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

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 revi...

Real-Space Evidence of Trimeric, Tetrameric, and Pentameric Uracil Clusters Induced by Alkali Metals

“…These biologically relevant complexes with the magical aggregation number have potential in forming sophisticated nanostructures, whose configuration and stability are thus fundamentally important in different disciplines. 27,28 As a peculiar nucleobase in RNA, uracil with its magic number clusters induced by alkali metals has attracted tremendous interest over the past decades with theoretical investigations [12][13][14][15]17,18 and spectroscopy studies 16,19,20 performed in solution and gas phase. The G clusters induced by alkali metals have been successfully introduced to the surface science community and extensively studied by scanning tunneling microscopy (STM), 22−25 which provides atomic-scale structural information.…”

“…Alkali metals, generally cationized in the cellular environments, are known as significant participants in several biological processes and play a vital role in some nucleic acid structures, such as inhibiting the chain initiation process by RNA polymerases and stabilizing nucleobase quartets within the telomere. , These functions of alkali metals are realized by interacting with negatively charged phosphate groups and nucleic acid bases through the electrostatic interaction, which further affects the syntheses, replication, and structural integrity of DNA and RNA. − Therefore, the interactions between alkali metals and nucleobases are significant and have attracted a lot of attention. − Among others, extensive studies reported that alkali metals, specifically lithium (Li), sodium (Na), and potassium (K), can significantly increase self-aggregation of the nucleobases and lead to the formation of uniquely stable magic number clusters, ,,,, such as the well-studied guanine (G) quartet stabilized by Na or K, − uracil (U) and thymine (T) quintets stabilized by K, etc. These biologically relevant complexes with the magical aggregation number have potential in forming sophisticated nanostructures, whose configuration and stability are thus fundamentally important in different disciplines. , As a peculiar nucleobase in RNA, uracil with its magic number clusters induced by alkali metals has attracted tremendous interest over the past decades with theoretical investigations − ,, and spectroscopy studies ,, performed in solution and gas phase. The G clusters induced by alkali metals have been successfully introduced to the surface science community and extensively studied by scanning tunneling microscopy (STM), − which provides atomic-scale structural information.…”