Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
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.
Received: 09 January 2018
Published: 08 February 2018
Fig 1 STM images and DFT models of the G-K porous network 42. (a) High-resolution STM image of the ordered G-K network. (b) DFT model of the G-K network with K atoms indicated as green spots. Adapted from American Chemical Society publisher.
Fig 2 STM image and DFT model of the G-quartet network on Au(111) 43. (a) High-resolution STM image of the G4K1 network. (b) The DFT proposed model of the G4K1 network is superimposed on the close-up STM image. Adapted from Royal Society of Chemistry publisher.
Fig 3 Schematic illustration of the formation of a G ribbon structure and a G-quartet-M complex on Au (111), where M represents Na, K or Ca 44.
Fig 4 STM images and Charge-density-difference maps showing the formation of a G-quartet-Na, G-quartet-K and G-quartet-Ca complexes on Au(111) 44. (a, d, g) Large-scale STM images of G4Na1, G4K1, G4Ca1 structures. (b, e, h) Close-up STM images providing more details of the structures of G4Na1, G4K1, G4Ca1. (c, f, i) Charge-density-difference maps of G4Na1, G4K1, G4Ca1 structures. Adapted from John Wiley and Sons publisher.
Fig 5 STM images showing the conversion from irregular G molecules and close-packed G/7H nanostructure to G-quartetNa network structure on Au(111) respectively with the aid of NaCl (the NaCl/guanine deposition ratio is higher than 1 : 4) 53. Adapted from American Chemical Society publisher.
Fig 6 Schematic illustration of the structural formation of organic motifs mediated by both Na and Cl ions provided by NaCl 54. Adapted from Royal Society of Chemistry publisher.
Fig 7 STM images showing the conversion of cytosine from one-dimensional chains to zero-dimensional clusters induced by Ni atoms 62. (a) The chemical structure of the cytosine molecule, A and D represent the binding sites of the molecule: hydrogen donor (electron acceptor) and hydrogen acceptor (electron donor) for hydrogen bonding and metal–organic coordination bonding. (b) STM image of 1-D zigzag chains formed by cytosine molecules on Au(111). (c) STM image of 0-D clusters formed by codeposition of cytosine molecules and Ni atoms on Au(111). Adapted from Royal Society of Chemistry publisher.
Fig 8 STM images, DFT-based optimized structural models, and simulated STM image of G/9H and Ni-coordinated metallosupramolecular network on Au(111) 45. (a) STM image shows the self-assembled nanostructures with each island being homochiral (as indicated by R and L) formed by G/9H and Ni after annealing at 420 K. The inset shows the chemical structure of G/9H and Ni. (b, c) DFT-optimized structural models of R and L chiral metallosupramolecular network structures that are superimposed on the corresponding high-resolution close-up STM images where good agreements are achieved. The green parallelogram represents the unit cell of the nanostructure. (d) Simulated STM image (the gray part) is partially superimposed on the STM image. Adapted from American Chemical Society publisher.
Fig 9 STM images, DFT-based optimized structural models, and simulated STM image of the co-deposition of uracil and Ni atoms on Au(111); STM manipulations demonstrating the whole reversible switching process between a parallelogrammic cluster and two triangular clusters 67. (a, b) STM images showing the formation of triangular and parallelogrammic clusters on Au(111), respectively.(c, d) Close-up STM images showing two triangular clusters with distinct orientations (indicated in blue and green) and a parallelogrammic cluster, respectively. (e) Simulated STM images of triangular and parallelogrammic clusters superimposed with the DFT-optimized models on Au(111); the substrate is omitted for clarity. (f–i) STM manipulations demonstrating the whole reversible switching process between a parallelogrammic cluster and two triangular clusters. The green arrows indicate the directions of the STM manipulations. Adapted from John Wiley and Sons publisher.
Fig 10 Schematic illustration on the constitutional dynamics between two distinct metal-organic coordination trimers on Au(111) surface. R and L denote the chiralities of individual molecules 68. Adapted from John Wiley and Sons publisher.
Fig 11 Illustration of iodine-induced structural transformation and stabilization of elementary metal-organic motifs 33. Adapted from by John Wiley and Sons publisher.
Fig 12 Schematic Illustration of the Formation of the G-Quartet-Fe Complex on Au(111) 46. Adapted from American Chemical Society publisher.
Fig 13 Schematic illustration of the reversible structural transformations among G4Fe1, heterochiral G3Fe1, G4Fe2 and G3Fe3 together with homochiral G3Fe1 motifs in response to Fe atoms and 9eG molecules 79. Adapted from John Wiley and Sons publisher.
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