Dynamic and Electronic Transport Properties of DNA Translocation through Graphene Nanopores

Abstract

Graphene layers have been targeted in the last years as excellent host materials for sensing a remarkable variety of gases and molecules. Such sensing abilities can also benefit other important scientific fields such as medicine and biology. This has automatically led scientists to probe graphene as a potential platform for sequencing DNA strands. In this work, we use robust numerical tools to model the dynamic and electronic properties of molecular sensor devices composed of a graphene nanopore through which DNA molecules are driven by external electric fields. We performed molecular dynamic simulations to determine the relation between the intensity of the electric field and the translocation time spent by the DNA to pass through the pore. Our results reveal that one can have extra control on the DNA passage when four additional graphene layers are deposited on the top of the main graphene platform containing the pore in a 2 × 2 grid arrangement. In addition to the dynamic analysis, we carried electronic transport calculations on realistic pore structures with diameters reaching nanometer scales. The transmission obtained along the graphene sensor at the Fermi level is affected by the presence of the DNA. However, it is rather hard to distinguish the respective nucleobases. This scenario can be significantly altered when the transport is conducted away from the Fermi level of the graphene platform. Under an energy shift, we observed that the graphene pore manifests selectiveness toward DNA nucleobases.

Graphene nanodevices for DNA sequencing

“…Similar results were obtained from various theoretical calculations, where electronic transport was studied using DFT and NEGF for different types of ribbons (width ∼3 nm and pore diameter ∼1.5nm) in the absence and presence of each of the four DNA nucleobases [72][73][74][75][76][77][78][79].…”

“…Base-distinct current variations were found, in the order of ∼1 µA at 100mV bias, much larger than what can be expected for armchair edged ribbons where these edge currents are absent. These results were, however, contradicted by a self-consistent DFT study on zigzag GNRs [75] that showed that the respective bases can only be distinguished when transport is conducted away from the Fermi level. In another interesting study, ribbons with a finite length along the ribbon were compared to quantum point contact structures, which essentially are ribbons in the limit of zero length [76].…”

“…Theoretical studies show that an armchair ribbon will be semiconducting [66][67][68][69] and that a zigzag-edged ribbon is metallic with a current profile that peaks at the edges [66,[69][70][71]. Both armchair and zigzag nanoribbons have been proposed to present promising platforms for DNA sequencing in a large number of theoretical reports [72][73][74][75][76][77][78][79], and experimentalists have begun to explore this approach [80][81][82][83][84][85].…”

Thermally modulated biomolecule transport through nanoconfined channels

“…It is generally believed that the premise of this method is how to obtain proper nanopores and how to design effective fluidic device. Till now, natural nanopores in biomembranes [15,16] and artificial nanopores in inorganic films [17][18][19] are two major types of pores used in this area, while nanopores in polymer membranes obtained by track-etching method also can provide other possible choices [20][21][22][23]. Since the transport of mass and charge in the confined nanochannels, novel phenomena which cannot be observed in the bulk solutions will occur [24][25][26].…”

Graphene/hexagonal boron nitride/graphene nanopore for electrical detection of single molecules

“…[1][2][3][4][5][6][7][8][9] By fabricating nanogaps or nanopores on the graphene sheet and then propelling single molecules to electrophoretically translocate through the gap/pore, information regarding the target molecules can be recorded and used for characterizing the molecules. This information can be either the longitudinal ionic current blockage due to the transient dwelling of molecule in the gap/pore, [2][3][4]9 or the transverse tunneling current through the molecule measured by the electrodes embedded in the pore.…”