DNA Translocation through Graphene Nanopores

Abstract

In the past few years, nanopores have emerged as a new powerful tool to interrogate single molecules. They have been successfully used to rapidly characterize biopolymers like DNA 3,4 , RNA 5 , as well as DNA-ligand complexes 6 and local protein structures along DNA 7 at the single-molecule level. A key driving force for nanopore research in the past decade has been the prospect of DNA sequencing. However, a major roadblock for achieving high-resolution DNA sequencing with pores is the finite length of the channel constituting the pore (Fig. 1A). In a long nanopore, the current blockade resulting from DNA translocation is due to a large number of bases (for typical devices ~10-100 bases) present in the pore. Here, we demonstrate that this limitation can be overcome by realizing an ultimately thin nanopore in a graphene monolayer. We obtain single-layer graphene (Fig. 1B) by mechanical exfoliation from graphite on SiO 2 13 . Monolayer graphene is identified by its particular optical contrast 14 in the optical microscope and by Raman measurements (Fig. 1C). At ~ 1590 cm -1 , we measure the socalled G resonance peak and at ~2690 cm -1 the 2D resonance peak. In the case of multilayer graphene, the 2D resonance peak splits off in multiple peaks in contrast to monolayer graphene which has a very sharp single resonance peak. In this way, we are well able to distinguish single-layer graphene from multilayer graphene 15 .Next we select a monolayer of graphene and transfer it onto a SiN support membrane with a 5 micron sized hole 16 by use of our recently developed 'wedging transfer' technique 17 . This transfer procedure is straightforward: flakes can be overlaid to support membranes in less than an hour. Briefly, a hydrophobic polymer is spun onto a hydrophilic substrate (here plasma-oxidized SiO 2 ) with graphene flakes, and wedged off the substrate by sliding it at an angle in water. Graphene flakes are peeled off the SiO 2 along with the -4 -polymer. The polymer is then floating on the water surface, located near a target SiN substrate, the water level is lowered, and the flakes are positioned onto the SiN membrane with micrometer lateral precision. In the final step the polymer is dissolved.We then drill a nanopore into the graphene monolayer using the highly focused electron beam of a transmission electron microscope (TEM). The acceleration voltage is 300 kV, well above the 80-140 kV knock-out voltage for carbon atoms in graphene 18 (see Methods).Drilling the holes by TEM is a robust well-reproducible procedure (we drilled 31 holes with diameters ranging from 2 to 40 nm, in monolayer as well as in multilayer graphene; some examples of pores are shown in Fig. 2). Because of the high acceleration voltage of the electron beam, drilling could potentially induce damage to the graphene around the pore. However, electron beam diffraction measurements across the hole ( Fig. 2B and C) confirm the crystallinity of the monolayer surrounding the hole, as evidenced by the well-defined hexagonal diffraction patterns (Fig. 2C).Su...

Janus graphene from asymmetric two-dimensional chemistry

“…Graphene is composed of carbon atoms that are held together by strong covalent bonds, which are theoretically predicted 35 and experimentally confirmed [36][37][38][39][40] to be impermeable to small atoms and molecules as a perfect nanoballoon at room temperature. This is a prerequisite for its bifacially nonsymmetrical modification.…”

“…More importantly, we observed that the functionalities on one side are capable of influencing the chemical reactivity as well as surface wettability of the opposite side, indicative of a communication between X and Y through the mediated single carbon layer. Such novel structures would offer an excellent alternative to study asymmetric chemistry of graphene, control the selfassembly of graphene-based new functional structures 41 and advance the potential applications of graphene functional derivatives as a 2D sensor or actuator for biochemical detection 33,[38][39][40] .…”

Graphene nanodevices for DNA sequencing

“…In 2010, three independent groups published experimental data of double-stranded DNA translocations through graphene nanopores [35] [36] [30]. Their approaches were equivalent: 5-25 nm diameter pores ( Fig.…”

Direct visualization of reversible dynamics in a Si6 cluster embedded in a graphene pore

“…As the molecules translocate they partially block ion flow through the pore, detected as a transient decrease in ionic current. Significant information (diameter, length and size) about DNA molecules was obtained through this translocation technique using graphene pores [9][10][11] .…”