Source: http://www.whxb.pku.edu.cn/EN/10.3866/PKU.WHXB201802081
Timestamp: 2019-04-22 03:07:32+00:00

Document:
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.
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.
1 Snoussi K. ; Halle B. Biochemistry 2008, 47 (46), 12219.
2 Luedtke N. W. Chim. Int. J. Chem. 2009, 63 (3), 134.
3 Bochman M. L. ; Paeschke K. ; Zakian V. A. Nat. Rev. Genet. 2012, 13 (11), 770.
4 Koirala D. ; Dhakal S. ; Ashbridge B. ; Sannohe Y. ; Rodriguez R. ; Sugiyama H. ; Balasubramanian S. ; Mao H. Nat. Chem. 2011, 3 (10), 782.
5 Nicoludis J. M. ; Miller S. T. ; Jeffrey P. D. ; Barrett S. P. ; Rablen P. R. ; Lawton T. J. ; Yatsunyk L. A. J. Am. Chem. Soc. 2012, 134 (50), 20446.
6 Nicoludis J. M. ; Barrett S. P. ; Mergny J. L. ; Yatsunyk L. A. Nucleic Acids Res. 2012, 40 (12), 5432.
7 Davis J. T. Angew. Chem. Int. Ed. 2004, 43 (6), 668.
8 Lippert B. ; Gupta D. Dalton Trans. 2009, No. 24, 4619.
9 Gupta D. ; Huelsekopf M. ; Cerdà M. M. ; Ludwig R. ; Lippert B. Inorg. Chem. 2004, 43 (11), 3386.
10 Katritzky A. R. ; Karelson M. J. Am. Chem. Soc. 1991, 113 (5), 1561.
11 Goodman M. F. Nature 1995, 378 (6554), 237.
12 Wang W. ; Hellinga H. W. ; Beese L. S. Proc. Natl. Acad. Sci. U.S.A. 2011, 108 (43), 17644.
13 Zamora F. ; Kunsman M. ; Sabat M. ; Lippert B. Inorg. Chem. 1997, 36 (8), 1583.
14 Martínez A. J. Chem. Phys. 2005, 123 (2), 024311.
15 Zhao Y. P. ; Ai H. Q. ; Chen J. P. ; Yang A. B. ; Qi Z. N. Acta Phys. -Chim Sin. 2010, 26 (12), 3322.
15 赵永平; 艾洪奇; 陈金鹏; 杨爱彬; 齐中囡. 物理化学学报, 2010, 26 (12), 3322.
16 Kabelac M. ; Hobza P. J. Phys. Chem. B 2006, 110 (29), 14515.
17 Russo N. ; Toscano M. ; Grand A. J. Am. Chem. Soc. 2001, 123 (42), 10272.
18 Ciesielski A. ; Lena S. ; Masiero S. ; Spada G. P. ; Samorì P. Angew. Chem. Int. Ed. 2010, 49 (11), 1963.
19 Furukawa M. ; Tanaka H. ; Kawai T. Surf. Sci. 1997, 392 (1-3), L33.
20 Furukawa M. ; Tanaka H. ; Kawai T. Surf. Sci. 2000, 445 (1), 1.
21 Tanaka H. ; Yoshinobu J. ; Kawai M. ; Kawai T. Jpn. J. Appl. Phys. 1996, 35 (2B), L244.
22 Kawai T. J. Korean Phys. Soc. 1997, 31, S44.
23 Tanaka H. ; Kawai T. Jpn. J. Appl. Phys. 1996, 35 (6B), 3759.
24 Tanaka H. ; Nakagawa T. ; Kawai T. Surf. Sci. 1996, 364 (2), L575.
25 Otero R. ; Lukas M. ; Kelly R. E. A. ; Xu W. ; Laegsgaard E. ; Stensgaard I. ; Kantorovich L. N. ; Besenbacher F. Science 2008, 319 (5861), 312.
26 Tan Q. ; Zhang C. ; Wang N. ; Zhu X. ; Sun Q. ; Jacobsen M. F. ; Gothelf K. V. ; Besenbacher F. ; Hu A. ; Xu W. Chem. Commun. 2014, 50 (3), 356.
27 Otero R. ; Xu W. ; Lukas M. ; Kelly R. E. A. ; Laegsgaard E. ; Stensgaard I. ; Kjems J. ; Kantorovich L. N. ; Besenbacher F. Angew. Chem. Int. Ed. 2008, 47 (50), 9673.
28 Xu W. ; Wang J. G. ; Jacobsen M. F. ; Mura M. ; Yu M. ; Kelly R. E. A. ; Meng Q. Q. ; Laegsgaard E. ; Stensgaard I. ; Linderoth T. R. ; et al Angew. Chem. Int. Ed. 2010, 49 (49), 9373.
29 Wang L. ; Shi H. X. ; Wang W. Y. ; Shi H. ; Shao X. Acta Phys. -Chim. Sin. 2017, 33 (2), 393.
29 王利; 石何霞; 王文元; 施宏; 邵翔. 物理化学学报, 2017, 33 (2), 393.
30 Chen A. X. ; Wang H. ; Duan S. ; Zhang H. M. ; Xu X. ; Chi L. F. Acta Phys. -Chim. Sin. 2017, 33 (5), 1010.
30 陈爱喜; 汪宏; 段赛; 张海明; 徐昕; 迟力峰. 物理化学学报, 2017, 33 (5), 1010.
31 Zhang C. ; Xie L. ; Ding Y. ; Sun Q. ; Xu W. ACS Nano 2016, 10 (3), 3776.
32 Zhang C. ; Xie L. ; Ding Y. ; Xu W. Chem. Commun. 2018, 54, 771.
33 Xie L. ; Zhang C. ; Ding Y. ; Xu W. Angew. Chem. Int. Ed. 2017, 56 (18), 5077.
34 Zhang Y. ; Ding Y. ; Xie L. ; Ma H. ; Yao X. ; Zhang C. ; Yuan C. ; Xu W. Chem. Phys. 2017, 18 (24), 3544.
35 Ida R. ; Wu G. J. Am. Chem. Soc. 2008, 130 (11), 3590.
36 Kwan I. C. M. ; Wong A. ; She Y. M. ; Smith M. E. ; Wu G. Chem. Commun. 2008, (6), 682.
37 Kwan I. C. M. ; Mo X. ; Wu G. J. Am. Chem. Soc. 2007, 129 (8), 2398.
38 Kwan I. C. M. ; She Y. M. ; Wu G. Chem. Commun. 2007, No. 41, 4286.
39 Hurley L. H. Nat. Rev. Cancer 2002, 2 (3), 188.
40 Neidle S. ; Parkinson G. Nat. Rev. Drug Discov. 2002, 1 (5), 383.
41 González-Rodríguez D. ; Janssen P. G. A. ; Martín-Rapún R. ; De Cat I. ; De Feyter S. ; Schenning A. P. H. J. ; Meijer E. W. J. Am. Chem. Soc. 2010, 132 (13), 4710.
42 Xu W. ; Wang J. ; Yu M. ; L?gsgaard E. ; Stensgaard I. ; Linderoth T. R. ; Hammer B. ; Wang C. ; Besenbacher F. J. Am. Chem. Soc. 2010, 132 (45), 15927.
43 Xu W. ; Tan Q. ; Yu M. ; Sun Q. ; Kong H. ; Laegsgaard E. ; Stensgaard I. ; Kjems J. ; Wang J. G. ; Wang C. ; et al Chem. Commun. 2013, 49 (65), 7210.
44 Zhang C. ; Wang L. ; Xie L. ; Kong H. ; Tan Q. ; Cai L. ; Sun Q. ; Xu W. ChemPhysChem 2015, 16 (10), 2099.
45 Kong H. ; Sun Q. ; Wang L. ; Tan Q. ; Zhang C. ; Sheng K. ; Xu W. ACS Nano 2014, 8 (2), 1804.
46 Wang L. ; Kong H. ; Zhang C. ; Sun Q. ; Cai L. ; Tan Q. ; Besenbacher F. ; Xu W. ACS Nano 2014, 8 (11), 11799.
47 Langer H. ; Doltsinis N. L. J. Chem. Phys. 2003, 118 (12), 5400.
48 Lopes R. P. ; Marques M. P. M. ; Valero R. ; Tomkinson J. ; de Carvalho L. A. E. B. Spectroscopy 2012, 27 (5-6), 273.
49 W?ckerlin C. ; Iacovita C. ; Chylarecka D. ; Fesser P. ; Jung T. A. ; Ballav N. Chem. Commun. 2011, 47 (32), 9146.
50 Skomski D. ; Abb S. ; Tait S. L. J. Am. Chem. Soc. 2012, 134 (34), 14165.
51 Skomski D. ; Tait S. L. J. Phys. Chem. C 2013, 117 (6), 2959.
52 Shimizu T. K. ; Jung J. ; Imada H. ; Kim Y. Angew. Chem. Int. Ed. 2014, 53 (50), 13729.
53 Zhang C. ; Xie L. ; Wang L. ; Kong H. ; Tan Q. ; Xu W. J. Am. Chem. Soc. 2015, 137 (36), 11795.
54 Xie L. ; Zhang C. ; Ding Y. E. W. ; Yuan C. ; Xu W. Chem. Commun. 2017, 53 (62), 8767.
55 Xu W. ; Kelly R. E. A. ; Gersen H. ; L?gsgaard E. ; Stensgaard I. ; Kantorovich L. N. ; Besenbacher F. Small 2009, 5 (17), 1952.
56 Liu J. ; Lin T. ; Shi Z. ; Xia F. ; Dong L. ; Liu P. N. ; Lin N. J. Am. Chem. Soc. 2011, 133 (46), 18760.
57 Xu W. ; Kelly R. E. A. ; Otero R. ; Sch?ck M. ; L?gsgaard E. ; Stensgaard I. ; Kantorovich L. N. ; Besenbacher F. Small 2007, 3 (12), 2011.
58 Schlickum U. ; Klappenberger F. ; Decker R. ; Zoppellaro G. ; Klyatskaya S. ; Ruben M. ; Kern K. ; Brune H. ; Barth J. V. J. Phys. Chem. C 2010, 114 (37), 15602.
59 Abdurakhmanova N. ; Floris A. ; Tseng T. C. ; Comisso A. ; Stepanow S. ; De Vita A. ; Kern K. Nat. Commun. 2012, 3, 940.
60 Shi Z. ; Liu J. ; Lin T. ; Xia F. ; Liu P. N. ; Lin N. J. Am. Chem. Soc. 2011, 133 (16), 6150.
61 Yu M. ; Xu W. ; Kalashnyk N. ; Benjalal Y. ; Nagarajan S. ; Masini F. ; L?gsgaard E. ; Hliwa M. ; Bouju X. ; Gourdon A. ; et al Nano Res. 2012, 5 (12), 903.
62 Kong H. ; Wang L. ; Tan Q. ; Zhang C. ; Sun Q. ; Xu W. Chem. Commun. 2014, 50 (24), 3242.
63 Padermshoke A. ; Katsumoto Y. ; Masaki R. ; Aida M. Chem. Phys. Lett. 2008, 457 (1), 232.
64 Auw?rter W. ; Seufert K. ; Bischoff F. ; Ecija D. ; Vijayaraghavan S. ; Joshi S. ; Klappenberger F. ; Samudrala N. ; Barth J. V. Nat. Nanotechnol. 2012, 7 (1), 41.
65 Pan S. ; Fu Q. ; Huang T. ; Zhao A. ; Wang B. ; Luo Y. ; Yang J. ; Hou J. Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (36), 15259.
66 Kumagai T. ; Hanke F. ; Gawinkowski S. ; Sharp J. ; Kotsis K. ; Waluk J. ; Persson M. ; Grill L. Nat. Chem. 2014, 6 (1), 41.
67 Kong H. ; Wang L. ; Sun Q. ; Zhang C. ; Tan Q. ; Xu W. Angew. Chem. Int. Ed. 2015, 54 (22), 6526.
68 Kong H. ; Zhang C. ; Xie L. ; Wang L. ; Xu W. Angew. Chem. Int. Ed. 2016, 55 (25), 7157.
69 Zhang C. ; Sun Q. ; Chen H. ; Tan Q. ; Xu W. Chem. Commun. 2015, 51 (3), 495.
70 Fan Q. ; Gottfried J. M. ; Zhu J. Acc. Chem. Res. 2015, 48 (8), 2484.
71 Sun Q. ; Cai L. ; Ma H. ; Yuan C. ; Xu W. ACS Nano 2016, 10 (7), 7023.
72 Sun Q. ; Cai L. ; Ma H. ; Yuan C. ; Xu W. Chem. Commun. 2016, 52 (35), 6009.
73 Bieri M. ; Nguyen M. T. ; Gr?ning O. ; Cai J. ; Treier M. ; A?t-Mansour K. ; Ruffieux P. ; Pignedoli C. A. ; Passerone D. ; Kastler M. J. ; et al Am. Chem. Soc. 2010, 132 (46), 16669.
74 Lafferentz L. ; Eberhardt V. ; Dri C. ; Africh C. ; Comelli G. ; Esch F. ; Hecht S. ; Grill L. Nat. Chem. 2012, 4 (3), 215.
75 Kaposi T. ; Joshi S. ; Hoh T. ; Wiengarten A. ; Seufert K. ; Paszkiewicz M. ; Klappenberger F. ; Ecija D. ; ?or?evi? L. ; Marangoni T. ACS Nano 2016, 10 (8), 7665.
76 Rastgoo-Lahrood A. ; Bj?rk J. ; Lischka M. ; Eichhorn J. ; Kloft S. ; Fritton M. ; Strunskus T. ; Samanta D. ; Schmittel M. ; Heckl W. M. ; et al Angew. Chem. Int. Ed. 2016, 55 (27), 7650.
77 Wang T. ; Lv H. ; Fan Q. ; Feng L. ; Wu X. ; Zhu J. Angew. Chem. Int. Ed. 2017, 56 (17), 4762.
78 Langner A. ; Tait S. L. ; Lin N. ; Chandrasekar R. ; Meded V. ; Fink K. ; Ruben M. ; Kern K. Angew. Chem. Int. Ed. 2012, 51 (18), 4327.
79 Zhang C. ; Wang L. ; Xie L. ; Ding Y. ; Xu W. Chem. Eur. J. 2017, 23 (10), 2356.
80 Fukuma T. ; Higgins M. J. ; Jarvis S. P. Phys. Rev. Lett. 2007, 98 (10), 106101.
 Qianqian WANG,Dajun LIU,Xingquan HE. Metal-Organic Framework-Derived Fe-N-C Nanohybrids as Highly-Efficient Oxygen Reduction Catalysts [J]. Acta Phys. -Chim. Sin., 2019, 35(7): 740-748.
 Xiaodong YANG,Chi CHEN,Zhiyou ZHOU,Shigang SUN. Advances in Active Site Structure of Carbon-Based Non-Precious Metal Catalysts for Oxygen Reduction Reaction [J]. Acta Phys. -Chim. Sin., 2019, 35(5): 472-485.
 Yanfang LIU,Bing HU,Yazhi YIN,Guoliang LIU,Xinlin HONG. One-Pot Surfactant-Free Synthesis of Transition Metal/ZnO Nanocomposites for Catalytic Hydrogenation of CO2 to Methanol [J]. Acta Phys. -Chim. Sin., 2019, 35(2): 223-229.
 Yongjun LI,Yuliang LI. Chemical Modification and Functionalization of Graphdiyne [J]. Acta Phys. -Chim. Sin., 2018, 34(9): 992-1013.
 Xiangyan SHEN,Jianjiang HE,Ning WANG,Changshui HUANG. Graphdiyne for Electrochemical Energy Storage Devices [J]. Acta Phys. -Chim. Sin., 2018, 34(9): 1029-1047.
 Yanfang SHEN,Longjiu CHENG. Electronic Stability of Eight-electron Tetrahedral Pd4 Clusters [J]. Acta Phys. -Chim. Sin., 2018, 34(7): 830-836.
 Xueting LIN,Mingli FU,Hui HE,Junliang WU,Limin CHEN,Daiqi YE,Yun HU,Yifan WANG,William WEN. Synthesis of MnOx-CeO2 Using Metal-Organic Framework as Sacrificial Template and Its Performance in the Toluene Catalytic Oxidation Reaction [J]. Acta Phys. -Chim. Sin., 2018, 34(6): 719-730.
 Yeliang ZHAO,Bing WANG. Effect of Substrate on the Electron Spin Resonance Spectra of N@C60 Molecules [J]. Acta Phys. -Chim. Sin., 2018, 34(12): 1312-1320.
 Yan WANG,Xiong LI,Shanwei HU,Qian XU,Huanxin JU,Junfa ZHU. Morphologies and Electronic Structures of Calcium-Doped Ceria Model Catalysts and Their Interaction with CO2 [J]. Acta Phys. -Chim. Sin., 2018, 34(12): 1381-1389.
 Hengwei WANG,Junling LU. Atomic Layer Deposition: A Gas Phase Route to Bottom-up Precise Synthesis of Heterogeneous Catalyst [J]. Acta Phys. -Chim. Sin., 2018, 34(12): 1334-1357.
 Hui-Jun YAN,Biao LI,Ning JIANG,Ding-Guo XIA. First-Principles Study:the Structural Stability and Sulfur Anion Redox of Li1-xNiO2-ySy [J]. Acta Phys. -Chim. Sin., 2017, 33(9): 1781-1788.
 Wei-Yun XU,Li-Li WANG,Yi-Ming MI,Xin-Xin ZHAO. Effect of Adsorption of Fe Atoms on the Structure and Properties of WS2 Monolayer [J]. Acta Phys. -Chim. Sin., 2017, 33(9): 1765-1772.

References: V. 
 V. 
 V. 
 V. 
 V. 
 V.