Elsevier

Chemical Physics Letters

Volume 730, September 2019, Pages 70-75
Chemical Physics Letters

Research paper
Silicene nanosheet device with nanopore to identify the nucleobases – A first-principles perspective

https://doi.org/10.1016/j.cplett.2019.05.038Get rights and content

Highlights

  • The silicene nanosheet with nanopore (Si-NP) is designed and its stability and electronic properties are explored.

  • The nucleobase passage through nanopore leads to change the electronic properties of silicene nanosheet.

  • The modulation in the band structure of Si-NP results in the resistance change of the material.

  • The results suggest that silicene sheets with nanopore can be used to sequence the DNA or RNA passing through it.

Abstract

We studied the sequencing of nucleobases upon passage through the silicene nanopores using non-equilibrium Green’s function formalism along with density functional theory. The silicene nanosheet is segmented into three regions, where the nanopore is created, and the edges of nanopore are functionalized with hydrogen. The density of states, transmission spectrum, and current-voltage characteristics are studied, and the variation in the magnitude of current leads to identify the type of nucleobase. The results of the proposed study clearly indicate silicene sheets with nanopore can be used to sequence the DNA or RNA passing through it.

Introduction

The building block of deoxyribonucleic acid (DNA) is nucleotide. The genetic information is encoded by the ordered arrangement of the nucleic acid chain that gives valuable information of the living being [1], [2]. Hence, sequencing the whole genome gives the fundamental understanding behind the biologically relevant issues mainly in hereditary pathologies [3]. Moreover, the recent advancement in the nanopore sequencer involves the change in the current, flowing through molecular device upon passage of nucleobase along the pore [4], [5]. Furthermore, monolayer materials such as graphene, silicene, germanene, and phosphorene are used as a molecular device to identify the sequence of the genome. Moreover, the advantage of using monolayer based molecular device gives a fast sequencing of DNA with much more accuracy [6], [7], [8]. It is well known that a nanopore may electrophoretically translocate DNA/RNA and proteins in the salt solution, which leads to ionic current blockage. Thus, the ionic signals will be the fingerprint that can be used to detect the DNA sequence [9]. The challenge to sequence DNA with the help of nanopore is in the design mechanism, which leads to reliable and fast identification of the nucleotides present in the DNA strand while they pass through the nanopore [10]. To achieve the goal of the work, we used silicene sheet with nanopore to recognize the nucleobases. On passage of DNA nucleotides, it gives rise to the disparity in the transverse current. Moreover, the base material silicene is entrenched as the left and right electrode, after the passage of nucleotide, the current through the silicene molecular device leads to variation. Besides, there are numerous reports based on graphene, which is used to detect the presence of nucleotide upon passage through the nanopore [11], [12]. However, the graphene material possesses sp2 hybridization, which gives rise to metal like property. In contrast, silicene sheets exhibit buckled structure with sp3 hybridization [13], [14]. Thus, the band gap can be opened in the silicene base material, which can be efficiently used as a base material for chemical and biosensors [15], [16]. The recent advancement in the research leads to the search for nano biodevice in order to differentiate the various nucleobases that pass through the nanopore device. Moreover, the design of novel solid-state nanopore device remains a challenging task to the researchers. At this juncture, we would like to address why silicene base material is chosen and what is the motivation behind the proposed work? The seed for the stimulus behind the present work is from Ralph H Scheicher group [17]. Rodrigo G Amorim et al. [17] have reported silicene sheet as the base material to sequence DNA. Then what is the difference in the proposed work? In the current work, we designed a nanopore in silicene molecular device, which upon passage through the pore generates the current across the device. The magnitude of the current will serve as a precursor to identify the nucleobase in the strand. Besides, the other important advantages of using nanopore device are (i) it produces the current signal upon passage of nucleobases, which serves as a promising sequencing technique, (ii) a tunneling recognition scheme gives a promising signal across the electrodes that can capture the passage of single-stranded DNA. The other challenging task in the design of a molecular device for identification of nucleobases is with the alignment of the electrode concerning the nucleobases, which is guided through the minute opening in the molecular device so-called nanopore. The novel prospect of the current work is to identify the nucleobases that pass through the nanopore of silicene molecular device. Based on the current fluctuations through the silicene device, the nucleobases namely adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) can be identified. The entire results have been discussed based on the density of states, transmission and current-voltage characteristics of silicene nanopore molecular device.

Section snippets

Computational details

The electronic and transport properties of silicene sheet upon passage of nucleobase were studied using density functional theory (DFT) in combination with non-equilibrium Green’s function (NEGF) implemented using SIESTA code [18]. The electronic transport properties of silicene nanopore device are studied using TranSIESTA. In the current work, Generalized Gradient Approximation (GGA) for exchange-correlation functional along with Perdew-Burke-Ernzerhof (PBE) is used [19], [20]. The valence

Structural geometry of silicene molecular device

Initially, the formation energy of the silicene nanopore sheet (Si-NP) should be ascertained for its stability. The computed value of formation energy is observed to be −3.74 eV, which clearly suggest that the silicene sheet is stable and can be used as a base substrate for detecting the nucleobases in the DNA. The calculation for formation energy of silicene sheets is calculated based on our previous reports [24], [25]. Besides, the geometric stability of the base material also confirmed with

Inferences and future outlook

To sum up, we explored the ability of silicene nanosheet with nanopore device to identify the different nucleobases that pass through it using DFT along with NEGF method. The phonon band structure and formation energy are used to ensure the structural stability of silicene sheet with the nanopore. The electronic properties of Si-NP infer that it can be used as a base material for constructing the molecular device. Furthermore, we discussed the detection of nucleobases through the DOS,

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

The authors wish to express their sincere thanks to Nano Mission Council (No. SR/NM/NS-1011/2017(G)) Department of Science & Technology, India for the financial support.

References (49)

  • A.S. Rad et al.

    Application of pristine and Ni-decorated B12P12 nano-clusters as superior media for acetylene and ethylene adsorption: DFT calculations

    Comput. Theor. Chem.

    (2017)
  • H. Ullah et al.

    Polypyrrole/TiO2 composites for the application of photocatalysis

    Sensors Actuators, B Chem.

    (2017)
  • A.A. Peyghan et al.

    A first-principles study of the adsorption behavior of CO on Al- and Ga-doped single-walled BN nanotubes

    Appl. Surf. Sci.

    (2013)
  • S. Dharani et al.

    Nucleobases adsorption studies on silicane layer: a first-principles investigation

    J. Mol. Graph. Model.

    (2018)
  • E.C. Anota et al.

    In silico characterization of nitric oxide adsorption on a magnetic [B24N36 fullerene/(TiO2)2]− nanocomposite

    Appl. Surf. Sci.

    (2017)
  • P. Snehha et al.

    Doped aluminum nanocones as an efficient electron field emitter: a first-principles investigation

    Inorg. Chem. Commun.

    (2018)
  • R. Bhuvaneswari et al.

    First-principles insights on the electronic and field emission properties of Ga and Al doped germanium nanocones

    J. Electron Spectros. Relat. Phenomena.

    (2018)
  • C.M. Tan et al.

    Spin filtering and rectifying effects in the zinc methyl phenalenyl molecule between graphene nanoribbon leads

    Org. Electron. Phys., Mater. Appl. 28

    (2016)
  • R. Chandiramouli

    Antimonene nanosheet device for detection of explosive vapors – A first-principles inspection

    Chem. Phys. Lett.

    (2018)
  • H.P.J. Buermans et al.

    Next generation sequencing technology: advances and applications

    Biochim. Biophys. Acta - Mol. Basis Dis.

    (1842)
  • J. Knoch et al.

    Rare hereditary diseases with defects in DNA-repair

    Eur. J. Dermatol.

    (2012)
  • R.H. Scheicher et al.

    DNA sequencing with nanopores from an ab initio perspective

    J. Mater. Sci.

    (2012)
  • J. Prasongkit, A. Grigoriev, B. Pathak, R. Ahuja, theoretical study of electronic transport through DNA nucleotides in...
  • J. Prasongkit et al.

    Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene

    Sci. Rep.

    (2015)
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