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

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Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases biosensors Article Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases Hikmet Hakan Gürel 1,* and Bahadır Salmankurt 1,2,3 1 Information Systems Engineering Department, Technology Faculty, Umuttepe Campus, Kocaeli University, Kocaeli 41001, Turkey; [email protected] 2 Department of Physics, Art and Science Faculty, Esentepe Campus, Sakarya University, Sakarya 54187, Turkey 3 Remote Education Center, Sakarya University of Applied Sciences, Sakarya 54187, Turkey * Correspondence: [email protected] 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 experimen- tally 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 ger- manene 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. Citation: Gürel, H.H.; Salmankurt, B. Our results show that it is possible to get remarkable changes in transmittance due to the adsorption Quantum Simulation of the Silicene of nucleobases, especially for G, A, and C. These results indicate that silicene and germanene are and Germanene for Sensing and both good candidates for the applications in fast sequencing devices for DNA/RNA nucleobases. Sequencing of DNA/RNA Additionally, our present results have the potential to give insight into experimental studies and can Nucleobases. Biosensors 2021, 11, 59. be valuable for advancements in biosensing and nanobiotechnology. https://doi.org/10.3390/bios11030059 Received: 30 December 2020 Keywords: 2D material; silicene; germanene; DNA/RNA nucleobases; DFT; biosensor Accepted: 19 February 2021 Published: 24 February 2021 Publisher’s Note: MDPI stays neutral 1. Introduction with regard to jurisdictional claims in Experimental synthesis of two-dimensional (2D) graphene [1] has led to the discovery published maps and institutional affil- of new 2D materials such as silicene [2], germanene [3], h-BN [4], MoS2 [5], stanine [6], iations. and so forth. It is possible to form interfaces between 2D inorganic monolayers and biomolecules. These interfaces lead us to the discovery of several biomedical applications such as biosensors and smart drugs [7–10]. Advancements in nanotechnology allow us to detect the nanoscale events at the level of a single molecule by using 2D sensing platforms. Copyright: © 2021 by the authors. DNA/RNA consists of molecules called nucleotides. Each nucleotide has a nitrogen base, Licensee MDPI, Basel, Switzerland. a sugar group, and a phosphate group. The five types of nitrogen bases are Adenine (A), This article is an open access article Guanine (G), Cytosine (C), Thymine (T), and Uracil (U). The properties of genetic codes are distributed under the terms and determined by the order of the nucleobases. Sensing and sequencing of DNA/RNA nucle- conditions of the Creative Commons obases are important in disease diagnosis, forensic science, and genomics [11]. Because Attribution (CC BY) license (https:// of the extraordinary physical, mechanical, chemical, and tunable electronic properties, creativecommons.org/licenses/by/ 2D materials have started to be preferred in the sensing of nucleobases. For instance, 4.0/). Biosensors 2021, 11, 59. https://doi.org/10.3390/bios11030059 https://www.mdpi.com/journal/biosensors Biosensors 2021, 11, 59 2 of 14 Biosensors 2021, 11, 59 2 of 13 properties, 2D materials have started to be preferred in the sensing of nucleobases. For instance, graphene, silicene, germanene, monolayer transition‐metal dichalcogenides, graphene,MXenes, silicene,h‐BN, and germanene, phosphorene monolayer are used transition-metal for the detection dichalcogenides, of DNA/RNA MXenes, nucleobases h- BN,and and amino phosphorene acids [12–29]. are used for the detection of DNA/RNA nucleobases and amino acidsOver [12–29 the]. recent years, graphene counterparts such as silicene and germanene have gainedOver valuable the recent attention years, graphene in the scientific counterparts community. such as silicene Silicene and was germanene successfully have grown gained valuable attention in the scientific community. Silicene was successfully grown experimentally on Ag [2,30–32], Ir [33], and ZrB2 [34] substrate and germanene were also experimentally on Ag [2,30–32], Ir [33], and ZrB [34] substrate and germanene were also grown on the Pt (111) surface [35]. Although2 silicene and germanene stand out with their grown on the Pt (111) surface [35]. Although silicene and germanene stand out with their propertiesproperties similar similar to graphene,to graphene, they arethey different are different from graphene from graphene in terms of in their terms structural of their struc‐ properties.tural properties. They have They a buckled have a honeycombbuckled honeycomb crystal geometry crystal (see geometry Figure1b,c), (see which Figure 1b,c), provideswhich provides for sp3 bonding. for sp3 bonding. Because of Because their crystal of their structure, crystal interaction structure, ofinteraction molecules of and molecules atomsand atoms with silicene with silicene and germanane and germanane monolayers monolayers is stronger than is stronger with graphene. than with This graphene. makes This themmakes potential them potential candidates candidates for the applications for the applications of sensing devices. of sensing devices. FigureFigure 1. 1.( a()a Favorable) Favorable adsorption adsorption sites: sites: hollow, hollow, top, bridge, top, bridge, and valley and forvalley silicene for silicene and germanene. and ger‐ Buckledmanene. structure Buckled of structure (b) silicene of ( andb) silicene (c) germanene. and (c) germanene. Buckling and Buckling Si-Si and and Ge-Ge Si‐ distancesSi and Ge are‐Ge dis‐ presented.tances are ( dpresented.) High-symmetry (d) High points‐symmetry of silicene points and germanene. of silicene Bandand germanene. structure of bareBand (e )structure silicene of bare and(e) silicene (f) germanene. and (f) germanene. DespiteDespite the the importance importance of theof the interactions interactions of 2D of materials 2D materials with biomolecules, with biomolecules, there there are still limited studies with silicene and germanene. A covalent bonding mechanism are still limited studies with silicene and germanene. A covalent bonding mechanism be‐ between DNA/RNA nucleobases with silicene and germanene is absent in similar previous studies.tween DNA/RNA Quantum simulations nucleobases have with been silicene very effective and germanene in understanding is absent the in interaction similar previous mechanismstudies. Quantum of 2D materials simulations and biomoleculeshave been very and effective may play in an understanding important role the in the interaction developmentmechanism of of 2D effective materials and reliable and biomolecules biosensors. With and themay increase play an and important widespread role use in the de‐ ofvelopment high-performance of effective computing and reliable resources, biosensors. it has become With the clear increase how powerful and widespread the first use of principlehigh‐performance of the Density computing Functional resources, Theory (DFT)it has isbecome in modeling clear how such systems.powerful Metal- the first prin‐ dopedciple of monolayers the Density have Functional better binding Theory capabilities (DFT) is compared in modeling to pristine such monolayers systems. Metal [17]. ‐doped Goldmonolayers atoms have have some better advantages binding over capabilities other metal compared atoms. The to color pristine of gold monolayers nanoparticles [17]. Gold depends on their shape and size; they are highly preferred in nanomedicine. atoms have some advantages over other metal atoms. The color of gold nanoparticles de‐ In this work, we have calculated the binding of DNA/RNA nucleobases (NB) with pristinepends on silicene/germanene their shape and size; and Au- they and are Li-decorated highly preferred silicene/germanene in nanomedicine. by using the quantumIn this simulations work, we technique have calculated based on the the binding Density Functionalof DNA/RNA Theory nucleobases (DFT), with (NB) with vanpristine der Waals silicene/germanene (vdW) correction and and Au electronic‐ and Li transport‐decorated properties, silicene/germanene such as changes by in using the thequantum transmittance simulations and conductance technique based produced on the by adsorptionDensity
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