1
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Sun X, Hua W, Liu X, Jin J, Zhang J, Tian J, Zheng B, Jiang W, Yao D, Liang H. Programming of Supercrystals Using Replicable DNA-Functionalized Colloids. Angew Chem Int Ed Engl 2024; 63:e202403492. [PMID: 38482742 DOI: 10.1002/anie.202403492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Indexed: 04/09/2024]
Abstract
The development of self-replicating systems is of great importance in research on the origin of life. As the most iconic molecules, nucleic acids have provided prominent examples of the fabrication of self-replicating artificial nanostructures. However, it is still challenging to construct sophisticated synthetic systems that can create large-scale or three-dimensionally ordered nanomaterials using self-replicating nanostructures. By integrating a template system containing DNA-functionalized colloidal seeds with a simplified DNA strand-displacement circuit programmed subsystem to produce DNA-functionalized colloidal copies, we developed a facile enthalpy-mediated strategy to control the replication and catalytic assembly of DNA-functionalized colloids in a time-dependent manner. The replication efficiency and crystal quality of the resulting superlattice structures can be effectively increased by regulating the molar ratio of the template to the copy colloids. By constructing binary systems from two types of gold nanoparticles (or proteins), superlattice structures with different crystal symmetries can be obtained through the replication and catalytic assembly processes. This programmable enthalpy-mediated approach was easily leveraged to achieve the phase transformation and catalytic amplification of colloidal crystals starting from different initial template crystals. This work offers a potential way to construct self-replicating artificial systems that exhibit complicated phase behaviors and can produce large-scale superlattice nanomaterials.
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Affiliation(s)
- Xiaoyun Sun
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wenqiang Hua
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Xiaoyu Liu
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jing Jin
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jianing Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jie Tian
- Material Test and Analysis Lab, Engineering and Materials Science Experiment Center, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Zheng
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, China
| | - Wei Jiang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Dongbao Yao
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
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2
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Tower J. Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging. FRONTIERS IN AGING 2024; 5:1376060. [PMID: 38818026 PMCID: PMC11137231 DOI: 10.3389/fragi.2024.1376060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024]
Abstract
Rules of biology typically involve conservation of resources. For example, common patterns such as hexagons and logarithmic spirals require minimal materials, and scaling laws involve conservation of energy. Here a relationship with the opposite theme is discussed, which is the selectively advantageous instability (SAI) of one or more components of a replicating system, such as the cell. By increasing the complexity of the system, SAI can have benefits in addition to the generation of energy or the mobilization of building blocks. SAI involves a potential cost to the replicating system for the materials and/or energy required to create the unstable component, and in some cases, the energy required for its active degradation. SAI is well-studied in cells. Short-lived transcription and signaling factors enable a rapid response to a changing environment, and turnover is critical for replacement of damaged macromolecules. The minimal gene set for a viable cell includes proteases and a nuclease, suggesting SAI is essential for life. SAI promotes genetic diversity in several ways. Toxin/antitoxin systems promote maintenance of genes, and SAI of mitochondria facilitates uniparental transmission. By creating two distinct states, subject to different selective pressures, SAI can maintain genetic diversity. SAI of components of synthetic replicators favors replicator cycling, promoting emergence of replicators with increased complexity. Both classical and recent computer modeling of replicators reveals SAI. SAI may be involved at additional levels of biological organization. In summary, SAI promotes replicator genetic diversity and reproductive fitness, and may promote aging through loss of resources and maintenance of deleterious alleles.
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Affiliation(s)
- John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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3
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Wu H, Chen QX, Su Y, Chen Z. The Role of Hydrogen Bonds in Thermally Responsive Crystallization-Driven Template Autocatalysis. Angew Chem Int Ed Engl 2024:e202404838. [PMID: 38654551 DOI: 10.1002/anie.202404838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Autocatalysis has been recognized to be involved in the emergence of life and intrinsic to biomolecular replication. Recently, an efficient template autocatalysis driven by solvent-free crystallization has been reported. Herein, we unveil the role of intermolecular hydrogen bonds formed by amides in crystallization-driven template autocatalysis (CDTA), which involves the autocatalytic activity, template selectivity, and thermal responsiveness. We found that the thermal-induced cis-trans isomerization of amides possibly affects the H-bonding-mediated template ability of products for autocatalytic transformation. As a result, CDTA can be reversibly inhibited and activated by tuning the reaction temperatures. Our work sheds light on the significance of noncovalent H-bonding interactions in artificial self-replicators.
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Affiliation(s)
- Huimin Wu
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Qing-Xuan Chen
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Yang Su
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
| | - Zhen Chen
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
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4
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Komáromy D, Monzón DM, Marić I, Monreal Santiago G, Ottelé J, Altay M, Schaeffer G, Otto S. Generalist versus Specialist Self-Replicators. Chemistry 2024; 30:e202303837. [PMID: 38294075 DOI: 10.1002/chem.202303837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
Darwinian evolution, including the selection of the fittest species under given environmental conditions, is a major milestone in the development of synthetic living systems. In this regard, generalist or specialist behavior (the ability to replicate in a broader or narrower, more specific food environment) are of importance. Here we demonstrate generalist and specialist behavior in dynamic combinatorial libraries composed of a peptide-based and an oligo(ethylene glycol) based building block. Three different sets of macrocyclic replicators could be distinguished based on their supramolecular organization: two prepared from a single building block as well as one prepared from an equimolar mixture of them. Peptide-containing hexamer replicators were found to be generalists, i. e. they could replicate in a broad range of food niches, whereas the octamer peptide-based replicator and hexameric ethyleneoxide-based replicator were proven to be specialists, i. e. they only replicate in very specific food niches that correspond to their composition. However, sequence specificity cannot be demonstrated for either of the generalist replicators. The generalist versus specialist nature of these replicators was linked to their supramolecular organization. Assembly modes that accommodate structurally different building blocks lead to generalist replicators, while assembly modes that are more restrictive yield specialist replicators.
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Affiliation(s)
- Dávid Komáromy
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Diego M Monzón
- Instituto de Bio-Orgánica "Antonio González" (IUBO-AG), Departamento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, 38206, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Ivana Marić
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Guillermo Monreal Santiago
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jim Ottelé
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Meniz Altay
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gaël Schaeffer
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Sijbren Otto
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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5
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Markovitch O, Wu J, Otto S. Binding of Precursors to Replicator Assemblies Can Improve Replication Fidelity and Mediate Error Correction. Angew Chem Int Ed Engl 2024; 63:e202317997. [PMID: 38380789 DOI: 10.1002/anie.202317997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
Copying information is vital for life's propagation. Current life forms maintain a low error rate in replication, using complex machinery to prevent and correct errors. However, primitive life had to deal with higher error rates, limiting its ability to evolve. Discovering mechanisms to reduce errors would alleviate this constraint. Here, we introduce a new mechanism that decreases error rates and corrects errors in synthetic self-replicating systems driven by self-assembly. Previous work showed that macrocycle replication occurs through the accumulation of precursor material on the sides of the fibrous replicator assemblies. Stochastic simulations now reveal that selective precursor binding to the fiber surface enhances replication fidelity and error correction. Centrifugation experiments show that replicator fibers can exhibit the necessary selectivity in precursor binding. Our results suggest that synthetic replicator systems are more evolvable than previously thought, encouraging further evolution-focused experiments.
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Affiliation(s)
- Omer Markovitch
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Juntian Wu
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
| | - Sijbren Otto
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
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6
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Liu K, Blokhuis A, van Ewijk C, Kiani A, Wu J, Roos WH, Otto S. Light-driven eco-evolutionary dynamics in a synthetic replicator system. Nat Chem 2024; 16:79-88. [PMID: 37653230 DOI: 10.1038/s41557-023-01301-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Darwinian evolution involves the inheritance and selection of variations in reproducing entities. Selection can be based on, among others, interactions with the environment. Conversely, the replicating entities can also affect their environment generating a reciprocal feedback on evolutionary dynamics. The onset of such eco-evolutionary dynamics marks a stepping stone in the transition from chemistry to biology. Yet the bottom-up creation of a molecular system that exhibits eco-evolutionary dynamics has remained elusive. Here we describe the onset of such dynamics in a minimal system containing two synthetic self-replicators. The replicators are capable of binding and activating a co-factor, enabling them to change the oxidation state of their environment through photoredox catalysis. The replicator distribution adapts to this change and, depending on light intensity, one or the other replicator becomes dominant. This study shows how behaviour analogous to eco-evolutionary dynamics-which until now has been restricted to biology-can be created using an artificial minimal replicator system.
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Affiliation(s)
- Kai Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Alex Blokhuis
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Chris van Ewijk
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Armin Kiani
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Juntian Wu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands.
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7
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Dev D, Wagner N, Pramanik B, Sharma B, Maity I, Cohen-Luria R, Peacock-Lopez E, Ashkenasy G. A Peptide-Based Oscillator. J Am Chem Soc 2023; 145:26279-26286. [PMID: 37984498 DOI: 10.1021/jacs.3c09377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Living organisms are replete with rhythmic and oscillatory behavior at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recent studies of synthetic oscillators that mimic such functions have shown decayed cycles in batch-mode reactions or sustained oscillatory kinetics under flow conditions. Considering the hypothesized functionality of peptides in early chemical evolution and their central role in current bio-nanotechnology, we now reveal a peptide-based oscillator. Oscillatory behavior was achieved by coupling coiled-coil-based replication processes as positive feedback to controlled initiation and inhibition pathways in a continuously stirred tank reactor (CSTR). Our results stress that assembly into the supramolecular structure and specific interactions with the replication substrates are crucial for oscillations. The replication-inhibition processes were first studied in batch mode, which produced a single damped cycle. Thereafter, combined experimental and theoretical characterization of the replication process in a CSTR under different flow and environmental (pH, redox) conditions demonstrated reasonably sustained oscillations. We propose that studies in this direction might pave the way to the design of robust oscillation networks that mimic the autonomous behavior of proteins in cells (e.g., in the cyanobacterial circadian clock) and hence hint at feasible pathways that accelerated the transition from simple peptides to extant enzymes.
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Affiliation(s)
- Dharm Dev
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bapan Pramanik
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bhawna Sharma
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Centre for Nano and Material Sciences, Jain Global Campus, Bangalore, Karnataka 560070, India
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Enrique Peacock-Lopez
- Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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8
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Root-Bernstein R, Brown AW. Novel Apparatuses for Incorporating Natural Selection Processes into Origins-of-Life Experiments to Produce Adaptively Evolving Chemical Ecosystems. Life (Basel) 2022; 12:life12101508. [PMID: 36294944 PMCID: PMC9605314 DOI: 10.3390/life12101508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022] Open
Abstract
Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.
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Affiliation(s)
- Robert Root-Bernstein
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence:
| | - Adam W. Brown
- Department of Art, Art History and Design, Michigan State University, East Lansing, MI 48824, USA
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9
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Escárcega-Bobadilla MV, Maldonado-Domínguez M, Romero-Ávila M, Zelada-Guillén GA. Turing patterns by supramolecular self-assembly of a single salphen building block. iScience 2022; 25:104545. [PMID: 35747384 PMCID: PMC9209723 DOI: 10.1016/j.isci.2022.104545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/15/2022] [Accepted: 06/02/2022] [Indexed: 11/02/2022] Open
Abstract
In the 1950s, Alan Turing showed that concerted reactions and diffusion of activating and inhibiting chemical species can autonomously generate patterns without previous positional information, thus providing a chemical basis for morphogenesis in Nature. However, access to these patterns from only one molecular component that contained all the necessary information to execute agonistic and antagonistic signaling is so far an elusive goal, since two or more participants with different diffusivities are a must. Here, we report on a single-molecule system that generates Turing patterns arrested in the solid state, where supramolecular interactions are used instead of chemical reactions, whereas diffusional differences arise from heterogeneously populated self-assembled products. We employ a family of hydroxylated organic salphen building blocks based on a bis-Schiff-base scaffold with portions responsible for either activation or inhibition of assemblies at different hierarchies through purely supramolecular reactions, only depending upon the solvent dielectric constant and evaporation as fuel.
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Affiliation(s)
- Martha V Escárcega-Bobadilla
- School of Chemistry, National Autonomous University of Mexico (UNAM), Circuito Escolar s/n, Ciudad Universitaria, 04510 Mexico City, Mexico
| | - Mauricio Maldonado-Domínguez
- School of Chemistry, National Autonomous University of Mexico (UNAM), Circuito Escolar s/n, Ciudad Universitaria, 04510 Mexico City, Mexico.,Department of Computational Chemistry, J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Margarita Romero-Ávila
- School of Chemistry, National Autonomous University of Mexico (UNAM), Circuito Escolar s/n, Ciudad Universitaria, 04510 Mexico City, Mexico
| | - Gustavo A Zelada-Guillén
- School of Chemistry, National Autonomous University of Mexico (UNAM), Circuito Escolar s/n, Ciudad Universitaria, 04510 Mexico City, Mexico
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10
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Schaeffer G, Eleveld MJ, Ottelé J, Kroon PC, Frederix PWJM, Yang S, Otto S. Stochastic Emergence of Two Distinct Self-Replicators from a Dynamic Combinatorial Library. J Am Chem Soc 2022; 144:6291-6297. [PMID: 35357150 PMCID: PMC9011346 DOI: 10.1021/jacs.1c12591] [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] [Indexed: 11/30/2022]
Abstract
![]()
Unraveling how chemistry
can give rise to biology is one of the
greatest challenges of contemporary science. Achieving life-like properties
in chemical systems is therefore a popular topic of research. Synthetic
chemical systems are usually deterministic: the outcome is determined
by the experimental conditions. In contrast, many phenomena that occur
in nature are not deterministic but caused by random fluctuations
(stochastic). Here, we report on how, from a mixture of two synthetic
molecules, two different self-replicators emerge in a stochastic fashion.
Under the same experimental conditions, the two self-replicators are
formed in various ratios over several repeats of the experiment. We
show that this variation is caused by a stochastic nucleation process
and that this stochasticity is more pronounced close to a phase boundary.
While stochastic nucleation processes are common in crystal growth
and chiral symmetry breaking, it is unprecedented for systems of synthetic
self-replicators.
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Affiliation(s)
- Gaël Schaeffer
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcel J Eleveld
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Peter C Kroon
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Pim W J M Frederix
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Shuo Yang
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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11
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Hatai J, Altay Y, Sood A, Kiani A, Eleveld MJ, Motiei L, Margulies D, Otto S. An Optical Probe for Real-Time Monitoring of Self-Replicator Emergence and Distinguishing between Replicators. J Am Chem Soc 2022; 144:3074-3082. [PMID: 35139307 PMCID: PMC8874894 DOI: 10.1021/jacs.1c11594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Self-replicating
systems play an important role in research on
the synthesis and origin of life. Monitoring of these systems has
mostly relied on techniques such as NMR or chromatography, which are
limited in throughput and demanding when monitoring replication in
real time. To circumvent these problems, we now developed a pattern-generating
fluorescent molecular probe (an ID-probe) capable of discriminating
replicators of different chemical composition and monitoring the process
of replicator formation in real time, giving distinct signatures for
starting materials, intermediates, and final products. Optical monitoring
of replicators dramatically reduces the analysis time and sample quantities
compared to most currently used methods and opens the door for future
high-throughput experimentation in protocell environments.
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Affiliation(s)
- Joydev Hatai
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Yigit Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ankush Sood
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Armin Kiani
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcel J Eleveld
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Leila Motiei
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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12
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Abstract
As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials.
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Affiliation(s)
- Sijbren Otto
- Centre for Systems Chemistry, Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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13
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Steiner M, Reiher M. Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis. Top Catal 2022; 65:6-39. [PMID: 35185305 PMCID: PMC8816766 DOI: 10.1007/s11244-021-01543-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/11/2022]
Abstract
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to catalysis: (i) automation allows one to consider orders of magnitude more structures in a systematic and open-ended fashion than what would be accessible by manual inspection. Eventually, full resolution in terms of structural varieties and conformations as well as with respect to the type and number of potentially important elementary reaction steps (including decomposition reactions that determine turnover numbers) may be achieved. (ii) Fast electronic structure methods with uncertainty quantification warrant high efficiency and reliability in order to not only deliver results quickly, but also to allow for predictive work. (iii) A high degree of autonomy reduces the amount of manual human work, processing errors, and human bias. Although being inherently unbiased, it is still steerable with respect to specific regions of an emerging network and with respect to the addition of new reactant species. This allows for a high fidelity of the formalization of some catalytic process and for surprising in silico discoveries. In this work, we first review the state of the art in computational catalysis to embed autonomous explorations into the general field from which it draws its ingredients. We then elaborate on the specific conceptual issues that arise in the context of autonomous computational procedures, some of which we discuss at an example catalytic system.
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Affiliation(s)
- Miguel Steiner
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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14
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Vela-Gallego S, Pardo-Botero Z, Moya C, de la Escosura A. Collective Adaptability in a Replication Network of Minimal Nucleobase Sequences. Chem Sci 2022; 13:10715-10724. [PMID: 36320689 PMCID: PMC9491195 DOI: 10.1039/d2sc02419e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/05/2022] [Indexed: 12/05/2022] Open
Abstract
A major challenge for understanding the origins of life is to explore how replication networks can engage in an evolutionary process. Herein, we shed light on this problem by implementing a network constituted by two different types of extremely simple biological components: the amino acid cysteine and the canonical nucleobases adenine and thymine, connected through amide bonds to the cysteine amino group and oxidation of its thiol into three possible disulfides. Supramolecular and kinetic analyses revealed that both self- and mutual interactions between such dinucleobase compounds drive their assembly and replication pathways. Those pathways involving sequence complementarity led to enhanced replication rates, suggesting a potential bias for selection. The interplay of synergistic dynamics and competition between replicators was then simulated, under conditions that are not easily accessible with experiments, in an open reactor parametrized and constrained with the unprecedentedly complete experimental kinetic data obtained for our replicative network. Interestingly, the simulations show bistability, as a selective amplification of different species depending on the initial mixture composition. Overall, this network configuration can favor a collective adaptability to changes in the availability of feedstock molecules, with disulfide exchange reactions serving as 'wires' that connect the different individual auto- and cross-catalytic pathways. A replication network of minimal nucleobase sequences is built from simple biological components. The network shows collective adaptability to changes in the environment, while disulfide exchange wires different auto- and cross-catalytic pathways.![]()
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Affiliation(s)
- Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
| | | | - Cristian Moya
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
- Institute for Advanced Research in Chemistry (IAdChem) Cantoblanco 28049 Madrid Spain
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15
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Sevim İ. Design of Subreplicating Systems from an Existing Self-Replicating Diels-Alder Reaction System by Isosteric Replacement. J Org Chem 2021; 86:14964-14973. [PMID: 34633828 DOI: 10.1021/acs.joc.1c01695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The key feature of non-enzymatic self-replicating systems is the formation of catalytically active ternary complexes in which product templates direct precursors into spatial proximity to allow the formation of new covalent bonds. It is possible to create new replicating species by simply evaluating the ternary active complex of an existing replicating system and applying proper isosteric replacements. In this study, we have evaluated the formerly reported self-replicating Diels-Alder reaction having 61 and 33% selectivity for two diastereomeric replicators. An isosteric replacement on the spacer part connecting recognition and reactive sites of the maleimide component was applied by considering the symmetry of catalytically active ternary complexes, and it was shown that self-replication was conserved. Analysis of the new system showed 77 and 21% diastereoselectivity for the two new replicating species. Seeding experiments indicated autocatalytic activity of both replicators. In other words, both replicators compete with each other by catalyzing their own formation from the same reagent source. Another modification was applied by aiming selective blocking of the autocatalytic cycle of the competing diastereomer. The new system showed a diastereoselectivity of about 94% for the favored replicator. The kinetic data of both systems were analyzed by modeling with SimFit simulations.
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Affiliation(s)
- İlhan Sevim
- Lehrstuhl für Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
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16
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Feng Y, Philp D. A Molecular Replication Process Drives Supramolecular Polymerization. J Am Chem Soc 2021; 143:17029-17039. [PMID: 34617739 DOI: 10.1021/jacs.1c06404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Supramolecular polymers are materials in which the connections between monomers in the polymer main chain are non-covalent bonds. This area has seen rapid expansion in the last two decades and has been exploited in several applications. However, suitable contiguous hydrogen-bond arrays can be difficult to synthesize, placing some limitations on the deployment of supramolecular polymers. We have designed a hydrogen-bonded polymer assembled from a bifunctional monomer composed of two replicating templates separated by a rigid spacer. This design allows the autocatalytic formation of the polymer main chain through the self-templating properties of the replicators and drives the synthesis of the bifunctional monomer from its constituent components in solution. The template-directed 1,3-dipolar cycloaddition reaction between nitrone and maleimide proceeds with high diastereoselectivity, affording the bifunctional monomer. The high binding affinity between the self-complementary replicating templates that allows the bifunctional monomer to polymerize in solution is derived from the positive cooperativity associated with this binding process. The assembly of the polymer in solution has been investigated by diffusion-ordered NMR spectroscopy. Both microcrystalline and thin films of the polymeric material can be prepared readily and have been characterized by powder X-ray diffraction and scanning electron microscopy. These results demonstrate that the approach described here is a valid one for the construction of supramolecular polymers and can be extended to systems where the rigid spacer between the replicating templates is replaced by one carrying additional function.
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Affiliation(s)
- Yuanning Feng
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Douglas Philp
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
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17
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Howlett M, Scanes RJH, Fletcher SP. Selection between Competing Self-Reproducing Lipids: Succession and Dynamic Activation. JACS AU 2021; 1:1355-1361. [PMID: 34604845 PMCID: PMC8479773 DOI: 10.1021/jacsau.1c00138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 06/09/2023]
Abstract
Models of chemical evolution are central to advancing origins of life research. To design more lifelike systems, we must expand our understanding of molecular selection mechanisms. Here, we show two selection modes that produce evolving populations of self-reproducing species, formed through thiol-disulfide exchange. Competition between thiol precursors can give clear succession patterns based on steric factors, an intrinsic property. A separate, emergent selection mechanism-dynamic activating metathesis-was found when exploring competing disulfide precursors. These experiments reveal that additional species generated in the mixture open up alternative reaction pathways to form self-reproducing products. Thus, increased compositional complexity provides certain species with a unique competitive advantage at the expense of others.
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Affiliation(s)
- Michael
G. Howlett
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Oxford OX1 3TA, United Kingdom
| | - Robert J. H. Scanes
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Oxford OX1 3TA, United Kingdom
| | - Stephen P. Fletcher
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Oxford OX1 3TA, United Kingdom
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18
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Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks. Proc Natl Acad Sci U S A 2021; 118:2015285118. [PMID: 33622789 DOI: 10.1073/pnas.2015285118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.
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19
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Schaufelberger F, Ramström O. Activated Self-Resolution and Error-Correction in Catalytic Reaction Networks*. Chemistry 2021; 27:10335-10340. [PMID: 33780566 DOI: 10.1002/chem.202100208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 01/02/2023]
Abstract
Understanding the emergence of function in complex reaction networks is a primary goal of systems chemistry and origin-of-life studies. Especially challenging is to create systems that simultaneously exhibit several emergent functions that can be independently tuned. In this work, a multifunctional complex reaction network of nucleophilic small molecule catalysts for the Morita-Baylis-Hillman (MBH) reaction is demonstrated. The dynamic system exhibited triggered self-resolution, preferentially amplifying a specific catalyst/product set out of a many potential alternatives. By utilizing selective reversibility of the products of the reaction set, systemic thermodynamically driven error-correction could also be introduced. To achieve this, a dynamic covalent MBH reaction based on adducts with internal H-transfer capabilities was developed. By careful tuning of the substituents, rate accelerations of retro-MBH reactions of up to four orders of magnitude could be obtained. This study thus demonstrates how efficient self-sorting of catalytic systems can be achieved through an interplay of several complex emergent functionalities.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH - Royal Institute of Technology Teknikringen 36, 10044 Stockholm (Sweden)
| | - Olof Ramström
- Department of Chemistry, KTH - Royal Institute of Technology Teknikringen 36, 10044 Stockholm (Sweden).,Department of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA, 01854, USA.,Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182, Kalmar, Sweden
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20
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Komáromy D, Tiemersma-Wegman T, Kemmink J, Portale G, Adamski PR, Blokhuis A, Aalbers FS, Marić I, Santiago GM, Ottelé J, Sood A, Saggiomo V, Liu B, van der Meulen P, Otto S. Stoichiometry alone can steer supramolecular systems on complex free energy surfaces with high selectivity. Chem 2021. [DOI: 10.1016/j.chempr.2021.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Liu B, Beatty MA, Pappas CG, Liu K, Ottelé J, Otto S. Self‐Sorting in Dynamic Combinatorial Libraries Leads to the Co‐Existence of Foldamers and Self‐Replicators. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Meagan A. Beatty
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Charalampos G. Pappas
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Kai Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
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22
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Liu B, Beatty MA, Pappas CG, Liu K, Ottelé J, Otto S. Self-Sorting in Dynamic Combinatorial Libraries Leads to the Co-Existence of Foldamers and Self-Replicators. Angew Chem Int Ed Engl 2021; 60:13569-13573. [PMID: 33949062 PMCID: PMC8252005 DOI: 10.1002/anie.202101052] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 12/27/2022]
Abstract
Nature segregates fundamental tasks such as information storage/transmission and catalysis between two different compound classes (e.g. polynucleotides for replication and folded polyamides for catalysis). This division of labor is likely a product of evolution, raising the question of how simpler systems in which replicators and folded macromolecules co-exist may emerge in the transition from chemistry to biology. In synthetic systems, achieving co-existence of replicators and foldamers in a single molecular network remains an unsolved problem. Previous work on dynamic molecular networks has given rise to either self-replicating fibers or well-defined foldamer structures (or completely un-sorted complex systems). We report a system in which two cross-reactive dithiol (nucleobase- and peptide-based) building blocks self-sort into a replicator fiber and foldamer that both emerge spontaneously and co-exist. The self-sorting behavior remains prevalent across different building block ratios as two phases of emergence occur: replicator growth followed by foldamer formation. This is attributed to the autocatalytic formation of the replicator fiber, followed by enrichment of the system in the remaining building block, which is subsequently incorporated into a foldamer.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Meagan A Beatty
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Kai Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
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23
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Yang S, Schaeffer G, Mattia E, Markovitch O, Liu K, Hussain AS, Ottelé J, Sood A, Otto S. Chemical Fueling Enables Molecular Complexification of Self-Replicators*. Angew Chem Int Ed Engl 2021; 60:11344-11349. [PMID: 33689197 PMCID: PMC8251556 DOI: 10.1002/anie.202016196] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/09/2021] [Indexed: 12/21/2022]
Abstract
Unravelling how the complexity of living systems can (have) emerge(d) from simple chemical reactions is one of the grand challenges in contemporary science. Evolving systems of self-replicating molecules may hold the key to this question. Here we show that, when a system of replicators is subjected to a regime where replication competes with replicator destruction, simple and fast replicators can give way to more complex and slower ones. The structurally more complex replicator was found to be functionally more proficient in the catalysis of a model reaction. These results show that chemical fueling can maintain systems of replicators out of equilibrium, populating more complex replicators that are otherwise not readily accessible. Such complexification represents an important requirement for achieving open-ended evolution as it should allow improved and ultimately also new functions to emerge.
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Affiliation(s)
- Shuo Yang
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Gael Schaeffer
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Elio Mattia
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Omer Markovitch
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
- Origins CenterUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Kai Liu
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Andreas S. Hussain
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Jim Ottelé
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Ankush Sood
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Sijbren Otto
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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24
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Yang S, Schaeffer G, Mattia E, Markovitch O, Liu K, Hussain AS, Ottelé J, Sood A, Otto S. Chemical Fueling Enables Molecular Complexification of Self‐Replicators**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shuo Yang
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gael Schaeffer
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Elio Mattia
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Omer Markovitch
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- Origins Center University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Kai Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Andreas S. Hussain
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ankush Sood
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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25
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Kühnlein A, Lanzmich SA, Braun D. tRNA sequences can assemble into a replicator. eLife 2021; 10:e63431. [PMID: 33648631 PMCID: PMC7924937 DOI: 10.7554/elife.63431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/28/2021] [Indexed: 11/29/2022] Open
Abstract
Can replication and translation emerge in a single mechanism via self-assembly? The key molecule, transfer RNA (tRNA), is one of the most ancient molecules and contains the genetic code. Our experiments show how a pool of oligonucleotides, adapted with minor mutations from tRNA, spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The pool of cross-complementary hairpins self-selected by agglomeration and sedimentation. The metastable DNA hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. The molecular assembly could encode and replicate binary sequences with a replication fidelity corresponding to 85-90 % per nucleotide. The replication by a self-assembly of tRNA-like sequences suggests that early forms of tRNA could have been involved in molecular replication. This would link the evolution of translation to a mechanism of molecular replication.
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Affiliation(s)
- Alexandra Kühnlein
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Simon A Lanzmich
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Dieter Braun
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
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26
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Maity I, Dev D, Basu K, Wagner N, Ashkenasy G. Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Indrajit Maity
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
- Institute for Macromolecular Chemistry Freiburg Institute for Advanced Studies Albert Ludwigs University of Freiburg 79104 Freiburg Germany
| | - Dharm Dev
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Kingshuk Basu
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Nathaniel Wagner
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Gonen Ashkenasy
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
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27
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Maity I, Dev D, Basu K, Wagner N, Ashkenasy G. Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network. Angew Chem Int Ed Engl 2021; 60:4512-4517. [PMID: 33006406 PMCID: PMC7984337 DOI: 10.1002/anie.202012837] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Indexed: 12/23/2022]
Abstract
Living cells exploit bistable and oscillatory behaviors as memory mechanisms, facilitating the integration of transient stimuli into sustained molecular responses that control downstream functions. Synthetic bistable networks have also been studied as memory entities, but have rarely been utilized to control orthogonal functions in coupled dynamic systems. We herein present a new cascade pathway, for which we have exploited a well-characterized switchable peptide-based replicating network, operating far from equilibrium, that yields two alternative steady-state outputs, which in turn serve as the input signals for consecutive processes that regulate various features of Au nanoparticle shape and assembly. This study further sheds light on how bridging together the fields of systems chemistry and nanotechnology may open up new opportunities for the dynamically controlled design of functional materials.
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Affiliation(s)
- Indrajit Maity
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
- Institute for Macromolecular ChemistryFreiburg Institute for Advanced StudiesAlbert Ludwigs University of Freiburg79104FreiburgGermany
| | - Dharm Dev
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Kingshuk Basu
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Nathaniel Wagner
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Gonen Ashkenasy
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
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28
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Qu T, Calabrese P, Singhavi P, Tower J. Incorporating antagonistic pleiotropy into models for molecular replicators. Biosystems 2020; 201:104333. [PMID: 33359635 DOI: 10.1016/j.biosystems.2020.104333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/15/2022]
Abstract
In modern cells, chromosomal genes composed of DNA encode multi-subunit protein/RNA complexes that catalyze the replication of the chromosome and cell. One prevailing theory for the origin of life posits an early stage involving self-replicating macromolecules called replicators, which can be considered genes capable of self-replication. One prevailing theory for the genetics of aging in humans and other organisms is antagonistic pleiotropy, which posits that a gene can be beneficial in one context, and detrimental in another context. We previously reported that the conceptual simplicity of molecular replicators facilitates the generation of two simple models involving antagonistic pleiotropy. Here a third model is proposed, and each of the three models is presented with improved definition of the time variable. Computer simulations were used to calculate the proliferation of a hypothetical two-subunit replicator (AB), when one of the two subunits (B) exhibits antagonistic pleiotropy, leading to an advantage for B to be unstable. In model 1, instability of B yields free A subunits, which in turn stimulate the activity of other AB replicators. In model 2, B is lost and sometimes replaced by a more active mutant form, B'. In model 3, B becomes damaged and loses activity, and its instability allows it to be replaced by a new B. For each model, conditions were identified where instability of B was detrimental, and where instability of B was beneficial. The results are consistent with the hypothesis that antagonistic pleiotropy can promote molecular instability and system complexity, and provide further support for a model linking aging and evolution.
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Affiliation(s)
- Tianjiao Qu
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peter Calabrese
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Pratik Singhavi
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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29
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Yue L, Wang S, Zhou Z, Willner I. Nucleic Acid Based Constitutional Dynamic Networks: From Basic Principles to Applications. J Am Chem Soc 2020; 142:21577-21594. [DOI: 10.1021/jacs.0c09891] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liang Yue
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- 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
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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30
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Ren Y, Kravchenko O, Ramström O. Configurational and Constitutional Dynamics of Enamine Molecular Switches. Chemistry 2020; 26:15654-15663. [PMID: 33044767 PMCID: PMC7756271 DOI: 10.1002/chem.202003478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Indexed: 12/11/2022]
Abstract
Dual configurational and constitutional dynamics in systems based on enamine molecular switches has been systematically studied. pH-responsive moieties, such as 2-pyridyl and 2-quinolinyl units, were required on the "stator" part, also providing enamine stability through intramolecular hydrogen-bonding (IMHB) effects. Upon protonation or deprotonation, forward and backward switching could be rapidly achieved. Extension of the stator π-system in the 2-quinolinyl derivative provided a higher E-isomeric equilibrium ratio under neutral conditions, pointing to a means to achieve quantitative forward/backward isomerization processes. The "rotor" part of the enamine switches exhibited constitutional exchange ability with primary amines. Interestingly, considerably higher exchange rates were observed with amines containing ester groups, indicating potential stabilization of the transition state through IMHB. Acids, particularly BiIII , were found to efficiently catalyze the constitutional dynamic processes. In contrast, the enamine and the formed dynamic enamine system showed excellent stability under basic conditions. This coupled configurational and constitutional dynamics expands the scope of dynamic C-C and C-N bonds and potentiates further studies and applications in the fields of molecular machinery and systems chemistry.
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Affiliation(s)
- Yansong Ren
- Department of ChemistryKTH—Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Oleksandr Kravchenko
- Department of ChemistryKTH—Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Olof Ramström
- Department of ChemistryKTH—Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
- Department of ChemistryUniversity of Massachusetts LowellOne University Ave.LowellMA01854USA
- Department of Chemistry and Biomedical SciencesLinnaeus University39182KalmarSweden
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31
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Schaufelberger F, Seigel K, Ramström O. Hydrogen-Bond Catalysis of Imine Exchange in Dynamic Covalent Systems. Chemistry 2020; 26:15581-15588. [PMID: 32427370 DOI: 10.1002/chem.202001666] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 12/28/2022]
Abstract
The reversibility of imine bonds has been exploited to great effect in the field of dynamic covalent chemistry, with applications such as preparation of functional systems, dynamic materials, molecular machines, and covalent organic frameworks. However, acid catalysis is commonly needed for efficient equilibration of imine mixtures. Herein, it is demonstrated that hydrogen bond donors such as thioureas and squaramides can catalyze the equilibration of dynamic imine systems under unprecedentedly mild conditions. Catalysis occurs in a range of solvents and in the presence of many sensitive additives, showing moderate to good rate accelerations for both imine metathesis and transimination with amines, hydrazines, and hydroxylamines. Furthermore, the catalyst proved simple to immobilize, introducing both reusability and extended control of the equilibration process.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden
| | - Karolina Seigel
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden
| | - Olof Ramström
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden.,Department of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA, 01854, USA.,Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182, Kalmar, Sweden
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32
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Robust Dynamics of Synthetic Molecular Systems as a Consequence of Broken Symmetry. Symmetry (Basel) 2020. [DOI: 10.3390/sym12101688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The construction of molecular robot-like objects that imitate living things is an important challenge for current chemists. Such molecular devices are expected to perform their duties robustly to carry out mechanical motion, process information, and make independent decisions. Dissipative self-organization plays an essential role in meeting these purposes. To produce a micro-robot that can perform the above tasks autonomously as a single entity, a function generator is required. Although many elegant review articles featuring chemical devices that mimic biological mechanical functions have been published recently, the dissipative structure, which is the minimum requirement for mimicking these functions, has not been sufficiently discussed. This article aims to show clearly that dissipative self-organization is a phenomenon involving autonomy, robustness, mechanical functions, and energy transformation. Moreover, it reports the results of recent experiments with an autonomous light-driven molecular device that achieves all of these features. In addition, a chemical model of cell-amplification is also discussed to focus on the generation of hierarchical movement by dissipative self-organization. By reviewing this research, it may be perceived that mainstream approaches to synthetic chemistry have not always been appropriate. In summary, the author proposes that the integration of catalytic functions is a key issue for the creation of autonomous microarchitecture.
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33
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Hanopolskyi AI, Smaliak VA, Novichkov AI, Semenov SN. Autocatalysis: Kinetics, Mechanisms and Design. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anton I. Hanopolskyi
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Viktoryia A. Smaliak
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Alexander I. Novichkov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Sergey N. Semenov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
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34
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Larsen D, Beeren SR. Tuning the Outcome of Enzyme-Mediated Dynamic Cyclodextrin Libraries to Enhance Template Effects. Chemistry 2020; 26:11032-11038. [PMID: 32445426 DOI: 10.1002/chem.202001076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/15/2020] [Indexed: 12/11/2022]
Abstract
Enzyme-mediated dynamic combinatorial chemistry combines the concept of thermodynamically controlled covalent self-assembly with the inherent biological relevance of enzymatic transformations. A system of interconverting cyclodextrins has been explored, in which the glycosidic linkage is rendered dynamic by the action of cyclodextrin glucanotransferase (CGTase). External factors, such as pH, temperature, solvent, and salinity are reported to modulate the composition of the dynamic cyclodextrin library. Dynamic libraries of cyclodextrins (CDs) could be obtained in wide ranges of pH (5.0-9.0), temperature (5-37 °C), and salinity (up to 7.5 m NaNO3 ), and with high organic solvent content (50 % by volume of ethanol), showing that enzyme-mediated dynamic systems can be robust and not limited to physiological conditions. Furthermore, it is demonstrated how strategic choice of reaction conditions can enhance template effects, in this case, to achieve highly selective production of α-CD, an otherwise challenging target due to competition from the structurally similar β-CD.
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Affiliation(s)
- Dennis Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark
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35
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36
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Sevim İ, Pankau WM, von Kiedrowski G. Re-Evaluation of a Fulvene-Based Self-Replicating Diels-Alder Reaction System. Chemistry 2020; 26:9032-9035. [PMID: 32638430 DOI: 10.1002/chem.201905594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/04/2020] [Indexed: 11/06/2022]
Abstract
We re-evaluate our claim of a high diastereoselectivity in the self-relicating Diels-Alder reaction between maleimide 1 and fulvene 3. It was shown that the system has a diastereoselectivity of 1.8:1 for NN-4:NX-4, which is contrary to the 16:1 ratio claimed by Dieckmann et al. The analysis of 1 H NMR monitoring of the reaction revealed that both replicators show sigmoidal growth which is typical for auto-catalytic systems.
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Affiliation(s)
- İlhan Sevim
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Wolf Matthias Pankau
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Günter von Kiedrowski
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
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37
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Ayme J, Dhers S, Lehn J. Triple Self-Sorting in Constitutional Dynamic Networks: Parallel Generation of Imine-Based Cu I , Fe II , and Zn II Complexes. Angew Chem Int Ed Engl 2020; 59:12484-12492. [PMID: 32286724 PMCID: PMC7383593 DOI: 10.1002/anie.202000818] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 12/20/2022]
Abstract
Three imine-based metal complexes, having no overlap in terms of their compositions, have been simultaneously generated from the self-sorting of a constitutional dynamic library (CDL) containing three amines, three aldehydes, and three metal salts. The hierarchical ordering of the stability of the three metal complexes assembled and the leveraging of the antagonistic and agonistic relationships existing between the constituents within the constitutional dynamic network corresponding to the CDL were pivotal in achieving the sorting. Examination of the process by NMR spectroscopy showed that the self-sorting of the FeII and ZnII complexes depended on an interplay between the thermodynamic driving forces and a kinetic trap involved in their assembly. These results also exemplify the concept of "simplexity"-the fact that the output of a self-assembling system may be simplified by increasing its initial compositional complexity-as the two complexes could self-sort only in the presence of the third pair of organic components, those of the CuI complex.
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Affiliation(s)
- Jean‐François Ayme
- Institute of NanotechnologyKarlsruhe Institute of Technology76344Eggenstein-LeopoldshafenGermany
- Laboratoire de Chimie SupramoléculaireInstitut de Science et d'Ingénierie SupramoléculairesUniversité de Strasbourg8 allée Gaspard Monge67000StrasbourgFrance
| | - Sébastien Dhers
- Laboratoire de Chimie SupramoléculaireInstitut de Science et d'Ingénierie SupramoléculairesUniversité de Strasbourg8 allée Gaspard Monge67000StrasbourgFrance
| | - Jean‐Marie Lehn
- Institute of NanotechnologyKarlsruhe Institute of Technology76344Eggenstein-LeopoldshafenGermany
- Laboratoire de Chimie SupramoléculaireInstitut de Science et d'Ingénierie SupramoléculairesUniversité de Strasbourg8 allée Gaspard Monge67000StrasbourgFrance
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38
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Ayme J, Dhers S, Lehn J. Triple Self‐Sorting in Constitutional Dynamic Networks: Parallel Generation of Imine‐Based Cu
I
, Fe
II
, and Zn
II
Complexes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jean‐François Ayme
- Institute of Nanotechnology Karlsruhe Institute of Technology 76344 Eggenstein-Leopoldshafen Germany
- Laboratoire de Chimie Supramoléculaire Institut de Science et d'Ingénierie Supramoléculaires Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
| | - Sébastien Dhers
- Laboratoire de Chimie Supramoléculaire Institut de Science et d'Ingénierie Supramoléculaires Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
| | - Jean‐Marie Lehn
- Institute of Nanotechnology Karlsruhe Institute of Technology 76344 Eggenstein-Leopoldshafen Germany
- Laboratoire de Chimie Supramoléculaire Institut de Science et d'Ingénierie Supramoléculaires Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
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39
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From self-replication to replicator systems en route to de novo life. Nat Rev Chem 2020; 4:386-403. [PMID: 37127968 DOI: 10.1038/s41570-020-0196-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2020] [Indexed: 01/01/2023]
Abstract
The process by which chemistry can give rise to biology remains one of the biggest mysteries in contemporary science. The de novo synthesis and origin of life both require the functional integration of three key characteristics - replication, metabolism and compartmentalization - into a system that is maintained out of equilibrium and is capable of open-ended Darwinian evolution. This Review takes systems of self-replicating molecules as starting points and describes the steps necessary to integrate additional characteristics of life. We analyse how far experimental self-replicators have come in terms of Darwinian evolution. We also cover models of replicator communities that attempt to solve Eigen's paradox, whereby accurate replication needs complex machinery yet obtaining such complex self-replicators through evolution requires accurate replication. Successful models rely on a collective metabolism and a way of (transient) compartmentalization, suggesting that the invention and integration of these two characteristics is driven by evolution. Despite our growing knowledge, there remain numerous key challenges that may be addressed by a combined theoretical and experimental approach.
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40
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Robertson CC, Kosikova T, Philp D. Encoding Multiple Reactivity Modes within a Single Synthetic Replicator. J Am Chem Soc 2020; 142:11139-11152. [PMID: 32414236 DOI: 10.1021/jacs.0c03527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Establishing programmable and self-sustaining replication networks in pools of chemical reagents is a key challenge in systems chemistry. Self-replicating templates are formed from two constituent components with complementary recognition and reactive sites via a slow bimolecular pathway and a fast template-directed pathway. Here, we re-engineer one of the components of a synthetic replicator to encode an additional recognition function, permitting the assembly of a binary complex between the components that mediates replicator formation through a template-independent pathway, which achieves maximum rate acceleration at early time points in the replication process. The complementarity between recognition sites creates a key conformational equilibrium between the catalytically inert product, formed via the template-independent pathway, and the catalytically active replicator that mediates the template-directed pathway. Consequently, the rapid formation of the catalytically inert isomer kick-starts replication through the template-directed pathway. Through kinetic analyses, we demonstrate that the presence of the two recognition-mediated reactivity modes results in enhanced template formation in comparison to that of systems capable of exploiting only a single recognition-mediated pathway. Finally, kinetic simulations reveal that the conformational equilibrium and both the relative and absolute efficiencies of the recognition-mediated pathways affect the extent to which self-replicating systems can benefit from this additional template-independent reactivity mode. These results allow us to formulate the rules that govern the coupling of replication processes to alternative recognition-mediated reactivity modes. The interplay between template-directed and template-independent pathways for replicator formation has significant relevance to ongoing efforts to design programmable and adaptable replicator networks.
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Affiliation(s)
- Craig C Robertson
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Douglas Philp
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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41
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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42
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Liu B, Pappas CG, Ottelé J, Schaeffer G, Jurissek C, Pieters PF, Altay M, Marić I, Stuart MCA, Otto S. Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids. J Am Chem Soc 2020; 142:4184-4192. [PMID: 32023041 PMCID: PMC7059183 DOI: 10.1021/jacs.9b10796] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
The conditions that led to the formation
of the first organisms
and the ways that life originates from a lifeless chemical soup are
poorly understood. The recent hypothesis of “RNA-peptide coevolution”
suggests that the current close relationship between amino acids and
nucleobases may well have extended to the origin of life. We now show
how the interplay between these compound classes can give rise to
new self-replicating molecules using a dynamic combinatorial approach.
We report two strategies for the fabrication of chimeric amino acid/nucleobase
self-replicating macrocycles capable of exponential growth. The first
one relies on mixing nucleobase- and peptide-based building blocks,
where the ligation of these two gives rise to highly specific chimeric
ring structures. The second one starts from peptide nucleic acid (PNA)
building blocks in which nucleobases are already linked to amino acids
from the start. While previously reported nucleic acid-based self-replicating
systems rely on presynthesis of (short) oligonucleotide sequences,
self-replication in the present systems start from units containing
only a single nucleobase. Self-replication is accompanied by self-assembly,
spontaneously giving rise to an ordered one-dimensional arrangement
of nucleobase nanostructures.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Christoph Jurissek
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Priscilla F Pieters
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Meniz Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ivana Marić
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marc C A Stuart
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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43
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Selection from a pool of self-assembling lipid replicators. Nat Commun 2020; 11:176. [PMID: 31924788 PMCID: PMC6954257 DOI: 10.1038/s41467-019-13903-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/06/2019] [Indexed: 11/22/2022] Open
Abstract
Replication and compartmentalization are fundamental to living systems and may have played important roles in life’s origins. Selection in compartmentalized autocatalytic systems might provide a way for evolution to occur and for life to arise from non-living systems. Herein we report selection in a system of self-reproducing lipids where a predominant species can emerge from a pool of competitors. The lipid replicators are metastable and their out-of-equilibrium population can be sustained by feeding the system with starting materials. Phase separation is crucial for selective surfactant formation as well as autocatalytic kinetics; indeed, no selection is observed when all reacting species are dissolved in the same phase. Selectivity is attributed to a kinetically controlled process where the rate of monomer formation determines which replicator building blocks are the fittest. This work reveals how kinetics of a phase-separated autocatalytic reaction may be used to control the population of out-of-equilibrium replicators in time. Selection in compartmentalized self-replicating systems might provide a way for life to arise from abiotic environments. Here, the authors explore selection in a system of transient autocatalytic lipids and find that autocatalytic kinetics and phase separation are the key selection factors.
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44
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Affiliation(s)
- Jean‐François Lutz
- Université de Strasbourg, CNRSInstitut Charles Sadron, UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
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45
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Solà J, Jimeno C, Alfonso I. Exploiting complexity to implement function in chemical systems. Chem Commun (Camb) 2020; 56:13273-13286. [DOI: 10.1039/d0cc04170j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.
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Affiliation(s)
- Jordi Solà
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| | - Ciril Jimeno
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
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46
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Ayme JF, Lehn JM. Self-sorting of two imine-based metal complexes: balancing kinetics and thermodynamics in constitutional dynamic networks. Chem Sci 2019; 11:1114-1121. [PMID: 34084368 PMCID: PMC8146771 DOI: 10.1039/c9sc04988f] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A major hurdle in the development of complex constitutional dynamic networks (CDNs) is the lack of strategies to simultaneously control the output of two (or more) interconnected dynamic processes over several species, namely reversible covalent imine bond formation and dynamic metal–ligand coordination. We have studied in detail the self-sorting process of 11 constitutional dynamic libraries containing two different amines, aldehydes and metal salts into two imine-based metal complexes, having no overlap in terms of their compositions. This study allowed us to determine the factors influencing the fidelity of this process (concentration, electronic and steric parameters of the organic components, and nature of the metal cations). In all 11 systems, the outcome of the process was primarily determined by the ability of the octahedral metal ion to select its pair of components from the initial pool of components, with the composition of the weaker tetrahedral complex being imposed by the components rejected by the octahedral metal ions. Different octahedral metal ions required different levels of precision in the “assembling instructions” provided by the organic components of the CDN to guide it towards a sorted output. The concentration of the reaction mixture, and the electronic and steric properties of the initial components of the library were all found to influence the lifetime of unwanted metastable intermediates formed during the assembling of the two complexes. Constitutional dynamic networks have been developed to simultaneously control the output of two interconnected dynamic processes over several species of the same reaction mixture.![]()
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Affiliation(s)
- Jean-François Ayme
- Institute of Nanotechnology, Karlsruhe Institute of Technology 76344 Eggenstein-Leopoldshafen Germany.,Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
| | - Jean-Marie Lehn
- Institute of Nanotechnology, Karlsruhe Institute of Technology 76344 Eggenstein-Leopoldshafen Germany.,Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
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Huck J, Kosikova T, Philp D. Compositional Persistence in a Multicyclic Network of Synthetic Replicators. J Am Chem Soc 2019; 141:13905-13913. [PMID: 31403776 DOI: 10.1021/jacs.9b06697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The emergence of collections of simple chemical entities that create self-sustaining reaction networks, embedding replication and catalysis, is cited as a potential mechanism for the appearance on the early Earth of systems that satisfy minimal definitions of life. In this work, a functional reaction network that creates and maintains a set of privileged replicator structures through auto- and cross-catalyzed reaction cycles is created from the pairwise combinations of four reagents. We show that the addition of individual preformed templates to this network, representing instructions to synthesize a specific replicator, induces changes in the output composition of the system that represent a network-level response. Further, we establish through sets of serial transfer experiments that the catalytic connections that exist between the four replicators in this network and the system-level behavior thereby encoded impose limits on the compositional variability that can be induced by repeated exposure to instructional inputs, in the form of preformed templates, to the system. The origin of this persistence is traced through kinetic simulations to the properties and inter-relationships between the critical ternary complexes formed by the auto- and crosscatalytic templates. These results demonstrate that in an environment where there is no continuous selection pressure the network connectivity, described by the catalytic relationships and system-level interactions between the replicators, is persistent, thereby limiting the ability of this network to adapt and evolve.
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Affiliation(s)
- Jürgen Huck
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , Fife KY16 9ST , U.K
| | - Tamara Kosikova
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , Fife KY16 9ST , U.K
| | - Douglas Philp
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , Fife KY16 9ST , U.K
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Strom KR, Szostak JW, Prywes N. Transfer of Sequence Information and Replication of Diimine Duplexes. J Org Chem 2019; 84:3754-3761. [PMID: 30855962 PMCID: PMC7547894 DOI: 10.1021/acs.joc.9b00095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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The
ability of the biopolymers RNA and DNA to store and transfer
information is essential to life. Herein, we demonstrate template-directed
replication in a set of dimer duplexes that use reversible covalent
bonds to form base-pairing interactions. Binary sequence information
was encoded as a sequence of aniline and benzaldehyde subunits linked
together by a diethynyl benzene backbone. These dimers formed sequence-specific,
imine-linked duplexes, which could be separated and used as templates
for the synthesis of daughter duplexes with identical sequences.
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Affiliation(s)
- Kyle R Strom
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States
| | - Noam Prywes
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States
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Grzelczak M. Colloidal systems chemistry. Replication, reproduction and selection at nanoscale. J Colloid Interface Sci 2019; 537:269-279. [PMID: 30448648 DOI: 10.1016/j.jcis.2018.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/25/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
Development of synthetic systems carrying life-like features is a long-standing challenge in chemistry and material science. Poor understanding of mechanisms ruling the emergence of life-like features in an inanimate matter makes the challenge even more exciting. The growing field of systems chemistry takes the lead in defining life-like dynamic signatures in minimalistic (macro)molecular systems through the development of multicomponent synthetic models using tools from organic and supramolecular chemistry. Recent progress in nanoscience makes available a range of novel materials that can undoubtedly enrich systems chemistry. Therefore, with the aim of placing nano- and colloidal science within the context of systems chemistry, the recent experimental and theoretical developments dealing with the use of nanoparticles and their assemblies in the realisation of the concepts such as replication, reproduction and selection are discussed.
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Affiliation(s)
- Marek Grzelczak
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, Donostia - San Sebastián 20018, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
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Abstract
The continuous consumption of chemical energy powers biological systems so that they can operate functional supramolecular structures. A goal of modern science is to understand how simple chemical mixtures may transition from non-living components to truly emergent systems and the production of new lifelike materials and machines. In this work a replicator can be maintained out-of-equilibrium by the continuous consumption of chemical energy. The system is driven by the autocatalytic formation of a metastable surfactant whose breakdown products are converted back into building blocks by a chemical fuel. The consumption of fuel allows the high-energy replicators to persist at a steady state, much like a simple metabolic cycle. Thermodynamically-driven reactions effect a unidirectional substrate flux as the system tries to regain equilibrium. The metastable replicator persists at a higher concentration than achieved even transiently in a closed system, and its concentration is responsive to the rate of fuel supply. Understanding how simple chemical mixtures transition into truly emergent systems is essential to create new lifelike materials. Here, the authors show a self-replicating system that can be maintained out-of-equilibrium by an oxidant fuel in analogy to simple metabolic cycles.
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