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Wang K, Deng P, Lin H, Sun W, Shen J. DNA-Based Conductors: From Materials Design to Ultra-Scaled Electronics. SMALL METHODS 2024:e2400694. [PMID: 39049716 DOI: 10.1002/smtd.202400694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/04/2024] [Indexed: 07/27/2024]
Abstract
Photolithography has been the foundational fabrication paradigm in current high-performance electronics. However, due to the limitation in fabrication resolution, scaling beyond a 20-nm critical dimension for metal conductors presents a significant challenge for photolithography. Structural DNA nanotechnology emerges as a promising alternative to photolithography, allowing for the site-specific assembly of nano-materials at single-molecule resolution. Substantial progresses have been achieved in the ultra-scaled DNA-based conductors, exhibiting novel transport characteristics and small critical dimensions. This review highlights the structure-transport property relationship for various DNA-based conductors and their potential applications in quantum /semiconductor electronics, going beyond the conventional scope focusing mainly on the shape diversity of DNA-templated metals. Different material synthesis methods and their morphological impacts on the conductivities are discussed in detail, with particular emphasis on the conducting mechanisms, such as insulating, metallic conducting, quantum tunneling, and superconducting. Furthermore, the ionic gating effect of self-assembled DNA structures in electrolyte solutions is examined. This review also suggests potential solutions to address current challenges in DNA-based conductors, encouraging multi-disciplinary collaborations for the future development of this exciting area.
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Affiliation(s)
- Kexin Wang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Pu Deng
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Huili Lin
- School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Wei Sun
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
- Zhangjiang Laboratory, Shanghai, 201210, China
| | - Jie Shen
- School of Materials Science and Engineering, Peking University, Beijing, 100871, China
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2
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Polycarpou G, Skourtis SS. Intra-strand phosphate-mediated pathways in microsolvated double-stranded DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:375301. [PMID: 38848732 DOI: 10.1088/1361-648x/ad559d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/07/2024] [Indexed: 06/09/2024]
Abstract
We argue that dry DNA charge transport in molecular junctions, over distances of tens of nanometers, can take place via independent intra-strand pathways involving the phosphate groups. Such pathways explain recent single-molecule experiments that compare currents in intact and nicked 100 base-pair double-stranded DNA. We explore the conditions that favor independent intra-strand transport channels with the participation of the phosphate groups, as opposed to purely base-mediated transport involving the pi-stacked bases and inter-strand transitions. Our computations demonstrate how long-distance transport pathways in DNA are tuned by the degree of solvation, which affects the level of dynamic disorder in the pi-stacking, and the energies of phosphate-group molecular orbitals.
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3
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Song Y, Gao Y, Fang H. Unexpected large charge transfer rate mediated by adenine in twisted DNA structure. Phys Rev E 2024; 109:064412. [PMID: 39020924 DOI: 10.1103/physreve.109.064412] [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: 06/21/2023] [Accepted: 04/15/2024] [Indexed: 07/20/2024]
Abstract
DNA exhibits remarkable charge transfer ability, which is crucial for its biological functions and potential electronic applications. The charge transfer process in DNA is widely recognized as primarily mediated by guanine, while the contribution of other nucleobases is negligible. Using the tight-binding models in conjunction with first-principles calculations, we investigated the charge transfer behavior of homogeneous GC and AT pairs. We found that the charge transfer rate of adenine significantly changes. With overstretching, the charge transfer rate of adenine can even surpass that of guanine, by as much as five orders of magnitude at a twist angle of around 26°. Further analysis reveals that it is attributed to the turnover of the relative coupling strength between homogeneous GC and AT base pairs, which is caused by the symmetry exchange between the two highest occupied molecular orbitals of base pairs occurring at different twist angles. Given the high degree of flexibility of DNA in vivo and in vitro conditions, these findings prompt us to reconsider the mechanism of biological functions concerning the charge transfer in DNA molecules and further open the potential of DNA as a biomaterial for electronic applications.
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4
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Subramanian V, Das S, Gavini V. Tucker Tensor Approach for Accelerating Fock Exchange Computations in a Real-Space Finite-Element Discretization of Generalized Kohn-Sham Density Functional Theory. J Chem Theory Comput 2024; 20:3566-3579. [PMID: 38661129 DOI: 10.1021/acs.jctc.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The evaluation of Fock exchange is often the computationally most expensive part of hybrid functional density functional theory calculations in a systematically improvable, complete basis. In this work, we employ a Tucker tensor based approach that substantially accelerates the evaluation of the action of Fock exchange by transforming three-dimensional convolutional integrals into a tensor product of one-dimensional convolution integrals. Our numerical implementation uses a parallelization strategy that balances the memory and communication bottlenecks, alongside overlapping compute and communication operations to enhance computational efficiency and parallel scalability. The accuracy and computational efficiency are demonstrated on various systems, including Pt clusters of various sizes and a TiO2 cluster with 3684 electrons.
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Affiliation(s)
- Vishal Subramanian
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sambit Das
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vikram Gavini
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Wang L, Bin Q, Liu H, Zhang Y, Wang S, Luo S, Chen Z, Zhang M, Yu K. New insights into the on-site monitoring of probiotics eDNA using biosensing technology for heat-stress relieving in coral reefs. Biosens Bioelectron 2024; 243:115790. [PMID: 37906999 DOI: 10.1016/j.bios.2023.115790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023]
Abstract
Coral probiotics can improve the tolerance of corals to heat stress, thus mitigating the process of coral thermal bleaching. Sensitive and specific detection of coral probiotics at low abundances is highly desirable but remains challenging, especially for rapid and on-site detection of coral probiotics. Since the electrochemical biosensor has been recently used in the field of environmental DNA (eDNA) detection, herein, an efficient electrochemical biosensor was developed based on CoS2/CoSe2-NC HNCs electrode material with a specific DNA probe for the C. marina detection. After optimization, the lower limit of detection (LOD) values of such biosensors for the target DNA and genomic DNA were 1.58 fM and 6.5 pM, respectively. On this basis, a portable device was constructed for the practical detection of C. marina eDNA, and its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). For each analysis, the average cost was only ∼ $1.08 and could be completed within 100 min with reliable sensitivity and specificity. Overall, the biosensor could reflect the protective effect of probiotics on coral heat stress, and the proposed technique will put new insights into the rapid and on-site detection of coral probiotics to assist corals against global warming.
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Affiliation(s)
- Liwei Wang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China; Guangxi, Key Laboratory of Processing for Non-ferrous Metallic and Featured Materials, Nanning, 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qi Bin
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Hongjie Liu
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Yibo Zhang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Shaopeng Wang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Songlin Luo
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Zhenghua Chen
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China
| | - Man Zhang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China.
| | - Kefu Yu
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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6
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Liu L, Zou Y, Xia T, Zhang J, Xiong M, Long L, Wang K, Hao N. A double-quenching paperclip ECL biosensing platform for ultrasensitive detection of antibiotic resistance genes (mecA) based on Ti 3C 2 MXene-Au NPs as a coreactant accelerator. Biosens Bioelectron 2023; 240:115651. [PMID: 37666010 DOI: 10.1016/j.bios.2023.115651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
The global spread of environmental biological pollutants, such as antibiotic-resistant bacteria and their antibiotic resistance genes (ARGs), has emerged as a critical public health concern. It is imperative to address this pressing issue due to its potential implications for public health. Herein, a DNA paperclip probe with double-quenching function of target cyclic cleavage was proposed, and an electrochemiluminescence (ECL) biosensing platform was constructed using Ti3C2 MXene in-situ reduction growth of Au NPs (TCM-Au) as a coreactant accelerator, and applied to the sensitive detection of ARGs. Thanks to the excellent catalytic performance, large surface area and Au-S affinity of TCM-Au, the ECL performance of CdS QDs have been significantly improved. By cleverly utilizing the negative charge of the paperclip nucleic acid probe and its modification group, double-quenching of the ECL signal was achieved. This innovative approach, combined with target cyclic amplification, facilitated specific and sensitive detection of the mecA gene. This biosensing platform manifested highly selective and sensitive determination of mecA genes in the range of 10 fM to 100 nM and a low detection limit of 2.7 fM. The credible detectability and anti-interference were demonstrated in Yangtze river and Aeration tank outlet, indicating its promising application toward pollution monitoring of ARGs.
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Affiliation(s)
- Liqi Liu
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Yi Zou
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Tiantian Xia
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Jiadong Zhang
- Key Laboratory for Palygorskite Science and Applied Technology of Jiangsu, National & Local Joint Engineering Research Center for Mineral Salt Deep Utilization, School of Chemical Engineering, Huaiyin Institute of Technology, Huaian, 223003, PR China
| | - Meng Xiong
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, PR China
| | - Lingliang Long
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Kun Wang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China.
| | - Nan Hao
- School of Chemistry and Materials Science, Nanjing University of Information Science & Technology, Nanjing, 210044, PR China.
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7
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Chandra S, Williams A, Maksudov F, Kliuchnikov E, Pattiya Arachchillage KGG, Piscitelli P, Castillo A, Marx KA, Barsegov V, Artes Vivancos JM. Charge transport in individual short base stacked single-stranded RNA molecules. Sci Rep 2023; 13:19858. [PMID: 37963922 PMCID: PMC10645971 DOI: 10.1038/s41598-023-46263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure the electrical conductance of particular 5-base and 10-base single-stranded (ss) RNA sequences capable of base stacking. These ssRNA sequences show single-molecule conductance values around [Formula: see text] ([Formula: see text]), while equivalent-length ssDNAs result in featureless conductance histograms. Circular dichroism (CD) spectra and MD simulations reveal the existence of extended ssRNA conformations versus folded ssDNA conformations, consistent with their different electrical behaviors. Computational molecular modeling and Machine Learning-assisted interpretation of CD data helped us to disentangle the structural and electronic factors underlying CT, thus explaining the observed electrical behavior differences. RNA with a measurable conductance corresponds to sequences with overall extended base-stacking stabilized conformations characterized by lower HOMO energy levels delocalized over a base-stacking mediating CT pathway. In contrast, DNA and a control RNA sequence without significant base-stacking tend to form closed structures and thus are incapable of efficient CT.
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Affiliation(s)
- Subrata Chandra
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Ajoke Williams
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | | | | | - Patrick Piscitelli
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Aderlyn Castillo
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA.
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8
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Wang J, Zhao Y, Li S, Shen L, Zhang H, Ding C, Wei C, Wang Y, Li Y, Hong W, Li M. Composition and sequence-controlled conductance of crystalline unimolecular monolayers. SCIENCE ADVANCES 2023; 9:eadh0667. [PMID: 37327333 DOI: 10.1126/sciadv.adh0667] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/12/2023] [Indexed: 06/18/2023]
Abstract
Understanding how the charge travels through sequence-controlled molecules has been a formidable challenge because of simultaneous requirements in well-controlled synthesis and well-manipulated orientation. Here, we report electrically driven simultaneous synthesis and crystallization as a general strategy to study the conductance of composition and sequence-controlled unioligomer and unipolymer monolayers. The structural disorder of molecules and conductance variations on random positions can be extremely minimized, by uniform synthesis of monolayers unidirectionally sandwiched between electrodes, as an important prerequisite for the reproducible measurement on the micrometer scale. These monolayers show tunable current density and on/off ratios in four orders of magnitude with controlled multistate and massive negative differential resistance (NDR) effects. The conductance of monolayer mainly depends on the metal species in homo-metal monolayers, while the sequence becomes a matter in hetero-metal monolayers. Our work demonstrates a promising way to release an ultra-rich variety of electrical parameters and optimize the functions and performances of multilevel resistive devices.
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Affiliation(s)
- Jinxin Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yongjie Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shumu Li
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing Mass Spectrum Center, Beijing 100190, China
| | - Lingyun Shen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Hao Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Caijun Ding
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Chang Wei
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yanfang Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Yongfang Li
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Mao Li
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
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9
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Demir B, Mohammad H, Anantram MP, Oren EE. DNA-Au (111) interactions and transverse charge transport properties for DNA-based electronic devices. Phys Chem Chem Phys 2023. [PMID: 37309195 DOI: 10.1039/d2cp05009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA's charge transfer and self-assembly characteristics have made it a hallmark of molecular electronics for the past two decades. A fast and efficient charge transfer mechanism with programmable properties using DNA nanostructures is required for DNA-based nanoelectronic applications and devices. The ability to integrate DNA with inorganic substrates becomes critical in this process. Such integrations may affect the conformation of DNA, altering its charge transport properties. Thus, using molecular dynamics simulations and first-principles calculations in conjunction with Green's function approach, we explore the impact of the Au (111) substrate on the conformation of DNA and analyze its effect on the charge transport. Our results indicate that DNA sequence, leading to its molecular conformation on the Au substrate, is critical to engineer charge transport properties. We demonstrate that DNA fluctuates on a gold substrate, sampling various distinct conformations over time. The energy levels, spatial locations of molecular orbitals and the DNA/Au contact atoms can differ between these distinct conformations. Depending on the sequence, at the HOMO, the charge transmission differs up to 60 times between the top ten conformations. We demonstrate that the relative positions of the nucleobases are critical in determining the conformations and the coupling between orbitals. We anticipate that these results can be extended to other inorganic surfaces and pave the way for understanding DNA-inorganic interface interactions for future DNA-based electronic device applications.
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Affiliation(s)
- Busra Demir
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey.
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
- Department of Electrical and Computer Engineering, University of Washington, 98195 Seattle, WA, USA
| | - 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, 98195 Seattle, WA, USA
| | - Ersin Emre Oren
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey.
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
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10
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Gao D, Tang Z, Chen X, Wu R, Tian Y, Min Q, Zhang JR, Chen Z, Zhu JJ. Reversible Regulation of Long-Distance Charge Transport in DNA Nanowires by Dynamically Controlling Steric Conformation. NANO LETTERS 2023; 23:4201-4208. [PMID: 37188354 DOI: 10.1021/acs.nanolett.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Understanding of DNA-mediated charge transport (CT) is significant for exploring circuits at the molecular scale. However, the fabrication of robust DNA wires remains challenging due to the persistence length and natural flexibility of DNA molecules. Moreover, CT regulation in DNA wires often relies on predesigned sequences, which limit their application and scalability. Here, we addressed these issues by preparing self-assembled DNA nanowires with lengths of 30-120 nm using structural DNA nanotechnology. We employed these nanowires to plug individual gold nanoparticles into a circuit and measured the transport current in nanowires with an optical imaging technique. Contrary to the reported cases with shallow or no length dependence, a fair current attenuation was observed with increasing nanowire length, which experimentally confirmed the prediction of the incoherent hopping model. We also reported a mechanism for the reversible CT regulation in DNA nanowires, which involves dynamic transitions in the steric conformation.
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Affiliation(s)
- Di Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zhuodong Tang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xueqin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Rong Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zixuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, People's Republic of China
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11
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Panneer Selvam S, Cho S. Phosphate-driven H 2O 2 decomposition on DNA-bound bio-inspired activated carbon-based sensing platform for biological and food samples. Food Chem 2023; 421:136234. [PMID: 37119688 DOI: 10.1016/j.foodchem.2023.136234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
Hydrogen peroxide (H2O2) is one of the most important reactive oxygen species (ROS). Increased endogenous H2O2 levels indicate oxidative stress and could be a potential marker of many diseases, including Alzheimer's, cardiovascular diseases, and diabetes. However, consuming H2O2-incorporated food has adverse effects on humans and is a serious health concern. We used salmon testes DNA with bio-inspired activated carbon (AC) as an electrocatalyst for developing a novel H2O2 sensor. The phosphate backbone of DNA contains negatively charged oxygen groups that specifically attract protons from H2O2 reduction. We observed a linearity range of 0.01-250.0 μM in the H2O2 reduction peak current with a detection limit of 2.5 and 45.7 nM for chronoamperometric and differential pulse voltammetric studies. High biocompatibility of the sensor was achieved by the DNA, facilitating endogenous H2O2 detection. Moreover, this non-enzymatic sensor could also help in the rapid screening of H2O2-contaminated foods.
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Affiliation(s)
- Sathish Panneer Selvam
- Department of Electronic Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13210, Korea
| | - Sungbo Cho
- Department of Electronic Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13210, Korea; Gachon Advanced Institute for Health Science & Technology, Gachon University, Incheon 21999, Korea.
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12
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Kanungo B, Rufus ND, Gavini V. Efficient All-Electron Time-Dependent Density Functional Theory Calculations Using an Enriched Finite Element Basis. J Chem Theory Comput 2023; 19:978-991. [PMID: 36656153 DOI: 10.1021/acs.jctc.2c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We present an efficient and systematically convergent approach to all-electron real-time time-dependent density functional theory (TDDFT) calculations using a mixed basis, termed as enriched finite element (EFE) basis. The EFE basis augments the classical finite element basis (CFE) with a compactly supported numerical atom-centered basis, obtained from atomic ground-state DFT calculations. Particularly, we orthogonalize the enrichment functions with respect to the classical finite element basis to ensure good conditioning of the resultant basis. We employ the second-order Magnus propagator in conjunction with an adaptive Krylov subspace method for efficient time evolution of the Kohn-Sham orbitals. We rely on a priori error estimates to guide our choice of an adaptive finite element mesh as well as the time step to be used in the TDDFT calculations. We observe close to optimal rates of convergence of the dipole moment with respect to spatial and temporal discretizations. Notably, we attain a 50-100 times speedup for the EFE basis over the CFE basis. We also demonstrate the efficacy of the EFE basis for both linear and nonlinear responses by studying the absorption spectra in sodium clusters, the linear to nonlinear response transition in the green fluorescence protein chromophore, and the higher harmonic generation in the magnesium dimer. Lastly, we attain good parallel scalability of our numerical implementation of the EFE basis for up to ∼1000 processors, using a benchmark system of a 50-atom sodium nanocluster.
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Affiliation(s)
- Bikash Kanungo
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan48109, United States
| | - Nelson D Rufus
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan48109, United States
| | - Vikram Gavini
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan48109, United States.,Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan48109, United States
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13
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Chen X, Yan B, Yao G. Towards atom manufacturing with framework nucleic acids. NANOTECHNOLOGY 2023; 34:172002. [PMID: 36669170 DOI: 10.1088/1361-6528/acb4f2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Atom manufacturing has become a blooming frontier direction in the field of material and chemical science in recent years, focusing on the fabrication of functional materials and devices with individual atoms or with atomic precision. Framework nucleic acids (FNAs) refer to nanoscale nucleic acid framework structures with novel properties distinct from those of conventional nucleic acids. Due to their ability to be precisely positioned and assembled at the nanometer or even atomic scale, FNAs are ideal materials for atom manufacturing. They hold great promise for the bottom-up construction of electronic devices by precisely arranging and integrating building blocks with atomic or near-atomic precision. In this review, we summarize the progress of atom manufacturing based on FNAs. We begin by introducing the atomic-precision construction of FNAs and the intrinsic electrical properties of DNA molecules. Then, we describe various approaches for the fabrication of FNAs templated materials and devices, which are classified as conducting, insulating, or semiconducting based on their electrical properties. We highlight the role of FNAs in the fabrication of functional electronic devices with atomic precision, as well as the challenges and opportunities for atom manufacturing with FNAs.
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Affiliation(s)
- Xiaoliang Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Bingjie Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Guangbao Yao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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14
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Zinelli R, Soni S, Cornelissen JJLM, Michel-Souzy S, Nijhuis CA. Charge Transport across Proteins inside Proteins: Tunneling across Encapsulin Protein Cages and the Effect of Cargo Proteins. Biomolecules 2023; 13:174. [PMID: 36671559 PMCID: PMC9855946 DOI: 10.3390/biom13010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Charge transport across proteins can be surprisingly efficient over long distances-so-called long-range tunneling-but it is still unclear as to why and under which conditions (e.g., presence of co-factors, type of cargo) the long-range tunneling regime can be accessed. This paper describes molecular tunneling junctions based on an encapsulin (Enc), which is a large protein cage with a diameter of 24 nm that can be loaded with various types of (small) proteins, also referred to as "cargo". We demonstrate with dynamic light scattering, transmission electron microscopy, and atomic force microscopy that Enc, with and without cargo, can be made stable in solution and immobilized on metal electrodes without aggregation. We investigated the electronic properties of Enc in EGaIn-based tunnel junctions (EGaIn = eutectic alloy of Ga and In that is widely used to contact (bio)molecular monolayers) by measuring the current density for a large range of applied bias of ±2.5 V. The encapsulated cargo has an important effect on the electrical properties of the junctions. The measured current densities are higher for junctions with Enc loaded with redox-active cargo (ferritin-like protein) than those junctions without cargo or redox-inactive cargo (green fluorescent protein). These findings open the door to charge transport studies across complex biomolecular hierarchical structures.
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Affiliation(s)
- Riccardo Zinelli
- Hybrid Materials for Opto-Electronics Group, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
- Biomolecular NanoTechnology, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
| | - Saurabh Soni
- Hybrid Materials for Opto-Electronics Group, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Biomolecular NanoTechnology, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
| | - Sandra Michel-Souzy
- Biomolecular NanoTechnology, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
| | - Christian A. Nijhuis
- Hybrid Materials for Opto-Electronics Group, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
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15
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Heo W, Seo J, Lee Y, Kim Y. Fluid-driven DNA stretching for single-molecule studies on chromatin-associated proteins. Biochem Biophys Res Commun 2022; 634:122-128. [DOI: 10.1016/j.bbrc.2022.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022]
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16
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Sharma N, Srivastava S. Diagnosis of Pancreatic Cancer Using miRNA30e Biosensor. Interdiscip Sci 2022; 14:804-813. [PMID: 35781212 DOI: 10.1007/s12539-022-00531-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
This work describes miRNA-based electrochemical biosensor for detection of miRNA30e, a pancreatic cancer biomarker. The screen-printed gold electrode was functionalized using cysteine hydrochloride followed by immobilization of synthesized colloidal gold nanorods (10-12 nm diameter and 25-65 nm length). The gold nanorods modified electrode surface was amino functionalized for covalent attachment of single-stranded DNA probe against miRNA30e (miR30e). This platform was utilized for electrochemical measurements and response analysis of target miRNA30e. Electrochemical impedance spectroscopic measurements showed very poor sensitivity (13.51 Ω/µg/mL/cm2) using charge transfer resistance calibration plots. Cyclic voltammetry and differential pulse voltammetry-based miR30e quantification showed decreasing current response with increasing concentration of miR30e with detection range of 0.1 fg/mL-0.1 µg/mL (14.9 aM-14.9 nM). The sensitivity of DPV sensing (104.4 µA/µg/mL/cm2) was found to be 1.3 times higher than that of CV-based quantification (79.6 µA/µg/mL/cm2). miRNA-based biosensors have the potential of replacing current invasive, time consuming and technically difficult diagnostic procedures. Furthermore, the lower limit of detection of 14.9 aM miRNA30e makes it a promising tool for detection of cancer at early stages and hence increasing survival rate.
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Affiliation(s)
- Namita Sharma
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, UP, India
| | - Sudha Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, UP, India.
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17
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Nandi S, Coane C, Villegas AE, Ray A, Di Felice R. The impact of G-quadruplex dynamics on inter-tetrad electronic couplings: a hybrid computational study. Phys Chem Chem Phys 2022; 24:22513-22522. [PMID: 36106845 DOI: 10.1039/d2cp03505g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The G-quadruplex is a fascinating nucleic acid motif with implications in biology, medicine, and nanotechnologies. G-quadruplexes can form in the telomeres at the edges of chromosomes and in other guanine-rich regions of the genome. They can also be engineered for exploitation as biological materials for nanodevices. Their higher stiffness and higher charge transfer rates make them better candidates in nanodevices than duplex DNA. For the development of molecular nanowires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that structural changes have on electron transport. Here, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure-function relationship is complex. A single helix shape parameter alone does not embody such complexity, but rather a combination of distances and angles between stacked bases influences charge transfer efficiency. By analyzing linear combinations of shape descriptors for different topologies, we identify the structural features that most affect charge transfer efficiency. We discuss the transferability of the proposed model and the limiting effects of inherent flexibility.
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Affiliation(s)
- Samprita Nandi
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Colin Coane
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Angel-Emilio Villegas
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Angana Ray
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rosa Di Felice
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA. .,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.,CNR Institute of Nanoscience, 41125 Modena, Italy
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18
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Lai Liang F, Segal D. Long-range charge transport in homogeneous and alternating-rigidity chains. J Chem Phys 2022; 157:104106. [DOI: 10.1063/5.0101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the interplay of intrinsic-electronic and environmental factors in long-range charge transport across molecular chains with up to N ∼ 80 monomers. We describe the molecular electronic structure of the chain with a tight-binding Hamiltonian. Thermal effects in the form of electron decoherence and inelastic scattering are incorporated with the Landauer–Büttiker probe method. In short chains of up to ten units, we observe the crossover between coherent (tunneling, ballistic) motion and thermally-assisted conduction, with thermal effects enhancing the current beyond the quantum coherent limit. We further show that unconventional (nonmonotonic with size) transport behavior emerges when monomer-to-monomer electronic coupling is made large. In long chains, we identify a different behavior, with thermal effects suppressing the conductance below the coherent-ballistic limit. With the goal to identify a minimal model for molecular chains displaying unconventional and effective long-range transport, we simulate a modular polymer with alternating regions of high and low rigidity. Simulations show that, surprisingly, while charge correlations are significantly affected by structuring environmental conditions, reflecting charge delocalization, the electrical resistance displays an averaging effect, and it is not sensitive to this patterning. We conclude by arguing that efficient long-range charge transport requires engineering both internal electronic parameters and environmental conditions.
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Affiliation(s)
- Francisco Lai Liang
- Department of Chemistry and Centre for Quantum Information and Quantum Control, University of Toronto, 80 Saint George St., Toronto, Ontario M5S 3H6, Canada
| | - Dvira Segal
- Department of Chemistry and Centre for Quantum Information and Quantum Control, University of Toronto, 80 Saint George St., Toronto, Ontario M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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19
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Pavc D, Sebastian N, Spindler L, Drevenšek-Olenik I, Podboršek GK, Plavec J, Šket P. Understanding self-assembly at molecular level enables controlled design of DNA G-wires of different properties. Nat Commun 2022; 13:1062. [PMID: 35217667 PMCID: PMC8881451 DOI: 10.1038/s41467-022-28726-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022] Open
Abstract
A possible engineering of materials with diverse bio- and nano-applications relies on robust self-assembly of oligonucleotides. Bottom-up approach utilizing guanine-rich DNA oligonucleotides can lead to formation of G-wires, nanostructures consisting of continuous stacks of G-quartets. However, G-wire structure and self-assembly process remain poorly understood, although they are crucial for optimizing properties needed for specific applications. Herein, we use nuclear magnetic resonance to get insights at molecular level on how chosen short, guanine-rich oligonucleotides self-assemble into G-wires, whereas complementary methods are used for their characterization. Additionally, unravelling mechanistic details enable us to guide G-wire self-assembly in a controlled manner. MD simulations provide insight why loop residues with considerably different properties, i.e., hydrogen-bond affinity, stacking interactions, electronic effects and hydrophobicity extensively increase or decrease G-wire length. Our results provide fundamental understanding of G-wire self-assembly process useful for future design of nanomaterials with specific properties. G-wire structures have potential applications in bio-nanotechnology, however, this is limited by a lack of understanding about the assembly process and structures formed. Here, the authors use nuclear magnetic resonance and molecular dynamic simulations to understand the guiding principles of G-wire assembly.
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Affiliation(s)
- Daša Pavc
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Nerea Sebastian
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia
| | - Lea Spindler
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia.,Faculty of Mechanical Engineering, University of Maribor, 2000, Maribor, Slovenia
| | - Irena Drevenšek-Olenik
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia.,Faculty of Mathematics and Physics, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Gorazd Koderman Podboršek
- Department of Materials Chemistry, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.,EN-FIST, Center of Excellence, 1000, Ljubljana, Slovenia
| | - Primož Šket
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.
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20
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Chandra S, Gunasinghe Pattiya Arachchillage KG, Kliuchnikov E, Maksudov F, Ayoub S, Barsegov V, Artés Vivancos JM. Single-molecule conductance of double-stranded RNA oligonucleotides. NANOSCALE 2022; 14:2572-2577. [PMID: 35107112 DOI: 10.1039/d1nr06925j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA oligonucleotides are crucial for a range of biological functions and in many biotechnological applications. Herein, we measured, for the first time, the conductance of individual double-stranded (ds)RNA molecules and compared it with the conductance of single DNA : RNA hybrids. The average conductance values are similar for both biomolecules, but the distribution of conductance values shows an order of magnitude higher variability for dsRNA, indicating higher molecular flexibility of dsRNA. Microsecond Molecular Dynamics simulations explain this difference and provide structural insights into the higher stability of DNA : RNA duplex with atomic level of detail. The rotations of 2'-OH groups of the ribose rings and the bases in RNA strands destabilize the duplex structure by weakening base stacking interactions, affecting charge transport, and making single-molecule conductance of dsRNA more variable (dynamic disorder). The results demonstrate that a powerful combination of state-of-the-art biomolecular electronics techniques and computational approaches can provide valuable insights into biomolecules' biophysics with unprecedented spatial resolution.
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Affiliation(s)
- Subrata Chandra
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | | | - Evgenii Kliuchnikov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Steven Ayoub
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
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21
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Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity. Proc Natl Acad Sci U S A 2022; 119:2112812119. [PMID: 35074874 PMCID: PMC8812571 DOI: 10.1073/pnas.2112812119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Detection of molecular interactions is the foundation for many important biotechnology applications in society and industry, such as drug discovery, diagnostics, and DNA sequencing. This report describes a broadly applicable platform for detecting molecular interactions at the single-molecule scale, in real-time, label-free, and potentially highly multiplexable fashion, using single-molecule sensors on a highly scalable semiconductor sensor array chip. Such chips are both practically manufacturable in the near term, and have a durable long-term scaling roadmap, thus providing an ideal way to bring the power of modern chip technology to the broad area of biosensing. This work also realizes a 50-year-old scientific vision of integrating single molecules into electronic chips to achieve the ultimate miniaturization of electronics. For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.
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22
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Kogikoski S, Dutta A, Bald I. Spatial Separation of Plasmonic Hot-Electron Generation and a Hydrodehalogenation Reaction Center Using a DNA Wire. ACS NANO 2021; 15:20562-20573. [PMID: 34875168 PMCID: PMC8717627 DOI: 10.1021/acsnano.1c09176] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Using hot charge carriers far from a plasmonic nanoparticle surface is very attractive for many applications in catalysis and nanomedicine and will lead to a better understanding of plasmon-induced processes, such as hot-charge-carrier- or heat-driven chemical reactions. Herein we show that DNA is able to transfer hot electrons generated by a silver nanoparticle over several nanometers to drive a chemical reaction in a molecule nonadsorbed on the surface. For this we use 8-bromo-adenosine introduced in different positions within a double-stranded DNA oligonucleotide. The DNA is also used to assemble the nanoparticles into nanoparticles ensembles enabling the use of surface-enhanced Raman scattering to track the decomposition reaction. To prove the DNA-mediated transfer, the probe molecule was insulated from the source of charge carriers, which hindered the reaction. The results indicate that DNA can be used to study the transfer of hot electrons and the mechanisms of advanced plasmonic catalysts.
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Affiliation(s)
- Sergio Kogikoski
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
- Department
of Analytical Chemistry, Institute of Chemistry, State University of Campinas (UNICAMP), P.O. Box 6154, 13083-970, Campinas São Paulo, Brazil
| | - Anushree Dutta
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Ilko Bald
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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23
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Gupta N, Wilkinson EA, Karuppannan SK, Bailey L, Vilan A, Zhang Z, Qi DC, Tadich A, Tuite EM, Pike AR, Tucker JHR, Nijhuis CA. Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions. J Am Chem Soc 2021; 143:20309-20319. [PMID: 34826219 PMCID: PMC8662729 DOI: 10.1021/jacs.1c09549] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 11/29/2022]
Abstract
Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.
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Affiliation(s)
- Nipun
Kumar Gupta
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
| | - Edward A. Wilkinson
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Senthil Kumar Karuppannan
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Lily Bailey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Ayelet Vilan
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Ziyu Zhang
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Dong-Chen Qi
- Centre
for Materials Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Anton Tadich
- Australian
Synchrotron Clayton, 800 Blackburn Rd, Clayton, Victoria 3168, Australia
| | - Eimer M. Tuite
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Andrew R. Pike
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Christian A. Nijhuis
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science and Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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24
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Djurišić I, Jovanović VP, Dražić MS, Tomović AŽ, Zikic R. Predicting Finite-Bias Tunneling Current Properties from Zero-Bias Features: The Frontier Orbital Bias Dependence at an Exemplar Case of DNA Nucleotides in a Nanogap. NANOMATERIALS 2021; 11:nano11113021. [PMID: 34835784 PMCID: PMC8624643 DOI: 10.3390/nano11113021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/06/2023]
Abstract
The electrical current properties of single-molecule sensing devices based on electronic (tunneling) transport strongly depend on molecule frontier orbital energy, spatial distribution, and position with respect to the electrodes. Here, we present an analysis of the bias dependence of molecule frontier orbital properties at an exemplar case of DNA nucleotides in the gap between H-terminated (3, 3) carbon nanotube (CNT) electrodes and its relation to transversal current rectification. The electronic transport properties of this simple single-molecule device, whose characteristic is the absence of covalent bonding between electrodes and a molecule between them, were obtained using density functional theory and non-equilibrium Green's functions. As in our previous studies, we could observe two distinct bias dependences of frontier orbital energies: the so-called strong and the weak pinning regimes. We established a procedure, from zero-bias and empty-gap characteristics, to estimate finite-bias electronic tunneling transport properties, i.e., whether the molecular junction would operate in the weak or strong pinning regime. We also discuss the use of the zero-bias approximation to calculate electric current properties at finite bias. The results from this work could have an impact on the design of new single-molecule applications that use tunneling current or rectification applicable in high-sensitivity sensors, protein, or DNA sequencing.
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25
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Pattiya Arachchillage KGG, Chandra S, Piso A, Qattan T, Artes Vivancos JM. RNA BioMolecular Electronics: towards new tools for biophysics and biomedicine. J Mater Chem B 2021; 9:6994-7006. [PMID: 34494636 DOI: 10.1039/d1tb01141c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The last half-century has witnessed the birth and development of a new multidisciplinary field at the edge between materials science, nanoscience, engineering, and chemistry known as Molecular Electronics. This field deals with the electronic properties of individual molecules and their integration as active components in electronic circuits and has also been applied to biomolecules, leading to BioMolecular Electronics and opening new perspectives for single-molecule biophysics and biomedicine. Herein, we provide a brief introduction and overview of the BioMolecular electronics field, focusing on nucleic acids and potential applications for these measurements. In particular, we review the recent demonstration of the first single-molecule electrical detection of a biologically-relevant nucleic acid. We also show how this could be used to study biomolecular interactions and applications in liquid biopsy for early cancer detection, among others. Finally, we discuss future perspectives and challenges in the applications of this fascinating research field.
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Affiliation(s)
| | - Subrata Chandra
- Department of Chemistry, University of Massachusetts Lowell, One University Ave, 01854 Lowell, MA, USA.
| | - Angela Piso
- Department of Chemistry, University of Massachusetts Lowell, One University Ave, 01854 Lowell, MA, USA.
| | - Tiba Qattan
- Department of Chemistry, University of Massachusetts Lowell, One University Ave, 01854 Lowell, MA, USA.
| | - Juan M Artes Vivancos
- Department of Chemistry, University of Massachusetts Lowell, One University Ave, 01854 Lowell, MA, USA.
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Qu Z, Zhang Y, Dai Z, Hao Y, Zhang Y, Shen J, Wang F, Li Q, Fan C, Liu X. DNA Framework-Engineered Long-Range Electrostatic Interactions for DNA Hybridization Reactions. Angew Chem Int Ed Engl 2021; 60:16693-16699. [PMID: 33991031 DOI: 10.1002/anie.202106010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Indexed: 11/06/2022]
Abstract
Long-range electrostatic interactions beyond biomolecular interaction interfaces have not been extensively studied due to the limitation in engineering electric double layers in physiological fluids. Here we find that long-range electrostatic interactions play an essential role in kinetic modulation of DNA hybridizations. Protein and gold nanoparticles with different charges are encapsulated in tetrahedral frameworks to exert diverse electrostatic effects on site-specifically tethered single DNA strands. Using this strategy, we have successfully modulated the hybridization kinetics in both bulk solution and single molecule level. Experimental and theoretical studies reveal that long-range Coulomb interactions are the key factor for hybridization rates. This work validates the important role of long-range electrostatic forces in nucleic acid-biomacromolecule complexes, which may encourage new strategies of gene regulation, antisense therapy, and nucleic acid detection.
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Affiliation(s)
- Zhibei Qu
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yinan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China.,Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | - Zheze Dai
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yaya Hao
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yichi Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
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Qu Z, Zhang Y, Dai Z, Hao Y, Zhang Y, Shen J, Wang F, Li Q, Fan C, Liu X. DNA Framework‐Engineered Long‐Range Electrostatic Interactions for DNA Hybridization Reactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhibei Qu
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
| | - Yinan Zhang
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
- Center for Molecular Design and Biomimetics The Biodesign Institute School of Molecular Sciences Arizona State University Tempe AZ 85281 USA
| | - Zheze Dai
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
| | - Yaya Hao
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
| | - Yichi Zhang
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering Frontiers Science Centre for Transformative Molecules Shanghai Jiao Tong University Shanghai 200240 China
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Mantela M, Morphis A, Lambropoulos K, Simserides C, Di Felice R. Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study. J Phys Chem B 2021; 125:3986-4003. [PMID: 33857373 DOI: 10.1021/acs.jpcb.0c11489] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.
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Affiliation(s)
- Marilena Mantela
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Andreas Morphis
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Konstantinos Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
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Aggarwal A, Sahoo AK, Bag S, Kaliginedi V, Jain M, Maiti PK. Fine-tuning the DNA conductance by intercalation of drug molecules. Phys Rev E 2021; 103:032411. [PMID: 33862831 DOI: 10.1103/physreve.103.032411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/08/2021] [Indexed: 11/07/2022]
Abstract
In this work we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modeling approach where extensive ab initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites, which leads to modifications of the density of states in the near-Fermi-energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance or tune the DNA conductance, which opens new possibilities for their potential applications in nanoelectronics.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Veerabhadrarao Kaliginedi
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manish Jain
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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Aggarwal A, Vinayak V, Bag S, Bhattacharyya C, Waghmare UV, Maiti PK. Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model. J Chem Inf Model 2020; 61:106-114. [PMID: 33320660 DOI: 10.1021/acs.jcim.0c01072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Vinayak Vinayak
- Undergraduate Program, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Chiranjib Bhattacharyya
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560012, India
| | - Umesh V Waghmare
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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