Graphene nanopores and nanodevices


Graphene bears great potential for biosensing and DNA sequencing due to its atomically thin membrane and unique electrical properties. Our group was the first to report single DNA translocations through graphene nanopores using ionic current measurements [1]. In these ionic current measurements, a voltage is applied across a graphene membrane with a nanopore, which induces an ionic current through the pore. Negatively charged DNA will be driven through the nanopore while physically blocking the current, resulting in a resistive spike (Fig 1). As graphene is atomically thin it could theoretically provide maximal resolution. However, the noise levels in the ionic current are high [3], and the DNA translocates too fast to read DNA sequence data, which is why new approaches are tested.

Ionic current detection through a nanopore in a graphene membrane

Fig. 1: Top right: The passage of a DNA molecule causes a resistive spike in the measured ionic current through the nanopore [1]. Bottom left: high resolution TEM image of a nanopore in a graphene membrane (scalebar 1nm) [2]. Bottom right: With this approach we can distinguish non-folded, partially folded and folded events [1].

We now aim to explore whether we can develop an ultra-sensitive platform for single-DNA detection by measuring modulations of the inplane current of a graphene nanostructures. We employ STEM for the sculpting of freestanding graphene at high temperatures (600 C) to make nanopores as well as nanostructures like narrow ribbons, while preserving the crystallinity of the graphene due to a self-repair mechanism (Fig. 2).  At beam dwell times of 5 μs the graphene can be imaged without damage, while at dwell times of 10 ms the graphene is sculpted [4][5][6]. By cutting along the right crystal orientation, one can control the edge shape of the graphene nanostructure (zig-zag or armchair) [5].

Crystalline graphene nanostructures through high temperature STEM sculpting

Fig. 2: Top: Illustration of graphene’s self-repair process at high temperature. Approximately 20 seconds after a highly defective area is created by an intense e-beam, the graphene recovers its single-crystallinity [4]. Bottom: HRTEM image of a nanoribbon in monolayer graphene. The overlaid white line indicates an armchair edge [5]. (This work was done in collaboration with Henny Zandbergen, HREM group, Kavli Institute of Nanoscience, Delft)

With our expertise in sculpting crystalline graphene nanostructures we aim to make a highly sensitive DNA detector. A broad range of theoretical studies on graphene nanostructures propose that sequencing should indeed be possible [7]. We currently explore exciting different setups.


Fig. 3: Four new concepts using graphene nanostructures for DNA sequencing [7], based on (a) Ionic current detection through a nanopore in a graphene membrane. (b) Detection of tunnelling current modulations across a graphene nanogap due to the passage of a DNA molecule. (c) Variations in the inplane current through a graphene nanoribbon due to the traversal of a DNA molecule. (d) Changes in the graphene current due to physisorption of DNA bases on to a graphene nanostructure.

Now that we can sculpt graphene nanostructures in a controlled way, the challenge remains to translocate DNA through/along these narrow graphene ribbons and the assembly of functional devices with reasonable yields. It remains to be seen whether an inplane graphene current is modulated by a translocating DNA molecule and whether sequencing with these approach can be realized.

Graphene nanoribbon with a nanopore (credits: H. Zandbergen)

Fig. 4: High-resolution TEM image of a graphene nanoribbon with a nanopore in the middle (credits: Henny Zandbergen, HREM Group, Kavli Institute of Nanoscience)


[1] G.F. Schneider et al., Nano Lett., 10, 3163–3167 (2010)
[2] G.F. Schneider et al., Nature Communications 4, (2013)
[3] S.J. Heerema et al., Nanotechnology 26, 074001, (2015)
[4] B. Song et al. Nano Lett., 11, 2247–2250 (2011)
[5] Q. Xu et al., ACS Nano 7, 1566-1572 (2013)
[6] L. Vicarelli et al., ACS Nano 9 (4), 3428–3435 (2015)
[7] S.J. Heerema and C. Dekker, Nature Nanotechnology, 11, 127–136 (2016)



Due to the extreme thinness and low atomic mobility compared to standard bulk Au electrodes, conducting graphene layers show promise for use in single molecule devices, offering both high resolution and stability during transport measurements. We are developing graphene nanogap electrodes as a means to contact single molecules. Measurement of the tunnelling current across the gap in the presence of a molecule allows the extraction of spectroscopic features from the molecular junction, opening up the potential for sensing and sequencing at single molecule resolution.


Our current work focuses on the fabrication of small graphene nanogaps (<2 nm width) using mechanically controlled break junctions. This approach consists in patterning and suspending a graphene bridge on top of a flexible substrate in a 3-point bending setup. The displacement of the pushing rod bending the substrate induces stretching of the graphene bridge until the breaking point is reached. The advantage of this design is that the spacing can be tuned with sub-nm precision while also enabling the recording of potentially hundreds of breaking traces through breaking/fusing cycles (i.e. bending/unbending of the substrate). Conductance traces can then subsequently be recorded under various conditions of temperature and gas atmosphere, as well as in solution using a customised liquid cell setup.




This project is done in collaboration with the van der Zant lab in Quantum Nanoscience.



Solid-state nanopores are a promising technique for rapid, low cost and accurate sequencing of long DNA fragments. However, a huge challenge in sequencing technology is the high DNA translocation speed through the nanopore which are currently too quick for measurement resolution. A way to arrest or stall this motion is to induce large optical gradients to slow down the DNA. By coupling graphene with a plasmonic antenna, we demonstrate through FDTD simulations that we are able to create highly confined field intensities at the edge of the nanopore for interaction with the DNA. Moreover, these simulations show that the plasmonic response of graphene can be tuned – unlike conventional plasmonic structures with fixed responses after fabrication. Using high-resolution e-beam lithography, we are able to fabricate and experimentally realize these devices for use in DNA translocation experiments.


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The only microscopy technique capable of sub-Angstrom resolution is scanning/transmission electron microscopy (S/TEM). We use advanced TEM techniques to visualize extremely small biological molecules such as DNA. Two-dimensional (2D) DNA origami is an excellent microscopy test object as it features the same scattering properties as double stranded DNA while it comes with a bigger and defined size, which helps the observation and investigation (panel a). Panel b depicts a liquid-cell AFM image of these structures after folding and purification. When the origami plates are deposited on carbon membranes (panel c), one can obtain a nice STEM image with all the features in the computer design such as the smaller cavity and the dsDNA loop at the bottom of the plates.

Graphene gained an interest in the TEM community as a support substrate because it can be as thin as one carbon atom, which provides the lowest cross-section for elastic and inelastic scattering. Can graphene also facilitate the imaging of DNA with TEM (panel d)? Despite its promises, we observed distorted DNA origami nanoplates on graphene (panel e). However, after non-covalent functionalization of the graphene, likely by preventing π-π interaction of the DNA bases with graphene, we can observe less distorted origami plate (panel d). In addition, we are exploring different combinations of substrates and TEM techniques to improve the imaging of DNA naostructures, both in dry and wet conditions.



Related publication:

  1. Kabiri, A.N. Ananth, J. van der Torre, A. Katan, J.-Y. Hong, S. Malladi, J. Kong, H. Zandbergen, C. Dekker. Small. Submitted

This project is done in collaboration with the High Resolution Microscopy Group (Henny Zandbergen) at Quantum Nanoscience.