1
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Taketomi Y, Yamaguchi Y, Sakurai S, Tanaka M. Evaluation of DNA-mediated electron transfer using a hole-trapping nucleobase under crowded conditions. Org Biomol Chem 2022; 20:2043-2047. [PMID: 35005766 DOI: 10.1039/d1ob01669e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effects of a crowded environment on DNA-mediated electron transfer were evaluated using a pyrene-modified oligonucleotide containing a hole-trapping nucleobase in poly(ethylene glycol) mixed solutions. Rapid decompositions of hole-trapping bases in condensed and noncondensed DNA showed that more efficient electron transfer occurred under crowded conditions than in dilute solutions.
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Affiliation(s)
- Yuuki Taketomi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Yuuki Yamaguchi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Shunsuke Sakurai
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Makiko Tanaka
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
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2
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Pavc D, Sebastian N, Spindler L, Drevenšek-Olenik I, Podboršek GK, Plavec J, Šket P. Understanding self-assembly at molecular level enables controlled design of DNA G-wires of different properties. Nat Commun 2022; 13:1062. [PMID: 35217667 PMCID: PMC8881451 DOI: 10.1038/s41467-022-28726-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022] Open
Abstract
A possible engineering of materials with diverse bio- and nano-applications relies on robust self-assembly of oligonucleotides. Bottom-up approach utilizing guanine-rich DNA oligonucleotides can lead to formation of G-wires, nanostructures consisting of continuous stacks of G-quartets. However, G-wire structure and self-assembly process remain poorly understood, although they are crucial for optimizing properties needed for specific applications. Herein, we use nuclear magnetic resonance to get insights at molecular level on how chosen short, guanine-rich oligonucleotides self-assemble into G-wires, whereas complementary methods are used for their characterization. Additionally, unravelling mechanistic details enable us to guide G-wire self-assembly in a controlled manner. MD simulations provide insight why loop residues with considerably different properties, i.e., hydrogen-bond affinity, stacking interactions, electronic effects and hydrophobicity extensively increase or decrease G-wire length. Our results provide fundamental understanding of G-wire self-assembly process useful for future design of nanomaterials with specific properties. G-wire structures have potential applications in bio-nanotechnology, however, this is limited by a lack of understanding about the assembly process and structures formed. Here, the authors use nuclear magnetic resonance and molecular dynamic simulations to understand the guiding principles of G-wire assembly.
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Affiliation(s)
- Daša Pavc
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Nerea Sebastian
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia
| | - Lea Spindler
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia.,Faculty of Mechanical Engineering, University of Maribor, 2000, Maribor, Slovenia
| | - Irena Drevenšek-Olenik
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia.,Faculty of Mathematics and Physics, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Gorazd Koderman Podboršek
- Department of Materials Chemistry, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.,EN-FIST, Center of Excellence, 1000, Ljubljana, Slovenia
| | - Primož Šket
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.
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3
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Wu J, Liyarita BR, Zhu H, Liu M, Hu X, Shao F. Self-Assembly of Dendritic DNA into a Hydrogel: Application in Three-Dimensional Cell Culture. ACS APPLIED MATERIALS & INTERFACES 2021; 13:49705-49712. [PMID: 34658242 DOI: 10.1021/acsami.1c14445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
With inherent biocompatibility, biodegradability, and unique programmability, hydrogels with a DNA framework show great potential in three-dimensional (3D) cell culture. Here, a DNA hydrogel was assembled by a dendritic DNA with four branches. The hydrogel showed tunable mechanical strength and reversible thixotropy even under a nanomolar DNA concentration. The cell culture medium can be converted into the hydrogel isothermally at physiological temperature. This DNA hydrogel allows both cancer and somatic cells to be seeded in situ and to achieve high proliferation and viability. The bis-entity of dendritic branches enabled the specific loading of bioactive clues to regulate cell behaviors. Thus, the dendritic DNA-assembled hydrogel could serve as a highly biocompatible, readily functionalizing, and easy-casting gel platform for 3D cell culture.
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Affiliation(s)
- Jingyuan Wu
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, 637371 Singapore
| | - Bella Rosa Liyarita
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, 637371 Singapore
| | - Haishuang Zhu
- ZJU-UIUC Institute, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, Zhejiang 314400, China
| | - Ming Liu
- Temasek Laboratories@NTU, Nanyang Technological University, 637371 Singapore
| | - Xiao Hu
- School of Materials Science and Engineering and Environment Chemistry and Materials Centre, NEWRI, Nanyang Technological University, 637371 Singapore
| | - Fangwei Shao
- ZJU-UIUC Institute, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, Zhejiang 314400, China
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4
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NDI-induced Topological Conversion of Human Telomeric G-Quadruplexes from Hybrid-2 to Parallel Form. Chem Res Chin Univ 2021. [DOI: 10.1007/s40242-021-1022-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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5
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Hao X, Wang C, Wang Y, Li C, Hou J, Zhang F, Kang C, Gao L. Topological conversion of human telomeric G-quadruplexes from hybrid to parallel form induced by naphthalene diimide ligands. Int J Biol Macromol 2020; 167:1048-1058. [PMID: 33188810 DOI: 10.1016/j.ijbiomac.2020.11.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
G-quadruplexes (GQs) have become promising anti-cancer therapeutic targets, which are formed by the folding of a guanine-rich repeat DNA/RNA sequence at human telomeres or oncogene promoters. Polymorphism has been observed for the folding topologies of intramolecular GQs. Here we report the topological conversion of human telomeric GQ induced by naphthalene diimide (NDI) ligands in K+ solution. The ligands selectively induce metastable hybrid-type GQs to highly stable parallel-type GQ at physiological temperature (37 °C) in dilute aqueous solutions and under crowding conditions that mimic cellular bioenvironment. According to spectroscopic analyses, the topological conversion is speculated to undergo stepwise unfolding of hybrid-type GQ through intermediate states to parallel-type GQ. The results will prompt further studies on the designs of ligands with GQ conformation regulation functions and nanotechnological systems based on nucleic acids with dynamic regulation of GQ conformation.
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Affiliation(s)
- Xueyu Hao
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Yu Wang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China
| | - Chunjie Li
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jingwei Hou
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Feng Zhang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Chuanqing Kang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China.
| | - Lianxun Gao
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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6
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Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Guanine Radicals Generated in Telomeric G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions. Molecules 2020; 25:E2094. [PMID: 32365780 PMCID: PMC7248781 DOI: 10.3390/molecules25092094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022] Open
Abstract
The study deals with the primary species, ejected electrons, and guanine radicals, leading to oxidative damage, that is generated in four-stranded DNA structures (guanine quadruplexes) following photo-ionization by low-energy UV radiation. Performed by nanosecond transient absorption spectroscopy with 266 nm excitation, it focusses on quadruplexes formed by folding of GGG(TTAGGG)3 single strands in the presence of K+ ions, TEL21/K+. The quantum yield for one-photon ionization (9.4 × 10-3) was found to be twice as high as that reported previously for TEL21/Na+. The overall population of guanine radicals decayed faster, their half times being, respectively, 1.4 and 6.7 ms. Deprotonation of radical cations extended over four orders of magnitude of time; the faster step, concerning 40% of their population, was completed within 500 ns. A reaction intermediate, issued from radicals, whose absorption spectrum peaked around 390 nm, was detected.
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Affiliation(s)
- Evangelos Balanikas
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
| | - Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
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7
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Martínez-Fernández L, Esposito L, Improta R. Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives. Photochem Photobiol Sci 2020; 19:436-444. [DOI: 10.1039/d0pp00065e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química
- Facultad de Ciencias
- Modulo 13 Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC Cantoblanco
- 28049 Madrid
| | | | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini
- CNR
- I-80134 Napoli
- Italy
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8
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The Dynamics of Hole Transfer in DNA. Molecules 2019; 24:molecules24224044. [PMID: 31703470 PMCID: PMC6891780 DOI: 10.3390/molecules24224044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.
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9
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Archer SA, Raza A, Dröge F, Robertson C, Auty AJ, Chekulaev D, Weinstein JA, Keane T, Meijer AJHM, Haycock JW, MacNeil S, Thomas JA. A dinuclear ruthenium(ii) phototherapeutic that targets duplex and quadruplex DNA. Chem Sci 2019; 10:3502-3513. [PMID: 30996941 PMCID: PMC6430095 DOI: 10.1039/c8sc05084h] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/14/2019] [Indexed: 02/06/2023] Open
Abstract
With the aim of developing a sensitizer for photodynamic therapy, a previously reported luminescent dinuclear complex that functions as a DNA probe in live cells was modified to produce a new iso-structural derivative containing RuII(TAP)2 fragments (TAP = 1,4,5,8-tetraazaphenanthrene). The structure of the new complex has been confirmed by a variety of techniques including single crystal X-ray analysis. Unlike its parent, the new complex displays Ru → L-based 3MLCT emission in both MeCN and water. Results from electrochemical studies and emission quenching experiments involving guanosine monophosphate are consistent with an excited state located on a TAP moiety. This hypothesis is further supported by detailed DFT calculations, which take into account solvent effects on excited state dynamics. Cell-free steady-state and time-resolved optical studies on the interaction of the new complex with duplex and quadruplex DNA show that the complex binds with high affinity to both structures and indicate that its photoexcited state is also quenched by DNA, a process that is accompanied by the generation of the guanine radical cation sites as photo-oxidization products. Like the parent complex, this new compound is taken up by live cells where it primarily localizes within the nucleus and displays low cytotoxicity in the absence of light. However, in complete contrast to [{RuII(phen)2}2(tpphz)]4+, the new complex is therapeutically activated by light to become highly phototoxic toward malignant human melanoma cell lines showing that it is a promising lead for the treatment of this recalcitrant cancer.
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Affiliation(s)
- Stuart A Archer
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
| | - Ahtasham Raza
- Materials Science & Engineering , University of Sheffield , Mappin St , Sheffield S1 3JD , UK . ;
| | - Fabian Dröge
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
| | - Craig Robertson
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
| | - Alexander J Auty
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
| | - Dimitri Chekulaev
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
| | - Julia A Weinstein
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
| | - Theo Keane
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
| | - Anthony J H M Meijer
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
| | - John W Haycock
- Materials Science & Engineering , University of Sheffield , Mappin St , Sheffield S1 3JD , UK . ;
| | - Sheila MacNeil
- Materials Science & Engineering , University of Sheffield , Mappin St , Sheffield S1 3JD , UK . ;
| | - James A Thomas
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , UK . ; Tel: +44 (0)114 222 9325
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10
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G-quadruplex Nanowires To Direct the Efficiency and Selectivity of Electrocatalytic CO 2
Reduction. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Martínez‐Fernández L, Banyasz A, Markovitsi D, Improta R. Topology Controls the Electronic Absorption and Delocalization of Electron Holes in Guanine Quadruplexes. Chemistry 2018; 24:15185-15189. [DOI: 10.1002/chem.201803222] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/21/2022]
Affiliation(s)
| | - Akos Banyasz
- LIDYL, CEA, CNRSUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | | | - Roberto Improta
- LIDYL, CEA, CNRSUniversité Paris-Saclay 91191 Gif-sur-Yvette France
- Istituto di Biostrutture e BioimmaginiCNR Via Mezzocannone 16 80134 Napoli Italy
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12
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He L, Sun X, Zhang H, Shao F. G-quadruplex Nanowires To Direct the Efficiency and Selectivity of Electrocatalytic CO2
Reduction. Angew Chem Int Ed Engl 2018; 57:12453-12457. [DOI: 10.1002/anie.201806652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/13/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Lei He
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University, Singapore; 21 Nanyang Link Singapore 637371 Singapore
| | - Xiaofu Sun
- Center for Programmable Materials; School of Materials Science and Engineering; Nanyang Technological University; 50 Nanyang Avenue Singapore 639798 Singapore
| | - Hua Zhang
- Center for Programmable Materials; School of Materials Science and Engineering; Nanyang Technological University; 50 Nanyang Avenue Singapore 639798 Singapore
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University, Singapore; 21 Nanyang Link Singapore 637371 Singapore
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