Electronic Conductance and Current Modulation through Graphdiyne Nanopores for DNA Sequencing

Abstract

Solid-state nanopore devices have emerged as one of the most promising technologies that may decode the sequence of DNA nucleobases by reading electronic conductance and electric current signals. Herein we study the potential of atomically thick graphdiyne (GDY) to act as an all-electronic nanopore (NP)-based DNA sequencing device. The first-principles density functional theory method is used to study the structural properties, interaction energy (E i) values, translocation time (τ), charge transfer [Q(e)] values, charge density difference [Δρ­(r)], molecular orbital (MO) positions, and electronic density of states (DOS) properties of the GDYNP and GDYNP + nucleobase (nucleobases: adenine (A), guanine (G), thymine (T), and cytosine (C)) systems. Our results suggest that the GDYNP system could be a suitable device for the detection of nucleobases due to their specific translocation times inside the GDYNP device. The Δρ­(r) results reveal that the charge fluctuates around the GDYNP edges close to the target nucleobase. This charge reorganization causes the modulation of charge transport in the GDYNP device. Furthermore, the GDYNP device is used to read-out the conductance and current signals of each DNA nucleobase while located inside the GDYNP by using nonequilibrium Green’s functions formalism. Our findings show a change in conductance with respect to the reference bare “GDYNP” device for energy values below/above the Fermi energy. The conductance as well as current sensitivity (%) values (C > G > T > A) indicates that the nucleobases could possibly be sequenced through the GDYNP device. Further, each nucleobase transmits unique current signals when transported through the GDYNP device. A distinction between purine- and pyrimidine-type nucleobases seems possible due to their different current signals. Thus, our study highlights the potentials that would motivate research toward the development of the GDYNP device, which may be even a better DNA nucleobase detector compared to graphene-based devices.

First-Principles Density Functional Theory Study on Graphene and Borophene Nanopores for Individual Identification of DNA Nucleotides

“…Inspired by the progress and challenges of biological nanopore-based DNA sequencing, researchers from the academia and industry are committed toward the development of a biomimetic solid-state nanopore device. − A plethora of two-dimensional (2D) materials has attracted considerable interest and attention from the scientific community due to their unique structural, physical, chemical, electronic, and transport properties, not to mention their novel applications in sensing, optoelectronic, and biomedical devices. Recently, several 2D material-based nanopores have been widely studied and found to be quite promising for DNA sequencing due to their thickness, which is comparable with the spacing between two nucleotides in DNA.…”

Identification of DNA nucleotides by conductance and tunnelling current variation through borophene nanogaps

“…55,56 Hence, dAMP has the higher resident time inside the pore, while dCMP can translocate effortlessly through the nanogap, with a comparatively shorter resident time inside it. 57…”

Conductance and tunnelling current characteristics for individual identification of synthetic nucleic acids with a graphene device

“…At zero-bias, we have computed the conductance G = G 0 T(E F ), where G 0 = 2e 2 /h represents the quantum conductance, e (charge of the electron) and h (Plank's constant); respectively. 3,4,8,9,[38][39][40][41][42][43][44] The integration of eqn (3) provides the current i.e., I(V b ) (current under applied bias voltage (V b )), which can be computed by using the below equation:…”

“…where f (E À m L ) and f (E À m R ) represents the Fermi-Dirac functions for the electrons in the L and R nanoelectrodes, respectively. 3,4,8,9,31,[38][39][40][41][42][43][44][45][46][47][48]…”

“…6 The experimental proof of artificial genetic characters presents a challenge to a low-cost, label-and amplification-free, rapid, and controlled next-generation sequencing (NGS) technique such as nanogap, nanopore, and nanochannel-based smart sensors for healthcare applications. 3,4,[7][8][9][10][11][12][13][14][15][16] In NGS, DNA nucleobases can electrophoretically be passed through nanogaps or nanopores, which changes the ionic or tunneling/ transverse currents, which can be used in real-time sequencing. On the other hand, nanochannel-based devices are also quite promising for NGS applications.…”