have data on this next year," he added.

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