吴惠丰^1,2,
张明兴^1,3,
李斐¹,
曹天贵¹,
李雪花⁴,
赵建民¹
1. 中国科学院烟台海岸带研究所 中国科学院环境过程与生态修复重点实验室, 烟台 264003;
2. 青岛海洋科学与技术国家实验室 海洋渔业科学与食物产出过程功能实验室, 青岛 266237;
3. 中国科学院大学, 北京 100049;
4. 大连理工大学环境学院 工业生态与环境工程教育部重点实验室, 大连 116024

作者简介: 吴惠丰(1977-),男,研究员,研究方向为生态毒理学和计算毒理学,E-mail:hfwu@yic.ac.cn.

基金项目: 国家自然科学基金(41530642,21677173)；中国科学院青年创新促进会资助(2017255)


中图分类号: X171.5

Studies on the Interaction between Graphene and p53-DNA by Molecular Dynamics Simulations and Spectroscopic Methods

Wu Huifeng^1,2,
Zhang Mingxing^1,3,
Li Fei¹,
Cao Tiangui¹,
Li Xuehua⁴,
Zhao Jianmin¹
1. Key Laboratory of Coastal Environmental Processes and Ecological Remediation of Chinese Academy of Sciences, Yantai Institute of Coastal Zone Research(YIC), Chinese Academy of Sciences, Yantai 264003, China;
2. Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China;
3. University of Chinese Academy of Sciences, Beijing 100049, China;
4. Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China

CLC number: X171.5

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摘要:石墨烯(graphene, G)及其衍生物由于具有独特的理化性质,被广泛应用于能源、生物医学等领域,但尚缺乏其对生物体和环境潜在危害的研究。采用分子动力学模拟并结合光谱学方法(紫外可见吸收光谱、紫外变温实验及荧光光谱),分析了石墨烯与抑癌基因p53启动子区DNA片段(p53-DNA)间的相互作用,并探讨了相关作用机制。石墨烯的部分芳香环与p53-DNA碱基的芳香环之间存在π-π堆积作用,两者可以通过嵌插作用进行结合,同时还通过沟槽作用进一步结合。光谱实验进一步证实,在石墨烯作用下,p53-DNA的熔点(T_m)值升高,EB-DNA体系发生静态荧光淬灭,说明石墨烯能与p53-DNA结合;同时,p53-DNA与石墨烯结合后在260 nm处的吸光度升高,说明石墨烯对p53-DNA的双螺旋结构具有一定的破坏作用。上述研究结果从分子水平上分析了石墨烯与p53-DNA间的相互作用机制,有助于进一步阐明石墨烯的毒性作用机理。
关键词: 石墨烯/
p53-DNA/
相互作用/
分子动力学模拟/
光谱法

Abstract:Graphene and its derivatives have been widely used in the fields ranging from energy to biomedicine because of its peculiar physical and chemical properties. However, limited attention has been paid to potential hazards of graphene to organisms and environments. In this study, the interaction between graphene and the promoter region of p53 gene (p53-DNA) was investigated using molecular dynamics simulation (MD) technology and spectroscopic methods based on the combination of UV-vis absorption, DNA melting point test and fluorescent spectra, followed by the illustration of the interaction mechanism. MD results showed that some aromatic moieties of graphene could intercalate into the p53-DNA base pairs, which relied on π-π stacking interaction between aromatic moieties of graphene and p53-DNA base, and the other parts of graphene could further combine with p53-DNA by groove binding. Moreover, spectroscopic tests exhibited that graphene could increase the melting point (Tm) of p53-DNA and lead to static fluorescence quenching of EB-DNA system, suggesting that graphene was indeed able to bind with p53-DNA. Meanwhile, the ascent of absorbance of 260 nm was found in the p53-DNA as a result of the combination of graphene and p53-DNA, which meant graphene posed some effect on the double helix structure of p53-DNA. In conclusion, the mechanism of interaction between graphene and p53-DNA was investigated at molecular level in this study, which contributed to a further understanding of the toxicological effects of graphene.
Key words:graphene(G)/
p53-DNA/
binding interaction/
molecular dynamics simulations/
spectroscopic methods.