Graphene Comes to Nanopore Gene Sequencing

Graphene is thin enough to fit in between each base of a DNA molecule, so it could solve some of nanopore gene sequencing's problems

2 min read
Graphene Comes to Nanopore Gene Sequencing

Nanopore sequencing—the ability to sequence a strand of DNA by reading its electronic signature as it slithers through a nanoscale pore in a membrane— has always held great promise, but it has been frustratingly difficult to realize its full potential. There have been attempts to boost the faint signal produced as the DNA passes through the nanopore. Other research has aimed to slow the speed at which the DNA passes through the nanopore to improve the measurement. Some researchers have even created a molecular motor that doesn’t just slow the DNA down but controls it’s movement through the nanopore.

Now researchers at the Ecole Polytechnique Fédérale de Lausanne (EPFL) in Switzerland have turned to the wonder material graphene as the membrane.

The original technique on which this latest iteration of nanopore sequencing is based suffered from the nanopore frequently clogging up as well as a general lack of precision in the measurements.

“We thought that we would be able to solve these problems by creating a membrane as thin as possible while maintaining the orifice’s strength”, said Aleksandra Radenovic from the Laboratory of Nanoscale Biology at EPFL in a press release.

The EPFL research, which was published in the journal Nature Nanotechnology (“Detecting the translocation of DNA through a nanopore using graphene nanoribbons”),  showed that the typical insulating membrane that is used nanopore schemes is as thick as 15 DNA bases—the chemical rungs of DNA's ladder-like helix. But graphene is only 0.335 nm thick, which is equal to the spacing between two bases in a DNA chain, making it possible to individually analyze the passage of the DNA bases as the squiggle through the nanopore.

While the researchers believe that graphene will ultimately lead to a higher precision nanopore sequencing technique, the speed at which the DNA molecule pass through the nanopore remains a problem. In only 5 milliseconds 50 000 DNA bases can pass through. So the signal given off by the DNA passing through the pore is too faint to read.

“However, the possibility of detecting the passage of DNA with graphene nanoribbons is a breakthrough as well as a significant opportunity”, added Radenovic in the release.

Illustration: EPFL

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This CAD Program Can Design New Organisms

Genetic engineers have a powerful new tool to write and edit DNA code

11 min read
A photo showing machinery in a lab

Foundries such as the Edinburgh Genome Foundry assemble fragments of synthetic DNA and send them to labs for testing in cells.

Edinburgh Genome Foundry, University of Edinburgh

In the next decade, medical science may finally advance cures for some of the most complex diseases that plague humanity. Many diseases are caused by mutations in the human genome, which can either be inherited from our parents (such as in cystic fibrosis), or acquired during life, such as most types of cancer. For some of these conditions, medical researchers have identified the exact mutations that lead to disease; but in many more, they're still seeking answers. And without understanding the cause of a problem, it's pretty tough to find a cure.

We believe that a key enabling technology in this quest is a computer-aided design (CAD) program for genome editing, which our organization is launching this week at the Genome Project-write (GP-write) conference.

With this CAD program, medical researchers will be able to quickly design hundreds of different genomes with any combination of mutations and send the genetic code to a company that manufactures strings of DNA. Those fragments of synthesized DNA can then be sent to a foundry for assembly, and finally to a lab where the designed genomes can be tested in cells. Based on how the cells grow, researchers can use the CAD program to iterate with a new batch of redesigned genomes, sharing data for collaborative efforts. Enabling fast redesign of thousands of variants can only be achieved through automation; at that scale, researchers just might identify the combinations of mutations that are causing genetic diseases. This is the first critical R&D step toward finding cures.

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