The Singapore National Research Foundation has awarded a $3 million fellowship to Slaven Garaj, formerly of the Nanopore Group at Harvard University, to develop a graphene nanopore sequencing device.
Garaj, an assistant professor at the National University of Singapore, told In Sequence that he began setting up his new lab this September at Singapore’s Graphene Research Center.
Garaj said he plans to continue work begun initially with the Harvard Nanopore Group led by Daniel Branton and Jene Golovchenko. The Harvard group published a proof of principle in Nature in 2010 showing that a layer of graphene immersed in ionic solution becomes a trans-electrode with a less than one nanometer effective insulating thickness, making graphene "an ideal substrate for very high-resolution, high-throughput nanopore-based single-molecule detectors."
This fall, the Harvard Nanopore Group also received a grant — $3.6 million from the National Human Genome Research Institute's Advanced DNA Sequencing Technology Program — to develop a scalable graphene nanopore sequencing device that will identify DNA subunits on unlabeled, single-stranded genomic DNA molecules.
According to Garaj, the field is large enough that the initial steps he and the Harvard lab made together should now be able to support multiple paths forward.
Though he declined to detail technical plans for his new lab’s approach, he said the first step will be to "investigate ways of translocating DNA through the graphene pores, and also establish ways to increase the sensitivity either using better graphene, or by chemically modifying graphene."
Garaj said he has had some early talks with potential partners — both academic and potentially commercial — but said he could not discuss any possibilities in detail.
Oxford Nanopore announced in 2011 that it had licensed technology from Harvard University for graphene-based nanopore sequencing. Under the terms of the agreement, the company has exclusive rights to develop and commercialize methods developed in the Harvard Nanopore lab (IS 3/15/2011).
Garaj said he could not comment on whether that agreement would have any impact on his work going forward.
He said his work will expand off the 2010 Nature paper, which demonstrated that "graphene had really remarkable possibilities for DNA sequencing.” For instance, "it's very important to have a sufficient resolution along the molecule so you can detect only one base after another at a time without averaging over multiple bases. So in that respect graphene is really ideal because it is the thinnest material possible," Garaj said.
“What we have demonstrated is that there is a real possibility toward atomic resolution. But we have not seen atomic resolution,” he said.
There is now "a large landscape over where [the research] can go, and at this point each of us are following our intuition on how to proceed. But we have the same goal — to establish a DNA sequencing platform based on the graphene."
The group will have to tackle three main issues. "For one, we have to show that the graphene nanopores have sufficient sensitivity to distinguish between different nucleobases," he said.
Another challenge is controling the passage of the DNA molecule. "Currently with many nanopore sequencing techniques, the DNA molecule is just passing too quickly through a pore," he said.
Finally, more work needs to be done to show that graphene nanopores can offer single-molecule resolution along the length of DNA without averaging over several bases, Garaj said.
Garaj, with his Harvard colleagues, has recently submitted another paper for publication, demonstrating high sensitivity for graphene nanopores. "We didn't show distinction between different nucleobases," he said. "But it indicates that the sensitivity is really large." The study is available ahead of print from the arXiv e-print service.
According to the paper, the group has shown "remarkably large sensitivities (0.5 nA/A) … obtained when the nanopore is tailored to have a diameter close to that of the polymer of interest."
"Our results have been obtained with double-stranded DNA (dsDNA). Smaller graphene nanopores that can be tuned to the diameter of single-stranded DNA (ssDNA) for sequencing have only recently been demonstrated. Our results indicate that nanopore sensors based on such pores will provide excellent resolution and base discrimination, and will be robust competitors to protein nanopores that have recently demonstrated sequencing capability," the group wrote.
According to Garaj, nanopore sequencing does not have a "simple solution." Thus, graphene will be only "one part" of his ultimate plan to develop a nanopore sequencing technology.
Moving forward with his NRF fellowship grant, Garaj said he hopes to gain support and insight through "cross-pollination" with colleagues at Singapore’s Graphene Research Center, who he said represent a "group of excellent researchers addressing different graphene subjects."
Garaj said he is currently building up his lab and hiring researchers.
Though he and the Harvard Nanopore team are both working forward from the same starting point, Garaj stressed that graphene offers wide enough possibilities that the two groups will likely move in different directions going forward.
"I believe the whole landscape can end up really wide, so even if we started from the same point, I'm pretty sure we will go in different directions. I think we are already diverging," he said.