超高真空条件下碱基与金属在Au(111)表面的相互作用

doi:10.3866/PKU.WHXB201802081

Abstract

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

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[J]. Acta Phys. -Chim. Sin. 2018, 34(12), 1321-1333. doi: 10.3866/PKU.WHXB201802081

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Interactions between Bases and Metals on Au(111) under Ultrahigh Vacuum Conditions

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