First-Principles Simulation of the Interaction Between DNA Nucleotides and One-Dimensional Carbon Chain in Electrical Based Sequencing
Electrical DNA sequencing has attracted significant attention in recent years due to its simplified sequencing protocol, compact sequencing system, and relatively low sequencing cost. In the design and fabrication of the sequencing device, carbon-based nanomaterials such as graphene have been explor...
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IEEE
2024-01-01
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| Series: | IEEE Open Journal of Nanotechnology |
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| Online Access: | https://ieeexplore.ieee.org/document/10663936/ |
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| author | Zeina Salman Jin-Woo Kim Steve Tung |
| author_facet | Zeina Salman Jin-Woo Kim Steve Tung |
| author_sort | Zeina Salman |
| collection | DOAJ |
| description | Electrical DNA sequencing has attracted significant attention in recent years due to its simplified sequencing protocol, compact sequencing system, and relatively low sequencing cost. In the design and fabrication of the sequencing device, carbon-based nanomaterials such as graphene have been explored as a promising sensing material that provides an excellent combination of spatial resolution and base specificity. Using first-principles simulation, we determined the effect on the electrical conductivity of a one-dimensional carbon chain due to the presence of four DNA bases. The simulation results indicate that the interaction between the carbon chain and different DNA bases leads to different levels of conductivity change in the carbon chain. Quantitatively, base A is the most difficult base to detect due to its relatively small current change. Furthermore, the results also show that the relative orientation of the bases with respect to the carbon chain can affect the induced current change in the chain. This information can be used to optimize the structural design of future sequencing devices. Collectively, the first-principles simulation results suggest the integration of a one-dimensional carbon chain with supporting nanofluidic designs can provide a viable approach towards the development of a compact, robust, and high-resolution DNA sequencing system. |
| format | Article |
| id | doaj-art-5e108e974c124f369655f1b51a6a7c3b |
| institution | Kabale University |
| issn | 2644-1292 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | IEEE |
| record_format | Article |
| series | IEEE Open Journal of Nanotechnology |
| spelling | doaj-art-5e108e974c124f369655f1b51a6a7c3b2025-01-24T00:02:24ZengIEEEIEEE Open Journal of Nanotechnology2644-12922024-01-015394610.1109/OJNANO.2024.345195410663936First-Principles Simulation of the Interaction Between DNA Nucleotides and One-Dimensional Carbon Chain in Electrical Based SequencingZeina Salman0Jin-Woo Kim1https://orcid.org/0000-0002-7119-8208Steve Tung2https://orcid.org/0000-0003-3713-4494Department of Mechanical Engineering, University of Arkansas, Fayetteville, AR, USADepartment of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR, USADepartment of Mechanical Engineering, University of Arkansas, Fayetteville, AR, USAElectrical DNA sequencing has attracted significant attention in recent years due to its simplified sequencing protocol, compact sequencing system, and relatively low sequencing cost. In the design and fabrication of the sequencing device, carbon-based nanomaterials such as graphene have been explored as a promising sensing material that provides an excellent combination of spatial resolution and base specificity. Using first-principles simulation, we determined the effect on the electrical conductivity of a one-dimensional carbon chain due to the presence of four DNA bases. The simulation results indicate that the interaction between the carbon chain and different DNA bases leads to different levels of conductivity change in the carbon chain. Quantitatively, base A is the most difficult base to detect due to its relatively small current change. Furthermore, the results also show that the relative orientation of the bases with respect to the carbon chain can affect the induced current change in the chain. This information can be used to optimize the structural design of future sequencing devices. Collectively, the first-principles simulation results suggest the integration of a one-dimensional carbon chain with supporting nanofluidic designs can provide a viable approach towards the development of a compact, robust, and high-resolution DNA sequencing system.https://ieeexplore.ieee.org/document/10663936/DNA sequencingone-dimensional materialpi stackingquantum simulation |
| spellingShingle | Zeina Salman Jin-Woo Kim Steve Tung First-Principles Simulation of the Interaction Between DNA Nucleotides and One-Dimensional Carbon Chain in Electrical Based Sequencing IEEE Open Journal of Nanotechnology DNA sequencing one-dimensional material pi stacking quantum simulation |
| title | First-Principles Simulation of the Interaction Between DNA Nucleotides and One-Dimensional Carbon Chain in Electrical Based Sequencing |
| title_full | First-Principles Simulation of the Interaction Between DNA Nucleotides and One-Dimensional Carbon Chain in Electrical Based Sequencing |
| title_fullStr | First-Principles Simulation of the Interaction Between DNA Nucleotides and One-Dimensional Carbon Chain in Electrical Based Sequencing |
| title_full_unstemmed | First-Principles Simulation of the Interaction Between DNA Nucleotides and One-Dimensional Carbon Chain in Electrical Based Sequencing |
| title_short | First-Principles Simulation of the Interaction Between DNA Nucleotides and One-Dimensional Carbon Chain in Electrical Based Sequencing |
| title_sort | first principles simulation of the interaction between dna nucleotides and one dimensional carbon chain in electrical based sequencing |
| topic | DNA sequencing one-dimensional material pi stacking quantum simulation |
| url | https://ieeexplore.ieee.org/document/10663936/ |
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