An electro-optical system for improving graphene nanopore DNA sequencing

Document Type : Article

Author

Department of Electrical and Computer Engineering, Tarbiat Modares University, Tehran, P.O. Box 14115-194, Iran

Abstract

I propose a new electro-optical system for sequencing single-stranded DNA molecules. The localized plasmons in graphene combined with the nanopore-based DNA translocation have been suggested for sequencing DNA molecules and decreasing the translocation speed. These localized surface plasmon resonances in the graphene nanopore have three dominant modes. Every-mode peak wavelength is shifted while the DNA nucleobases are presented to the nanopore. The ultraviolet photodiodes with narrow-band filters can separate each mode individually. Then, the electrical-current to voltage convertor, differential pairs based on the bipolar transistors, combine all modes in the effective output voltage. The output voltage level of the circuit is sensitive to the DNA presence and is unique for each DNA nucleobase. Analyzes have been performed for different central wavelengths and spectral width of the light source. Results show that the best sensitivity to the DNA molecule is 6.04, and the best selectivity is 1.1. These factors are directly related to the method's applicability for DNA translocation sensing and DNA sequencing; they are enormously improved. The proposed method and results shed light on a higher selectivity for DNA nucleobases which is the main bottleneck for nanopore DNA sequencing.

Keywords

References

References:
1. Taheri, H.E. and Mirhassani, M. "A low-power, high-resolution, adaptive sensitivity readout circuit with selective detection range for capacitive biosensors", AEU-Int. J. Electron. C., 131, 153599 (2021). https://doi.org/10.1016/j.aeue.2020.153599.
2. Buvaneswari, B. and Balamurugan, N.B. "2D analytical modeling and simulation of dual material DG MOSFET for biosensing application", AEUInt. J. Electron. C., 99, pp. 193-200 (2019).https://doi.org/10.1016/j.aeue.2018.11.039.
3. Sariki, A., Rao, K.V., Chandrasekar, L., et al. "Is accumulation or inversion mode dielectric modulated FET better for label-free biosensing?: A comparative investigation", AEU-Int. J. Electron. C., 137, 153791 (2021). https://doi.org/10.1016/j.aeue.2021.153791.
4. Khosravian, E., Mashayekhi, H.R., and Farmani, A. "Tunable plasmonics photodetector in near-infrared wavelengths using graphene chemical doping method", AEU-Int. J. Electron. C., 127, 153472 (2020). https://doi.org/10.1016/j.aeue.2020.153472.
5. Li, J., Yu, D., and Zhao, Q. "Solid-state nanoporebased DNA single molecule detection and sequencing", Microchim. Acta, 183(3), pp. 941-953 (2016). https://doi.org/10.1007/s00604-015-1542-4.
6. Arjmandi-Tash, H., Belyaeva, L.A., and Schneider, G.F. "Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond", Chem. Soc. Rev., 45(3), pp.476-493 (2016). https://doi.org/10.1039/C5CS00512D.
7. Pud, S., Verschueren, D., Vukovic, N., et al. "Selfaligned plasmonic nanopores by optically controlled dielectric breakdown", Nano Lett., 15(10), pp. 7112- 7117 (2015). https://doi.org/10.1021/acs.nanolett.5b03239.
8. Nam, S., Choi, I., Fu, C.C., et al. "Graphene nanopore with a self-integrated optical antenna", Nano Lett., 14(10), pp. 5584-5589 (2014).https://doi.org/10.1021/nl503159d.
9. Faramarzi, V., Ahmadi, V., Fotouhi, B., et al. "A potential sensing mechanism for DNA nucleobases by optical properties of GO and MoS2 nanopores", Sci. Rep., 9(1), pp. 1-11 (2019). https://doi.org/10.1038/s41598-019-41165-6.
10. Abasifard, M. Ahmadi, V. Fotouhi, B., et al. "DNA nucleobases sensing by localized plasmon resonances in graphene quantum dots with nanopore: A first principle approach", J. Phys. Chem. C., 123(41), pp. 25309-25319 (2019). https://doi.org/10.1021/acs.jpcc.9b05040.
11. Belkin, M., Chao, S.H., Jonsson, M.P., et al. "Plasmonic nanopores for trapping, controlling displacement, and sequencing of DNA", ACS Nano, 9(11), pp.10598-10611 (2015). https://doi.org/10.1021/acsnano.5b04173.
12. Faramarzi, V., Ahmadi, V., Heidari, M., et al. "Interband plasmon-enhanced optical absorption of DNA nucleobases through the graphene nanopore", Opt. Lett., 47(1), pp. 194-197 (2022). https://doi.org/10.1364/OL.443993.
13. Fotouhi, B., Ahmadi, V., and Abasifard, M. "Controlling DNA translocation speed through graphene nanopore via plasmonic fields", Sci. Iran, 25(3), pp. 1849-1856 (2018). https://doi.org/10.24200/SCI.2018.20419.
14. Gao, Y. and Neuhauser, D. "Dynamical quantumelectrodynamics embedding: Combining timedependent density functional theory and the near-field method", J. Chem. Phys., 137(7), 074113 (2012). https://doi.org/10.1063/1.4745847.
15. Pinchuk, A. "Optical constants and dielectric function of DNA's nucleotides in UV range", J. Quant. Spectrosc. Rad., 85(2), pp. 211-215 (2004). https://doi.org/10.1016/j.jqsrt.2003.08.004.
16. S12742-254 Datasheet, S12742-254.PDF, [Online]. Available: https://www.hamamatsu.com/eu/en /product/type/S12742-254/index.html.
17. Razavi, B., Fundamentals of Microelectronics, Ed., 3rd, John Wiley & Sons (2021).
18. MAX477 Datasheet, MAX477.PDF, [Online]. Available: https://www.alldatasheet.com/datasheet -pdf/pdf/ 73451/MAXIM/MAX477.html.
19. 2N3904 Datasheet, 2N3904.PDF, [Online]. Available: https://www.alldatasheet.com/datasheet-pdf/pdf/ 855281/ISC/2N3904.html.
20. Nurrohman, D.T. and Chiu, N.F. "A review of graphene-based surface plasmon resonance and surface-enhanced Raman scattering biosensors: Current status and future prospects", Nanomaterials., 11(1), p. 216 (2016). https://doi.org/10.3390/nano11010216.
21. Cui, L., Wang, J., and Sun, M. "Graphene plasmon for optoelectronics", Reviews in Physics, 6, 100054 (2021). https://doi.org/10.1016/j.revip.2021.100054.
22. Faramarzi, V., Ahmadi, V., Hwang, M.T., et al. "Highly sensitive crumpled 2D material-based plasmonic biosensors", Biomed. Opt. Express, 12(7), pp. 4544-4559 (2021). https://doi.org/10.1364/BOE.428537.
Scientia Iranica
Volume 30, Issue 6
Transactions on Computer Science & Engineering and Electrical Engineering (D)
November and December 2023
Pages 2162-2169

Files

History

  • Receive Date: 11 October 2021
  • Revise Date: 05 January 2022
  • Accept Date: 14 February 2022

Share

How to cite

Statistics