Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment
Molecular interactions between carbon nanoparticles (CNPs) and a double-stranded deoxyribonucleic acid (dsDNA) fragment were investigated using molecular dynamics (MD) simulations. Six types of CNPs including fullerenes (C60 and C70), (8,0) single-walled carbon nanotube (SWNT), (8,0) double-walled c...
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| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | Journal of Chemistry |
| Online Access: | http://dx.doi.org/10.1155/2015/531610 |
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| _version_ | 1832563989528182784 |
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| author | Zhuang Wang Hao Fang Se Wang Fan Zhang Degao Wang |
| author_facet | Zhuang Wang Hao Fang Se Wang Fan Zhang Degao Wang |
| author_sort | Zhuang Wang |
| collection | DOAJ |
| description | Molecular interactions between carbon nanoparticles (CNPs) and a double-stranded deoxyribonucleic acid (dsDNA) fragment were investigated using molecular dynamics (MD) simulations. Six types of CNPs including fullerenes (C60 and C70), (8,0) single-walled carbon nanotube (SWNT), (8,0) double-walled carbon nanotube (DWNT), graphene quantum dot (GQD), and graphene oxide quantum dot (GOQD) were studied. Analysis of the best geometry indicates that the dsDNA fragment can bind to CNPs through pi-stacking and T-shape. Moreover, C60, DWNT, and GOQD bind to the dsDNA molecules at the minor groove of the nucleotide, and C70, SWNT, and GQD bind to the dsDNA molecules at the hydrophobic ends. Estimated interaction energy implies that van der Waals force may mainly contribute to the mechanisms for the dsDNA-C60, dsDNA-C70, and dsDNA-SWNT interactions and electrostatic force may contribute considerably to the dsDNA-DWNT, dsDNA-GQD, and dsDNA-GOQD interactions. On the basis of the results from large-scale MD simulations, it was found that the presence of the dsDNA enhances the dispersion of C60, C70, and SWNT in water and has a slight impact on DWNT, GQD, and GOQD. |
| format | Article |
| id | doaj-art-63609dc652cb440aa785ebfd29630e94 |
| institution | Kabale University |
| issn | 2090-9063 2090-9071 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Chemistry |
| spelling | doaj-art-63609dc652cb440aa785ebfd29630e942025-02-03T01:12:05ZengWileyJournal of Chemistry2090-90632090-90712015-01-01201510.1155/2015/531610531610Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA FragmentZhuang Wang0Hao Fang1Se Wang2Fan Zhang3Degao Wang4Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (AEET), Jiangsu Engineering Technology Research Centre of Environmental Cleaning Materials (ECM), School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, ChinaJiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (AEET), Jiangsu Engineering Technology Research Centre of Environmental Cleaning Materials (ECM), School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, ChinaJiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (AEET), Jiangsu Engineering Technology Research Centre of Environmental Cleaning Materials (ECM), School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, ChinaJiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (AEET), Jiangsu Engineering Technology Research Centre of Environmental Cleaning Materials (ECM), School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, ChinaEnvironmental Science and Engineering College, Dalian Maritime University, Dalian 116026, ChinaMolecular interactions between carbon nanoparticles (CNPs) and a double-stranded deoxyribonucleic acid (dsDNA) fragment were investigated using molecular dynamics (MD) simulations. Six types of CNPs including fullerenes (C60 and C70), (8,0) single-walled carbon nanotube (SWNT), (8,0) double-walled carbon nanotube (DWNT), graphene quantum dot (GQD), and graphene oxide quantum dot (GOQD) were studied. Analysis of the best geometry indicates that the dsDNA fragment can bind to CNPs through pi-stacking and T-shape. Moreover, C60, DWNT, and GOQD bind to the dsDNA molecules at the minor groove of the nucleotide, and C70, SWNT, and GQD bind to the dsDNA molecules at the hydrophobic ends. Estimated interaction energy implies that van der Waals force may mainly contribute to the mechanisms for the dsDNA-C60, dsDNA-C70, and dsDNA-SWNT interactions and electrostatic force may contribute considerably to the dsDNA-DWNT, dsDNA-GQD, and dsDNA-GOQD interactions. On the basis of the results from large-scale MD simulations, it was found that the presence of the dsDNA enhances the dispersion of C60, C70, and SWNT in water and has a slight impact on DWNT, GQD, and GOQD.http://dx.doi.org/10.1155/2015/531610 |
| spellingShingle | Zhuang Wang Hao Fang Se Wang Fan Zhang Degao Wang Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment Journal of Chemistry |
| title | Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment |
| title_full | Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment |
| title_fullStr | Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment |
| title_full_unstemmed | Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment |
| title_short | Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment |
| title_sort | simulating molecular interactions of carbon nanoparticles with a double stranded dna fragment |
| url | http://dx.doi.org/10.1155/2015/531610 |
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