151
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Alapan Y, Yigit B, Beker O, Demirörs AF, Sitti M. Shape-encoded dynamic assembly of mobile micromachines. NATURE MATERIALS 2019; 18:1244-1251. [PMID: 31235903 DOI: 10.1038/s41563-019-0407-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Field-directed and self-propelled colloidal assembly have been used to build micromachines capable of performing complex motions and functions. However, integrating heterogeneous components into micromachines with specified structure, dynamics and function is still challenging. Here, we describe the dynamic self-assembly of mobile micromachines with desired configurations through pre-programmed physical interactions between structural and motor units. The assembly is driven by dielectrophoretic interactions, encoded in the three-dimensional shape of the individual parts. Micromachines assembled from magnetic and self-propelled motor parts exhibit reconfigurable locomotion modes and additional rotational degrees of freedom that are not available to conventional monolithic microrobots. The versatility of this site-selective assembly strategy is demonstrated on different reconfigurable, hierarchical and three-dimensional micromachine assemblies. Our results demonstrate how shape-encoded assembly pathways enable programmable, reconfigurable mobile micromachines. We anticipate that the presented design principle will advance and inspire the development of more sophisticated, modular micromachines and their integration into multiscale hierarchical systems.
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Affiliation(s)
- Yunus Alapan
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Berk Yigit
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Onur Beker
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Ahmet F Demirörs
- Complex Materials, Department of Materials, ETH Zurich, Zurich, Switzerland
| | - Metin Sitti
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany.
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152
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Xie Q, Chen X, Wu T, Wang T, Cao Y, Granick S, Li Y, Jiang L. Synthetic asters as elastic and radial skeletons. Nat Commun 2019; 10:4954. [PMID: 31672981 PMCID: PMC6823511 DOI: 10.1038/s41467-019-13009-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/16/2019] [Indexed: 12/21/2022] Open
Abstract
The radial geometry with rays radiated from a common core occurs ubiquitously in nature for its symmetry and functions. Herein, we report a class of synthetic asters with well-defined core-ray geometry that can function as elastic and radial skeletons to harbor nano- and microparticles. We fabricate the asters in a single, facile, and high-yield step that can be readily scaled up; specifically, amphiphilic gemini molecules self-assemble in water into asters with an amorphous core and divergently growing, twisted crystalline ribbons. The asters can spontaneously position microparticles in the cores, along the radial ribbons, or by the outer rims depending on particle sizes and surface chemistry. Their mechanical properties are determined on single- and multiple-aster levels. We further maneuver the synthetic asters as building blocks to form higher-order structures in virtue of aster-aster adhesion induced by ribbon intertwining. We envision the astral structures to act as rudimentary spatial organizers in nanoscience for coordinated multicomponent systems, possibly leading to emergent, synergistic functions. Nanosystems capable of organisation and the formation of structures are of interest in nanotechnology. Here, the authors report on synthetic asters made of gemini surfactant which are able to position microparticles based on size and chemical composition which can also be organised into higher order structures.
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Affiliation(s)
- Qingqiao Xie
- College of Chemistry and Materials Science, Jinan University, Guangzhou, 510632, China
| | - Xixi Chen
- Institute of Nanophotonics, Jinan University, 511443, Guangzhou, China
| | - Tianli Wu
- Institute of Nanophotonics, Jinan University, 511443, Guangzhou, China
| | - Tiankuo Wang
- Collaborative Innovation Center of Advanced Microstructures, Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
| | - Steve Granick
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.,Departments of Chemistry and Physics, UNIST, Ulsan, 44919, Republic of Korea
| | - Yuchao Li
- Institute of Nanophotonics, Jinan University, 511443, Guangzhou, China.
| | - Lingxiang Jiang
- College of Chemistry and Materials Science, Jinan University, Guangzhou, 510632, China. .,Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
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153
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Marolf DM, Jones MR. Measurement Challenges in Dynamic and Nonequilibrium Nanoscale Systems. Anal Chem 2019; 91:13324-13336. [DOI: 10.1021/acs.analchem.9b02702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- David M. Marolf
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Matthew R. Jones
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Materials Science and Nanoengineering, Rice University, Houston, Texas 77005, United States
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154
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Jepsen MDE, Sørensen RS, Maffeo C, Aksimentiev A, Kjems J, Birkedal V. Single molecule analysis of structural fluctuations in DNA nanostructures. NANOSCALE 2019; 11:18475-18482. [PMID: 31577314 PMCID: PMC6825326 DOI: 10.1039/c9nr03826d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA origami is an excellent tool for building complex artificial nanostructures. Functionalization of these structures provides the possibility of precise organization of matter at the nanoscale. In practice, efforts in this endeavour can be impeded by electrostatic repulsion or other dynamics at the molecular scale, resulting in uncompliant local structures. Using single molecule FRET microscopy combined with coarse-grained Brownian dynamics simulations, we investigated here the local structure around the lid of a DNA origami box, which can be opened by specific DNA keys. We found that FRET signals for the closed box depend on buffer ion concentrations and small changes to the DNA structure design. Simulations provided a view of the global and local structure and showed that the distance between the box wall and lid undergoes fluctuations. These results provide methods to vizualise and improve the local structure of three-dimensional DNA origami assemblies and offer guidance for exercising control over placement of chemical groups and ligands.
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Affiliation(s)
- Mette D E Jepsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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155
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Afrose SP, Bal S, Chatterjee A, Das K, Das D. Designed Negative Feedback from Transiently Formed Catalytic Nanostructures. Angew Chem Int Ed Engl 2019; 58:15783-15787. [PMID: 31476101 DOI: 10.1002/anie.201910280] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Ayan Chatterjee
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Krishnendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
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156
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Afrose SP, Bal S, Chatterjee A, Das K, Das D. Designed Negative Feedback from Transiently Formed Catalytic Nanostructures. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910280] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Ayan Chatterjee
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Krishnendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
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157
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Hebel M, Riegger A, Zegota MM, Kizilsavas G, Gačanin J, Pieszka M, Lückerath T, Coelho JAS, Wagner M, Gois PMP, Ng DYW, Weil T. Sequence Programming with Dynamic Boronic Acid/Catechol Binary Codes. J Am Chem Soc 2019; 141:14026-14031. [PMID: 31436970 PMCID: PMC6743217 DOI: 10.1021/jacs.9b03107] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Indexed: 12/25/2022]
Abstract
The development of a synthetic code that enables a sequence programmable feature like DNA represents a key aspect toward intelligent molecular systems. We developed herein the well-known dynamic covalent interaction between boronic acids (BAs) and catechols (CAs) into synthetic nucleobase analogs. Along a defined peptide backbone, BA or CA residues are arranged to enable sequence recognition to their complementary strand. Dynamic strand displacement and errors were elucidated thermodynamically to show that sequences are able to specifically select their partners. Unlike DNA, the pH dependency of BA/CA binding enables the dehybridization of complementary strands at pH 5.0. In addition, we demonstrate the sequence recognition at the macromolecular level by conjugating the cytochrome c protein to a complementary polyethylene glycol chain in a site-directed fashion.
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Affiliation(s)
- Marco Hebel
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Andreas Riegger
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Maksymilian M. Zegota
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Gönül Kizilsavas
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jasmina Gačanin
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Michaela Pieszka
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Thorsten Lückerath
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jaime A. S. Coelho
- Research Institute
for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Manfred Wagner
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Pedro M. P. Gois
- Research Institute
for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - David Y. W. Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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158
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Linsenmeier M, Kopp MRG, Grigolato F, Emmanoulidis L, Liu D, Zürcher D, Hondele M, Weis K, Capasso Palmiero U, Arosio P. Dynamics of Synthetic Membraneless Organelles in Microfluidic Droplets. Angew Chem Int Ed Engl 2019; 58:14489-14494. [DOI: 10.1002/anie.201907278] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Marie R. G. Kopp
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Leonidas Emmanoulidis
- Institute of Molecular Biology and Biophysics Department of Biology ETH Zurich 8093 Zurich Switzerland
| | - Dany Liu
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Dominik Zürcher
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Maria Hondele
- Department of Biology Institute of Biochemistry ETH Zürich 8093 Zurich Switzerland
| | - Karsten Weis
- Department of Biology Institute of Biochemistry ETH Zürich 8093 Zurich Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
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159
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Linsenmeier M, Kopp MRG, Grigolato F, Emmanoulidis L, Liu D, Zürcher D, Hondele M, Weis K, Capasso Palmiero U, Arosio P. Dynamics of Synthetic Membraneless Organelles in Microfluidic Droplets. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Marie R. G. Kopp
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Leonidas Emmanoulidis
- Institute of Molecular Biology and Biophysics Department of Biology ETH Zurich 8093 Zurich Switzerland
| | - Dany Liu
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Dominik Zürcher
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Maria Hondele
- Department of Biology Institute of Biochemistry ETH Zürich 8093 Zurich Switzerland
| | - Karsten Weis
- Department of Biology Institute of Biochemistry ETH Zürich 8093 Zurich Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
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160
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Li J, Liu X, Abdelmohsen LKEA, Williams DS, Huang X. Spatial Organization in Proteinaceous Membrane-Stabilized Coacervate Protocells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902893. [PMID: 31298806 DOI: 10.1002/smll.201902893] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/21/2019] [Indexed: 06/10/2023]
Abstract
As a model protocell, the membrane-free coacervate microdroplet is widely utilized in functional studies to provide insights into the physicochemical properties of the cell and to engineer cytomimetic soft technologies; however, the lack of a discrete membrane contributes to its instability and limits further application. Herein, a strategy is developed to fabricate a hybrid protocell based on the self-assembly of a proteinaceous membrane at the surface of coacervate microdroplets driven by a combination of electrostatic adhesion and steric/hydrophilic surface buoyancy. The semipermeable proteinaceous membrane can enhance coacervate stability obviously without compromising sequestration behavior. Significantly, such hybrid protocells demonstrate spatial organization whereby various functional enzymes can be located in discrete regions, which facilitates an on/off modulation for a cascade enzymatic reaction along with enhanced chemical communication between subpopulations.
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Affiliation(s)
- Junbo Li
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xiaoman Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Loai K E A Abdelmohsen
- Bio-Organic Chemistry Institute for Complex Molecular Systems, Eindhoven University of Technology, Helix, het Kranenveld (STO 3.50) P. O. Box 513, Eindhoven, 5600, MB, The Netherlands
| | - David S Williams
- Department of Chemistry, Swansea University, Swansea, SA2 8PP, UK
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
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161
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Godde B, Jouaiti A, Mauro M, Marquardt R, Chaumont A, Robert V. The Motion of an Azobenzene Light‐Controlled Switch: A Joint Theoretical and Experimental Approach. CHEMSYSTEMSCHEM 2019. [DOI: 10.1002/syst.201900003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Bérangère Godde
- Laboratoire de Tectonique MoléculaireUMR UDS-CNRS 7140icFRCUniversité de Strasbourg Institut Le Bel, 4, rue B. Pascal F-67000 Strasbourg France
| | - Abdelaziz Jouaiti
- Laboratoire de Tectonique MoléculaireUMR UDS-CNRS 7140icFRCUniversité de Strasbourg Institut Le Bel, 4, rue B. Pascal F-67000 Strasbourg France
| | - Matteo Mauro
- Institut de Physique et Chimie des Matériaux de StrasbourgUMR UDS-CNRS 7504Université de Strasbourg 23, rue du Loess F-67000 Strasbourg France
| | - Roberto Marquardt
- Laboratoire de Chimie QuantiqueInstitut de Chimie, UMR UDS-CNRS 7177Université de Strasbourg Institut Le Bel, 4, rue B. Pascal F-67000 Strasbourg France
| | - Alain Chaumont
- Laboratoire de Chimie Moléculaire de l'Etat SolideUMR UDS-CNRS 7140Université de Strasbourg Institut Le Bel 4, rue B. Pascal F-67000 Strasbourg France
| | - Vincent Robert
- Laboratoire de Chimie QuantiqueInstitut de Chimie, UMR UDS-CNRS 7177Université de Strasbourg Institut Le Bel, 4, rue B. Pascal F-67000 Strasbourg France
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162
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Ahmed S, Chatterjee A, Das K, Das D. Fatty acid based transient nanostructures for temporal regulation of artificial peroxidase activity. Chem Sci 2019; 10:7574-7578. [PMID: 31588307 PMCID: PMC6761916 DOI: 10.1039/c9sc02648g] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/21/2019] [Indexed: 12/01/2022] Open
Abstract
Natural systems access transient high energy self-assembled structures for temporal regulation of different biological functions through dissipative processes. Compartmentalization within self-assembled structures is used by living systems to organize vital biochemical reactions that define cellular metabolism. Herein, we demonstrate a simple fatty acid based system where a redox active base (dimethylaminomethyl ferrocene, Fc-NMe2 ) acts as a countercation to access unique hexagonal compartments resulting in the formation of a self-supporting gel. An oxidizing environment helps in the dissipation of energy by converting Fc-NMe2 to oxidized waste and the gel autonomously undergoes transition to a sol. Hence, the system requires the addition of the fuel Fc-NMe2 to access the temporal gel state. Notably, these transient compartments were able to temporally upregulate and downregulate hemin-catalyzed oxidation reactions mimicking peroxidase, a ubiquitous enzyme in extant biology. An order of magnitude variation in k cat values was observed with time and the chemical reaction persists as long as the gel state was present.
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Affiliation(s)
- Sahnawaz Ahmed
- Department of Chemical Sciences , Centre for Advanced Functional Materials , Indian Institute of Science Education and Research (IISER) Kolkata , Mohanpur 741246 , India .
| | - Ayan Chatterjee
- Department of Chemical Sciences , Centre for Advanced Functional Materials , Indian Institute of Science Education and Research (IISER) Kolkata , Mohanpur 741246 , India .
| | - Krishnendu Das
- Department of Chemical Sciences , Centre for Advanced Functional Materials , Indian Institute of Science Education and Research (IISER) Kolkata , Mohanpur 741246 , India .
| | - Dibyendu Das
- Department of Chemical Sciences , Centre for Advanced Functional Materials , Indian Institute of Science Education and Research (IISER) Kolkata , Mohanpur 741246 , India .
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163
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Abstract
Chemical processes in closed systems inevitably relax to equilibrium. Living systems avoid this fate and give rise to a much richer diversity of phenomena by operating under nonequilibrium conditions. Recent experiments in dissipative self-assembly also demonstrated that by opening reaction vessels and steering certain concentrations, an ocean of opportunities for artificial synthesis and energy storage emerges. To navigate it, thermodynamic notions of energy, work and dissipation must be established for these open chemical systems. Here, we do so by building upon recent theoretical advances in nonequilibrium statistical physics. As a central outcome, we show how to quantify the efficiency of such chemical operations and lay the foundation for performance analysis of any dissipative chemical process.
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164
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Criado-Gonzalez M, Fores JR, Carvalho A, Blanck C, Schmutz M, Kocgozlu L, Schaaf P, Jierry L, Boulmedais F. Phase Separation in Supramolecular Hydrogels Based on Peptide Self-Assembly from Enzyme-Coated Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:10838-10845. [PMID: 31334660 DOI: 10.1021/acs.langmuir.9b01420] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spatial localization of biocatalysts, such as enzymes, has recently proven to be an effective process to direct supramolecular self-assemblies in a spatiotemporal way. In this work, silica nanoparticles (NPs) functionalized covalently by alkaline phosphatase (NPs@AP) induce the localized growth of self-assembled peptide nanofibers from NPs by dephosphorylation of Fmoc-FFpY peptides (Fmoc: fluorenylmethyloxycarbonyl; F: phenylalanine; Y: tyrosine; p: phosphate group). The fibrillary nanoarchitecture around NPs@AP underpins a homogeneous hydrogel, which unexpectedly undergoes a macroscopic shape change over time. This macroscopic change is due to a phase separation leading to a dense phase (in NPs and nanofibers) in the center of the vial and surrounded by a dilute one, which still contains NPs and peptide self-assemblies. We thus hypothesize that the phase separation is not a syneresis process. Such a change is only observed when the enzymes are localized on the NPs. The dense phase contracts with time until reaching a constant volume after several days. For a given phosphorylated peptide concentration, the dense phase contracts faster when the NPs@AP concentration is increased. For a given NPs@AP concentration, it condenses faster when the peptide concentration increases. We hypothesize that the appearance of a dense phase is not only due to attractive interactions between NPs@AP but also to the strong interactions of self-assembled peptide nanofibers with the enzymes, covalently fixed on the NPs.
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Affiliation(s)
- Miryam Criado-Gonzalez
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
- Institut National de la Santé et de la Recherche Médicale, UMR-S 1121, "Biomatériaux et Bioingénierie" , 67087 Strasbourg , France
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Fédération de Médecine Translationnelle de Strasbourg and Fédération des Matériaux et Nanoscience d'Alsace , 67000 Strasbourg , France
| | - Jennifer Rodon Fores
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Alain Carvalho
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Christian Blanck
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Marc Schmutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Leyla Kocgozlu
- Institut National de la Santé et de la Recherche Médicale, UMR-S 1121, "Biomatériaux et Bioingénierie" , 67087 Strasbourg , France
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Fédération de Médecine Translationnelle de Strasbourg and Fédération des Matériaux et Nanoscience d'Alsace , 67000 Strasbourg , France
| | - Pierre Schaaf
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
- Institut National de la Santé et de la Recherche Médicale, UMR-S 1121, "Biomatériaux et Bioingénierie" , 67087 Strasbourg , France
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Fédération de Médecine Translationnelle de Strasbourg and Fédération des Matériaux et Nanoscience d'Alsace , 67000 Strasbourg , France
| | - Loïc Jierry
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Fouzia Boulmedais
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
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165
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166
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Li Z, Zeman CJ, Valandro SR, Bantang JPO, Schanze KS. Adenosine Triphosphate Templated Self-Assembly of Cationic Porphyrin into Chiral Double Superhelices and Enzyme-Mediated Disassembly. J Am Chem Soc 2019; 141:12610-12618. [PMID: 31329440 DOI: 10.1021/jacs.9b04133] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembly of small molecules through noncovalent interactions into nanoscale architectures has been extensively studied in supramolecular chemistry. However, it is still challenging to develop a biologically inspired self-assembly system that functions in water with complex structure and dynamics by analogy with those found in nature. Here, we report a new water-soluble cationic porphyrin that undergoes adenosine triphosphate (ATP)-templated self-assembly into right-handed double-helical supramolecular structures. Direct observation of the porphyrin-ATP assembly by transmission electron microscopy has been accomplished. The assemblies consist of superhelical fibers with length greater than 1 μm and width ∼46 nm. The chiral superhelical fibers show reversible disassembly to monomers upon hydrolysis of ATP catalyzed by alkaline phosphatase (ALP), and the nanofibers can be re-formed with subsequent addition of ATP. Moreover, transient self-assembly of a chiral double helix is formed when ALP is present to consume ATP.
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Affiliation(s)
- Zhiliang Li
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States.,Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Charles J Zeman
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States.,Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Silvano R Valandro
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Jose Paolo O Bantang
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Kirk S Schanze
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
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167
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Zhang H, Zeng H, Priimagi A, Ikkala O. Programmable responsive hydrogels inspired by classical conditioning algorithm. Nat Commun 2019; 10:3267. [PMID: 31332196 PMCID: PMC6646376 DOI: 10.1038/s41467-019-11260-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/26/2019] [Indexed: 01/19/2023] Open
Abstract
Living systems have inspired research on non-biological dynamic materials and systems chemistry to mimic specific complex biological functions. Upon pursuing ever more complex life-inspired non-biological systems, mimicking even the most elementary aspects of learning is a grand challenge. We demonstrate a programmable hydrogel-based model system, whose behaviour is inspired by associative learning, i.e., conditioning, which is among the simplest forms of learning. Algorithmically, associative learning minimally requires responsivity to two different stimuli and a memory element. Herein, nanoparticles form the memory element, where a photoacid-driven pH-change leads to their chain-like assembly with a modified spectral behaviour. On associating selected light irradiation with heating, the gel starts to melt upon the irradiation, originally a neutral stimulus. A logic diagram describes such an evolution of the material response. Coupled chemical reactions drive the system out-of-equilibrium, allowing forgetting and memory recovery. The findings encourage to search non-biological materials towards associative and dynamic properties. Living systems inspired research on systems chemistry to mimic specific complex biological functions, but mimicking even the most elementary aspects of learning is a grand challenge. Here the authors demonstrate a programmable hydrogel-based model system, whose behaviour is inspired by associative learning.
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168
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Biagini C, Fielden SDP, Leigh DA, Schaufelberger F, Di Stefano S, Thomas D. Dissipative Catalysis with a Molecular Machine. Angew Chem Int Ed Engl 2019; 58:9876-9880. [PMID: 31111628 PMCID: PMC6900173 DOI: 10.1002/anie.201905250] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Indexed: 11/29/2022]
Abstract
We report on catalysis by a fuel-induced transient state of a synthetic molecular machine. A [2]rotaxane molecular shuttle containing secondary ammonium/amine and thiourea stations is converted between catalytically inactive and active states by pulses of a chemical fuel (trichloroacetic acid), which is itself decomposed by the machine and/or the presence of additional base. The ON-state of the rotaxane catalyzes the reduction of a nitrostyrene by transfer hydrogenation. By varying the amount of fuel added, the lifetime of the rotaxane ON-state can be regulated and temporal control of catalysis achieved. The system can be pulsed with chemical fuel several times in succession, with each pulse activating catalysis for a time period determined by the amount of fuel added. Dissipative catalysis by synthetic molecular machines has implications for the future design of networks that feature communication and signaling between the components.
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Affiliation(s)
- Chiara Biagini
- School of ChemistryUniversity of ManchesterOxford RoadM13 9PLManchesterUK
- Edificio Cannizzaro (VEC)Dipartimento di ChimicaUniversità degli Studi di Roma “La Sapienza”Piazzale Aldo Moro 500185RomaItaly
| | | | - David A. Leigh
- School of ChemistryUniversity of ManchesterOxford RoadM13 9PLManchesterUK
| | | | - Stefano Di Stefano
- Edificio Cannizzaro (VEC)Dipartimento di ChimicaUniversità degli Studi di Roma “La Sapienza”Piazzale Aldo Moro 500185RomaItaly
| | - Dean Thomas
- School of ChemistryUniversity of ManchesterOxford RoadM13 9PLManchesterUK
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169
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Ryzhkov NV, Andreeva DV, Skorb EV. Coupling pH-Regulated Multilayers with Inorganic Surfaces for Bionic Devices and Infochemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8543-8556. [PMID: 31018639 DOI: 10.1021/acs.langmuir.9b00633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This article summarizes more than 10 years of cooperation with Prof. Helmuth Möhwald. Here we describe how the research moved from light-regulated feedback sustainable systems and control biodevices to the current focus on infochemistry in aqueous solution. An important advanced characteristic of such materials and devices is the pH concentration gradient in aqueous solution. A major part of the article focuses on the use of localized illumination for proton generation as a reliable, minimal-reagent-consuming, stable light-promoted proton pump. The in situ scanning vibration electrode technique (SVET) and scanning ion-selective electrode technique (SIET) are efficient for the spatiotemporal evolution of ions on the surface. pH-sensitive polyelectrolyte (PEs) multilayers with different PE architectures are composed with a feedback loop for bionic devices. We show here that pH-regulated PE multilayers can change their properties-film thickness and stiffness, permeability, hydrophilicity, and/or fluorescence-in response to light or electrochemical or biological processes instead of classical acid/base titration.
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Affiliation(s)
| | - Daria V Andreeva
- Centre for Advanced 2D Materials and Graphene Research Centre , National University of Singapore , 117546 Singapore
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170
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Heinen L, Walther A. Programmable dynamic steady states in ATP-driven nonequilibrium DNA systems. SCIENCE ADVANCES 2019; 5:eaaw0590. [PMID: 31334349 PMCID: PMC6641946 DOI: 10.1126/sciadv.aaw0590] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/11/2019] [Indexed: 05/17/2023]
Abstract
Inspired by the dynamics of the dissipative self-assembly of microtubules, chemically fueled synthetic systems with transient lifetimes are emerging for nonequilibrium materials design. However, realizing programmable or even adaptive structural dynamics has proven challenging because it requires synchronization of energy uptake and dissipation events within true steady states, which remains difficult to orthogonally control in supramolecular systems. Here, we demonstrate full synchronization of both events by ATP-fueled activation and dynamization of covalent DNA bonds via an enzymatic reaction network of concurrent ligation and cleavage. Critically, the average bond ratio and the frequency of bond exchange are imprinted into the energy dissipation kinetics of the network and tunable through its constituents. We introduce temporally and structurally programmable dynamics by polymerization of transient, dynamic covalent DNA polymers with adaptive steady-state properties in dependence of ATP fuel and enzyme concentrations. This approach enables generic access to nonequilibrium soft matter systems with adaptive and programmable dynamics.
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Affiliation(s)
- Laura Heinen
- Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany
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171
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Biagini C, Fielden SDP, Leigh DA, Schaufelberger F, Di Stefano S, Thomas D. Dissipative Catalysis with a Molecular Machine. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905250] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Chiara Biagini
- School of ChemistryUniversity of Manchester Oxford Road M13 9PL Manchester UK
- Edificio Cannizzaro (VEC)Dipartimento di ChimicaUniversità degli Studi di Roma “La Sapienza” Piazzale Aldo Moro 5 00185 Roma Italy
| | | | - David A. Leigh
- School of ChemistryUniversity of Manchester Oxford Road M13 9PL Manchester UK
| | | | - Stefano Di Stefano
- Edificio Cannizzaro (VEC)Dipartimento di ChimicaUniversità degli Studi di Roma “La Sapienza” Piazzale Aldo Moro 5 00185 Roma Italy
| | - Dean Thomas
- School of ChemistryUniversity of Manchester Oxford Road M13 9PL Manchester UK
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172
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Yucknovsky A, Mondal S, Burnstine-Townley A, Foqara M, Amdursky N. Use of Photoacids and Photobases To Control Dynamic Self-Assembly of Gold Nanoparticles in Aqueous and Nonaqueous Solutions. NANO LETTERS 2019; 19:3804-3810. [PMID: 31124686 DOI: 10.1021/acs.nanolett.9b00952] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Dynamic self-assembly of nanoparticles (NPs) for the formation of aggregates takes place out of thermodynamic equilibrium and is sustained by external energy supply. Herein, we present light energy driven dynamic self-assembly process of AuNPs, decorated with pH sensitive ligands. The process is being controlled by the use of photoacids and photobases that undergo excited state proton or hydroxide transfer, respectively, due to their large p Ka change between their ground and excited electronic states. The unique design is underlined by record subsecond conversion rates between the assembled and disassembled AuNPs states, and the ability to control the process using only light of different wavelengths. Measurements in both aqueous and nonaqueous solutions resulted in different self-assembly mechanisms, hence showing the wide versatility of photoacids and photobases for dynamic processes.
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Affiliation(s)
- Anna Yucknovsky
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Somen Mondal
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Alex Burnstine-Townley
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Mohammad Foqara
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Nadav Amdursky
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
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173
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Seo J, Kim S, Park HH, Nam JM. Biocomputing with Nanostructures on Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900998. [PMID: 31026121 DOI: 10.1002/smll.201900998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.
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Affiliation(s)
- Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Ha H Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
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174
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Kroiss D, Aramini JM, McPhee SA, Tuttle T, Ulijn RV. Unbiased Discovery of Dynamic Peptide‐ATP Complexes. CHEMSYSTEMSCHEM 2019. [DOI: 10.1002/syst.201900013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Daniela Kroiss
- Nanoscience Initiative at Advanced Science Research Center (ASRC)The Graduate Center of the City University of New York 85 St. Nicholas Terrace New York NY 10031 USA
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New York 365 Fifth Avenue New York NY 10016 USA
- Department of ChemistryHunter College, City University of New York 695 Park Avenue New York NY 10065 USA
| | - James M. Aramini
- Structural Biology Initiative at ASRCThe Graduate Center of the City University of New York 85 St. Nicholas Terrace New York NY 10031 USA
| | - Scott A. McPhee
- Nanoscience Initiative at Advanced Science Research Center (ASRC)The Graduate Center of the City University of New York 85 St. Nicholas Terrace New York NY 10031 USA
| | - Tell Tuttle
- WestCHEM and Department of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - Rein V. Ulijn
- Nanoscience Initiative at Advanced Science Research Center (ASRC)The Graduate Center of the City University of New York 85 St. Nicholas Terrace New York NY 10031 USA
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New York 365 Fifth Avenue New York NY 10016 USA
- Department of ChemistryHunter College, City University of New York 695 Park Avenue New York NY 10065 USA
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175
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Del Grosso E, Ragazzon G, Prins LJ, Ricci F. Fuel‐Responsive Allosteric DNA‐Based Aptamers for the Transient Release of ATP and Cocaine. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812885] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Erica Del Grosso
- Dipartimento di Scienze e Tecnologie ChimicheUniversity of Rome Tor Vergata Via della Ricerca Scientifica Rome 00133 Italy
| | - Giulio Ragazzon
- Department of Chemical SciencesUniversity of Padua Via Marzolo 1 35131 Padua Italy
| | - Leonard J. Prins
- Department of Chemical SciencesUniversity of Padua Via Marzolo 1 35131 Padua Italy
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie ChimicheUniversity of Rome Tor Vergata Via della Ricerca Scientifica Rome 00133 Italy
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176
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Ke H, Yang LP, Xie M, Chen Z, Yao H, Jiang W. Shear-induced assembly of a transient yet highly stretchable hydrogel based on pseudopolyrotaxanes. Nat Chem 2019; 11:470-477. [DOI: 10.1038/s41557-019-0235-8] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 02/25/2019] [Indexed: 11/09/2022]
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177
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Roszak R, Bajczyk MD, Gajewska EP, Hołyst R, Grzybowski BA. Propagation of Oscillating Chemical Signals through Reaction Networks. Angew Chem Int Ed Engl 2019; 58:4520-4525. [PMID: 30397988 DOI: 10.1002/anie.201808821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 12/20/2022]
Abstract
Akin to electronic systems that can tune to and process signals of select frequencies, systems/networks of chemical reactions also "propagate" time-varying concentration inputs in a frequency-dependent manner. Whereas signals of low frequencies are transmitted, higher frequency inputs are dampened and converted into steady-concentration outputs. Such behavior is observed in both idealized reaction chains as well as realistic signaling cascades, in the latter case explaining the experimentally observed responses of such cascades to input calcium oscillations. These and other results are supported by numerical simulations within the freely available Kinetix web application we developed to study chemical systems of arbitrary architectures, reaction kinetics, and boundary conditions.
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Affiliation(s)
- Rafał Roszak
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Michał D Bajczyk
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Ewa P Gajewska
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Bartosz A Grzybowski
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, Warsaw, 02-224, Poland.,IBS Center for Soft and Living Matter and Department of Chemistry, UNIST, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, South Korea
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178
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Del Grosso E, Ragazzon G, Prins LJ, Ricci F. Fuel-Responsive Allosteric DNA-Based Aptamers for the Transient Release of ATP and Cocaine. Angew Chem Int Ed Engl 2019; 58:5582-5586. [PMID: 30715777 DOI: 10.1002/anie.201812885] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/18/2019] [Indexed: 11/11/2022]
Abstract
We show herein that allostery offers a key strategy for the design of out-of-equilibrium systems by engineering allosteric DNA-based nanodevices for the transient loading and release of small organic molecules. To demonstrate the generality of our approach, we used two model DNA-based aptamers that bind ATP and cocaine through a target-induced conformational change. We re-engineered these aptamers so that their affinity towards their specific target is controlled by a DNA sequence acting as an allosteric inhibitor. The use of an enzyme that specifically cleaves the inhibitor only when it is bound to the aptamer generates a transient allosteric control that leads to the release of ATP or cocaine from the aptamers. Our approach confirms that the programmability and predictability of nucleic acids make synthetic DNA/RNA the perfect candidate material to re-engineer synthetic receptors that can undergo chemical fuel-triggered release of small-molecule cargoes and to rationally design non-equilibrium systems.
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Affiliation(s)
- Erica Del Grosso
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Giulio Ragazzon
- Department of Chemical Sciences, University of Padua, Via Marzolo 1, 35131, Padua, Italy
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padua, Via Marzolo 1, 35131, Padua, Italy
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
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179
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Grzelczak M. Colloidal systems chemistry. Replication, reproduction and selection at nanoscale. J Colloid Interface Sci 2019; 537:269-279. [PMID: 30448648 DOI: 10.1016/j.jcis.2018.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/25/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
Development of synthetic systems carrying life-like features is a long-standing challenge in chemistry and material science. Poor understanding of mechanisms ruling the emergence of life-like features in an inanimate matter makes the challenge even more exciting. The growing field of systems chemistry takes the lead in defining life-like dynamic signatures in minimalistic (macro)molecular systems through the development of multicomponent synthetic models using tools from organic and supramolecular chemistry. Recent progress in nanoscience makes available a range of novel materials that can undoubtedly enrich systems chemistry. Therefore, with the aim of placing nano- and colloidal science within the context of systems chemistry, the recent experimental and theoretical developments dealing with the use of nanoparticles and their assemblies in the realisation of the concepts such as replication, reproduction and selection are discussed.
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Affiliation(s)
- Marek Grzelczak
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, Donostia - San Sebastián 20018, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
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180
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Abstract
The continuous consumption of chemical energy powers biological systems so that they can operate functional supramolecular structures. A goal of modern science is to understand how simple chemical mixtures may transition from non-living components to truly emergent systems and the production of new lifelike materials and machines. In this work a replicator can be maintained out-of-equilibrium by the continuous consumption of chemical energy. The system is driven by the autocatalytic formation of a metastable surfactant whose breakdown products are converted back into building blocks by a chemical fuel. The consumption of fuel allows the high-energy replicators to persist at a steady state, much like a simple metabolic cycle. Thermodynamically-driven reactions effect a unidirectional substrate flux as the system tries to regain equilibrium. The metastable replicator persists at a higher concentration than achieved even transiently in a closed system, and its concentration is responsive to the rate of fuel supply. Understanding how simple chemical mixtures transition into truly emergent systems is essential to create new lifelike materials. Here, the authors show a self-replicating system that can be maintained out-of-equilibrium by an oxidant fuel in analogy to simple metabolic cycles.
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181
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Jain A, Dhiman S, Dhayani A, Vemula PK, George SJ. Chemical fuel-driven living and transient supramolecular polymerization. Nat Commun 2019; 10:450. [PMID: 30683874 PMCID: PMC6347607 DOI: 10.1038/s41467-019-08308-9] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/03/2019] [Indexed: 01/04/2023] Open
Abstract
Temporal control over self-assembly process is a desirable trait in the quest towards adaptable and controllable materials. The ability to devise synthetic ways to control the growth, as well as decay of materials has long been a property which only the biological systems could perform seamlessly. A common synthetic strategy which works on the biological principles such as chemical fuel-driven control over temporal self-assembly profile has not been completely realized synthetically. Here we show, we filled this dearth by showing that a chemical fuel driven self-assembling system can not only be grown in a controlled manner, but it can also result in precise control over the assembly and disassembly kinetics. Herein, we elaborate strategies which clearly show that once a chemical fuel driven self-assembly is established it can be made receptive to multiple molecular cues such that the inherent growth and decay characteristics are programmed into the ensemble.
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Affiliation(s)
- Ankit Jain
- Supramolecular Chemistry Laboratory, New Chemistry Unit, School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Shikha Dhiman
- Supramolecular Chemistry Laboratory, New Chemistry Unit, School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Ashish Dhayani
- Institute for Stem Cell Biology and Regenerative Medicine (InStem), UAS-GKVK Post, Bellary Road, Bangalore, 560065, India
- The School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401, India
| | - Praveen K Vemula
- Institute for Stem Cell Biology and Regenerative Medicine (InStem), UAS-GKVK Post, Bellary Road, Bangalore, 560065, India.
| | - Subi J George
- Supramolecular Chemistry Laboratory, New Chemistry Unit, School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India.
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182
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Catalytic transport of molecular cargo using diffusive binding along a polymer track. Nat Chem 2019; 11:359-366. [DOI: 10.1038/s41557-018-0204-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/04/2018] [Indexed: 01/17/2023]
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183
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Tuning the life-time of supramolecular hydrogels using ROS-responsive telechelic peptide-polymer conjugates. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.11.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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184
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Barreto GR, Kawai C, Tofanello A, Neves AAR, Araujo-Chaves JC, Belleti E, Lanfredi AJC, Crespilho FN, Nantes-Cardoso IL. Magnetoliposomes as model for signal transmission. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181108. [PMID: 30800363 PMCID: PMC6366231 DOI: 10.1098/rsos.181108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 11/23/2018] [Indexed: 06/09/2023]
Abstract
Liposomes containing magnetic nanoparticles (magnetoliposomes) have been extensively explored for targeted drug delivery. However, the magnetic effect of nanoparticles movement is also an attractive choice for the conduction of signals in communication systems at the nanoscale level because of the simple manipulation and efficient control. Here, we propose a model for the transmission of electrical and luminous signals taking advantage of magnetophoresis. The study involved three steps. Firstly, magnetite was synthesized and incorporated into fusogenic large unilamellar vesicles (LUVs) previously associated with a fluorescent label. Secondly, the fluorescent magnetite-containing LUVs delivered their contents to the giant unilamellar vesicles (GUVs), which were corroborated by magnetophoresis and fluorescence microscopy. In the third step, magnetophoresis of magnetic vesicles was used for the conduction of the luminous signal from a capillary to an optical fibre connected to a fluorescence detector. Also, the magnetophoresis effects on subsequent transmission of the electrochemical signal were demonstrated using magnetite associated with CTAB micelles modified with ferrocene. We glimpse that these magnetic supramolecular systems can be applied in micro- and nanoscale communication systems.
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Affiliation(s)
- G. R. Barreto
- Center of Natural Sciences and Humanities (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - C. Kawai
- Center of Natural Sciences and Humanities (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - A. Tofanello
- Center of Natural Sciences and Humanities (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - A. A. R. Neves
- Center of Natural Sciences and Humanities (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - J. C. Araujo-Chaves
- Center of Natural Sciences and Humanities (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - E. Belleti
- Center of Natural Sciences and Humanities (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - A. J. C. Lanfredi
- Center for Engineering and Applied Social Sciences (CECS), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - F. N. Crespilho
- São Carlos Institute of Chemistry, University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, São Paulo 13560-970, Brazil
| | - I. L. Nantes-Cardoso
- Center of Natural Sciences and Humanities (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil
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185
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Grzelczak M, Liz-Marzán LM, Klajn R. Stimuli-responsive self-assembly of nanoparticles. Chem Soc Rev 2019; 48:1342-1361. [DOI: 10.1039/c8cs00787j] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ligand-protected nanoparticles can serve as attractive building blocks for constructing complex chemical systems.
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Affiliation(s)
- Marek Grzelczak
- Donostia International Physics Center (DIPC)
- 20018 Donostia-San Sebastián
- Spain
- Ikerbasque
- Basque Foundation for Science
| | - Luis M. Liz-Marzán
- Ikerbasque
- Basque Foundation for Science
- 48013 Bilbao
- Spain
- CIC biomaGUNE and CIBER-BBN
| | - Rafal Klajn
- Department of Organic Chemistry
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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186
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BRITO ADRIANNEM, BELLETI ELISANGELA, MENEZES LUCIVALDOR, LANFREDI ALEXANDREJ, NANTES-CARDOS ISELIL. Proteins and Peptides at the Interfaces of Nanostructures. ACTA ACUST UNITED AC 2019; 91:e20181236. [DOI: 10.1590/0001-3765201920181236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/05/2019] [Indexed: 12/19/2022]
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187
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Abstract
Gels that display light-induced motile, life-like actions are reviewed and their potential applications as light-driven soft actuators are also discussed.
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Affiliation(s)
- Matteo Mauro
- Université de Strasbourg
- CNRS Institut de Physique et Chimie des Matériaux de Strasbourg
- UMR 7504
- 67000 Strasbourg
- France
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188
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Menezes L, Parma E, Machado EG, Nagao R. Quasiperiodic behavior in the electrodeposition of Cu/Sn multilayers: extraction of activation energies and wavelet analysis. Phys Chem Chem Phys 2019; 21:21057-21063. [DOI: 10.1039/c9cp03605a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The oscillatory electro-deposition of Cu/Sn in the presence of a surfactant shows quasiperiodic behavior, which is described by the coupling between a mainly activation and a mainly diffusion-controlled processes.
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Affiliation(s)
- Laura Menezes
- Institute of Chemistry
- University of Campinas
- CEP 13083-970 Campinas
- Brazil
| | - Eduardo Parma
- Institute of Chemistry
- University of Campinas
- CEP 13083-970 Campinas
- Brazil
| | - Eduardo G. Machado
- Institute of Chemistry
- University of Campinas
- CEP 13083-970 Campinas
- Brazil
- Center for Innovation on New Energies
| | - Raphael Nagao
- Institute of Chemistry
- University of Campinas
- CEP 13083-970 Campinas
- Brazil
- Center for Innovation on New Energies
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189
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Solís Muñana P, Ragazzon G, Dupont J, Ren CZ, Prins LJ, Chen JL. Substrate-Induced Self-Assembly of Cooperative Catalysts. Angew Chem Int Ed Engl 2018; 57:16469-16474. [PMID: 30302870 PMCID: PMC7159596 DOI: 10.1002/anie.201810891] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 12/12/2022]
Abstract
Dissipative self-assembly processes in nature rely on chemical fuels that activate proteins for assembly through the formation of a noncovalent complex. The catalytic activity of the assemblies causes fuel degradation, resulting in the formation of an assembly in a high-energy, out-of-equilibrium state. Herein, we apply this concept to a synthetic system and demonstrate that a substrate can induce the formation of vesicular assemblies, which act as cooperative catalysts for cleavage of the same substrate.
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Affiliation(s)
- Pablo Solís Muñana
- School of SciencesAuckland University of TechnologyPrivate Bag 92006Auckland1142New Zealand
| | - Giulio Ragazzon
- Department of Chemical SciencesUniversity of PadovaVia Marzolo 135131PadovaItaly
| | - Julien Dupont
- School of SciencesAuckland University of TechnologyPrivate Bag 92006Auckland1142New Zealand
| | - Chloe Z.‐J. Ren
- School of SciencesAuckland University of TechnologyPrivate Bag 92006Auckland1142New Zealand
| | - Leonard J. Prins
- Department of Chemical SciencesUniversity of PadovaVia Marzolo 135131PadovaItaly
| | - Jack L.‐Y. Chen
- School of SciencesAuckland University of TechnologyPrivate Bag 92006Auckland1142New Zealand
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190
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Solís Muñana P, Ragazzon G, Dupont J, Ren CZJ, Prins LJ, Chen JLY. Substrate-Induced Self-Assembly of Cooperative Catalysts. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 130:16707-16712. [PMID: 32313321 PMCID: PMC7159549 DOI: 10.1002/ange.201810891] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 11/22/2022]
Abstract
Dissipative self-assembly processes in nature rely on chemical fuels that activate proteins for assembly through the formation of a noncovalent complex. The catalytic activity of the assemblies causes fuel degradation, resulting in the formation of an assembly in a high-energy, out-of-equilibrium state. Herein, we apply this concept to a synthetic system and demonstrate that a substrate can induce the formation of vesicular assemblies, which act as cooperative catalysts for cleavage of the same substrate.
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Affiliation(s)
- Pablo Solís Muñana
- School of Sciences Auckland University of Technology Private Bag 92006 Auckland 1142 New Zealand
| | - Giulio Ragazzon
- Department of Chemical Sciences University of Padova Via Marzolo 1 35131 Padova Italy
| | - Julien Dupont
- School of Sciences Auckland University of Technology Private Bag 92006 Auckland 1142 New Zealand
| | - Chloe Z-J Ren
- School of Sciences Auckland University of Technology Private Bag 92006 Auckland 1142 New Zealand
| | - Leonard J Prins
- Department of Chemical Sciences University of Padova Via Marzolo 1 35131 Padova Italy
| | - Jack L-Y Chen
- School of Sciences Auckland University of Technology Private Bag 92006 Auckland 1142 New Zealand
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191
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Bal S, Das K, Ahmed S, Das D. Chemically Fueled Dissipative Self-Assembly that Exploits Cooperative Catalysis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811749] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Subhajit Bal
- Department of Chemical Sciences and Centre for Advanced Functional Materials; Indian Institute of Science Education and Research (IISER); Kolkata Mohanpur 741246 India
| | - Krishnendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials; Indian Institute of Science Education and Research (IISER); Kolkata Mohanpur 741246 India
| | - Sahnawaz Ahmed
- Department of Chemical Sciences and Centre for Advanced Functional Materials; Indian Institute of Science Education and Research (IISER); Kolkata Mohanpur 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials; Indian Institute of Science Education and Research (IISER); Kolkata Mohanpur 741246 India
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192
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Roszak R, Bajczyk MD, Gajewska EP, Hołyst R, Grzybowski BA. Propagation of Oscillating Chemical Signals through Reaction Networks. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rafał Roszak
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 Warsaw 02-224 Poland
| | - Michał D. Bajczyk
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 Warsaw 02-224 Poland
| | - Ewa P. Gajewska
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 Warsaw 02-224 Poland
| | - Robert Hołyst
- Institute of Physical Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 Warsaw 02-224 Poland
| | - Bartosz A. Grzybowski
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 Warsaw 02-224 Poland
- IBS Center for Soft and Living Matter and Department of Chemistry UNIST 50, UNIST-gil, Eonyang-eup, Ulju-gun Ulsan South Korea
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193
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Bal S, Das K, Ahmed S, Das D. Chemically Fueled Dissipative Self-Assembly that Exploits Cooperative Catalysis. Angew Chem Int Ed Engl 2018; 58:244-247. [PMID: 30395376 DOI: 10.1002/anie.201811749] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Indexed: 12/12/2022]
Abstract
In living systems, dissipative processes are driven by the endergonic hydrolysis of chemical fuels such as nucleoside triphosphates. Now, through a simple model system, a transient self-assembled state is realized by utilizing the catalytic effect of histidine on the formation and breaking of ester bonds. First, histidine facilitates the ester bond formation, which then rapidly co-assembles to form a self-supporting gel. An out-of-equilibrium state is realized owing to the cooperative catalysis by the proximal histidines in the assembled state, driving the second pathway and resulting in disassembly to sol. Cooperative effects that use the dual role of imidazoles as nucleophile and as proton donor is utilized to achieve transient assemblies. This simple system mimics the structural journey seen in microtubule formation where the substrate GTP facilitates the non-covalent assembly and triggers a cooperative catalytic process, leading to substrate hydrolysis and subsequent disassembly.
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Affiliation(s)
- Subhajit Bal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Krishnendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Sahnawaz Ahmed
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
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194
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Qian C, Wang R, Wu H, Ping J, Wu J. Recent advances in emerging DNA-based methods for genetically modified organisms (GMOs) rapid detection. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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195
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Tian L, Li M, Liu J, Patil AJ, Drinkwater BW, Mann S. Nonequilibrium Spatiotemporal Sensing within Acoustically Patterned Two-Dimensional Protocell Arrays. ACS CENTRAL SCIENCE 2018; 4:1551-1558. [PMID: 30555908 PMCID: PMC6276052 DOI: 10.1021/acscentsci.8b00555] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Indexed: 05/03/2023]
Abstract
Acoustically trapped periodic arrays of horseradish peroxidase (HRP)-loaded poly(diallydimethylammonium chloride) / adenosine 5'-triphosphate coacervate microdroplet-based protocells exhibit a spatiotemporal biochemical response when exposed to a codiffusing mixture of substrate molecules (o-phenylenediamine (o-PD) and hydrogen peroxide (H2O2)) under nonequilibrium conditions. Unidirectional propagation of the chemical concentration gradients gives rise to time- and position-dependent fluorescence signal outputs from individual coacervate microdroplets, indicating that the organized protocell assembly can dynamically sense encoded information in the advancing reaction-diffusion front. The methodology is extended to arrays comprising spatially separated binary populations of HRP- or glucose oxidase-containing coacervate microdroplets to internally generate a H2O2 signal that chemically connects the two protocell communities via a concerted biochemical cascade reaction. Our results provide a step toward establishing a systematic approach to study dynamic interactions between organized protocell consortia and propagating reaction-diffusion gradients, and offer a new methodology for exploring the complexity of protocellular communication networks operating under nonequilibrium conditions.
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Affiliation(s)
- Liangfei Tian
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Mei Li
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Juntai Liu
- School
of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K.
| | - Avinash J. Patil
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Bruce W. Drinkwater
- Faculty
of Engineering, Queens Building, University
of Bristol, Bristol BS8 1TR, U.K.
| | - Stephen Mann
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
- E-mail:
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196
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Abstract
Heterogeneous catalytic systems based on the use of stimuli-responsive materials can be switched from an “on” active state to an “off” inactive state, which contributes to endowing the catalysts with unique functional properties, such as adaptability, recyclability and precise spatial and temporal control on different types of chemical reactions. All these properties constitute a step toward the development of nature-inspired catalytic systems. Even if this is a niche area in the field of catalysis, it is possible to find in literature intriguing examples of dynamic catalysts, whose systematic analysis and review are still lacking. The aim of this work is to examine the recent developments of stimuli-responsive heterogeneous catalytic systems from the viewpoint of different approaches that have been proposed to obtain a dynamic control of catalytic efficiency. Because of the variety of reactions and conditions, it is difficult to make a quantitative comparison between the efficiencies of the considered systems, but the analysis of the different strategies can inspire the preparation of new smart catalytic systems.
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197
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Fukui T, Uchihashi T, Sasaki N, Watanabe H, Takeuchi M, Sugiyasu K. Direct Observation and Manipulation of Supramolecular Polymerization by High‐Speed Atomic Force Microscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomoya Fukui
- Molecular Design and Function GroupNational Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
| | - Takayuki Uchihashi
- Department of PhysicsNagoya University Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Norihiko Sasaki
- Molecular Design and Function GroupNational Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
- Department of Materials Physics and ChemistryGraduate School of EngineeringKyushu University Moto-oka 744 Nishi-ku Fukuoka 819-0395 Japan
| | - Hiroki Watanabe
- Department of PhysicsNagoya University Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Masayuki Takeuchi
- Molecular Design and Function GroupNational Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
| | - Kazunori Sugiyasu
- Molecular Design and Function GroupNational Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
- Department of Materials Physics and ChemistryGraduate School of EngineeringKyushu University Moto-oka 744 Nishi-ku Fukuoka 819-0395 Japan
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198
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Fukui T, Uchihashi T, Sasaki N, Watanabe H, Takeuchi M, Sugiyasu K. Direct Observation and Manipulation of Supramolecular Polymerization by High‐Speed Atomic Force Microscopy. Angew Chem Int Ed Engl 2018; 57:15465-15470. [DOI: 10.1002/anie.201809165] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Tomoya Fukui
- Molecular Design and Function GroupNational Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
| | - Takayuki Uchihashi
- Department of PhysicsNagoya University Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Norihiko Sasaki
- Molecular Design and Function GroupNational Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
- Department of Materials Physics and ChemistryGraduate School of EngineeringKyushu University Moto-oka 744 Nishi-ku Fukuoka 819-0395 Japan
| | - Hiroki Watanabe
- Department of PhysicsNagoya University Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Masayuki Takeuchi
- Molecular Design and Function GroupNational Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
| | - Kazunori Sugiyasu
- Molecular Design and Function GroupNational Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
- Department of Materials Physics and ChemistryGraduate School of EngineeringKyushu University Moto-oka 744 Nishi-ku Fukuoka 819-0395 Japan
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199
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Leira-Iglesias J, Tassoni A, Adachi T, Stich M, Hermans TM. Oscillations, travelling fronts and patterns in a supramolecular system. NATURE NANOTECHNOLOGY 2018; 13:1021-1027. [PMID: 30323361 DOI: 10.1038/s41565-018-0270-4] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/03/2018] [Indexed: 05/24/2023]
Abstract
Supramolecular polymers, such as microtubules, operate under non-equilibrium conditions to drive crucial functions in cells, such as motility, division and organelle transport1. In vivo and in vitro size oscillations of individual microtubules2,3 (dynamic instabilities) and collective oscillations4 have been observed. In addition, dynamic spatial structures, like waves and polygons, can form in non-stirred systems5. Here we describe an artificial supramolecular polymer made of a perylene diimide derivative that displays oscillations, travelling fronts and centimetre-scale self-organized patterns when pushed far from equilibrium by chemical fuels. Oscillations arise from a positive feedback due to nucleation-elongation-fragmentation, and a negative feedback due to size-dependent depolymerization. Travelling fronts and patterns form due to self-assembly induced density differences that cause system-wide convection. In our system, the species responsible for the nonlinear dynamics and those that self-assemble are one and the same. In contrast, other reported oscillating assemblies formed by vesicles6, micelles7 or particles8 rely on the combination of a known chemical oscillator and a stimuli-responsive system, either by communication through the solvent (for example, by changing pH7-9), or by anchoring one of the species covalently (for example, a Belousov-Zhabotinsky catalyst6,10). The design of self-oscillating supramolecular polymers and large-scale dissipative structures brings us closer to the creation of more life-like materials11 that respond to external stimuli similarly to living cells, or to creating artificial autonomous chemical robots12.
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Affiliation(s)
| | | | - Takuji Adachi
- University of Strasbourg, CNRS, ISIS UMR 7006, Strasbourg, France
| | - Michael Stich
- Non-linearity and Complexity Research Group, Systems Analytics Research Institute, Engineering and Applied Science, Aston University, Birmingham, UK
| | - Thomas M Hermans
- University of Strasbourg, CNRS, ISIS UMR 7006, Strasbourg, France.
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200
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Rodríguez-Arco L, Poma A, Ruiz-Pérez L, Scarpa E, Ngamkham K, Battaglia G. Molecular bionics - engineering biomaterials at the molecular level using biological principles. Biomaterials 2018; 192:26-50. [PMID: 30419394 DOI: 10.1016/j.biomaterials.2018.10.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/06/2018] [Accepted: 10/28/2018] [Indexed: 12/18/2022]
Abstract
Life and biological units are the result of the supramolecular arrangement of many different types of molecules, all of them combined with exquisite precision to achieve specific functions. Taking inspiration from the design principles of nature allows engineering more efficient and compatible biomaterials. Indeed, bionic (from bion-, unit of life and -ic, like) materials have gained increasing attention in the last decades due to their ability to mimic some of the characteristics of nature systems, such as dynamism, selectivity, or signalling. However, there are still many challenges when it comes to their interaction with the human body, which hinder their further clinical development. Here we review some of the recent progress in the field of molecular bionics with the final aim of providing with design rules to ensure their stability in biological media as well as to engineer novel functionalities which enable navigating the human body.
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Affiliation(s)
- Laura Rodríguez-Arco
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK.
| | - Alessandro Poma
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK
| | - Lorena Ruiz-Pérez
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK; The EPRSC/Jeol Centre of Liquid Electron Microscopy, University College London, London, WC1H 0AJ, UK
| | - Edoardo Scarpa
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK
| | - Kamolchanok Ngamkham
- Faculty of Engineering, King Mongkut's University of Technology Thonbury, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok, 10140, Thailand
| | - Giuseppe Battaglia
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK; The EPRSC/Jeol Centre of Liquid Electron Microscopy, University College London, London, WC1H 0AJ, UK.
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