中国物理B ›› 2023, Vol. 32 ›› Issue (1): 18701-018701.doi: 10.1088/1674-1056/ac5c3a

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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. 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
  • 收稿日期:2022-01-07 修回日期:2022-02-26 接受日期:2022-03-10 出版日期:2022-12-08 发布日期:2022-12-08
  • 通讯作者: Li Yang, Xiaoling Lei E-mail:yangli@mailbox.gxnu.edu.cn;leixiaoling@ecust.edu.cn
  • 基金资助:
    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.

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. 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
  • Received:2022-01-07 Revised:2022-02-26 Accepted:2022-03-10 Online:2022-12-08 Published:2022-12-08
  • Contact: Li Yang, Xiaoling Lei E-mail:yangli@mailbox.gxnu.edu.cn;leixiaoling@ecust.edu.cn
  • Supported by:
    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.

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摘要： 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.

关键词: double-strand DNA (dsDNA), molecular dynamics simulation, adsorption dynamic, graphene oxide

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.

Key words: double-strand DNA (dsDNA), molecular dynamics simulation, adsorption dynamic, graphene oxide

中图分类号:  (DNA)

  • 87.14.gk
68.47.Gh (Oxide surfaces) 87.10.Tf (Molecular dynamics simulation) 34.35.+a (Interactions of atoms and molecules with surfaces)