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. 2024 May 1;16(17):21427-21437.
doi: 10.1021/acsami.3c18400. Epub 2024 Apr 18.

Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS2 and Janus MoSSe Monolayers

Vasudeo Babar  1 , Sitansh Sharma  2 , Abdul Rajjak Shaikh  2 , Romina Oliva  3 , Mohit Chawla  1 , Luigi Cavallo  1
Affiliations

Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS2 and Janus MoSSe Monolayers

Vasudeo Babar et al. ACS Appl Mater Interfaces. .

Abstract

In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA nucleobase detection, owing to their impressive surface-to-volume ratio. This study employs density functional theory with van der Waals corrections to methodically scrutinize the adsorption behavior and electronic band structure properties of a DNA system composed of eight hachimoji nucleotide letters adsorbed on both MoS2 and MoSSe monolayers. Through a comprehensive conformational search, we pinpoint the most favorable adsorption sites, quantifying their adsorption energies and charge transfer properties. The analysis of electronic band structure unveils the emergence of flat bands in close proximity to the Fermi level post-adsorption, a departure from the pristine MoS2 and MoSSe monolayers. Furthermore, leveraging the nonequilibrium Green's function approach, we compute the current-voltage characteristics, providing valuable insights into the electronic transport properties of the system. All hachimoji bases exhibit physisorption with a horizontal orientation on both monolayers. Notably, base G demonstrates high sensitivity on both substrates. The obtained current-voltage (I-V) characteristics, both without and with base adsorption on MoS2 and the Se side of MoSSe, affirm excellent sensing performance. This research significantly advances our understanding of potential DNA sensing platforms and their electronic characteristics, thereby propelling the endeavor for personalized medicine through enhanced DNA sequencing technologies.

Keywords: 2D-materials; DNA sensing; MoS2; MoSSe; density functional theory.

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Conflict of interest statement

The authors declare the following competing financial interest(s): S.S. and A.R.S. were employed by the company STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India.

Figures

Figure 1
Figure 1
Molecular structures of hachimoji natural and modified DNA bases. In the representation, C, N, O, and H atoms are denoted by brown, gray, red, and pink balls, respectively.
Figure 2
Figure 2
Atomic structure with electronic band structure of the hexagonal unit cell in MoS2 and MoSSe monolayers. The Mo, S, and Se atoms are represented by purple, yellow, and green balls, respectively.
Figure 3
Figure 3
Lowest-energy configurations of natural (A, T, G, C) and modified (B, S, P, Z) base molecules on the MoS2 monolayer, with both top and side views. Mo, S, C, N, O, and H atoms are represented by purple, yellow, brown, gray, red, and pink balls, respectively.
Figure 4
Figure 4
Top and side perspectives of the lowest-energy conformations of natural (A, T, G, and C) and modified (B, S, P, and Z) base molecules on the selenium (Se) side of the MoSSe monolayer. Mo, S, Se, C, N, O, and H atoms are depicted by purple, yellow, green, brown, gray, red, and pink balls, respectively.
Figure 5
Figure 5
Visualization of 3D-NCI plots depicting interaction profiles for (a) G base, (b) T base, (c) B base, and (d) S base on the MoS2 surface. Additionally, (e) G base and (f) T base, along with (g) B base and (h) S base on MoSSe_Se surface. The accompanying neighboring graph showcases 2D-NCI plots representing the reduced density gradient (s) against the sign of the Laplacian of electron density (l2*r) in atomic units.
Figure 6
Figure 6
Top and side views of the charge density difference induced by adsorption base molecules on the MoS2 monolayer. Magenta and cyan isosurfaces represent charge accumulation and depletion, respectively (isosurface value: 5.0 × 10–4 electrons/Å3).
Figure 7
Figure 7
Top and side views of the charge density difference induced by adsorption base molecules on the MoSSe_Se monolayer. Magenta and cyan isosurfaces represent charge accumulation and depletion, respectively (isosurface value: 5.0 × 10–4 electrons/Å3).
Figure 8
Figure 8
Electronic band structure of the natural (A, T, G, C) and modified (B, S, P, Z) base molecules on the MoS2 monolayer. Molecular contributions are highlighted in red color.
Figure 9
Figure 9
Electronic band structure of the natural (A, T, G, C) and modified (B, S, P, Z) base molecules on the MoSSe_Se monolayer. Molecular contributions are highlighted in red color.
Figure 10
Figure 10
Transport setup and current–voltage characteristics of MoS2 and MoSSe_Se monolayers in armchair and zigzag directions, with and without adsorbed base molecules. The insets display the current value for base molecules on both monolayers at an applied voltage of 2.4 V. The horizontal line represents the current value for pure monolayers.
Figure 11
Figure 11
Sensitivity plots for base molecules on monolayers of MoS2 and MoSSe (Se side) at an applied voltage of 2.4 V.
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References

    1. Li F.; Huang Y.; Yang Q.; Zhong Z.; Li D.; Wang L.; Song S.; Fan C. A Graphene-Enhanced Molecular Beacon for Homogeneous DNA Detection. Nanoscale 2010, 2 (6), 1021–1026. 10.1039/b9nr00401g. - DOI - PubMed
    1. He S.; Song B.; Li D.; Zhu C.; Qi W.; Wen Y.; Wang L.; Song S.; Fang H.; Fan C. A Graphene Nanoprobe for Rapid, Sensitive, and Multicolor Fluorescent DNA Analysis. Adv. Funct. Mater. 2010, 20 (3), 453–459. 10.1002/adfm.200901639. - DOI
    1. Kumar S. Epigenomics of Plant Responses to Environmental Stress. Epigenomes 2018, 2 (1), 6.10.3390/epigenomes2010006. - DOI
    1. Hikida Y.; Kimoto M.; Yokoyama S.; Hirao I. Site-Specific Fluorescent Probing of RNA Molecules by Unnatural Base-Pair Transcription for Local Structural Conformation Analysis. Nat. Protoc. 2010, 5, 1312–1323. 10.1038/nprot.2010.77. - DOI - PubMed
    1. Kimoto M.; Mitsui T.; Yamashige R.; Sato A.; Yokoyama S.; Hirao I. A New Unnatural Base Pair System Between Fluorophore and Quencher Base Analogues for Nucleic Acid-Based Imaging Technology. J. Am. Chem. Soc. 2010, 132, 15418–15426. 10.1021/ja1072383. - DOI - PubMed