文献类型：期刊文献

英文题名：Unexpected sequence adsorption features of polynucleotide ssDNA on graphene oxide

作者：Ma, Huishu[1,2,3];Xu, Zhen[4];Fang, Haiping[5,6];Lei, Xiaoling[5,6]

机构：[1]Chinese Acad Sci, Div Interfacial Water, Shanghai Inst Appl Phys, POB 800-204, Shanghai 201800, Peoples R China;[2]Chinese Acad Sci, Key Lab Interfacial Phys & Technol, Shanghai Inst Appl Phys, POB 800-204, Shanghai 201800, Peoples R China;[3]Univ Chinese Acad Sci, Beijing 100049, Peoples R China;[4]Shanghai Univ Engn Sci, Coll Mech Engn, Shanghai 201620, Peoples R China;[5]East China Univ Sci & Technol, Dept Phys, Shanghai 200237, Peoples R China;[6]Chinese Acad Sci, Shanghai Adv Res Inst, Zhangjiang Lab, Shanghai 201210, Peoples R China

年份：2020

卷号：22

期号：20

起止页码：11740

外文期刊名：PHYSICAL CHEMISTRY CHEMICAL PHYSICS

收录：;EI(收录号：20202408806728);WOS:【SCI-EXPANDED(收录号:WOS:000538039300056)】；

基金：We gratefully acknowledge Prof. Guosheng Shi, Dr Rongzheng Wan and Dr Yongshun Song for helpful discussions and their crucial reading of this manuscript. We thank Alan Burns, PhD, from the Liwen Bianji, Edanz Group China (www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript. This work is supported by the NSFC (11305237 and 11974366), the Key Research Program of Chinese Academy of Sciences (Grant No. QYZDJ-SSW-SLH053), the supercomputer Center of the Chinese Academy of Sciences, and the Shanghai Supercomputer Center of China.

语种：英文

外文关键词：Adsorption - Bioinformatics - Nucleotides - Molecular dynamics - Graphene

摘要：The sequence features of single-stranded DNA (ssDNA) adsorbed on a graphene oxide (GO) surface are important for applications of the DNA/GO functional structure in biosensors, biomedicine, and materials science. In this study, molecular dynamics (MD) simulations were used to examine the adsorption of polynucleotide ssDNAs (A(12), C-12, G(12), and T-12) and single nucleotides (A, C, G, and T) on the GO surface. For the latter case, the nucleotide-GO interaction energy followed the trend G > A > C > T, even though it was influenced by specific adsorption sites. In the case of polynucleotides, unexpectedly polythymidine (T-12) had the strongest interaction with the GO surface. The angle distributions of the adsorbed nucleobases indicated that T-12 was more likely to form a quasi-parallel structure with GO compared to A(12), C-12, or G(12). This was attributed to the weakest pi-stacking interactions of thymine. Weaker intra-molecular base-stacking interactions made it easier to break the structures of pyrimidine bases relative to those of purine bases. Weaker inter-molecular base-stacking interactions between T-12 and the GO surface enabled T-12 to adjust its structure easily to a more stable one by slipping on the surface. This result provides a new understanding of polynucleotide ssDNA adsorption on GO surfaces, which will help in the design of functional DNA/GO structure-based platforms.