51
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Howlett MG, Engwerda AHJ, Scanes RJH, Fletcher SP. An autonomously oscillating supramolecular self-replicator. Nat Chem 2022; 14:805-810. [PMID: 35618766 DOI: 10.1038/s41557-022-00949-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/13/2022] [Indexed: 01/24/2023]
Abstract
A key goal of chemistry is to develop synthetic systems that mimic biology, such as self-assembling, self-replicating models of minimal life forms. Oscillations are often observed in complex biological networks, but oscillating, self-replicating species are unknown, and how to control autonomous supramolecular-level oscillating systems is also not yet established. Here we show how a population of self-assembling self-replicators can autonomously oscillate, so that simple micellar species repeatedly appear and disappear in time. The interplay of molecular and supramolecular events is key to observing oscillations: the repeated formation and disappearance of compartments is connected to a reaction network where molecular-level species are formed and broken down. The dynamic behaviour of our system across different length scales offers the opportunities for mass transport, as we demonstrate via reversible dye uptake. We believe these findings will inspire new biomimetic systems and may unlock nanotechnology systems such as (supra)molecular pumps, where compartment formation is controlled in time and space.
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52
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Mahato RR, Shandilya E, Not Applicable S, Maiti S. Regulating Spatial Localization and Reactivity Biasness of DNAzymes by Metal Ions and Oligonucleotides. Chembiochem 2022; 23:e202200154. [PMID: 35762518 DOI: 10.1002/cbic.202200154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/08/2022] [Indexed: 11/09/2022]
Abstract
Chemical gradient sensing behavior of catalytically active colloids and enzymes is an area of immense interest owing to their importance in understanding fundamental spatiotemporal complexity pattern in living systems and designing of dynamic materials. Herein, we have shown peroxidase activity of DNAzyme (G-quadruplex-hemin complex tagged in a micron-sized glass bead) can be modulated by metal ions and metal ion-binding oligonucleotides. Next we demonstrated both experimentally and theoretically that the localization and product formation ability of the DNAzyme containing particle remains biased to the more catalytically active zone where concentration of metal ion (Hg2+) inhibitor is low. Interestingly, this biased localization can be broken by introduction of Hg2+ binding oligonucleotide in the system. Additionally, macroscopically asymmetric catalytic product distributed zone has also been achieved on this process, showing possibility in regulation in autonomous spatially controlled chemical process. This demonstration of autonomous modulation of the localization pattern and spatially specific enhanced product forming ability of DNAzymes will further enable in designing of responsive nucleic acid-based motile materials and surfaces.
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Affiliation(s)
- Rishi Ram Mahato
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, INDIA
| | - Ekta Shandilya
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, INDIA
| | | | - Subhabrata Maiti
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, Knowledge City, Sector-81, S.A.S. Nagar, Manauli P.O., 140306, Mohali, INDIA
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53
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He JY, Deng HL, Shang X, Yang CL, Zuo SY, Yuan R, Liu HY, Xu WJ. Modulating the Fluorescence of Silver Nanoclusters Wrapped in DNA Hairpin Loops via Confined Strand Displacement and Transient Concatenate Ligation for Amplifiable Biosensing. Anal Chem 2022; 94:8041-8049. [PMID: 35617342 DOI: 10.1021/acs.analchem.2c01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
It is intriguing to modulate the fluorescence emission of DNA-scaffolded silver nanoclusters (AgNCs) via confined strand displacement and transient concatenate ligation for amplifiable biosensing of a DNA segment related to SARS-CoV-2 (s2DNA). Herein, three stem-loop structural hairpins for signaling, recognizing, and assisting are designed to assemble a variant three-way DNA device (3WDD) with the aid of two linkers, in which orange-emitting AgNC (oAgNC) is stably clustered and populated in the closed loop of a hairpin reporter. The presence of s2DNA initiates the toehold-mediated strand displacement that is confined in this 3WDD for repeatable recycling amplification, outputting numerous hybrid DNA-duplex conformers that are implemented for a transient "head-tail-head" tandem ligation one by one. As a result, the oAgNC-hosted hairpin loops are quickly opened in loose coil motifs, bringing a significant fluorescence decay of multiple clusters dependent on s2DNA. Demonstrations and understanding of the tunable spectral performance of a hairpin loop-wrapped AgNC via switching 3WDD conformation would be highly beneficial to open a new avenue for applicable biosensing, bioanalysis, or clinical diagnostics.
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Affiliation(s)
- Jia-Yang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hui-Lin Deng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xin Shang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chun-Li Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Si-Yu Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hong-Yan Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wen-Ju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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54
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Schnitter F, Rieß B, Jandl C, Boekhoven J. Memory, switches, and an OR-port through bistability in chemically fueled crystals. Nat Commun 2022; 13:2816. [PMID: 35595758 PMCID: PMC9122941 DOI: 10.1038/s41467-022-30424-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/29/2022] [Indexed: 11/12/2022] Open
Abstract
The ability to store information in chemical reaction networks is essential for the complex behavior we associate with life. In biology, cellular memory is regulated through transcriptional states that are bistable, i.e., a state that can either be on or off and can be flipped from one to another through a transient signal. Such memory circuits have been realized synthetically through the rewiring of genetic systems in vivo or through the rational design of reaction networks based on DNA and highly evolved enzymes in vitro. Completely bottom-up analogs based on small molecules are rare and hard to design and thus represent a challenge for systems chemistry. In this work, we show that bistability can be designed from a simple non-equilibrium reaction cycle that is coupled to crystallization. The crystals exert the necessary feedback on the reaction cycle required for the bistability resulting in an on-state with assemblies and an off-state without. Each state represents volatile memory that can be stored in continuously stirred tank reactors indefinitely even though molecules are turned over on a minute-timescale. We showcase the system’s abilities by creating a matrix display that can store images and by creating an OR-gate by coupling several switches together. In biology, information is stored and processed using highly evolved molecules in bistable states. Here, the authors demonstrate bistability in a synthetic system without the need for evolved biomolecules or autocatalytic networks.
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Affiliation(s)
- Fabian Schnitter
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Benedikt Rieß
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Christian Jandl
- Catalysis Research Centre, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany. .,Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2a, 85748, Garching, Germany.
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55
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Xie M, Wang Y, Liu L, Wang X, Jiang H. Luminescent gold-peptide spheric aggregates: selective and effective cellular targeting. J Colloid Interface Sci 2022; 614:502-510. [PMID: 35121508 DOI: 10.1016/j.jcis.2022.01.144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 01/17/2023]
Abstract
Although the restriction of intramolecular motion has been well recognized as the fundamental of aggregation induced emission enhancement (AIEE), the regulation mechanism of gold nanoclusters (AuNCs) based AIEE system are still unclear. In this paper, we have investigated the Zn2+-induced AIEE process of thiolate ligands (i.e., cysteine, glutathione and an 8-mer peptide) protected AuNCs, which shows a pH-dependent evolution from single AuNCs to spheric aggregates to irregular network. Using photoluminescent enhancement ratio as an index, the concept of "mid-pH" is proposed to indicate the optimal pH for the formation of spheric AuNCs aggregates. Importantly, the surface ligands allow the formation of spheric AuNCs aggregates at tunable mid-pH between 5.7 and 7.5. Owing to the appropriate size and surface peptide targetability, the spheric AuNCs aggregates can be successfully screened for targeted tumor cell uptake and imaging at physiological pH. The cell uptake mechanism study showed that AuNCs aggregates was specifically recognized by arginine-glycine-aspartic acid (RGD) sequence on the ligand and integrin αvβ3 on the cell surface, thus mainly through clathrin-mediated endocytosis. This work provides new sight to artificially regulate the construction of efficient cellular imaging probes.
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Affiliation(s)
- Mengyang Xie
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yihan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Liu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Hui Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
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56
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Bi-directional feedback controlled transience in Cucurbituril based tandem nanozyme. J Colloid Interface Sci 2022; 614:172-180. [DOI: 10.1016/j.jcis.2022.01.092] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/06/2022] [Accepted: 01/15/2022] [Indexed: 02/02/2023]
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57
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Kriukov DV, Koyuncu AH, Wong ASY. History Dependence in a Chemical Reaction Network Enables Dynamic Switching. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107523. [PMID: 35257479 DOI: 10.1002/smll.202107523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/02/2022] [Indexed: 06/14/2023]
Abstract
This work describes an enzymatic autocatalytic network capable of dynamic switching under out-of-equilibrium conditions. The network, wherein a molecular fuel (trypsinogen) and an inhibitor (soybean trypsin inhibitor) compete for a catalyst (trypsin), is kept from reaching equilibria using a continuous flow stirred tank reactor. A so-called 'linear inhibition sweep' is developed (i.e., a molecular analogue of linear sweep voltammetry) to intentionally perturb the competition between autocatalysis and inhibition, and used to demonstrate that a simple molecular system, comprising only three components, is already capable of a variety of essential neuromorphic behaviors (hysteresis, synchronization, resonance, and adaptation). This research provides the first steps in the development of a strategy that uses the principles in systems chemistry to transform chemical reaction networks into platforms capable of neural network computing.
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Affiliation(s)
- Dmitrii V Kriukov
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
| | - A Hazal Koyuncu
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
| | - Albert S Y Wong
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
- MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
- BRAINS (Center for Brain-inspired Nano Systems), University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
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58
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Jeong Y, Jin S, Palanikumar L, Choi H, Shin E, Go EM, Keum C, Bang S, Kim D, Lee S, Kim M, Kim H, Lee KH, Jana B, Park MH, Kwak SK, Kim C, Ryu JH. Stimuli-Responsive Adaptive Nanotoxin to Directly Penetrate the Cellular Membrane by Molecular Folding and Unfolding. J Am Chem Soc 2022; 144:5503-5516. [PMID: 35235326 DOI: 10.1021/jacs.2c00084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biological nanomachines, including proteins and nucleic acids whose function is activated by conformational changes, are involved in every biological process, in which their dynamic and responsive behaviors are controlled by supramolecular recognition. The development of artificial nanomachines that mimic the biological functions for potential application as therapeutics is emerging; however, it is still limited to the lower hierarchical level of the molecular components. In this work, we report a synthetic machinery nanostructure in which actuatable molecular components are integrated into a hierarchical nanomaterial in response to external stimuli to regulate biological functions. Two nanometers core-sized gold nanoparticles are covered with ligand layers as actuatable components, whose folding/unfolding motional response to the cellular environment enables the direct penetration of the nanoparticles across the cellular membrane to disrupt intracellular organelles. Furthermore, the pH-responsive conformational movements of the molecular components can induce the apoptosis of cancer cells. This strategy based on the mechanical motion of molecular components on a hierarchical nanocluster would be useful to design biomimetic nanotoxins.
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Affiliation(s)
- Youngdo Jeong
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea
| | - Soyeong Jin
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - L Palanikumar
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Huyeon Choi
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eunhye Shin
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Eun Min Go
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Changjoon Keum
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Seunghwan Bang
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Biomedical Engineering, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Dongkap Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Seungho Lee
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Minsoo Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Hojun Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kwan Hyi Lee
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Batakrishna Jana
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Myoung-Hwan Park
- Department of Chemistry & Life Science, Sahmyook University, Seoul 01795, Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Chaekyu Kim
- Fusion Biotechnology, Inc., Ulsan 44919, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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59
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Azevedo HS, Mata A. Embracing complexity in biomaterials design. BIOMATERIALS AND BIOSYSTEMS 2022; 6:100039. [PMID: 36824165 PMCID: PMC9934423 DOI: 10.1016/j.bbiosy.2022.100039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/23/2022] [Accepted: 02/06/2022] [Indexed: 10/19/2022] Open
Abstract
Animate materials, man-made materials behaving like living systems, are attracting enormous interest across a range of sectors, from construction and transport industry to medicine. In this leading opinion article, we propose that embracing complexity in biomaterials design offers untapped opportunities to create biomaterials with innovative life-like properties that extend their capabilities and unleash new paradigms in medical treatment.
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Affiliation(s)
- Helena S. Azevedo
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS UK,Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK,Corresponding authors.
| | - Alvaro Mata
- Department of Chemical & Environmental Engineering, University of Nottingham, Nottingham, NG7 2RD, UK,School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK,Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK,Corresponding authors.
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60
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Bistervels MH, Kamp M, Schoenmaker H, Brouwer AM, Noorduin WL. Light-Controlled Nucleation and Shaping of Self-Assembling Nanocomposites. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107843. [PMID: 34854142 DOI: 10.1002/adma.202107843] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/15/2021] [Indexed: 05/12/2023]
Abstract
Controlling self-assembly of nanocomposites is a fundamental challenge with exciting implications for next-generation advanced functional materials. Precursors for composites can be generated photochemically, but limited insight in the underlying processes has hindered precise hands-on guidance. In this study, light-controlled nucleation and growth is demonstrated for self-assembling composites according to precise user-defined designs. Carbonate is generated photochemically with UV light to steer the precipitation of nanocomposites of barium carbonate nanocrystals and amorphous silica (BaCO3 /SiO2 ). Using a custom-built optical setup, the self-assembly process is controlled by optimizing the photogeneration, diffusion, reaction, and precipitation of the carbonate species, using the radius and intensity of the UV-light irradiated area and reaction temperature. Exploiting this control, nucleation is induced and the contours and individual features of the growing composite are sculpted according to micrometer-defined light patterns. Moreover, moving light patterns are exploited to create a constant carbonate concentration at the growth front to draw lines of nanocomposites with constant width over millimeters with micrometer precision. Light-directed generation of local gradients opens previously unimaginable opportunities for guiding self-assembly into functional materials.
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Affiliation(s)
| | - Marko Kamp
- AMOLF, Science Park 104, Amsterdam, 1098 XG, The Netherlands
| | | | - Albert M Brouwer
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, 1090 GD, The Netherlands
| | - Willem L Noorduin
- AMOLF, Science Park 104, Amsterdam, 1098 XG, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, 1090 GD, The Netherlands
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61
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Liu G, Tan J, Cen J, Zhang G, Hu J, Liu S. Oscillating the local milieu of polymersome interiors via single input-regulated bilayer crosslinking and permeability tuning. Nat Commun 2022; 13:585. [PMID: 35102153 PMCID: PMC8803951 DOI: 10.1038/s41467-022-28227-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/31/2021] [Indexed: 11/09/2022] Open
Abstract
The unique permselectivity of cellular membranes is of crucial importance to maintain intracellular homeostasis while adapting to microenvironmental changes. Although liposomes and polymersomes have been widely engineered to mimic microstructures and functions of cells, it still remains a considerable challenge to synergize the stability and permeability of artificial cells and to imitate local milieu fluctuations. Herein, we report concurrent crosslinking and permeabilizing of pH-responsive polymersomes containing Schiff base moieties within bilayer membranes via enzyme-catalyzed acid production. Notably, this synergistic crosslinking and permeabilizing strategy allows tuning of the mesh sizes of the crosslinked bilayers with subnanometer precision, showing discriminative permeability toward maltooligosaccharides with molecular sizes of ~1.4-2.6 nm. The permselectivity of bilayer membranes enables intravesicular pH oscillation, fueled by a single input of glucose. This intravesicular pH oscillation can further drive the dissipative self-assembly of pH-sensitive dipeptides. Moreover, the permeabilization of polymersomes can be regulated by intracellular pH gradient as well, enabling the controlled release of encapsulated payloads.
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Affiliation(s)
- Guhuan Liu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, Anhui, China
| | - Jiajia Tan
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, Anhui, China
| | - Jie Cen
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, Anhui, China
| | - Guoying Zhang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, Anhui, China
| | - Jinming Hu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, Anhui, China.
| | - Shiyong Liu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, Anhui, China.
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62
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Chen R, Das K, Cardona MA, Gabrielli L, Prins LJ. Progressive Local Accumulation of Self-Assembled Nanoreactors in a Hydrogel Matrix through Repetitive Injections of ATP. J Am Chem Soc 2022; 144:2010-2018. [PMID: 35061942 PMCID: PMC8815075 DOI: 10.1021/jacs.1c13504] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cellular functions
are regulated with high spatial control through
the local activation of chemical processes in a complex inhomogeneous
matrix. The development of synthetic macroscopic systems with a similar
capacity allows fundamental studies aimed at understanding the relationship
between local molecular events and the emergence of functional properties
at the macroscopic level. Here, we show that a kinetically stable
inhomogeneous hydrogel matrix is spontaneously formed upon the local
injection of ATP. Locally, ATP templates the self-assembly of amphiphiles
into large nanoreactors with a much lower diffusion rate compared
to unassembled amphiphiles. The local depletion of unassembled amphiphiles
near the injection point installs a concentration gradient along which
unassembled amphiphiles diffuse from the surroundings to the center.
This allows for a progressive local accumulation of self-assembled
nanoreactors in the matrix upon repetitive cycles of ATP injection
separated by time intervals during which diffusion of unassembled
amphiphiles takes place. Contrary to the homogeneous matrix containing
the same components, in the inhomogeneous matrix the local upregulation
of a chemical reaction occurs. Depending on the way the same amount
of injected ATP is administered to the hydrogel matrix different macroscopic
distributions of nanoreactors are obtained, which affect the location
in the matrix where the chemical reaction is upregulated.
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Affiliation(s)
- Rui Chen
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Krishnendu Das
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Maria A. Cardona
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Luca Gabrielli
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Leonard J. Prins
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
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63
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Valiyev I, Ghosh A, Paul I, Schmittel M. Concurrent base and silver(I) catalysis pulsed by fuel acid. Chem Commun (Camb) 2022; 58:1728-1731. [PMID: 35024705 DOI: 10.1039/d1cc06398g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Treatment of a crown-ether receptor and a silver(I)-loaded cyclam derivative (NetState-I) with a fuel acid reversibly afforded the protonated cyclam and the silver(I)-loaded crown ether (NetState-II). While NetState-I was catalytically OFF, a base-catalysed Michael addition and a silver(I)-catalysed oxime cyclisation reaction was pulsed under dissipative conditions in NetState-II.
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Affiliation(s)
- Isa Valiyev
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Str. 2, Siegen D-57068, Germany.
| | - Amit Ghosh
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Str. 2, Siegen D-57068, Germany.
| | - Indrajit Paul
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Str. 2, Siegen D-57068, Germany.
| | - Michael Schmittel
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Str. 2, Siegen D-57068, Germany.
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64
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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65
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Mahato RR, Shandilya E, Maiti S. Perpetuating enzymatically-induced spatiotemporal pH and catalytic heterogeneity of a hydrogel by nanoparticles. Chem Sci 2022; 13:8557-8566. [PMID: 35974757 PMCID: PMC9337733 DOI: 10.1039/d2sc02317b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
The attainment of spatiotemporally inhomogeneous chemical and physical properties within a system is gaining attention across disciplines due to the resemblance to environmental and biological heterogeneity. Notably, the origin of natural pH gradients and how they have been incorporated in cellular systems is one of the most important questions in understanding the prebiotic origin of life. Herein, we have demonstrated a spatiotemporal pH gradient formation pattern on a hydrogel surface by employing two different enzymatic reactions, namely, the reactions of glucose oxidase (pH decreasing) and urease (pH increasing). We found here a generic pattern of spatiotemporal change in pH and proton transfer catalytic activity that was completely altered in a cationic gold nanoparticle containing hydrogel. In the absence of nanoparticles, the gradually generated macroscopic pH gradient slowly diminished with time, whereas the presence of nanoparticles helped to perpetuate the generated gradient effect. This behavior is due to the differential responsiveness of the interface of the cationic nanoparticle in temporally changing surroundings with increasing or decreasing pH or ionic contents. Moreover, the catalytic proton transfer ability of the nanoparticle showed a concerted kinetic response following the spatiotemporal pH dynamics in the gel matrix. Notably, this nanoparticle-driven spatiotemporally resolved gel matrix will find applicability in the area of the membrane-free generation and control of spatially segregated chemistry at the macroscopic scale. This work reports perpetuating effect in enzymatically generated spatiotemporal pH gradient across a hydrogel in presence of cationic gold nanoparticle; showing a new route in spatially resolved chemistry in a membrane-free environment.![]()
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Affiliation(s)
- Rishi Ram Mahato
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Manauli 140306 India
| | - Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Manauli 140306 India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Manauli 140306 India
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66
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Mangalath S, Karunakaran SC, Newnam G, Schuster GB, Hud NV. Supramolecular assembly-enabled homochiral polymerization of short (dA) n oligonucleotides. Chem Commun (Camb) 2021; 57:13602-13605. [PMID: 34852364 DOI: 10.1039/d1cc05420a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A goal of supramolecular chemistry is to create covalent polymers of precise composition and stereochemistry from complex mixtures by the reversible assembly of specific monomers prior to covalent bond formation. We illustrate the power of this approach with short oligomers of deoxyadenosine monophosphate ((dA)n3'p), n ≥ 3, which form supramolecular assemblies with cyanuric acid. The addition of a condensing agent to these assemblies results in their selective, non-enzymatic polymerization to form long polymers (e.g., (dA)1003'p). Significantly, mixtures of D- and L-(dA)53'p form homochiral covalent polymers, which demonstrates self-sorting of racemic monomers and covalent bond formation exclusively in homochiral assemblies.
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Affiliation(s)
- Sreejith Mangalath
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Gary Newnam
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Gary B Schuster
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
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67
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Dai K, Tena-Solsona M, Rodon Fores J, Bergmann AM, Boekhoven J. Morphological transitions in chemically fueled self-assembly. NANOSCALE 2021; 13:19864-19869. [PMID: 34825692 DOI: 10.1039/d1nr04954b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In chemically fueled self-assembly, a reaction cycle activates and deactivates molecules for self-assembly. The resulting assembly is dynamic and should be endowed with unique behavior in this kinetically controlled regime. Recent works have mainly focused on design rules for the activation of molecules for self-assembly, thereby assuming that disassembly upon deactivation inherently follows. However, that is not always the case. This work shows a family of peptides that assemble into colloids regulated through a chemical reaction cycle. Despite their similarity in assembly, we find that they follow a different disassembly pathway upon deactivation. The colloids from several peptides completely disassemble as fuel depletes while others transition into fibers. Our findings demonstrate that assembly and disassembly should be taken into account in chemically fueled self-assembly.
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Affiliation(s)
- Kun Dai
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Marta Tena-Solsona
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Jennifer Rodon Fores
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Alexander M Bergmann
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2a, 85748 Garching, Germany
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68
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Gentile S, Del Grosso E, Pungchai PE, Franco E, Prins LJ, Ricci F. Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA. J Am Chem Soc 2021; 143:20296-20301. [PMID: 34843256 PMCID: PMC8662731 DOI: 10.1021/jacs.1c09503] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We demonstrate a strategy that allows
for the spontaneous reconfiguration
of self-assembled DNA polymers exploiting RNA as chemical fuel. To
do this, we have rationally designed orthogonally addressable DNA
building blocks that can be transiently deactivated by RNA fuels and
subtracted temporarily from participation in the self-assembly process.
Through a fine modulation of the rate at which the building blocks
are reactivated we can carefully control the final composition of
the polymer and convert a disordered polymer in a higher order polymer,
which is disfavored from a thermodynamic point of view. We measure
the dynamic reconfiguration via fluorescent signals and confocal microscopy,
and we derive a kinetic model that captures the experimental results.
Our approach suggests a novel route toward the development of biomolecular
materials in which engineered chemical reactions support the autonomous
spatial reorganization of multiple components.
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Affiliation(s)
- Serena Gentile
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Passa E Pungchai
- Department of Bioengineering, University of California at Los Angeles, 410 Westwood Plaza, Los Angeles, California 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padua, Via Marzolo 1, 35131 Padua, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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69
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Wang C, O'Hagan MP, Willner B, Willner I. Bioinspired Artificial Photosynthetic Systems. Chemistry 2021; 28:e202103595. [PMID: 34854505 DOI: 10.1002/chem.202103595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 12/18/2022]
Abstract
Mimicking photosynthesis using artificial systems, as a means for solar energy conversion and green fuel generation, is one of the holy grails of modern science. This perspective presents recent advances towards developing artificial photosynthetic systems. In one approach, native photosystems are interfaced with electrodes to yield photobioelectrochemical cells that transform light energy into electrical power. This is exemplified by interfacing photosystem I (PSI) and photosystem II (PSII) as an electrically contacted assembly mimicking the native Z-scheme, and by the assembly of an electrically wired PSI/glucose oxidase biocatalytic conjugate on an electrode support. Illumination of the functionalized electrodes led to light-induced generation of electrical power, or to the generation of photocurrents using glucose as the fuel. The second approach introduces supramolecular photosensitizer nucleic acid/electron acceptor complexes as functional modules for effective photoinduced electron transfer stimulating the subsequent biocatalyzed generation of NADPH or the Pt-nanoparticle-catalyzed evolution of molecular hydrogen. Application of the DNA machineries for scaling-up the photosystems is demonstrated. A third approach presents the integration of artificial photosynthetic modules into dynamic nucleic acid networks undergoing reversible reconfiguration or dissipative transient operation in the presence of auxiliary triggers. Control over photoinduced electron transfer reactions and photosynthetic transformations by means of the dynamic networks is demonstrated.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael P O'Hagan
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bilha Willner
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
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70
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Zhan X, Zhao X, Gao Z, Ge R, Lu J, Wang L, Li J. Breakthroughs on tailoring membrane materials for ethanol recovery by pervaporation. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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71
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Nakamura K, Tanaka W, Sada K, Kubota R, Aoyama T, Urayama K, Hamachi I. Phototriggered Spatially Controlled Out-of-Equilibrium Patterns of Peptide Nanofibers in a Self-Sorting Double Network Hydrogel. J Am Chem Soc 2021; 143:19532-19541. [PMID: 34767720 DOI: 10.1021/jacs.1c09172] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Out-of-equilibrium patterns arising from diffusion processes are ubiquitous in nature, although they have not been fully exploited for the design of artificial materials. Here, we describe the formation of phototriggered out-of-equilibrium patterns using photoresponsive peptide-based nanofibers in a self-sorting double network hydrogel. Light irradiation using a photomask followed by thermal incubation induced the spatially controlled condensation of peptide nanofibers. According to confocal images and spectroscopic analyses, metastable nanofibers photodecomposed in the irradiated areas, where thermodynamically stable nanofibers reconstituted and condensed with a supply of monomers from the nonirradiated areas. These supramolecular events were regulated by light and diffusion to facilitate the creation of unique out-of-equilibrium patterns, including two lines from a one-line photomask and a line pattern of a protein immobilized in the hydrogel.
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Affiliation(s)
- Keisuke Nakamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kei Sada
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuma Aoyama
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
| | - Kenji Urayama
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.,JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Nishikyo-ku, Kyoto 615-8530, Japan
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72
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Abstract
Microbial growth is a clear example of organization and structure arising in nonequilibrium conditions. Due to the complexity of the microbial metabolic network, elucidating the fundamental principles governing microbial growth remains a challenge. Here, we present a systematic analysis of microbial growth thermodynamics, leveraging an extensive dataset on energy-limited monoculture growth. A consistent thermodynamic framework based on reaction stoichiometry allows us to quantify how much of the available energy microbes can efficiently convert into new biomass while dissipating the remaining energy into the environment and producing entropy. We show that dissipation mechanisms can be linked to the electron donor uptake rate, a fact leading to the central result that the thermodynamic efficiency is related to the electron donor uptake rate by the scaling law [Formula: see text] and to the growth yield by [Formula: see text] These findings allow us to rederive the Pirt equation from a thermodynamic perspective, providing a means to compute its coefficients, as well as a deeper understanding of the relationship between growth rate and yield. Our results provide rather general insights into the relation between mass and energy conversion in microbial growth with potentially wide application, especially in ecology and biotechnology.
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73
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Exploiting the fundamentals of biological organization for the advancement of biofabrication. Curr Opin Biotechnol 2021; 74:42-54. [PMID: 34798447 DOI: 10.1016/j.copbio.2021.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/26/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022]
Abstract
The field of biofabrication continues to progress, offering higher levels of spatial control, reproducibility, and functionality. However, we remain far from recapitulating what nature has achieved. Biological systems such as tissues and organs are assembled from the bottom-up through coordinated supramolecular and cellular processes that result in their remarkable structures and functionalities. In this perspective, we propose that incorporating such biological assembling mechanisms within fabrication techniques, offers an opportunity to push the boundaries of biofabrication. We dissect these mechanisms into distinct biological organization principles (BOPs) including self-assembly, compartmentalization, diffusion-reaction, disorder-to-order transitions, and out-of-equilibrium processes. We highlight recent work demonstrating the viability and potential of these approaches to enhance scalability, reproducibility, vascularization, and biomimicry; as well as current challenges to overcome.
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74
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Ouyang Y, Zhang P, Manis-Levy H, Paltiel Y, Willner I. Transient Dissipative Optical Properties of Aggregated Au Nanoparticles, CdSe/ZnS Quantum Dots, and Supramolecular Nucleic Acid-Stabilized Ag Nanoclusters. J Am Chem Soc 2021; 143:17622-17632. [PMID: 34643387 DOI: 10.1021/jacs.1c07895] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Transient, dissipative, aggregation and deaggregation of Au nanoparticles (NPs) or semiconductor quantum dots (QDs) leading to control over their transient optical properties are introduced. The systems consist of nucleic acid-modified pairs of Au NPs or pairs of CdSe/ZnS QDs, an auxiliary duplex L1/T1, and the nicking enzyme Nt.BbvCI as functional modules yielding transient aggregation/deaggregation of the NPs and dynamically controlling over their optical properties. In the presence of a fuel strand L1', the duplex L1/T1 is separated, leading to the release of T1 and the formation of duplex L1/L1'. The released T1 leads to aggregation of the Au NPs or to the T1-induced G-quadruplex bridged aggregated CdSe/ZnS QDs. Biocatalytic nicking of the L1/L1' duplex fragments L1' and the released L1 displaces T1 bridging the aggregated NPs or QDs, resulting in the dynamic recovery of the original NPs or QDs modules. The dynamic aggregation/deaggregation of the Au NPs is followed by the transient interparticle plasmon coupling spectral changes. The dynamic aggregation/deaggregation of the CdSe/ZnS QDs is probed by following the transient chemiluminescence generated by the hemin/G-quadruplexes bridging the QDs and by the accompanying transient chemiluminescence resonance energy transfer proceeding in the dynamically formed QDs aggregates. A third system demonstrating transient, dissipative, luminescence properties of a reaction module consisting of nucleic acid-stabilized Ag nanoclusters (NCs) is introduced. Transient dynamic formation and depletion of the supramolecular luminescent Ag NCs system via strand displacement accompanied by a nicking process are demonstrated.
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Affiliation(s)
- Yu Ouyang
- The Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Pu Zhang
- The Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Hadar Manis-Levy
- Department of Applied Physics, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yossi Paltiel
- Department of Applied Physics, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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75
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Yang P, Zhou R, Kong C, Fan L, Dong C, Chen J, Hou X, Li F. Stimuli-Responsive Three-Dimensional DNA Nanomachines Engineered by Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces. ACS NANO 2021; 15:16870-16877. [PMID: 34596378 DOI: 10.1021/acsnano.1c07598] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stimuli-responsive nanomachines are attractive tools for biosensing, imaging, and drug delivery. Herein, we demonstrate that the orientation of macromolecules and subsequent dynamic interactions at the biomolecule-nanoparticle (bio-nano) interfaces can be rationally controlled to engineer stimuli-responsive DNA nanomachines. The success of this design principle was demonstrated by engineering a series of antibody-responsive DNA walkers capable of moving persistently on a three-dimensional track made of DNA functionalized gold nanoparticles. We show that drastically different responses to antibodies could be achieved using DNA walkers of identical sequences but with varying number or sites of modifications. We also show that multiple interfacial factors could be combined to engineer stimuli-responsive DNA nanomachines with high sensitivity and modularity. The potential of our strategy for practical uses was finally demonstrated for the amplified detection of antibodies and small molecules in both buffer and human serum samples. Unlike many DNA-based nanomachines, the performance of which could be significantly hindered by the matrix of serum, our system shows a matrix-enhanced sensitivity as a result of the engineering approach at the bio-nano interface.
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Affiliation(s)
- Peng Yang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Chuipeng Kong
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
| | - Li Fan
- Institute of Environmental Science, College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, Shanxi, China, 030006
| | - Chuan Dong
- Institute of Environmental Science, College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, Shanxi, China, 030006
| | - Junbo Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
| | - Xiandeng Hou
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
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76
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Amano S, Borsley S, Leigh DA, Sun Z. Chemical engines: driving systems away from equilibrium through catalyst reaction cycles. NATURE NANOTECHNOLOGY 2021; 16:1057-1067. [PMID: 34625723 DOI: 10.1038/s41565-021-00975-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Biological systems exhibit a range of complex functions at the micro- and nanoscales under non-equilibrium conditions (for example, transportation and motility, temporal control, information processing and so on). Chemists also employ out-of-equilibrium systems, for example in kinetic selection during catalysis, self-replication, dissipative self-assembly and synthetic molecular machinery, and in the form of chemical oscillators. Key to non-equilibrium behaviour are the mechanisms through which systems are able to extract energy from the chemical reactants ('fuel') that drive such processes. In this Perspective we relate different examples of such powering mechanisms using a common conceptual framework. We discuss how reaction cycles can be coupled to other dynamic processes through positive (acceleration) or negative (inhibition) catalysis to provide the thermodynamic impetus for diverse non-equilibrium behaviour, in effect acting as a 'chemical engine'. We explore the way in which the energy released from reaction cycles is harnessed through kinetic selection in a series of what have sometimes been considered somewhat disparate fields (systems chemistry, molecular machinery, dissipative assembly and chemical oscillators), highlight common mechanistic principles and the potential for the synchronization of chemical reaction cycles, and identify future challenges for the invention and application of non-equilibrium systems. Explicit recognition of the use of fuelling reactions to power structural change in catalysts may stimulate the investigation of known catalytic cycles as potential elements for chemical engines, a currently unexplored area of catalysis research.
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Affiliation(s)
- Shuntaro Amano
- Department of Chemistry, University of Manchester, Manchester, UK
| | - Stefan Borsley
- Department of Chemistry, University of Manchester, Manchester, UK
| | - David A Leigh
- Department of Chemistry, University of Manchester, Manchester, UK.
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Zhanhu Sun
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
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77
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Mehan S, Herrmann L, Chapel JP, Jestin J, Berret JF, Cousin F. The desalting/salting pathway: a route to form metastable aggregates with tuneable morphologies and lifetimes. SOFT MATTER 2021; 17:8496-8505. [PMID: 34474458 DOI: 10.1039/d1sm00260k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We investigate the formation/re-dissociation mechanisms of hybrid complexes made from negatively charged PAA2k coated γ-Fe2O3 nanoparticles (NP) and positively charged polycations (PDADMAC) in aqueous solution in the regime of very high ionic strength (I). When the building blocks are mixed at large ionic strength (1 M NH4Cl), the electrostatic interaction is screened and complexation does not occur. If the ionic strength is then lowered down to a targeted ionic strength Itarget, there is a critical threshold Ic = 0.62 M at which complexation occurs, that is independent of the charge ratio Z and the pathway used to reduce salinity (drop-by-drop mixing or fast mixing). If salt is added back up to 1 M, the transition is not reversible and persistent out-of-equilibrium aggregates are formed. The lifetimes of such aggregates depends on Itarget: the closer Itarget to Ic is, the more difficult it is to dissolve the aggregates. Such peculiar behavior is driven by the inner structure of the complexes that are formed after desalting. When Itarget is far below Ic, strong electrostatic interactions induce the formation of dense, compact and frozen aggregates. Such aggregates can only poorly reorganize further on with time, which makes their dissolution upon resalting almost reversible. Conversely, when Itarget is close to Ic more open aggregates are formed due to weaker electrostatic interactions upon desalting. The system can thus rearrange with time to lower its free energy and reach more stable out-of-equilibrium states which are very difficult to dissociate back upon resalting, even at very high ionic strength.
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Affiliation(s)
- Sumit Mehan
- Laboratoire Léon Brillouin, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette Cedex, France.
| | - Laure Herrmann
- Université de Paris, CNRS, Matière et systèmes complexes, 75013 Paris, France
| | - Jean-Paul Chapel
- Centre de Recherche Paul Pascal (CRPP), UMR CNRS 5031, Université de Bordeaux, 33600 Pessac, France
| | - Jacques Jestin
- Laboratoire Léon Brillouin, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette Cedex, France.
| | | | - Fabrice Cousin
- Laboratoire Léon Brillouin, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette Cedex, France.
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78
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Bhardwaj SK, Mujawar M, Mishra YK, Hickman N, Chavali M, Kaushik A. Bio-inspired graphene-based nano-systems for biomedical applications. NANOTECHNOLOGY 2021; 32. [PMID: 34371491 DOI: 10.1088/1361-6528/ac1bdb] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 08/08/2021] [Indexed: 05/15/2023]
Abstract
The increasing demands of environmentally sustainable, affordable, and scalable materials have inspired researchers to explore greener nanosystems of unique properties which can enhance the performance of existing systems. Such nanosystems, extracted from nature, are state-of-art high-performance nanostructures due to intrinsic hierarchical micro/nanoscale architecture and generous interfacial interactions in natural resources. Among several, bio-inspired nanosystems graphene nanosystems have emerged as an essential nano-platform wherein a highly electroactive, scalable, functional, flexible, and adaptable to a living being is a key factor. Preliminary investigation project bio-inspired graphene nanosystems as a multi-functional nano-platform suitable for electronic devices, energy storage, sensors, and medical sciences application. However, a broad understanding of bio-inspired graphene nanosystems and their projection towards applied application is not well-explored yet. Considering this as a motivation, this mini-review highlights the following; the emergence of bio-inspired graphene nanosystems, over time development to make them more efficient, state-of-art technology, and potential applications, mainly biomedical including biosensors, drug delivery, imaging, and biomedical systems. The outcomes of this review will certainly serve as a guideline to motivate scholars to design and develop novel bio-inspired graphene nanosystems to develop greener, affordable, and scalable next-generation biomedical systems.
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Affiliation(s)
| | - Mubarak Mujawar
- Department of Electrical and Computer Engineering, College of Engineering and Computing, Florida International University, Miami, FL, 33174, United States of America
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alsion 2, DK-6400, Sønderborg, Denmark
| | - Nicoleta Hickman
- NanoBioTech Laboratory, Department of Natural Sciences, Division of Sciences, Art & Mathematics, Florida Polytechnic University, Lakeland, FL, 33805, United States of America
| | - Murthy Chavali
- Office of the Dean (Research) & Department of Chemistry, Faculty of Sciences, Alliance University, Bengaluru 562 106, Karnataka, India
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Department of Natural Sciences, Division of Sciences, Art & Mathematics, Florida Polytechnic University, Lakeland, FL, 33805, United States of America
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79
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Sheehan F, Sementa D, Jain A, Kumar M, Tayarani-Najjaran M, Kroiss D, Ulijn RV. Peptide-Based Supramolecular Systems Chemistry. Chem Rev 2021; 121:13869-13914. [PMID: 34519481 DOI: 10.1021/acs.chemrev.1c00089] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration.
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Affiliation(s)
- Fahmeed Sheehan
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States
| | - Deborah Sementa
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States
| | - Ankit Jain
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States
| | - Mohit Kumar
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, Barcelona 08028, Spain
| | - Mona Tayarani-Najjaran
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States
| | - Daniela Kroiss
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Avenue, New York, New York 10016, United States
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Avenue, New York, New York 10016, United States
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80
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81
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Stach OS, Breul K, Berač CM, Urschbach M, Seiffert S, Besenius P. Bridging Rigidity and Flexibility: Modulation of Supramolecular Hydrogels by Metal Complexation. Macromol Rapid Commun 2021; 43:e2100473. [PMID: 34505725 DOI: 10.1002/marc.202100473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Indexed: 11/11/2022]
Abstract
The combination of complementary, noncovalent interactions is a key principle for the design of multistimuli responsive hydrogels. In this work, an amphiphilic peptide, supramacromolecular hydrogelator which combines metal-ligand coordination induced gelation and thermoresponsive toughening is reported. Following a modular approach, the incorporation of the triphenylalanine sequence FFF into a structural (C3 EG ) and a terpyridine-functionalized (C3 Tpy ) C3 -symmetric monomer enables their statistical copolymerization into self-assembled, 1D nanorods in water, as investigated by circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). In the presence of a terpyridine functionalized telechelic polyethylene glycol (PEG) cross-linker, complex formation upon addition of different transition metal ions (Fe2+ , Zn2+ , Ni2+ ) induces the formation of soft, reversible hydrogels at a solid weight content of 1 wt% as observed by linear shear rheology. The viscoelastic behavior of Fe2+ and Zn2+ cross-linked hydrogels are basically identical, while the most kinetically inert Ni2+ coordinative bond leads to significantly weaker hydrogels, suggesting that the most dynamic rather than the most thermodynamically stable interaction supports the formation of robust and responsive hydrogel materials.
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Affiliation(s)
- Oliver S Stach
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
| | - Katharina Breul
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany.,Graduate School of Materials Science in Mainz, Staudingerweg 9, Mainz, 55128, Germany
| | - Christian M Berač
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany.,Graduate School of Materials Science in Mainz, Staudingerweg 9, Mainz, 55128, Germany
| | - Moritz Urschbach
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
| | - Sebastian Seiffert
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany.,Graduate School of Materials Science in Mainz, Staudingerweg 9, Mainz, 55128, Germany
| | - Pol Besenius
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany.,Graduate School of Materials Science in Mainz, Staudingerweg 9, Mainz, 55128, Germany
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82
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Das K, Gabrielli L, Prins LJ. Chemically Fueled Self-Assembly in Biology and Chemistry. Angew Chem Int Ed Engl 2021; 60:20120-20143. [PMID: 33704885 PMCID: PMC8453758 DOI: 10.1002/anie.202100274] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/12/2021] [Indexed: 12/23/2022]
Abstract
Life is a non-equilibrium state of matter maintained at the expense of energy. Nature uses predominantly chemical energy stored in thermodynamically activated, but kinetically stable, molecules. These high-energy molecules are exploited for the synthesis of other biomolecules, for the activation of biological machinery such as pumps and motors, and for the maintenance of structural order. Knowledge of how chemical energy is transferred to biochemical processes is essential for the development of artificial systems with life-like processes. Here, we discuss how chemical energy can be used to control the structural organization of organic molecules. Four different strategies have been identified according to a distinguishable physical-organic basis. For each class, one example from biology and one from chemistry are discussed in detail to illustrate the practical implementation of each concept and the distinct opportunities they offer. Specific attention is paid to the discussion of chemically fueled non-equilibrium self-assembly. We discuss the meaning of non-equilibrium self-assembly, its kinetic origin, and strategies to develop synthetic non-equilibrium systems.
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Affiliation(s)
- Krishnendu Das
- Department of Chemical Sciences|University of PadovaVia Marzolo 135131PadovaItaly
| | - Luca Gabrielli
- Department of Chemical Sciences|University of PadovaVia Marzolo 135131PadovaItaly
| | - Leonard J. Prins
- Department of Chemical Sciences|University of PadovaVia Marzolo 135131PadovaItaly
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83
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Wang J, Li Z, Zhou Z, Ouyang Y, Zhang J, Ma X, Tian H, Willner I. DNAzyme- and light-induced dissipative and gated DNA networks. Chem Sci 2021; 12:11204-11212. [PMID: 34522318 PMCID: PMC8386649 DOI: 10.1039/d1sc02091a] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/20/2021] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid-based dissipative, out-of-equilibrium systems are introduced as functional assemblies emulating transient dissipative biological transformations. One system involves a Pb2+-ion-dependent DNAzyme fuel strand-driven network leading to the transient cleavage of the fuel strand to “waste” products. Applying the Pb2+-ion-dependent DNAzyme to two competitive fuel strand-driven systems yields two parallel operating networks. Blocking the competitively operating networks with selective inhibitors leads, however, to gated transient operation of dictated networks, yielding gated catalytic operations. A second system introduces a “non-waste” generating out-of-equilibrium, dissipative network driven by light. The system consists of a trans-azobenzene-functionalized photoactive module that is reconfigured by light to an intermediary state consisting of cis-azobenzene units that are thermally recovered to the original trans-azobenzene-modified module. The cyclic transient photoinduced operation of the device is demonstrated. The kinetic simulation of the systems allows the prediction of the transient behavior of the networks under different auxiliary conditions. Functional DNA modules are triggered in the presence of appropriate inhibitors to yield transient gated catalytic functions, and a photoresponsive DNA module leads to “waste-free” operation of transient, dissipative dynamic transitions.![]()
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Affiliation(s)
- Jianbang Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Zhenzhen Li
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Zhixin Zhou
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Yu Ouyang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
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84
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A dissipative pathway for the structural evolution of DNA fibres. Nat Chem 2021; 13:843-849. [PMID: 34373598 DOI: 10.1038/s41557-021-00751-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
Biochemical networks interconnect, grow and evolve to express new properties as different chemical pathways are selected during a continuous cycle of energy consumption and transformation. In contrast, synthetic systems that push away from equilibrium usually return to the same self-assembled state, often generating waste that limits system recyclability and prevents the formation of adaptable networks. Here we show that annealing by slow proton dissipation selects for otherwise inaccessible morphologies of fibres built from DNA and cyanuric acid. Using single-molecule fluorescence microscopy, we observe that proton dissipation influences the growth mechanism of supramolecular polymerization, healing gaps within fibres and converting highly branched, interwoven networks into nanocable superstructures. Just as the growth kinetics of natural fibres determine their structural attributes to modulate function, our system of photoacid-enabled depolymerization and repolymerization selects for healed materials to yield organized, robust fibres. Our method provides a chemical route for error-checking, distinct from thermal annealing, that improves the morphologies and properties of supramolecular materials using out-of-equilibrium systems.
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85
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Mahato RR, Shandilya E, Dasgupta B, Maiti S. Dictating Catalytic Preference and Activity of a Nanoparticle by Modulating Its Multivalent Engagement. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01991] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rishi Ram Mahato
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Basundhara Dasgupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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86
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Teders M, Murray NR, Huck WTS. Reversible Photoswitchable Inhibitors Enable Wavelength‐Selective Regulation of Out‐of‐Equilibrium Bi‐enzymatic Systems. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Michael Teders
- Institute for Molecules and Materials Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Nicholas R. Murray
- Institute for Molecules and Materials Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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87
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Wang Y, Li C, Ma L, Wang X, Wang K, Lu X, Cai Y. Interfacial Liquid–Liquid Phase Separation-Driven Polymerization-Induced Electrostatic Self-Assembly. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00756] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ye Wang
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Chao Li
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Lei Ma
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xiyu Wang
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Kai Wang
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xinhua Lu
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yuanli Cai
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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88
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Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization. Nat Commun 2021; 12:2994. [PMID: 34016981 PMCID: PMC8138026 DOI: 10.1038/s41467-021-23206-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/26/2021] [Indexed: 11/08/2022] Open
Abstract
Autocatalytic and oscillatory networks of organic reactions are important for designing life-inspired materials and for better understanding the emergence of life on Earth; however, the diversity of the chemistries of these reactions is limited. In this work, we present the thiol-assisted formation of guanidines, which has a mechanism analogous to that of native chemical ligation. Using this reaction, we designed autocatalytic and oscillatory reaction networks that form substituted guanidines from thiouronium salts. The thiouronium salt-based oscillator show good stability of oscillations within a broad range of experimental conditions. By using nitrile-containing starting materials, we constructed an oscillator where the concentration of a bicyclic derivative of dihydropyrimidine oscillates. Moreover, the mixed thioester and thiouronium salt-based oscillator show unique responsiveness to chemical cues. The reactions developed in this work expand our toolbox for designing out-of-equilibrium chemical systems and link autocatalytic and oscillatory chemistry to the synthesis of guanidinium derivatives and the products of their transformations including analogs of nucleobases. So far, only a few chemical oscillators based on organic reactions have been developed. Here, the authors report both autocatalytic and oscillatory reaction networks that form substituted guanidines from thiouronium salts; when coupled to cascade cyclization, this reaction network produces oscillations in the production of pyrimidine-based heterocycles.
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89
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Panja S, Adams DJ. Stimuli responsive dynamic transformations in supramolecular gels. Chem Soc Rev 2021; 50:5165-5200. [PMID: 33646219 DOI: 10.1039/d0cs01166e] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Supramolecular gels are formed by the self-assembly of small molecules under the influence of various non-covalent interactions. As the interactions are individually weak and reversible, it is possible to perturb the gels easily, which in turn enables fine tuning of their properties. Synthetic supramolecular gels are kinetically trapped and usually do not show time variable changes in material properties after formation. However, such materials potentially become switchable when exposed to external stimuli like temperature, pH, light, enzyme, redox, and chemical analytes resulting in reconfiguration of gel matrix into a different type of network. Such transformations allow gel-to-gel transitions while the changes in the molecular aggregation result in alteration of physical and chemical properties of the gel with time. Here, we discuss various methods that have been used to achieve gel-to-gel transitions by modifying a pre-formed gel material through external perturbation. We also describe methods that allow time-dependent autonomous switching of gels into different networks enabling synthesis of next generation functional materials. Dynamic modification of gels allows construction of an array of supramolecular gels with various properties from a single material which eventually extend the limit of applications of the gels. In some cases, gel-to-gel transitions lead to materials that cannot be accessed directly. Finally, we point out the necessity and possibility of further exploration of the field.
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Affiliation(s)
- Santanu Panja
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Dave J Adams
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
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90
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Teders M, Pogodaev AA, Bojanov G, Huck WTS. Reversible Photoswitchable Inhibitors Generate Ultrasensitivity in Out-of-Equilibrium Enzymatic Reactions. J Am Chem Soc 2021; 143:5709-5716. [PMID: 33844531 PMCID: PMC8154525 DOI: 10.1021/jacs.0c12956] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Ultrasensitivity
is a ubiquitous emergent property of biochemical
reaction networks. The design and construction of synthetic reaction
networks exhibiting ultrasensitivity has been challenging, but would
greatly expand the potential properties of life-like materials. Herein,
we exploit a general and modular strategy to reversibly regulate the
activity of enzymes using light and show how ultrasensitivity arises
in simple out-of-equilibrium enzymatic systems upon incorporation
of reversible photoswitchable inhibitors (PIs). Utilizing a chromophore/warhead
strategy, PIs of the protease α-chymotrypsin were synthesized,
which led to the discovery of inhibitors with large differences in
inhibition constants (Ki) for the different
photoisomers. A microfluidic flow setup was used to study enzymatic
reactions under out-of-equilibrium conditions by continuous addition
and removal of reagents. Upon irradiation of the continuously stirred
tank reactor with different light pulse sequences, i.e., varying the
pulse duration or frequency of UV and blue light irradiation, reversible
switching between photoisomers resulted in ultrasensitive responses
in enzymatic activity as well as frequency filtering of input signals.
This general and modular strategy enables reversible and tunable control
over the kinetic rates of individual enzyme-catalyzed reactions and
makes a programmable linkage of enzymes to a wide range of network
topologies feasible.
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Affiliation(s)
- Michael Teders
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Aleksandr A Pogodaev
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Glenn Bojanov
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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91
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Pei D, Liu B, Zhao S, Shu X, Nie J, Chang Y. Controllable Release Mode Based on ATP Hydrolysis-Fueled Supra-Amphiphile Assembly. ACS APPLIED BIO MATERIALS 2021; 4:3532-3538. [DOI: 10.1021/acsabm.1c00060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Di Pei
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Bo Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Shuai Zhao
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Xin Shu
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jun Nie
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yincheng Chang
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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92
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Xu D, Shi R, Sun ZY, Lu ZY. Mechanism of periodic field driven self-assembly process. J Chem Phys 2021; 154:144904. [PMID: 33858165 DOI: 10.1063/5.0048072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dissipative self-assembly, a ubiquitous type of self-assembly in biological systems, has attracted a lot of attention in recent years. Inspired by nature, dissipative self-assembly driven by periodic external fields is often adopted to obtain controlled out-of-equilibrium steady structures and materials in experiments. Although the phenomena in dissipative self-assembly have been discovered in the past few decades, fundamental methods to describe dynamical self-assembly processes and responsiveness are still lacking. Here, we develop a theoretical framework based on the equations of motion and Floquet theory to reveal the dynamic behavior changing with frequency in the periodic external field driven self-assembly. Using the dissipative particle dynamics simulation method, we then construct a block copolymer model that can self-assemble in dilute solution to confirm the conclusions from the theory. Our theoretical framework facilitates the understanding of dynamic behavior in a periodically driven process and provides the theoretical guidance for designing the dissipative conditions.
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Affiliation(s)
- Duo Xu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Rui Shi
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Zhao-Yan Sun
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Changchun 130022, China
| | - Zhong-Yuan Lu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
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93
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Das K, Gabrielli L, Prins LJ. Chemically Fueled Self‐Assembly in Biology and Chemistry. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100274] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Krishnendu Das
- Department of Chemical Sciences
- University of Padova Via Marzolo 1 35131 Padova Italy
| | - Luca Gabrielli
- Department of Chemical Sciences
- University of Padova Via Marzolo 1 35131 Padova Italy
| | - Leonard J. Prins
- Department of Chemical Sciences
- University of Padova Via Marzolo 1 35131 Padova Italy
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94
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Stanzel M, Zhao L, Mohammadi R, Pardehkhorram R, Kunz U, Vogel N, Andrieu-Brunsen A. Simultaneous Nanolocal Polymer and In Situ Readout Unit Placement in Mesoporous Separation Layers. Anal Chem 2021; 93:5394-5402. [PMID: 33724794 PMCID: PMC8027984 DOI: 10.1021/acs.analchem.0c04446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/24/2021] [Indexed: 11/28/2022]
Abstract
Bioinspired solid-state nanopores and nanochannels have attracted interest in the last two decades, as they are envisioned to advance future sensing, energy conversion, and separation concepts. Although much effort has been made regarding functionalization of these materials, multifunctionality and accurate positioning of functionalities with nanoscale precision still remain challenging. However, this precision is necessary to meet transport performance and complexity of natural pores in living systems, which are often based on nonequilibrium states and compartmentalization. In this work, a nanolocal functionalization and simultaneous localized sensing strategy inside a filtering mesoporous film using precisely placed plasmonic metal nanoparticles inside mesoporous films with pore accessibility control is demonstrated. A single layer of gold nanoparticles is incorporated into mesoporous thin films with precise spatial control along the nanoscale layer thickness. The local surface plasmon resonance is applied to induce a photopolymerization leading to a nanoscopic polymer shell around the particles and thus nanolocal polymer placement inside the mesoporous material. As near-field modes are sensitive to the dielectric properties of their surrounding, the in situ sensing capability is demonstrated using UV-vis spectroscopy. It is demonstrated that the sensing sensitivity only slightly decreases upon functionalization. The presented nanolocal placement of responsive functional polymers into nanopores offers a simultaneous filtering and nanoscopic readout function. Such a nanoscale local control is envisioned to have a strong impact onto the development of new transport and sensor concepts, especially as the system can be developed into higher complexity using different metal nanoparticles and additional design of mesoporous film filtering properties.
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Affiliation(s)
- Mathias Stanzel
- Ernst-Berl
Institut für Technische und Makromolekulare Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Lucy Zhao
- Ernst-Berl
Institut für Technische und Makromolekulare Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Reza Mohammadi
- Institute
of Particle Technology, Friedrich-Alexander
University Erlangen-Nürnberg, Cauerstraße 4, 91058 Erlangen, Germany
| | - Raheleh Pardehkhorram
- Ernst-Berl
Institut für Technische und Makromolekulare Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Ulrike Kunz
- Department
of Materials and Earth Sciences, Physical Metallurgy Group, Technische Universität Darmstadt, Alarich-Weiss-Straße 2, 64287 Darmstadt, Germany
| | - Nicolas Vogel
- Institute
of Particle Technology, Friedrich-Alexander
University Erlangen-Nürnberg, Cauerstraße 4, 91058 Erlangen, Germany
| | - Annette Andrieu-Brunsen
- Ernst-Berl
Institut für Technische und Makromolekulare Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
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95
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Zhou Z, Ouyang Y, Wang J, Willner I. Dissipative Gated and Cascaded DNA Networks. J Am Chem Soc 2021; 143:5071-5079. [DOI: 10.1021/jacs.1c00486] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zhixin Zhou
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yu Ouyang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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96
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Constructing Large 2D Lattices Out of DNA-Tiles. Molecules 2021; 26:molecules26061502. [PMID: 33801952 PMCID: PMC8000633 DOI: 10.3390/molecules26061502] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.
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97
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Fan X, Walther A. Autonomous Transient pH Flips Shaped by Layered Compartmentalization of Antagonistic Enzymatic Reactions. Angew Chem Int Ed Engl 2021; 60:3619-3624. [PMID: 33098236 PMCID: PMC7898518 DOI: 10.1002/anie.202009542] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/10/2020] [Indexed: 12/13/2022]
Abstract
Transient signaling orchestrates complex spatiotemporal behaviour in living organisms via (bio)chemical reaction networks (CRNs). Compartmentalization of signal processing is an important aspect for controlling such networks. However, artificial CRNs mostly focus on homogeneous solutions to program autonomous self-assembling systems, which limits their accessible behaviour and tuneability. Here, we introduce layered compartments housing antagonistic pH-modulating enzymes and demonstrate that transient pH signals in a supernatant solution can be programmed based on spatial delays. This overcomes limitations of activity mismatches of antagonistic enzymes in solution and allows to flexibly program acidic and alkaline pH lifecycles beyond the possibilities of homogeneous solutions. Lag time, lifetime, and the pH minima and maxima can be precisely programmed by adjusting spatial and kinetic conditions. We integrate these spatially controlled pH flips with switchable peptides, furnishing time-programmed self-assemblies and hydrogel material system.
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Affiliation(s)
- Xinlong Fan
- ABMS Lab-Active Adaptive and Autonomous Bioinspired MaterialsInstitute for Macromolecular ChemistryUniversity of FreiburgStefan-Meier-Str. 3179104FreiburgGermany
- Freiburg Materials Research Center (FMF)University of FreiburgStefan-Meier-Str. 2179104FreiburgGermany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT)University of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
| | - Andreas Walther
- ABMS Lab-Active Adaptive and Autonomous Bioinspired MaterialsInstitute for Macromolecular ChemistryUniversity of FreiburgStefan-Meier-Str. 3179104FreiburgGermany
- Freiburg Materials Research Center (FMF)University of FreiburgStefan-Meier-Str. 2179104FreiburgGermany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT)University of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
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98
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Rao A, Roy S, Pillai PP. Temporal Changes in Interparticle Interactions Drive the Formation of Transiently Stable Nanoparticle Precipitates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1843-1849. [PMID: 33502873 DOI: 10.1021/acs.langmuir.0c03239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We demonstrate the power of fine-tuned interparticle interactions, emanating from appropriately functionalized surfaces, in creating self-assembled structures that show a transient switching between completely precipitated and redispersed stages of nanoparticles (NPs). The pH-dependent temporal changes in the strength of electrostatic interactions are explored to unveil a transient self-assembly response in plasmonic NPs. The assembly process was triggered by the electrostatic attraction between positively charged gold NPs (AuNPs) and an aggregating agent, ethylenediaminetetraacetic acid (EDTA). The autonomous changes in the pH and ionic strength of the solution, under the influence of atmospheric CO2, weaken the aggregating ability of EDTA and initiate the complete disassembly of [+] AuNP-EDTA precipitates. The use of a nondestructive mode of autonomous disassembly helped in achieving some of the desirable feats in the field of transient self-assembly such as easy removal of waste, formation of a transiently stable precipitate state, and negligible dampness in redispersion. The chemical strategy adopted in the present work, to introduce transientness, can act as a generic tool in creating the next generation of complex matter.
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Affiliation(s)
- Anish Rao
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Soumendu Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Pramod P Pillai
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
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99
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Xu X, Cölfen H. Ultracentrifugation Techniques for the Ordering of Nanoparticles. NANOMATERIALS 2021; 11:nano11020333. [PMID: 33513966 PMCID: PMC7912273 DOI: 10.3390/nano11020333] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 01/07/2023]
Abstract
A centrifugal field can provide an external force for the ordering of nanoparticles. Especially with the knowledge from in-situ characterization by analytical (ultra)centrifugation, nanoparticle ordering can be rationally realized in preparative (ultra)centrifugation. This review summarizes the work back to the 1990s, where intuitive use of centrifugation was achieved for the fabrication of colloidal crystals to the very recent work where analytical (ultra)centrifugation is employed to tailor-make concentration gradients for advanced materials. This review is divided into three main parts. In the introduction part, the history of ordering microbeads in gravity is discussed and with the size of particles reduced to nanometers, a centrifugal field is necessary. In the next part, the research on the ordering of nanoparticles in analytical and preparative centrifugation in recent decades is described. In the last part, the applications of the functional materials, fabricated from centrifugation-induced nanoparticle superstructures are briefly discussed.
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Affiliation(s)
- Xufeng Xu
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5612AE Eindhoven, The Netherlands;
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, Box 714, 78457 Konstanz, Germany
- Correspondence:
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100
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Evans JD, Krause S, Feringa BL. Cooperative and synchronized rotation in motorized porous frameworks: impact on local and global transport properties of confined fluids. Faraday Discuss 2021; 225:286-300. [DOI: 10.1039/d0fd00016g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simulations reveal the influence of rotating molecular motors and the importance of orientation and directionality for altering the transport properties of fluids. This has outlined that motors with specific rotation can generate directed diffusion.
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Affiliation(s)
- Jack D. Evans
- Department of Inorganic Chemistry
- Technische Universität Dresden
- 01062 Dresden
- Germany
| | - Simon Krause
- Centre for Systems Chemistry
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Ben L. Feringa
- Centre for Systems Chemistry
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
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