Electronic Transport through DNA Nucleotides in Atomically Thin

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Biological and Medical Applications of Materials and Interfaces

Electronic Transport through DNA Nucleotides in Atomically Thin Phosphorene Electrodes for Rapid DNA Sequencing Rameshwar L Kumawat, Priyanka Garg, Sourabh Kumar, and Biswarup Pathak ACS Appl. Mater. Interfaces, Just Accepted Manuscript • DOI: 10.1021/acsami.8b17239 • Publication Date (Web): 12 Dec 2018 Downloaded from http://pubs.acs.org on December 17, 2018

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ACS Applied Materials & Interfaces

Electronic Transport through DNA Nucleotides in Atomically Thin Phosphorene Electrodes for Rapid DNA Sequencing Rameshwar L. Kumawat,† Priyanka Garg,# Sourabh Kumar,# Biswarup Pathak †,#,* †Discipline

of Metallurgy Engineering and Materials Science, #Discipline of Chemistry, School of Basic Sciences and, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India Email: [email protected] Abstract Rapid progresses in developing the fast, low-cost, and reliable methods for DNA sequencing are envisaged for development of personalized medicine. In this respect, nanotechnology has paved the role for the development of advanced DNA sequencing techniques including sequencing with solid-state nanopores or nanogaps. Herein, we have explored the application of a black phosphorene based nanogap-device for DNA sequencing. Using densityfunctional-theory (DFT) based non-equilibrium Green’s function (NEGF) approach, we have computed transverse transmission and current-voltage (I-V) characteristics of all the four DNA nucleotides (dAMP, dGMP, dTMP, and dCMP) as functions of applied bias voltages. We deduce that it is in principle; possible to differentiate between all the four nucleotides by three sequencing runs at distinct applied bias voltages, i.e., at 0.2 V, 1.4 V, and 1.6 V, where individual identification of all the four nucleotides may be possible. Hence, we believe our study might be helpful for experimentalist towards the development of a phosphorene based nanodevice for DNA sequencing to diagnose critical diseases. Keywords: DNA sequencing, black phosphorene, non-equilibrium Green’s function, density functional theory, I−V characteristics

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1. Introduction Increasing demand for personalized medicine calls for a transformation in our health care system, which in turn demands for the development of new generation DNA sequencing based devices.1,2 In this respect, “$1000 Genome” project3 introduced by the National Institutes of Health (NIH) aims to develop personalized medicines4 based treatments by reducing the cost of the human genome sequence.5-8 Nanopore/Nanogap based DNA sequencing is one of the most growing third-generation DNA sequencing-based technologies that are presently foremost elegant to encounter such challenges as they have been growing rapidly to provide cheaper, faster, and accurate DNA sequencing.9-11 In 2012, Cherf and co-workers have reported that the information encoded in a DNA can be achieved through biological nanopores.12 However, in 2010, Schneider and co-workers and recently Garaj and co-workers have reported that the solid-state nanopore-based DNA sequencing is an emerging technology over biological nanopores.13,14 As such solid nanopore-based techniques help to achieve a single-nucleotide or base resolution.15 Furthermore, solid-state nanopores/nanogaps have better stability and high potential sequencing speeds over biological nanopores/nanogaps.16-18 In this regard, sequencing of the human genome (DNA) by solid-state nanopore/nanogap has progressed significantly. Several experimental and theoretical groups have used gold and various low dimensional materials based electrodes for rapid DNA sequencing.20-21 Graphene nanopores/nanogaps are excellent candidates to achieve single-nucleotide resolution due to its one atom-thickness.22 In a very recent report by Traversi and co-workers reported that the solid-state nanopore combined with the graphene nanoribbon can be used as a nanodevice for the nucleobase sensing.23 However, the surface properties of such graphene nanopores/nanogaps are very sensitive towards the target nucleotides. Moreover, such device

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generates high noise ratio and geometry deformation after the insertion of a DNA molecule into the pore/gap.24,25 This has prompted the exploration of other potential low dimensional materials such as silicene (Si), molybdenum disulfide (MoS2), boron-nitride (BN), and graphene-hBN, to name a few.26-31 Two-dimensional (2D) monolayer black phosphorus, known as “Phosphorene”, has been considered as a new alternative to graphene for the next-generation semiconductor-based devices.32,48 It exhibits a puckered honeycomb-like structural geometry along the armchair direction. Phosphorene based materials have received a lot of attention due to their biocompatibility, low cytotoxicity, unique optical, electronic, and mechanical properties. For example, phosphorene has a high anisotropic electrical conductivity, carrier mobility (~1000 cm2V-1s-1), and a wide tunable band gap.32-34 Recent experimental studies have confirmed the stability of black phosphorus nanostructures in the air and water.35-37 There are several experimental reports on the stability of black phosphorus in air and water. Such experiential studies have reported that an effective encapsulation of phosphorene by other 2D materials39, such as h-BN,40 graphene,41 Poly(methyl methacrylate) (PMMA),42 and Al2O343, can prevent from degradation under ambient conditions. Such encapsulation technologies (packaging and passivation) lead to improved device reliability and performance, which is very necessary for its applications in current nano-electronics.38,44-48 For example, Pei and co-workers have demonstrated a highly controllable method for fabrication of high quality, air-stable phosphorene films with a selected number of layers ranging from a few down to the monolayer. After that in 2017, Cupo and co-workers have theoretically and experimentally studied the black phosphorene nano-hole/nanopore with different radius.58-59 Several studies show the potential biomedical applications of phosphorus nanostructure as it does not affect the protein structures.49 Therefore, we believe that these advances must facilitate its

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development for DNA sequencing devices techniques.

All these reports indicate that

phosphorene can be a promising nanomaterial for bio-sensing30 applications. Furthermore, it would be interesting to find out whether the buckling nature in phosphorene is helpful for DNA sequencing or not. Inspired by all these reports, we have proposed phosphorene-based nanodevice for DNA sequencing. Using density-functional-theory (DFT) based non-equilibrium Green’s function (NEGF) approach,50-52 we have studied the transmission spectra and current as a function of bias voltage for the four nucleotides while passing through the phosphorene nanogap.

2. Model and Computational Methodology In this study, we have modeled a phosphorene nanodevice (Figure 1) for DNA sequencing where phosphorene used as electrodes as well as scattering region. The proposed device contains two phosphorene electrodes fixed oppositely in a nanogap and a target nucleotide as shown in Figure 1. A nanogap of ~1.45 nm is created along the armchair direction,53 as the electrical conductance in the armchair direction is one order higher than that in the zigzag direction.54 Such sized nanogap is good enough to allow the nucleotides (size ~ 1.0-1.2 nm) to pass through. The nucleotide is a part of single-stranded DNA (ssDNA) containing a base, a sugar, and a phosphate group. We have considered four target nucleotides for our study: (i) deoxy adenosine monophosphate (dAMP), (ii) deoxy guanidine monophosphate (dGMP), (iii) deoxy thymidine monophosphate (dTMP), and (iv) deoxy cytosine monophosphate (dCMP). The electronic calculations have been performed using the SIESTA code.50 Considering the optimized structures of armchair phosphorene nanogap and nucleotides, we placed each nucleotide inside the nanogap with H-terminated zigzag edges and the device is optimized.

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Left (L), and right (R) parts of the electrodes are periodic along the xz-plane. Furthermore, a periodic boundary condition has been adopted to avoid the electrostatic interactions. We have considered a large vacuum distance of ~16 Å, which is enough to avoid any interactions between the repeated images. We have used the GGA-PBE functional for the exchange-

Figure 1. Schematic of proposed phosphorene nanodevice with left (L), right (R) electrodes and scattering region. Top and side views of the fully optimized structures of the nanodevices with target nucleotides (a) dAMP, (b) dGMP, (c) dTMP, and (d) dCMP. Here, the transport direction is along the z-direction.

correlation-potentials. To model the atomic-core-electrons, the Troullier-Martins-normconserving51 pseudo-potentials are used, whereas double-zeta polarized (DZP) basis sets are used for valance electrons.52 A mesh cut off value of 200 Ry is utilized for the real-space integration. For the treatment of brillouin-zone sampling, a k-space grid of 4 × 1 × 2 has been employed. All the structures are optimized using the conjugate gradient algorithm (CG).

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The convergence tolerance is set to 0.0001 eV, and the atomic forces are smaller than 0.01 eV/Å.31 The electronic transport calculations are done within the framework of the Landauer55,57 methodology (DFT+NEGF methods) as employed in the TranSiesta code.50 The basis-set and the real-space integration engaged in the transport calculations are same as used for geometry optimization. The current is calculated using the integration of the transmission spectrum as

2e μ

I(V𝑏) = h ∫μL T(E,V𝑏)[f(E ― μL) ― f(E ― μR)]dE R

(1)

where T(E,V𝑏) is the transmission probability of the electrons. E is the energy of the electrons travelling from L (left) to R (right) electrode in the presence of an applied bias voltage Vb. Here, f(E ― μL, R) and μL, R are the Fermi-Dirac distribution of electrons and chemicalpotential of the electrodes, respectively.

3. Results and Discussion The proposed device has phosphorene zigzag edges, which are terminated with H atoms. This has been done to improve the interactions between electrodes and nucleotides, which in turn can improve the transmission. We have calculated zero bias transmission for all the four nucleotides to understand the coupling between electrodes and nucleotides and Figure 2a shows the zero bias transmission for all the four nucleotides while placed between the electrodes. In the -0.5 to -2.0 eV energy region of the transmission curve, we find distinct peaks for all the four nucleotides. The maximum intensity comes from dAMP, dGMP and dTMP and lowest intensity peaks come from dCMP. This could be due to the highest occupied molecular orbital states (HOMO) of the device, which appears close to the Fermi energy. Similarly, in the 0.1 to 2.0 eV energy regions, peaks with high intensities appear for 6


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dGMP, dAMP and dTMP and low intensity for dCMP. This could be due to the contribution of the lowest unoccupied molecular orbitals (LUMO) of the device. Furthermore, we have done density of states analysis (Figure 2b) and plotted the molecular orbitals (Figure 2c) corresponds to these peaks appear around the Fermi energy. Our detailed molecular orbital analysis shows (Figure 2c) that HOMOs are mainly localized on the nucleotides, whereas LUMOs are localized on the electrodes. Figure 2c shows that there is a strong overlap

Figure 2. (a) Zero-bias transmission spectrum as a function of energy plotted for all the four DNA nucleotides (dAMP, dGMP, dTMP, and dCMP). (b) DOS at zero-bias plotted for the four DNA nucleotides. The Fermi level (Ef) has been set to zero. (c) Molecular orbitals responsible for these transmission peaks labels with letters A, T, G, and C have been presented for all the four devices. Color code: (P:orange), (O:red), (N:blue), (C:grey), and (H:white).

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between electrode and nucleotide in case of dGMP, dTMP, and dAMP, where the overlap is less significant for the dCMP nucleotide. The zero-bias transmission as a function of energy is different for different nucleobases. This is because, there are two types of nucleobases: (i) purine (such as adenine and guanine), and (ii) pyrimidine based (cytosine and thymine). The pyrimidine based nucleobases are smaller in size than the purine based nucleobases and the number of hydrogen available for interactions are also different in these two cases. This is one of the reasons for weak coupling between dCMP and the phosphorene electrodes. As a result, pyrimidine base dCMP show less overlapping with phosphorene electrode. Our DOS plot in figure 2b also reveals that the orbital of dCMP does not significantly overlap with the phosphorene electrode. It can also be seen from figure 2c:C1 that the electron density is completely localized on the nucleobase which further confirms that there is a weak coupling between the phosphorene electrodes and dCMP. So, this is the reason that dCMP shows the lowest transmission intensity peaks. All these results indicate that all the three nucleotides (dGMP, dAMP, dTMP) are strongly coupling while dCMP shows somewhat weak coupling with the phosphorene electrodes. This is very much consistent with our transmission spectra. Furthermore, the existence of such peaks reveals that the DNA nucleotides can be identified under applied bias voltages, as these are the important factors for their tunneling transmittance. In addition, we have also investigated the effect of Hubbard U term (Ueffective = 1, 2, and 3) on the dGMP/dCMP + electrodes systems as they strongly/weakly couple with the phosphorene electrodes. However, we have not observed any change in their electronic structures (Figure S5, supporting information), which suggests that the single particle picture may be valid for such cases.

In order to electrically distinguish the four nucleotides, we have calculated the current signal for all the four DNA nucleotides (dAMP, dGMP, dTMP, and dCMP) while placed between

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phosphorene electrodes. We have used up to 2V voltages to understand the current vs. voltage pattern for all the four nucleotides. Figure 3 shows the I-V pattern for a specific orientation of all the four nucleotides. We have used a flowchart (Figure S1) to show that we could distinguish them sequentially. The I-V pattern curve shows that the current increases as we increase the bias voltage. Besides, the four nucleotides can be distinguished into three different runs as shown in (Figure 3b-d, Figure S1). At 0.2 V bias voltage, the current (I) for dGMP is nearly 2 orders of amount higher than that for dCMP (Figure 3b). This further indicates the good sensitivity of the proposed nanodevice. Thereafter, at 1.4 V, the current for dGMP is nearly 1.5 orders of amount higher than that for dAMP or dTMP ( Figure 3c). Further, at 1.6 V, we have noted significant current differences between all the four DNA nucleotides for their individual identification. The magnitude of the currents at 1.6 V voltage (Figure 3d) is in the following order: IdGMP > IdTMP > IdAMP > IdCMP. Therefore at 1.6 V (Figure S2), we could distinguish dAMP and dTMP (dTMP > dTMP). Moreover, dGMP and dTMP nucleotides can be differentiated from the other two DNA nucleotides for their

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Figure 3. (a) I-V pattern (current axis is presented on a logarithmic scale) curve for the four nucleotides (dAMP, dGMP, dTMP, and dCMP) while located in a nanogap. The bottom panel shows a view of the I-V pattern curve for the identification of nucleotides at three applied bias voltages, (b) 0.2 V, (c) 1.4 V, and (d) 1.6 V, used for identification of each DNA nucleotide. higher current values, which results in the closure of the Fermi-energy (Ef) of the proposed device to the broad HOMO peaks of dGMP and dTMP nucleotides (Figure 2). The other two nucleotides (dAMP, and dCMP), which have HOMO states further apart from the Fermienergy (Ef), unveil different current amounts, displaying tiny overlap with each other. Such differences in current between these two nucleobases are robust. In our investigation, the current increases the maximum for dGMP compared to the other three nucleotides. However, in all the four cases, the current values are very high (I > 10 ―10A), which is likely to avoid the electrical background noise in experimental investigations. Thus, the voltage window of 0.2 to 2 V will be good enough for a perfect differentiation of all the four DNA nucleotides. The 0.2-2 V bias window can be good for the device stability as graphene starts rupturing at 3.1 V.57 In this regard; we require a low bias voltage to distinguish all the four nucleotides. It is well known that the devices are driven out of the equilibrium condition under applied bias voltages. Therefore to understand their I-V pattern, we have analyzed the transmission spectra under applied biases (i.e. at 0.2, 1.4, and 1.6 V, respectively) for the four DNA nucleotides (Figure 4). These Figures show that the transmission peak shifts as we change the bias voltage. For example, all the transmission peaks move from high energy to low energy region as we increase the bias voltage. However, we find that the peak intensity is maximum for dGMP and dTMP, whereas low for dCMP. This is very much in agreement with our I-V curve too. Therefore, the observed molecular states of the target nucleotide and

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the electrodes are contributing in the transmission spectrum, which shows significant changes under applied bias voltages. Hence, the I-V pattern analysis shows unique variation in the low applied bias voltages region. Thus, all the four DNA nucleotides convey unique current signs under applied biases.

Figure 4. Bias-dependent transmission spectra of the four devices (a) dAMP, (b) dGMP, (c) dTMP, and (d) dCMP) under applied bias voltages of 0.2, 1.4, and 1.6 V. The Fermi level has been set to zero. The broken lines depict the voltage window of ± 𝑉/2. Furthermore, in the context of our phosphorene nanogap electrode device performance, we have considered the effect of rotational and lateral translation for all the nucleobases on the transmission spectrums to account the dynamical effects. We understand that the transport will most likely be dominated by the tail of the distribution of transmission values and not 11



necessarily that the lowest energy structure will provide the highest conductance. For this, we have considered the rotations of all four DNA nucleobases around the y-axis in the xz plane at 60°, and 90°and the corresponding transmission spectrums are also shown in Figure S3. The relative energy of these rotated configurations with respect to the original (zero degrees) orientation is also presented in Table S1. By rotating the nucleotides inside the gap, the transmission spectrum of the device varies along with their orientations. Further, comparing these results against the case of zero-degree rotation, we find a variation in the transmission spectrums. Moreover, for the dGMP nucleobase the largest deviation in the transmission spectra corresponds to the orientation, which has the highest energy (60°). For all other case, there is a negligible difference due to rotation. In addition by laterally shifting the nucleobases (left and right side) by 0.5 Å, we note there is a change to the transmission peaks (Figure S4). Therefore, we concluded that there is some unavoidable effects of lateral translations on the transmission though it won’t effect much the I-V pattern observed for the ground state structure.15,31 Similarly, solution can play an important role. Recently, Feliciano et al., have shown the effect of solvent (water) medium for the zero-bias transmission of graphene-nucleobase system. The small changes observed in the transmission plots undoubtedly describe the effect of screening, assisted by the water molecules. However, this will only affect the magnitude of the transverse electrical current. Solvent medium can provide better or less transverse electrical current. But the trend observed within systems doesn’t change.60 In a similar report by Lagerqvist and co-workers, they have shown the structural fluctuations in the nucleotides causing the change in transmission function. However, they have concluded that the direct effect of water on transmission can be neglected.61,62 In conclusion, the trend in I-V pattern will not be changed due to the solvent effects though there can be change in the magnitude of the transverse electrical current.

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4. Conclusion We have demonstrated the sensing application of phosphorene based nanogap-device for DNA sequencing. We find that phosphorene works as an ideal nano-electrode, and the zigzag H terminated phosphorene nanogap can interact with an incoming target nucleotide in a cooperative manner. By computing the I-V pattern and the transverse transmission spectrum of all the four target nucleotides in the nanodevice, we perceive that phosphorene nanogap based sequencing is indeed feasible to individually identify all the four DNA nucleotides. We find a noticeable difference in I-V signals into three different runs at 0.2, 1.4, and 1.6 V voltages, and observed the adequate sensitivity at 1.6 V. It is fascinating to observe that dAMP and dTMP show a comparatively smaller current value than the dGMP, which is significant enough to distinguish them. Moreover, dGMP and dCMP have nearly 2 orders of difference in current values. However, in the case of dGMP, the current trace is continuously increasing, whereas, in the case of dCMP, the current value is always lowest. This is due to the coupling of nucleobases with these electrodes; the induced density in the noticed nucleobases delivers a molecular level identification as noted over current-voltage. Hence, based on our results, we believe that it is possible to realize a phosphorene based nanodevice to distinguish between the four DNA nucleotides. 5. Supporting Information: Flowchart of I-V pattern to distinguish all the four nucleobases sequentially, The I-V pattern for individual identification of dAMP and dTMP at 1.6 V applied bias voltage, Effect of rotation and lateral translation of nucleobases on transmission spectra, Effect of Hubbard U term on the electronic structures of dGMP/dCMP. 6. Conflicts of interest There are no conflicts of interest to declare.

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7. Acknowledgments We thank IIT Indore for the lab and computing facilities. This work is supported by DSTSERB, (Project Number: EMR/2015/002057) New Delhi and CSIR [Grant number: 01(2886)/17/EMR (II)]. R.L.K. and P.G. thanks MHRD for research fellowships. S.K. thanks UGC fellowship.

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Electronic Transport through DNA Nucleotides in Atomically Thin

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