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Mohammad H, Anantram MP. Charge transport through DNA with energy-dependent decoherence. Phys Rev E 2023; 108:044403. [PMID: 37978586 DOI: 10.1103/physreve.108.044403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Abstract
Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron susceptible to decoherence. While knowledge of the Hamiltonian responsible for decoherence will provide a microscopic description, the interactions are complex and methods to calculate decoherence are unclear. One prominent phenomenological model to include decoherence is through fictitious probes that depend on spatially variant scattering rates. However, the built-in energy independence of the decoherence (E-indep) model overestimates the transmission in the bandgap and washes out distinct features inside the valence or conduction bands. In this study, we introduce a related model where the decoherence rate is energy-dependent (E-dep). This decoherence rate is maximum at energy levels and decays away from these energies. Our results show that the E-dep model allows for exponential transmission decay with the DNA length and maintains features within the bands' transmission spectra. We further demonstrate that we can obtain DNA conductance values within the experimental range. Our model can help study and design nanoelectronics devices that utilize weakly coupled molecular structures such as DNA.
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Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195, USA
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Mohammad H, Demir B, Akin C, Luan B, Hihath J, Oren EE, Anantram MP. Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics. NANOSCALE HORIZONS 2021; 6:651-660. [PMID: 34190284 DOI: 10.1039/d1nh00211b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively. The study on anthraquinone and anthraquinone-neomycin conjugate intercalation into short nucleic acids reveals some universal features: (1) the intercalation affects the transmission by two mechanisms: (a) inducing energy levels within the bandgap and (b) shifting the location of the Fermi energy with respect to the molecular orbitals of the nucleic acid, (2) the effect of intercalation was found to be dependent on the redox state of the intercalator: while oxidized anthraquinone decreases, reduced anthraquinone increases the conductance, and (3) the sequence of the intercalated nucleic acid further affects the transmission: lowering the AT-region length was found to enhance the electronic coupling of the intercalator with GC bases, hence yielding an increase of more than four times in conductance. We anticipate our study to inspire designing intercalator-nucleic acid complexes for potential use in molecular electronics via creating a multi-level gating effect.
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Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Caglanaz Akin
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research, Yorktown Heights, NY 10598, USA
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
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Wang DM, Jia J, Huang RF, Zhang X. A base-repair based electrochemiluminescent genotoxicity sensor that detects abasic sites in double-stranded DNA films. Chem Commun (Camb) 2021; 56:12558-12561. [PMID: 32940265 DOI: 10.1039/d0cc05186a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel genotoxicity sensor was developed based on the base repair process associated with the electrochemiluminescence (ECL) detection of abasic sites in a double-stranded DNA monolayer. This is the first time that an ECL sensor with the ability to identify the removed nucleobases in a DNA duplex has been studied. The successful detection of abasic sites created by DNA glycosylase indicates its further applications for examining some other specific types of DNA damage.
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Affiliation(s)
- Dong-Mei Wang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Jia Jia
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Rong-Fu Huang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
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