Oxidation degree dependent adsorption of ssDNA onto graphene-based surface

doi:10.1088/1674-1056/abf109

中国物理B ›› 2021, Vol. 30 ›› Issue (10): 106806-106806.doi: 10.1088/1674-1056/abf109

Oxidation degree dependent adsorption of ssDNA onto graphene-based surface

Huishu Ma(马慧姝)^1,2, Jige Chen(陈济舸)^1,4, Haiping Fang(方海平)^3,4, and Xiaoling Lei(雷晓玲)^3,†

1 Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
2 University of Chinese Academy of Sciences, Beijing 100049, China;
3 Department of Physics, East China University of Science and Technology, Shanghai 200237, China;
4 Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China

收稿日期:2021-01-07 修回日期:2021-03-04 接受日期:2021-03-23 发布日期:2021-09-17
通讯作者: Xiaoling Lei E-mail:leixiaoling@ecust.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11305237 and 11974366), the Fundamental Research Funds for the Central Universities, China, the Natural Science Foundation of Shanghai, China (Grant No. 19ZR1463200), and the Key Research Program of Chinese Academy of Sciences (Grant No. QYZDJ-SSW-SLH053).

Oxidation degree dependent adsorption of ssDNA onto graphene-based surface

Huishu Ma(马慧姝)^1,2, Jige Chen(陈济舸)^1,4, Haiping Fang(方海平)^3,4, and Xiaoling Lei(雷晓玲)^3,†

1 Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
2 University of Chinese Academy of Sciences, Beijing 100049, China;
3 Department of Physics, East China University of Science and Technology, Shanghai 200237, China;
4 Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China

Received:2021-01-07 Revised:2021-03-04 Accepted:2021-03-23 Published:2021-09-17
Contact: Xiaoling Lei E-mail:leixiaoling@ecust.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11305237 and 11974366), the Fundamental Research Funds for the Central Universities, China, the Natural Science Foundation of Shanghai, China (Grant No. 19ZR1463200), and the Key Research Program of Chinese Academy of Sciences (Grant No. QYZDJ-SSW-SLH053).

1. 2021-106806-SI.pdf(1361KB)

摘要/Abstract

摘要： DNA/GO composite plays a significant role in the research field of biotechnology and nanotechnology, and attracts a great deal of interest. However, it is still unclear how the oxidation degree of the graphene-based surface affects the adsorption process of single-strand DNA (ssDNA). In this paper, based on the molecular dynamics simulations, we find that ssDNA molecule is absorbed on the GO surface in the most stable state with the oxidation degree around 15%. The microscopic mechanism is attributed to the van Der Walls and the electrostatic interactions between the ssDNA molecule and the graphene-based surface, which is accompanied with the π-π stacking and hydrogen bond formation. The number of π-π stacking between ssDNA and GO reaches the maximum value when the oxidation degree is around 15% among all the GO surfaces. Our simulation results also reveal the coexistence of stretched and curved configurations as well as the adsorption orientation of ssDNA on the GO surface. Furthermore, it is found that the absorbed ssDNA molecules are more likely to move on the graphene-based surface of low oxidation degree, especially on pristine graphene. Our work provides the physics picture of ssDNA's physisorption dynamics onto graphene-based surface and it is helpful in designing DNA/GO nanomaterials.

关键词: single-strand DNA (ssDNA), molecular dynamics simulation, oxidation degrees, graphene-based surfaces

Abstract: DNA/GO composite plays a significant role in the research field of biotechnology and nanotechnology, and attracts a great deal of interest. However, it is still unclear how the oxidation degree of the graphene-based surface affects the adsorption process of single-strand DNA (ssDNA). In this paper, based on the molecular dynamics simulations, we find that ssDNA molecule is absorbed on the GO surface in the most stable state with the oxidation degree around 15%. The microscopic mechanism is attributed to the van Der Walls and the electrostatic interactions between the ssDNA molecule and the graphene-based surface, which is accompanied with the π-π stacking and hydrogen bond formation. The number of π-π stacking between ssDNA and GO reaches the maximum value when the oxidation degree is around 15% among all the GO surfaces. Our simulation results also reveal the coexistence of stretched and curved configurations as well as the adsorption orientation of ssDNA on the GO surface. Furthermore, it is found that the absorbed ssDNA molecules are more likely to move on the graphene-based surface of low oxidation degree, especially on pristine graphene. Our work provides the physics picture of ssDNA's physisorption dynamics onto graphene-based surface and it is helpful in designing DNA/GO nanomaterials.

Key words: single-strand DNA (ssDNA), molecular dynamics simulation, oxidation degrees, graphene-based surfaces

中图分类号: (Adsorption kinetics ?)

68.43.Mn

68.47.Gh (Oxide surfaces) 87.14.gk (DNA) 34.35.+a (Interactions of atoms and molecules with surfaces)

Huishu Ma(马慧姝), Jige Chen(陈济舸), Haiping Fang(方海平), and Xiaoling Lei(雷晓玲). Oxidation degree dependent adsorption of ssDNA onto graphene-based surface[J]. 中国物理B, 2021, 30(10): 106806-106806.

Huishu Ma(马慧姝), Jige Chen(陈济舸), Haiping Fang(方海平), and Xiaoling Lei(雷晓玲). Oxidation degree dependent adsorption of ssDNA onto graphene-based surface[J]. Chin. Phys. B, 2021, 30(10): 106806-106806.

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Oxidation degree dependent adsorption of ssDNA onto graphene-based surface

Oxidation degree dependent adsorption of ssDNA onto graphene-based surface

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