Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Abstract

Over the last decade, we have been witnessing the rise of two-dimensional (2D) materials. Several 2D materials with outstanding properties have been theoretically predicted and experimentally synthesized. 2D materials are good candidates for sensing and detecting various biomolecules because of their extraordinary properties, such as a high surface-to-volume ratio. Silicene and germanene are the monolayer honeycomb structures of silicon and germanium, respectively. Quantum simulations have been very effective in understanding the interaction mechanism of 2D materials and biomolecules and may play an important role in the development of effective and reliable biosensors. This article focuses on understanding the interaction of DNA/RNA nucleobases with silicene and germanane monolayers and obtaining the possibility of using silicene and germanane monolayers as a biosensor for DNA/RNA nucleobases’ sequencing using the first principle of Density Functional Theory (DFT) calculations with van der Waals (vdW) correction and nonequilibrium Green’s function method. Guanine (G), Cytosine (C), Adenine (A), Thymine (T), and Uracil (U) were examined as the analytes. The strength of adsorption between the DNA/RNA nucleobases and silicene and germanane is G > C > A > T > U. Moreover, our recent work on the investigation of Au- and Li-decorated silicene and germanane for detection of DNA/RNA nucleobases is presented. Our results show that it is possible to get remarkable changes in transmittance due to the adsorption of nucleobases, especially for G, A, and C. These results indicate that silicene and germanene are both good candidates for the applications in fast sequencing devices for DNA/RNA nucleobases. Additionally, our present results have the potential to give insight into experimental studies and can be valuable for advancements in biosensing and nanobiotechnology.

DNA/RNA sequencing using germanene nanoribbons via two dimensional molecular electronic spectroscopy: an ab initio study

“…The thermodynamic stability of germanene nanoribbons has already been discussed in the literature, where it has been shown that the low buckled form of germanene is energetically more favorable and behaves as a semi-metal. [72][73][74] Our calcu-lated values for a, b, and c are 3.96 Å, 0.64 Å, and 6.96 Å, respectively, in agreement with previous studies. 44,72 Fig.…”

“…Here, we follow the results on the adsorption behavior of nucleobases on germanene obtained from previous studies. 59,74 The separation distance is defined between nucleobase and AGeNR (d ) as the distance between the nearest atoms of the two subsystems. Although the initial positions and orientations of the nucleobase are arbitrarily chosen, however, since the interaction between the nucleobase and the substrate is mediated by weak vdW forces, 75 the variation of adsorption energy for different nucleobase-AGeNR configurations would be negligible.…”

A review on transport characteristics and bio-sensing applications of silicene

“…The order of their binding energy is given by G > C > T > A > U. A small band gap of 0.45 eV opens up when a silicene nanosheet interacts with G. A similar study carried out by Gürel and Salmankurt [41] have indicated the binding nature of DNA/RNA nucleobases on silicene. The gold (Au) and lithium (Li) decorations in silicene showcase the chemisorption in the surface.…”

“…In conjunction with the low thermal conductivity of silicene, these findings indicate that silicene-based nanostructures could be the basis of more efficient TE devices. Recently, it has been found that silicene can be used very efficiently as biosensor [38][39][40][41][42].…”

“…They have found from their computational study that adenine and thymine are physisorbed on silicene, whereas cytosine and guanine are weakly chemisorbed through the formation of a Si-O bond. Gürel and Salmankurt [41] have explored Au and Li decorated silicene and germanane for detection of DNA/RNA nucleobases. Their study has revealed that the adsorbed Li/Au atoms can significantly increase the binding between the nucleobases and silicene/germanene monolayers.…”