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物理化学学报  2018, Vol. 34 Issue (12): 1321-1333    DOI: 10.3866/PKU.WHXB201802081
所属专题: 表面物理化学
综述     
超高真空条件下碱基与金属在Au(111)表面的相互作用
王心怡,谢磊,丁元琪,姚心仪,张弛,孔惠慧,王利坤,许维*()
Interactions between Bases and Metals on Au(111) under Ultrahigh Vacuum Conditions
Xinyi WANG,Lei XIE,Yuanqi DING,Xinyi YAO,Chi ZHANG,Huihui KONG,Likun WANG,Wei XU*()
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摘要:

碱基是生命体中核酸的重要组成部分,用以携带遗传信息。碱基之间的互补配对行为在DNA和RNA的高保真复制过程中起到重要作用。除了碱基间的特异性识别,碱基分子与金属,盐类和一些小分子也可发生相互作用,特别是与某些金属原子或离子的相互作用会造成核酸的损伤,并可能进一步导致基因突变甚至诱发细胞的癌变。同时,基于DNA金属化形成的纳米器件逐渐成为纳米科技领域的研究热点。因此研究碱基与金属作用的现象和机制对于生物化学和纳米科学都十分重要。扫描隧道显微镜可以在实空间原子尺度下揭示纳米结构,密度泛函理论计算可以帮助确定反应机理。本文对近年来报道的利用以上两种方法在超高真空环境下碱基及其衍生物与碱金属、碱土金属和过渡金属的相互作用进行了介绍,总结了碱基与金属的作用位点及反应发生的机理,并进一步提出单原子尺度下的结构模型、可能的反应路径,进而揭示相互作用的本质。

关键词: 碱基金属静电作用配位作用扫描隧道显微镜密度泛函理论计算    
Abstract:

Nucleobases (guanine (G), adenine (A), thymine (T), cytosine (C), and uracil (U)) are important constituents of nucleic acids, which carry genetic information in all living organisms, and play vital roles in structure formation, functionalization, and biological catalytic processes. The principle of complementary base pairing is significant in the high-fidelity replication of DNA and RNA. In addition to their specific recognition, the interaction between bases and other reactants, such as metals, salts, and certain small molecules, may cause distinct effects. Specifically, the interactions between bases and certain metal atoms or ions could damage nucleic acids, inducing gene mutation and even carcinogenesis. In the meantime, nanoscale devices based on metal-DNA interactions have become the focus of research in nanotechnology. Therefore, extensive researches on the interactions between metals and bases and the corresponding mechanism are of great importance and may make improvements in the fields of both biochemistry and nanotechnology. Scanning tunneling microscopy (STM) is a powerful tool for effectively resolving nanostructures in real space and on the atomic scale under ultrahigh vacuum (UHV) conditions. Moreover, density functional theory (DFT) calculations could help elucidate the reaction pathways and their mechanisms. In this review, we summarize the distinct interactions between bases (including their derivatives) and various metal species (comprising alkali, alkaline earth, and transition metals) derived from metal sources and the corresponding salts on the Au(111) substrate reported recently based on the results obtained by a combination of above two methods. In general, bases afford N and/or O binding sites to interact with metal atoms, resulting in various motifs via coordination or electrostatic interactions, and form intermolecular hydrogen bonds to stabilize the whole system. On the basis of high-resolution STM images and DFT calculations, structural models and the possible reaction pathways are proposed, and their underlying mechanisms, which reveal the nature of the interactions, are thus obtained. Among them, we summarize the construction of G-quartet structures with different kinds of central metals like Na, K, and Ca, which are directly introduced by salts, and their relative stabilities are compared. In addition, salts can provide not only metal cations but also halogen anions in modulating the structure formation with bases. The halogen species enable the regulation of metal-organic motifs and induce phase transition by locating at specific hydrogen-rich sites. Moreover, reversible structural transformations of metal-organic nanostructures are realized owing to the intrinsic dynamic characteristic of coordination bonds, together with the coordination priority and diversity. Furthermore, the controllable scission and seamless stitching of metal-organic clusters, which contain two types of hierarchical interactions, have been successfully achieved through STM manipulations. Finally, this review offers a thorough comprehension on the interaction between bases and metals on Au(111) and provide fundamental insights into controllable fabrication of nanostructures of DNA bases. We also admit the limitation involved in detecting biological processes by on-surface model system, and speculate on future studies that would use more complicated biomolecules together with other technologies.

Key words: Bases    Metal    Electrostatic interaction    Coordination interaction    Scanning tunneling microscopy    Density functional theory calculation
收稿日期: 2018-01-09 出版日期: 2018-02-08
中图分类号:  O647  
基金资助: 国家自然科学基金(21473123);国家自然科学基金(21622307)
通讯作者: 许维     E-mail: xuwei@tongji.edu.cn
作者简介: 许维教授,出生于1981年。2008年在丹麦奥胡斯大学物理系获得理学博士学位,随后在美国宾夕法尼亚州立大学物理系从事博士后研究。2009年被聘为同济大学特聘教授加盟材料科学与工程学院,同时担任丹麦奥胡斯大学交叉学科纳米中心客座教授。主要从事利用超高真空扫描隧道显微镜(UHV-STM)高分辨成像及单分子操纵技术并结合密度泛函理论(DFT)计算研究固体表面物理化学相关课题
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引用本文:

王心怡,谢磊,丁元琪,姚心仪,张弛,孔惠慧,王利坤,许维. 超高真空条件下碱基与金属在Au(111)表面的相互作用[J]. 物理化学学报, 2018, 34(12): 1321-1333.

Xinyi WANG,Lei XIE,Yuanqi DING,Xinyi YAO,Chi ZHANG,Huihui KONG,Likun WANG,Wei XU. Interactions between Bases and Metals on Au(111) under Ultrahigh Vacuum Conditions. Acta Phys. -Chim. Sin., 2018, 34(12): 1321-1333.

链接本文:

http://www.whxb.pku.edu.cn/CN/10.3866/PKU.WHXB201802081        http://www.whxb.pku.edu.cn/CN/Y2018/V34/I12/1321

图1  G-K多孔结构的STM图和DFT模型42
图2  Au(111)表面上G4K1结构的STM图和DFT模型43
图3  Au(111)表面上形成G的带状结构和G4M1复合物的示意图,M代表Na、K和Ca 44
图4  在Au(111)表面上形成的G4Na1, G4K1, G4Ca1复合物的STM图和差分电荷密度图44
图5  Au(111)上无规则G分子和密排G/7H纳米结构在NaCl的辅助下分别向G4Na1网络结构转变过程的STM图(NaCl : G沉积量比例> 1 : 4) 53
图6  NaCl同时提供阴阳离子调节金属有机结构形成的示意图54
图7  镍原子诱导胞嘧啶由一维链转变为零维团簇的STM图62
图8  G/9H分子与Ni原子共沉积在Au(111)表面并加热至420 K后表面形成的金属有机网络结构的STM图像,DFT优化结构模型以及STM模拟图像45
图9  Au(111)表面上共沉积U分子和Ni原子后的STM图像、DFT优化结构模型和STM模拟图像以及STM操纵平行四边形和两个三角形团簇之间的可逆转变过程67
图10  两种不同的金属有机配位三聚体在Au(111)表面上的组分动态转变,R和L表示单个分子手性68
图11  碘诱导的金属有机结构的转变与稳定示意图33
图12  Au(111)上G4Fe1复合物的形成示意图46
图13  G4Fe1、异手性的G3Fe1、G4Fe2、G3Fe3和同手性的G3Fe1在Fe原子和9eG分子的诱导下发生的可逆性结构转变示意图79
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