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Chin. Phys. B, 2023, Vol. 32(1): 018701    DOI: 10.1088/1674-1056/ac5c3a

Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions

Mengjiao Wu(吴梦娇)1,2, Huishu Ma(马慧姝)3, Haiping Fang(方海平)4, Li Yang(阳丽)1,†, and Xiaoling Lei(雷晓玲)4,‡
1 College of Physics Science and Technology, Guangxi Normal University, Guilin 541004, China;
2 Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
3 Changzhou Vocational Institute of Mechatronic Technology, Professional Basic Department, Changzhou 213164, China;
4 School of Physics, East China University of Science and Technology, Shanghai 200237, China
Abstract  The adsorption dynamics of double-stranded DNA (dsDNA) molecules on a graphene oxide (GO) surface are important for applications of DNA/GO functional structures in biosensors, biomedicine and materials science. In this work, molecular dynamics simulations were used to examine the adsorption of different length dsDNA molecules (from 4 bp to 24 bp) on the GO surface. The dsDNA molecules could be adsorbed on the GO surface through the terminal bases and stand on the GO surface. For short dsDNA (4 bp) molecules, the double-helix structure was partially or totally broken and the adsorption dynamics was affected by the structural fluctuation of short dsDNA and the distribution of the oxidized groups on the GO surface. For long dsDNA molecules (from 8 bp to 24 bp) adsorption is stable. By nonlinear fitting of the contact angle between the axis of the dsDNA molecule and the GO surface, we found that a dsDNA molecule adsorbed on a GO surface has the chance of orienting parallel to the GO surface if the length of the dsDNA molecule is longer than 54 bp. We attributed this behavior to the flexibility of dsDNA molecules. With increasing length, the flexibility of dsDNA molecules also increases, and this increasing flexibility gives an adsorbed dsDNA molecule more chance of reaching the GO surface with the free terminal. This work provides a whole picture of adsorption of dsDNA molecules on the GO surface and should be of benefit for the design of DNA/GO based biosensors.
Keywords:  double-strand DNA (dsDNA)      molecular dynamics simulation      adsorption dynamic      graphene oxide  
Received:  07 January 2022      Revised:  26 February 2022      Accepted manuscript online:  10 March 2022
PACS:  87.14.gk (DNA)  
  68.47.Gh (Oxide surfaces)  
  87.10.Tf (Molecular dynamics simulation)  
  34.35.+a (Interactions of atoms and molecules with surfaces)  
Fund: Project supported by the National Natural Science Foundation of China (Grant No. 11974366), the Fundamental Research Funds for the Central Universities, China, the Supercomputer Center of the Chinese Academy of Sciences, and the Shanghai Supercomputer Center of China.
Corresponding Authors:  Li Yang, Xiaoling Lei     E-mail:;

Cite this article: 

Mengjiao Wu(吴梦娇), Huishu Ma(马慧姝), Haiping Fang(方海平), Li Yang(阳丽), and Xiaoling Lei(雷晓玲) Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions 2023 Chin. Phys. B 32 018701

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