Boosting DNA Recognition Sensitivity of Graphene Nanogaps through

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Boosting DNA Recognition Sensitivity of Graphene Nanogaps through Nitrogen Edge Functionalization Rodrigo G Amorim, Alexandre Reily Rocha, and Ralph H. Scheicher J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.6b04683 • Publication Date (Web): 05 Aug 2016 Downloaded from http://pubs.acs.org on August 7, 2016

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The Journal of Physical Chemistry

Boosting DNA Recognition Sensitivity of Graphene Nanogaps through Nitrogen Edge Functionalization Rodrigo G. Amorim,∗,†,‡ Alexandre R. Rocha,∗,¶ and Ralph H. Scheicher∗,† †Division of Materials Theory, Department of Physics and Astronomy, Box 516, Uppsala University, SE-751 20 Uppsala, Sweden. ‡Departamento de Física, ICEx, Universidade Federal Fluminense, Volta Redonda/RJ, Brazil ¶Instituto de Física Teórica, Universidade Estadual Paulista (UNESP), São Paulo, Brazil. E-mail: [email protected]; [email protected]; [email protected]

Abstract

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One of the challenges for next generation DNA sequencing is to have a robust, stable and reproducible nanodevice. In this work, we propose how to improve the sensing of DNA nucleobase using functionalized graphene nanogap as a solid state device. Two types of edge functionalization namely either hydrogen or nitrogen were considered. We showed that, independent of species involved in the edge passivation, the highest-to-lowest order of the nucleobase transmissions is not altered, but the intensity is affected by several orders of magnitude. Our results show that nitrogen edge tends to p-dope graphene, and most importantly, it contributes with resonance states close to the Fermi level which can be associated with the increased conductance. Finally, the translocation process of nucleobases passing through the nanogap was also investigated by varying their position from certain height (from 3Å to −3Å) with respect to the graphene sheet to show that nitrogenterminated sheets have enhanced sensitivity, as moving the nucleobase by approximately 1 Å reduces the conductance by up to three orders of magnitude.

Physical methods for DNA sequencing offer 1 several advantages over prevalent chemical methods. By avoiding amplification and expensive reagents, so-called physical methods could be significantly less expensive, thus allowing to lower the cost per genome to go below the 1000 USD mark 1 . But equally important is that physical methods allow for orders-of-magnitude longer base read lengths compared to chemical methods, thus making it realistically possible to de novo sequence whole genomes (i.e., without reference to the human genome blueprint) as well as to sequence parts of the genome which are difficult to assess with chemical methods (e.g., due to patterns repeating for longer stretches than the maximum base read length). For this reason, interest in physical methods for DNA sequencing has been growing over the past 15 years or so 2–8 . In particular, nanopores are at the forefront of applications for physical DNA sequencing. 9–12 Recently, nanogaps or nanopores in graphene have been suggested 13 for use in sequencing via transverse electrical current 14,15 because they would offer straightforward single-nucleobase resolution as it is effectively only one atomic layer thick. Due to experimental progress in the applica-

Introduction

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tion of graphene nanopores for DNA translocation 16–19 and more recently even simultaneous detection of DNA translocation through a nanopore in a graphene nanoribbon via both a drop in ionic current and an increase in transverse electrical current 15 , the application of graphene for DNA sequencing is appearing more and more feasible, and theoretical explorations of this system abound 9,10,20–23 . A crucial role is played by the edges of the graphene nanopore or nanogap 24,25 . The nucleotides of DNA interact with the atoms at the edges, which saturate the dangling bonds created when cutting the hexagonal network of carbon atoms. The saturating entities could be hydrogen, OH groups, O atoms, or N atoms. The latter were previously explored for graphene nanopores 21,26–28 and were found to have some favorable properties compared to H-terminated graphene. Recently a route towards functionalizing graphene edges with nitrogen has been obtained 23 . Here we focus on an in-depth understanding of the effect of N-terminated graphene edges in a nanogap and compare with H-termination. To this end, we theoretically study a graphene nanogap as a nanobiodevice to detect single nucleobases: Adenine (A), Cytosine (C), Guanine (G) and Thymine (T). Our goal and the main issue here is how to improve the sensitivity of this device using different edge functionalization. We employed two types of passivation (H and N), and calculated the tunneling conductance across a graphene nanogap - and through the nucleobases. We show that, depending of the edge termination, the system can be either p- or n-doped at the edges, which leads to edge states in the case of nitrogen, and up to five-order-of magnitude increase in conductance simply by changing the edge functionalization. Finally, we also studied the translational process of the nucleobases, i.e., calculated the transmissions for different heights with respect to the graphene gap in order to assess the sensitivity of the device.

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Methodology

The electronic structure and the tunneling transport through the nucleobase (A, C, G and T) were investigated using the setup shown in figure 1(a-b). We considered two semi-infinite graphene sheets with a nanogap in between, and the edges were functionalized with either hydrogen (H) or nitrogen (N). We then positioned the 4 different nucleobases (Figure 1c inside the graphene gap at different heights (in the y = ± 3 Å range relative to the graphene sheet). For electronic structure simulations we employed ab initio Density Functional Theory 29,30 (DFT) calculation as implemented in SIESTA 31 . We used the Gradient Generalized Approximation 32 (PBE-GGA) for the exchange-correlation functional, the valence electrons of Kohn-Sham wave-functions were expanded with a double-ζ polarized (DZP) basis set, and norm-conserving pseudopotentials 33 were used. All structures were fully relaxed using a conjugate gradient (CG) algorithm with residual forces in each component of the atoms smaller than 0.01 eV/Å. This procedure was performed in two steps. First the supercell containing two graphene sheets, and each of the nucleobases were separately relaxed. The C-C graphene gap distance, d, before the relaxation was 13.85 Å(figure 1 a-b), and after the structural relaxation we noted a variation of 3.6 (2.2%) for H (N) edge passivation. Subsequently each of the bases was inserted in the gap and the system was fully relaxed to obtain the pair of distances {d1 , d2 } (as defined in Figure 1d) between the base and either edge of the passivated sheet. The resulting distances are shown in Table S2 of the supplemental material. For the transport calculations the system was divided in three segments: right, and left electrodes and a so-called scattering region that considers a piece of each electrode as a buffer region (as shown in Figure 1d). The problem is solved via the non-equilibrium Green’s functions formalism, 34,35 using Transiesta 34 . A more detailed description of electronic transport can be found elsewhere 34,35 .


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Figure 1: Schematic setup used in the simulations. Graphene nanogap with two distinct edges: a) H; b) N; c) Setup of a nanogap containing a nucleobase, indicating the distances d1 and d2 between the base and each of the edges. d) Nucleobases (Adenine, Cytosine, Guanine and Thymine, respectively).

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Results

This is highlighted in Figure 3, which shows the sensitivity for different edge terminations and nuclebases taking Thymine in H-functionalized gaps as a reference.1 We note that the increase in conductance at the Fermi level for each base between H-terminated edges and its N-terminated counterpart is typically 4 to 5 orders of magnitude. This is also much larger than results reported for other functionalizations such as oxygen, hydroxyl groups, 23 or a nucleobase as an anchor. 12 We also note that the transmission is higher in the case of nitrogen for almost any choice of energy around EF . Finally, the I-V characteristics, calculated within the Buttiker-Landauer formalism 36 also shows significant sensitivity for a wide range of bias windows (Figure S2 of the supplemental material). We also examined the density of states for

The transmittance for each nucleobase placed in the graphene nanogap with either H- or N-functionalization is shown in Figure 2(a-b). For energies in the vicinity of the Fermi energy, for both terminations, the transmittance magnitudes exhibit the same hierarchy, namely G > A > C > T . As expected, the larger purine bases G and A bridge the tunneling gap better than the smaller pyrimidine bases C and T, resulting in the obtained overall order of transmittance amplitudes. Figure 2(c-f) presents a direct comparison of the energy-resolved transmittance curves for each nucleobase when placed in the graphene nanogap functionalized with either H or N. Nitrogen termination is seen to drastically raise the overall transmittance compared to the case of H-functionalization. In particular, the zero bias conductance, i.e., the value of the transmittance at E = EF , is always larger for Nfunctionalization than for H-functionalization.

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We define the sensitivity as S = gx /gref × 100, where gref is the reference conductance chosen as the conductance of a specific nucleotide, and gx corresponds the conductance for any other nucleotide


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Figure 3: Sensitivity at Fermi level of four nucleobases for H- (hashed) and N-functionalized (solid) nanogaps. Thymine in the H-terminated nanogap has the smallest conductance and was taken as a reference.

Figure 5: Charge density for a graphene nanogap with nucleobase in between where left handside panel is for hydrogen, and right is for nitrogen functionalization. The circular insets show zoomed in regions at the frontier between molecule and edge. The colors represent the charge density is given in linear scale going from 0.0 (red) to 1.1 (violet) and e/Bohr3 .

Figure 4: Projected density of states for the four nucleobases in the graphene nanogap. Panels on the left handside column correspond to the graphene nanogap with H functionalization and panels on the right handside column are for N functionalization. The black curve corresponds to the PDOS for all carbon atoms in the device except for the ones closest to the edge, which are shown in purple.

First we note that it is possible to directly correlate the resonances seen in the transmission curves with each of the nucleobases’ electronic states. For instance, analyzing the nature of the transmission peaks for Adenine in graphene functionalized with H (dashed line) in figure 2 c, we note that there are sharp resonances at ∼ -1 eV. As can be seen from the

all four nucleobases in the different functionalized graphene nanogaps. Figure 4 shows the projected density of states (PDOS) onto carbon atoms belonging to graphene, edge atoms (H or N) and the nucleobases.


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PDOS, states originating from the nucleobases are exactly at the same energies of the resonances found on the transmission curves (left panel of figure 4 a). Similar features can be seen for N-terminated nanogaps (right handside column in Figures 2 and 4), albeit they are shifted upwards, and the HOMO for each base remains closer to the Fermi level. This upward shift of the HOMO levels for all nucleobases is the reason the conductance at EF is significantly higher for nitrogen-saturated nanogaps. We note that the crucial difference between hydrogen and nitrogen is the fact that in the latter case, N states are also present at the resonances. This shift brings the lower lying occupied levels closer to EF , and a number of other conductance resonances are observed in Figure 2 in the case of nitrogen. The level alignment, and the enhancement in conductance can be understood from charge transfer occurring between the edges, and the graphene sheets. Upon functionalization, the atomic charge contribution was calculated using the Bader analysis 37 (not shown here), which indicates that the hydrogen atoms tend to be negatively charged, whereas nitrogen becomes p-doped. We also note that the nitrogen atoms on the edges tend to form hydrogen bonds with the NH2 and CH3 groups in each of the bases. This effect is clear when we look at the charge density for each system considered here (shown in Figure 5). The level alignment via hydrogen bonding leads to a more delocalized charge distribution between nucleobase and nitrogenterminated sheets (right handside column of Figure 5) compared to the H-saturated case (left handside column). Finally, we addressed the translocation through the nanogap from the electronic transport point of view. Thus we considered the graphene nanogap with N functionalization (the most efficient device in terms of transmission intensity), and each nucleobase starting from a height of 3 Å, passing through the equilibrium distance, i.e. best coupling (y = 0 in Figure 1 b), to y = −3 Å using displacements of 0.5 Å between each step. The transmissions as a function of energy and height are shown in figure 6(a-d). As expected, we note that

the resonance intensities decrease for all cases when the nucleobases are displaced away from the best coupling to ±3 Å, but the position of the resonance peak remains in the same place. In all cases this result is in line with a resonant tunneling regime. Figure 6e summarizes the zero bias conductance for each height. For the best coupling, the conductance is well resolved, i. e., the differences are large enough to distinguish the molecules. At the same time, there is a significant drop as we move away from y = 0. In fact that drop is ∼ 2 orders of magnitude for ∆y ∼ ±1Å. This means that the device would be highly sensitive to the translocation process, and that it would be possible to resolve a single base inside the gap. At the same time, the drop is not monotonic. This is particularly clear for adenine and cytosine. The increase in conductance around ±2 Åcomes from the increased coupling between the molecules, which has out-of-plane CH3 groups, and the nitrogen py orbitals.

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Conclusions

In conclusion, we studied graphene nanogaps edge-passivated with either H or N as a solid state nanodevice and how to improve the sensing of several orders of magnitude. We demonstrated that independent of the edge passivation the zero bias conductance has the same hierarchy for nucleobases (G > A > C > T ). The purines A and G have larger coupling compared with the pyrimidines C and T, due to the strong interaction between the base and the device. The device with N termination has a stronger coupling compared with H passivation and this fact is due to the hybridization between the states from the edge with the nucleobases could leads to charge transfer and level realignment. For the N termination we also investigated how the zero bias transmission decrease when the nucleobase passes through the gap. This combination of higher conductance and strong dependence of height from graphene nanogaps leads us to conclude the N-passivated edges give rise to highly sensitive and selective nanobiodevice.


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Supporting Information Available: A supplementary discussion about geometry distances, sensitivities, (I vs V) characteristics and nucleobase rotation are presented in the Supporting Information. This material is available free of charge via the Internet at http: //pubs.acs.org/.

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Acknowledgments

The authors would like to acknowledge financial support from STINT. A. R. R. acknowledges support from ICTP-SAIRF (FAPESP project 2011/11973-4) and the ICTP-Simons Foundation Associate Scheme. R.G.A. acknowledges financial support from the Carl Tryggers Stiftelse and R.H.S. thanks the Swedish Research Council for a Junior Research Position grant (VR, 621-2009-3628). Computational facilities were provided by SNIC (Sweden) and CENAPAD (Campinas - Brazil).

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Figure 2: Zero-bias transmission as a function of energy: graphene nanogap functionalized with (a) Hydrogen (dashed), and (b) Nitrogen atoms (solid) for all nucleobases; (c-f) transmittance comparison between H- and N-terminated edges of graphene nanogap with different nucleobases in between - A, C, G and T.


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Figure 6: For different heights we show zero bias transmittance in function of the energy for: a) Adenine; b) Cytosine; c) Guanine, d) Thymine and in e) the conductance in function of height for N-passivated edges device.


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Graphical TOC Entry

Graphene tunneling device with H/N-passivation are examined for biosensor application such as DNA sequencing. Were observed a conductance boosting comparing H with N nanodevices.


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Boosting DNA Recognition Sensitivity of Graphene Nanogaps through

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