‘DNA Translocation through Graphene Nanopores’ (published online in Nano Letters), reports a novel technique to fabricate tiny holes in a layer of graphene (a carbon layer with a thickness of only 1 atom) that managed to detect the motion of individual DNA molecules that travel through such a hole.

There is a worldwide race to develop fast, low-cost DNA sequencing strategies to read off the content of our genome. Particularly promising for the next generation of sequencing are devices that measure on single molecules. A single DNA molecule from one human cell (3 billion bases, 1 meter long if you would stretch it from head to tail) to be read – base per base – in real time while sliding between two of your fingers.

Postdoc Dr. Gregory Schneider in the group of professor Cees Dekker and colleagues from the Kavli Institute of Nanoscience have in mind. They now demonstrated a first step in that direction: to slide a single molecule of DNA through a tiny nanoscale hole made in the thinnest membrane that nature can offer, a 1-atom thin layer of graphene.

In this research, graphene is used because of that special property that makes single-atom-thin monolayers of graphene. The distance between two bases in DNA is very small, about half a nanometer, and to read off each base along the DNA, needs a recorder smaller than that half nanometer which is why atomically thin graphene membranes are crucial.

What Schneider and coworkers did was to fabricate a nanopore – in the graphene membrane, which represents the ideal recorder. They showed that single molecules of DNA in water can be pulled through such a graphene nanopore and each DNA molecule can be detected passing through the pore.

The detection technique is simple: upon applying an electrical voltage across the nanopore, ions in the solution start to flow through the hole and a current is detected. This current gets smaller whenever a DNA molecule enters the nanopore and partly blocks the ions flow. Each single DNA molecule that slides through the pore is detected by this current drop.

The DNA moves base per base through the nanopore. With atomically thin graphene nanopore there exists in principle the potential for reading off the DNA sequence, base per base. A number of groups worldwide have been trying to realise graphene nanopores. Schneider et al are the first to report their results.

DNA translocation through nanopores has been developed by Dekker lab and others, using SiN membranes. Graphene nanopores offer new opportunities – as well as sequencing. Since graphene, unlike SiN, is an excellent conductor, a next step is using the intrinsic conductive properties of graphene and a range of opportunities for scientific sensors and applications.

Graphene's switch on DNA fluorescence

 Illustration of how fluorescent-tagged DNA interacts with functionalised graphene. Both single-stranded DNA (a) and double-stranded DNA (b) are adsorbed onto a graphene surface, but the interaction is stronger with ssDNA, causing fluorescence on the ssDNA to darken more. (c) A complimentary DNA nears the ssDNA and causes the adsorbed ssDNA to detach from the graphene surface. (d) DNA adsorbed onto graphene is protected from being broken down. Implications are for future use in biosensors and drug delivery.

Zhiwen Tang, Yuehe Lin and colleagues from both Pacific Northwest National Lab  and Princeton University built nanostructures of graphene and DNA. They attached a fluorescent molecule to the DNA to track the interaction.

Tests showed that the fluorescence dimmed significantly when single-stranded DNA rested on graphene, but double-stranded DNA only darkened slightly - indicating that single-stranded DNA had a stronger interaction with graphene than its double-stranded cousin.

The researchers then examined whether they could take advantage of the difference in fluorescence and binding. Adding complementary DNA to single-stranded DNA-graphene structures, finds the fluorescence glowed anew.It suggested the two DNAs intertwined and left the graphene surface as a new molecule.

DNA's ability to turns its fluorescent light switch on and off when near graphene could be used to create a biosensor, the researchers propose. Possible applications for a DNA-graphene biosensor include diagnosing diseases like cancer, detecting toxins in tainted food and detecting pathogens from biological weapons.

Other tests also revealed that single-stranded DNA attached to graphene was less prone to being broken down by enzymes, which makes graphene-DNA structures especially stable. This could lead to drug delivery for gene therapy.

Tang discussed this research and some of its possible applications in medicine, food safety and biodefense. This research was funded by PNNL as part of its Transformations at complex interfaces