Top

Journal of Computational Electronics

Published in:

07-07-2021

Borospherene-based biomarker for DNA sequencing: a DFT study

Authors: Jupinder Kaur, Ravinder Kumar

Published in: Journal of Computational Electronics | Issue 5/2021

Activate our intelligent search to find suitable subject content or patents.

search-config

AI-assisted search

Off

Abstract

Density functional theory and non-equilibrium Green’s function were utilized to explore the feasibility of borospherene (B₄₀) as a biomarker for predicting the sequence of individual nucleobases in a DNA strand. In this context, total and adsorption energies, charge transfer, electron densities, transmission spectra, density of states (DOS), molecular energy spectra, HOMO–LUMO gaps, eigenstates, and current–voltage curve were determined. It is deduced that all DNA nucleobases were physisorbed on the surface of borospherene. On analysis of the transmission spectra and DOS, HOMO-mediated transmission was visualized in all the borospherene-nucleobase molecular junctions. The highest HOMO–LUMO gap was assayed by a borospherene-adenine device. The I–V curve showed a different current curve for all the devices, thus proving that borospherene is a suitable candidate to be explored as a biomarker for determining the sequence of nucleobases in DNA. In addition, negative differential resistance (NDR) is exhibited by the borospherene-cytosine complex, thus opening doors for utilizing it to design advanced electronic nano-devices in the future.

previous article Analysis and design of a passive spatial filter for sub-6 GHz 5G communication systems

next article Application of nitrogenated holey graphene for detection of volatile organic biomarkers in exhaled breath of humans with chronic kidney disease: a density functional theory study

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Kumar, D.: From evidence-based medicine to genomic medicine. Genom. Med. 1, 95 (2007)CrossRef

Kruglyak, L.: The road to genome-wide association studies. Nat. Rev. Genet. 9, 314 (2008)CrossRef

Cuniberti, G., Felice, R., di, : Charge transport in DNA-Based devices. Top. Curr. Chem. 23, 7183 (2004)

Xu, M.S., Endres, R.G., Arakawa, Y.: The electronic properties of DNA bases. Small 3, 1539 (2007)CrossRef

Porath, D., Bezryadin, A., de Vries, S., Dekker, C.: Direct measurements of electrical transport through DNA molecules. Nature 403, 635 (2000)CrossRef

Kyrpides, N.C., Porath, D.: Nat. Biotechnol. 27, 627 (2009)CrossRef

Chan, E.Y.M.: Advances in sequencing technology. Research 573, 13 (2005)

Lee, J.W., Meller, A.: Perspectives in Bioanalysis. Elsevier, Amsterdam (2007)

Dovichi, N.J., Zhang, J.Z.A.: How capillary electrophoresis sequenced the human genome. Chem. Int. Ed. 39, 4463 (2000)CrossRef

10.

Michael, Z., Massimiliano, D.: Colloquium: physical approaches to DNA sequencing and detection. Rev. Modern Phys. 80, 141 (2008)CrossRef

11.

Venkatesan, B.M., Bashir, R.: Nanopore sensors for nucleic acid analysis. Nat. Nanotechnol. 6, 615 (2011)CrossRef

12.

Wanunu, M.: Nanopores: a journey towards DNA sequencing. Phys. Life Rev. 9, 125 (2012)CrossRef

13.

Dekker, C.: Solid-state nanopores. Nat. Nanotechnol. 2, 209 (2007)CrossRef

14.

McNally, B., Singer, A., Yu, Z., Sun, Y., Weng, Z., Meller, A.: Optical recognition of converted DNA nucleotides single-molecule DNA sequencing using nanopore arrays. Nano Lett. 10, 2237 (2010)CrossRef

15.

Merchant, C.A., Healy, K., Wanunu, M., Ray, V., Peterman, N., Bartel, J., Fischbein, M.D., Venta, K., Luo, Z., Johnson, A.T.C., Drndić, M.: DNA translocation through graphene nanopores. Nano Lett. 10, 2915 (2010)CrossRef

16.

Schneider, G.F., Kowalczyk, S.W., Calado, V.E., Pandraud, G., Zandbergen, H.W., Vandersypen, L.M., Dekker, C.: DNA translocation through graphene nanopores. Nano Lett. 10, 3163 (2010)CrossRef

17.

Garaj, S., Hubbard, W., Reina, A., Kong, J., Branton, D., Golovchenko, J.A.: Graphene as a subnanometer trans-electrode membrane. Nature 467, 190 (2010)CrossRef

18.

Traversi, F., Raillon, C., Benameur, S.M., Liu, K., Khlybov, S., Tosun, M., Krasnozhon, D., Kis, A., Radenovic, A.: Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nat. Nanotechnol. 8, 939 (2013)CrossRef

19.

Ouyang, F.P., Peng, S.L., Zhang, H., Weng, L.B., Xu, H.: A biosensor based on graphene nanoribbon with nanopores: a first-principles devices-design. Chin. Phys. B 20, 058504 (2011)CrossRef

20.

Chang, P., Liu, H., Nikolić, B.K.: First-principles versus semi-empirical modelling of global and local electronic transport properties of graphene nanopore-based sensors for DNA sequencing. J. Comput. Electron. 13, 847–856 (2014). https://doi.org/10.1007/s10825-014-0614-8CrossRef

21.

Kroto, H.W., Heath, J.R., Obrien, S.C., Curl, R.E., Smalley, R.F.: C60: Buckminsterfullerene. Nature 318, 162–163 (1985)CrossRef

22.

Zhao, P., Liu, D.S., Liu, H.Y., Li, S.J., Chen, G.: Low bias negative differential resistance in C60 dimer modulated by gate voltage. Org. Electron. 14(4), 1109–1115 (2013)CrossRef

23.

Prinzbach, H., Weiler, A., Landenberger, P., Wahl, F., Worth, J., Scott, L.T., Gelmont, M., Olevano, D., Issendorff, B.V.: Gas-phase production and photoelectron spectroscopy of the smallest fullerene, C20. Nature 407, 60–63 (2000)CrossRef

24.

Kaur, M., Sawhney, R.S., Engles, D.: Non-equilibrium tunnelling through Au-C20-Au molecular bridge using density functional theory-non-equilibrium green functional aaproach. J. Mater. Res. 1(14), 1–10 (2016). https://doi.org/10.1557/jmr.2016.170CrossRef

25.

Kaur, M., Sawhney, R.S., Engles, D.: Proliferating miller indices of C20 fullerene device under DFT-NEGF regime. J. Mol. Gr. Model. 71, 32 (2016). https://doi.org/10.1016/j.jmgm.2016.10.017CrossRef

26.

Kaur, M., Sawhney, R.S., Engles, D., Kaur, R.: Design of fullerene-based biomarker for detection of lead impurities. ICT Express 2, 4 (2016). https://doi.org/10.1016/j.icte.2016.11.001CrossRef

27.

Kaur, M., Sawhney, R.S., Engles, D.: Transport in fullerene device coupled to Cu, Ag and Au electrodes. Mol. Phys. 114(22), 1–10 (2016). https://doi.org/10.1080/00268976.2016.1226442CrossRef

28.

Otani, M., Ono, T., Hirose, K.: First-principles study of electron transport through C20 cages. Phys. Rev. B 69(12), 121408(R) (2004)CrossRef

29.

An, Y.P., Yang, C.L., Wang, M.S., Ma, X.G., Wang, D.H.: Curr. Appl. Phys. 10(1), 260–265 (2009)CrossRef

30.

Baei, M.T., Soltani, A., Torabi, P., Hosseini, F.: Formation and electronic structure of C20 fullerene transition metal clusters. Monatsheftefür Chemie-Chemical Monthly 145(9), 1401–1405 (2014)CrossRef

31.

Singh, G., Kaur, M., Mahajan, S., Sawhney, R.S.: To inquire the effects of doping on current characteristics of fullerene molecular junction device. Mater. Today Proc. 3(6), 2422–2429 (2016)CrossRef

32.

Zhai, H.J., Zhao, Y.F., Li, W.L., Chen, Q., Bai, H., Hu, H.S., Piazza, Z.A., Tian, W.J., Lu, H.G., Wu, Y.B., Mu, Y.W., Wei, G.F., Liu, Z.P., Li, J., Li, S.D., Wang, L.S.: Observation of an all-boron fullerene. Nat. Chem. 6, 727–731 (2014)CrossRef

33.

He, R., Zeng, X.C.: Electronic structures and electronic spectra of all-boron fullerene B40. Chem. Commun. 51, 3185–3188 (2015)CrossRef

34.

Yang, Z., Ji, Y.L., Lan, G., Xu, L.C., Liu, X., Xu, B.: Design molecular rectifier and photodetector with all-boron fullerene. Solid State Commun. 217, 38–42 (2015)CrossRef

35.

Dong, H., Hou, T., Lee, S.T., Li, Y.: New Ti-decorated B40 fullerene as a promising hydrogen storage material. Sci Rep. 5, 9952 (2015). https://doi.org/10.1038/srep09952CrossRef

36.

Dong, H., Lin, B., Gilmore, K., Hou, T., Lee, S.T., Li, Y.: B40 fullerene: an efficient material for CO2 capture, storage and separation. Curr. Appl. Phys. 15, 1084 (2015). https://doi.org/10.1016/j.cap.2015.06.008CrossRef

37.

Gao, G., Ma, F., Jiao, Y., Sun, Q., Jiao, Y., Waclawik, E., Du, A.: Modelling CO2 adsorption and separation on experimentally-realized B40 fullerene. Comput. Mater. Sci. 108, 38–41 (2015). https://doi.org/10.1016/j.commatsci.2015.06.005CrossRef

38.

Moradi, M., Vahabi, V., Bodaghi, A.: Computational study on the fullerene-like B40 borospherene properties and interaction with ammonia. J. Mol. Liq. 223, 315–320 (2016). https://doi.org/10.1016/j.molliq.2016.07.147CrossRef

39.

Tang, C., Zhang, X.: The hydrogen storage capacity of Sc atoms decorated porous boron fullerene B40: a DFT study. Int. J. Hydrogen Energy 41, 16992–16999 (2016). https://doi.org/10.1016/j.ijhydene.2016.07.118CrossRef

40.

Maniei, Z., Shakerzadeh, E., Mahdavifar, Z.: Theoretical approach into potential possibility of efficient NO2 detection via B40 and Li@B40 fullerene. Chem. Phys. Lett. 691, 360–365 (2018). https://doi.org/10.1016/j.cplett.2017.11.045CrossRef

41.

Lin, B., Dong, H., Du, C., Hou, T., Lin, H., Li, Y.: B40 fullerene as a highly sensitive molecular device for NH3 detection at low bias: a first-principles study. Nanotechnology 27, 075501 (2016). https://doi.org/10.1088/0957-4484/27/7/075501CrossRef

42.

Kaur, J., Kumar, R., Vohra, R., Sawhney, R.S.: A pursuit to design highly sensitive fullerene-based sensors: adsorption and dissociation phenomenon of toxic sulfur gases on B40 fullerene. J. Mol. Model. 26, 17 (2020). https://doi.org/10.1007/s00894-019-4279-xCrossRef

43.

Kaur, R., Kaur, J.: The electronic transport properties of B40 fullerenes with chalcogens as anchor atoms. J. Mol. Model. 23, 351 (2017). https://doi.org/10.1007/s00894-017-3520-8CrossRef

44.

Kaur, J., Kaur, R.: To delve about the charge transport properties of p-block elements doped M@B40(M = Al, Si, P, S) molecular device. In: 8 th ICCCNT, pp. 1–4 (2017). https://doi.org/10.1109/ICCCNT.2017.8203969

45.

Atomistic Toolkit Manual, Quantumwise Inc. Atomistix toolkit version 13.8.0, Quantumwise A/S (http://quantumwise.com)

46.

Xue, Y., Datta, S., Ratner, M.A.: First-principles based matrix Green’s function approach to molecular electronic devices: general formalism. Chem. Phys. 281, 151 (2002). https://doi.org/10.1016/S0301-0104(02)00446-9CrossRef

47.

Brandbyge, M., Mozos, J.L., Ordejon, P., Taylor, J., Stokbro, K.: Density-functional method for nonequilibrium electron transport. Phys. Rev. B 65, 165401 (2002). https://doi.org/10.1103/PhysRevB.65.165401CrossRef

48.

Taylor, J., Guo, H., Wang, J.: Ab initio modelling of quantum transport properties of molecular electronic devices. Phys. Rev. B 63, 245407 (2001). https://doi.org/10.1103/PhysRevB.63.245407CrossRef

49.

Carlo, A.D.: Tight-binding methods for transport and optical properties in realistic nanostructures. Phys. B 314, 211–219 (2002)MathSciNetCrossRef

50.

Pecchia, A., Carlo, A.D.: Atomistic theory of transport in organic and inorganic nanostructures. Rep. Prog. Phys. 67, 1497–1562 (2004)CrossRef

51.

Magoga, M., Joachim, C.: Conductance and transparence of long molecular wires. Phys. Rev. B 56(8), 4722–4729 (1997). https://doi.org/10.1103/PhysRevB.56.4722CrossRef

52.

Corbel, S., Cerda, J., Sautet, P.: Ab initio calculations of scanning tunnelling microscopy images within a scattering formalism. Phys. Rev. B 60, 1989–1999 (1999)CrossRef

53.

Cerdá, J., Soria, F.: Accurate and transferable extended Huckle-type tight-binding parameters. Phys. Rev. B 61(12), 7965–7971 (2000). https://doi.org/10.1103/PhysRevB.61.7965CrossRef

54.

Emberly, E.G., Kirczenow, G.: Multiterminal molecular wire systems: a self-consistent theory and computer simulations of charging and transport. Phys. Rev. B 62(15), 10451–10458 (2001). https://doi.org/10.1103/PhysRevB.62.10451CrossRef

55.

Zahid, F., Paulsson, M., Polizzi, E., Ghosh, A.W., Siddiqui, L., Datta, S.: A self-consistent transport model for molecular conduction based on extended Huckle theory with full three-dimensional electrostatics. J. Chem. Phys. 123, 064707 (2005). https://doi.org/10.1063/1.1961289CrossRef

56.

Kienle, D., Cerda, J.I., Ghosh, A.W.: Extended Huckle theory for band structure, chemistry, and transport. I. Carbon nanotubes. J. Appl. Phys. 100, 043714 (2006). https://doi.org/10.1063/1.2259818CrossRef

57.

Kienle, D., Bevan, K.H., Liang, G.C., Siddiqui, L., Cerda, J.I., Ghosh, A.W.: Extended Huckle theory for band structure, chemistry, and transport. II. Silicon. J. Appl. Phys. 100, 043715 (2006). https://doi.org/10.1063/1.2259820CrossRef

58.

Fronzi, M., Ssoon, A., Delley, B., Traversa, E., Stampfly, C.: Stability and morphology of cerium oxide surfaces in an oxidizing environment: a first-principle investigation. J. Chem. Phys. 131, 104701 (2009). https://doi.org/10.1063/1.3191784CrossRef

59.

Fronzi, M., Soon, A., Delley, B., Traversa, E., Stampfly, C.: Water adsorption on the stoichiometric and reduced CeO2(111) surface: a first-principles investigation. Phys. Chem. Phys. 11, 9188–9199 (2009)CrossRef

60.

Perdew, J.P., Burke, K., Ernzerhof, M.: Gernalized gradient approximation made simple. Phys Rev. Lett. 77, 3865 (1996). https://doi.org/10.1103/PhysRevLett.77.3865CrossRef

61.

Walia, G.K., Randhawa, D.K.: Electronic and transport properties of silicene-based ammonia nanosensors: an ab initio study. Struct. Chem. 29, 257 (2018)CrossRef

62.

Landauer, R.: Conductance determined by transmission: probes and quantised constriction resistance. J. Phys. Condens. Matter 1, 8099 (1989)CrossRef

63.

Heurich, J., Cuevas, J.C., Wenzel, W., Schon, G.: Electrical transport through single-molecule junctions: from molecular orbitals to conduction channels. Phys. Rev. Lett. 88, 256803 (2002). https://doi.org/10.1103/PhysRevLett.88.256803CrossRef

64.

Lawson, J.W., Bauschlieher, C.W.: Transport in molecular junctions with different metallic contacts. Phys Rev. B Condens. Matter Mater. Phys. 74, 125401 (2006). https://doi.org/10.1103/PhysRevB.74.125401CrossRef

65.

Datta, S.: Electronic transport in mesoscopic systems. Cambridge University Press, Cambridge (1995)CrossRef

66.

Cheng, S., Sun, X., Zhao, L., Chen, J.: The interaction of guanine nucleobase with B40 borospherene. Eur. Phys. J. D 73, 88 (2019). https://doi.org/10.1140/epjd/e2019-90357-0CrossRef

Title: Borospherene-based biomarker for DNA sequencing: a DFT study
Authors: Jupinder Kaur
Ravinder Kumar
Publication date: 07-07-2021
Publisher: Springer US
Published in: Journal of Computational Electronics / Issue 5/2021
Print ISSN: 1569-8025
Electronic ISSN: 1572-8137
DOI: https://doi.org/10.1007/s10825-021-01731-6

Springer Professional

Abstract

Please log in to get access to your license.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Other articles of this Issue 5/2021

Analysis and design of a passive spatial filter for sub-6 GHz 5G communication systems

A new design for improving the performance of AlGaN/GaN high-electron-mobility transistors

Design and analysis of SHE-assisted STT MTJ/CMOS logic gates

Mathematical modelling of a novel heterojunction SIS front surface and interdigitated back-contact solar cell

Analytical breakdown voltage model for a partial SOI-LDMOS transistor with a buried oxide step structure

Method to enhance resonant interlayer tunneling in bilayer-graphene systems