1
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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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2
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Stingley KJ, Carpenter BA, Kean KM, Waters ML. Mismatched covalent and noncovalent templating leads to large coiled coil-templated macrocycles. Chem Sci 2023; 14:4935-4944. [PMID: 37181761 PMCID: PMC10171189 DOI: 10.1039/d3sc00231d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
Herein we describe the use of dynamic combinatorial chemistry to self-assemble complex coiled coil motifs. We amide-coupled a series of peptides designed to form homodimeric coiled coils with 3,5-dithiobenzoic acid (B) at the N-terminus and then allowed each B-peptide to undergo disulfide exchange. In the absence of peptide, monomer B forms cyclic trimers and tetramers, and thus we expected that addition of the peptide to monomer B would shift the equilibrium towards the tetramer to maximize coiled coil formation. Unexpectedly, we found that internal templation of the B-peptide through coiled coil formation shifts the equilibrium towards larger macrocycles up to 13 B-peptide subunits, with a preference for 4, 7, and 10-membered macrocycles. These macrocyclic assemblies display greater helicity and thermal stability relative to intermolecular coiled coil homodimer controls. The preference for large macrocycles is driven by the strength of the coiled coil, as increasing the coiled coil affinity increases the fraction of larger macrocycles. This system represents a new approach towards the development of complex peptide and protein assemblies.
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Affiliation(s)
- Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Benjamin A Carpenter
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Kelsey M Kean
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
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3
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Greenlee AJ, Chen H, Wendell CI, Moore JS. Tandem Imine Formation and Alkyne Metathesis Enabled by Catalyst Choice. J Org Chem 2022; 87:8429-8436. [PMID: 35678630 DOI: 10.1021/acs.joc.2c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three-rung molecular ladder 8 was prepared in one pot via tandem imine condensation and alkyne metathesis. Catalyst VI is demonstrated to successfully engender the metathesis of imine-bearing substrate 7, while catalyst III does not. The susceptibility of catalyst VI to deactivation by hydrolysis and ligand exchange is demonstrated. Assembly and disassembly of ladder 8 in one pot were demonstrated in the presence and absence of a Lewis acid catalyst.
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Affiliation(s)
- Andrew J Greenlee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Heyu Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chloe I Wendell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jeffrey S Moore
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Liu B, Wu J, Geerts M, Markovitch O, Pappas CG, Liu K, Otto S. Out-of-Equilibrium Self-Replication Allows Selection for Dynamic Kinetic Stability in a System of Competing Replicators. Angew Chem Int Ed Engl 2022; 61:e202117605. [PMID: 35179808 PMCID: PMC9314957 DOI: 10.1002/anie.202117605] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 12/16/2022]
Abstract
Among the key characteristics of living systems are their ability to self‐replicate and the fact that they exist in an open system away from equilibrium. Herein, we show how the outcome of the competition between two self‐replicators, differing in size and building block composition, is different depending on whether the experiments are conducted in a closed vial or in an open and out‐of‐equilibrium replication–destruction regime. In the closed system, the slower replicator eventually prevails over the faster competitor. In a replication‐destruction regime, implemented through a flow system, the outcome of the competition is reversed and the faster replicator dominates. The interpretation of the experimental observations is supported by a mass‐action‐kinetics model. These results represent one of the few experimental manifestations of selection among competing self‐replicators based on dynamic kinetic stability and pave the way towards Darwinian evolution of abiotic systems.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Juntian Wu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marc Geerts
- 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.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Kai Liu
- 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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5
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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: 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
![]()
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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6
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Liu B, Wu J, Geerts M, Markovitch O, Pappas CG, Liu K, Otto S. Out‐of‐equilibrium self‐replication allows selection for dynamic kinetic stability in a system of competing replicators. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bin Liu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Juntian Wu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Marc Geerts
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Omer Markovitch
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Charalampos G. Pappas
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Kai Liu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Sijbren Otto
- Stratingh Institute University of Groningen Centre for Systems Chemistry Nijenborgh 4 9747AG Groningen NETHERLANDS
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7
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Coste M, Suárez-Picado E, Ulrich S. Hierarchical self-assembly of aromatic peptide conjugates into supramolecular polymers: it takes two to tango. Chem Sci 2022; 13:909-933. [PMID: 35211257 PMCID: PMC8790784 DOI: 10.1039/d1sc05589e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/10/2021] [Indexed: 12/26/2022] Open
Abstract
Supramolecular polymers are self-assembled materials displaying adaptive and responsive "life-like" behaviour which are often made of aromatic compounds capable of engaging in π-π interactions to form larger assemblies. Major advances have been made recently in controlling their mode of self-assembly, from thermodynamically-controlled isodesmic to kinetically-controlled living polymerization. Dynamic covalent chemistry has been recently implemented to generate dynamic covalent polymers which can be seen as dynamic analogues of biomacromolecules. On the other hand, peptides are readily-available and structurally-rich building blocks that can lead to secondary structures or specific functions. In this context, the past decade has seen intense research activity in studying the behaviour of aromatic-peptide conjugates through supramolecular and/or dynamic covalent chemistries. Herein, we review those impressive key achievements showcasing how aromatic- and peptide-based self-assemblies can be combined using dynamic covalent and/or supramolecular chemistry, and what it brings in terms of the structure, self-assembly pathways, and function of supramolecular and dynamic covalent polymers.
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Affiliation(s)
- Maëva Coste
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Esteban Suárez-Picado
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Sébastien Ulrich
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM Montpellier France
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8
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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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9
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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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10
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Schröder HV, Zhang Y, Link AJ. Dynamic covalent self-assembly of mechanically interlocked molecules solely made from peptides. Nat Chem 2021; 13:850-857. [PMID: 34426684 PMCID: PMC8446321 DOI: 10.1038/s41557-021-00770-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022]
Abstract
Mechanically interlocked molecules (MIMs), such as rotaxanes and catenanes, have captured the attention of chemists both from a synthetic perspective and because of their role as simple prototypes of molecular machines. Although examples exist in nature, most synthetic MIMs are made from artificial building blocks and assembled in organic solvents. Synthesis of MIMs from natural biomolecules remains highly challenging. Here we report on a synthesis strategy for interlocked molecules solely made from peptides—mechanically interlocked peptides (MIPs). Fully peptidic, cysteine-decorated building blocks were self-assembled in water to generate disulfide-bonded dynamic combinatorial libraries consisting of multiple different rotaxanes, catenanes and daisy chains as well as more exotic structures. Detailed NMR spectroscopy and mass spectrometry characterization of a [2]catenane comprised of two peptide macrocycles revealed that this structure has rich conformational dynamics reminiscent of protein folding. Thus, MIPs can serve as a bridge between fully synthetic MIMs and those found in nature.
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Affiliation(s)
- Hendrik V Schröder
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Yi Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,Department of Chemistry, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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11
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Pappas CG, Mandal PK, Liu B, Kauffmann B, Miao X, Komáromy D, Hoffmann W, Manz C, Chang R, Liu K, Pagel K, Huc I, Otto S. Emergence of low-symmetry foldamers from single monomers. Nat Chem 2020; 12:1180-1186. [DOI: 10.1038/s41557-020-00565-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 09/21/2020] [Indexed: 12/20/2022]
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12
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Rodon Fores J, Criado‐Gonzalez M, Chaumont A, Carvalho A, Blanck C, Schmutz M, Boulmedais F, Schaaf P, Jierry L. Autonomous Growth of a Spatially Localized Supramolecular Hydrogel with Autocatalytic Ability. Angew Chem Int Ed Engl 2020; 59:14558-14563. [DOI: 10.1002/anie.202005377] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Jennifer Rodon Fores
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Miryam Criado‐Gonzalez
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche Médicale INSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de Strasbourg Faculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Alain Chaumont
- Université de Strasbourg Faculté de Chimie, UMR7140 1 rue Blaise Pascal 67008 Strasbourg Cedex France
| | - Alain Carvalho
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christian Blanck
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Marc Schmutz
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Fouzia Boulmedais
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Pierre Schaaf
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche Médicale INSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de Strasbourg Faculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Loïc Jierry
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
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13
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Rodon Fores J, Criado‐Gonzalez M, Chaumont A, Carvalho A, Blanck C, Schmutz M, Boulmedais F, Schaaf P, Jierry L. Autonomous Growth of a Spatially Localized Supramolecular Hydrogel with Autocatalytic Ability. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jennifer Rodon Fores
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Miryam Criado‐Gonzalez
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche Médicale INSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de Strasbourg Faculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Alain Chaumont
- Université de Strasbourg Faculté de Chimie, UMR7140 1 rue Blaise Pascal 67008 Strasbourg Cedex France
| | - Alain Carvalho
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christian Blanck
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Marc Schmutz
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Fouzia Boulmedais
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Pierre Schaaf
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche Médicale INSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de Strasbourg Faculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Loïc Jierry
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
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14
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Sattler LE, Otten CJ, Hilt G. Alternating Current Electrolysis for the Electrocatalytic Synthesis of Mixed Disulfide via Sulfur-Sulfur Bond Metathesis towards Dynamic Disulfide Libraries. Chemistry 2020; 26:3129-3136. [PMID: 31908043 PMCID: PMC7079035 DOI: 10.1002/chem.201904948] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Indexed: 11/24/2022]
Abstract
A novel approach of electrolysis using alternating current was applied in the sulfur–sulfur bond metathesis of symmetrical disulfides towards unsymmetrical disulfides. As initially expected, a statistical distribution in disulfides was obtained. Furthermore, the influence of electrode polarisation by alternating current was investigated on a two‐disulfide matrix. The highly dynamic nature of this chemistry resulted in the creation of dynamic disulfide libraries by expansion of the matrices, consisting of up to six symmetrical disulfides. In addition, mixing of matrices and stepwise expanding of a matrix by using alternating current electrolysis were realised.
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Affiliation(s)
- Lars Erik Sattler
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany.,Institut für Chemie, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, 26129, Oldenburg, Germany
| | - Chris Josef Otten
- Institut für Chemie, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, 26129, Oldenburg, Germany
| | - Gerhard Hilt
- Institut für Chemie, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, 26129, Oldenburg, Germany
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15
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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
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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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16
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Rodon Fores J, Criado-Gonzalez M, Schmutz M, Blanck C, Schaaf P, Boulmedais F, Jierry L. Protein-induced low molecular weight hydrogelator self-assembly through a self-sustaining process. Chem Sci 2019; 10:4761-4766. [PMID: 31160952 PMCID: PMC6509879 DOI: 10.1039/c9sc00312f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/07/2019] [Indexed: 01/18/2023] Open
Abstract
Controlling how, when and where a self-assembly process occurs is essential for the design of the next generation of smart materials. Along this route, enzyme-assisted self-assembly is a powerful tool developed during the last decade. Here we introduce another strategy allowing for spatiotemporal control over peptide self-assemblies. We use a Fmoc-peptide precursor in dynamic equilibrium with its low molecular weight hydrogelator (LMWH) through a reversible disulfide bond. In the absence of proteins, no self-assembly of the hydrogelator is observed. In the presence of proteins, their interactions with the precursor initiate a self-assembly process of the hydrogelator around them. This self-assembly displaces the equilibrium between precursor and LMWH according to Le Chatelier's principle, producing new hydrogelators available to pursue the self-assembly growth. One thus establishes a self-sustaining cycle fuelled by the self-assembly itself until full consumption of the LMWH. For proteins in solutions this process can lead to a supramolecular hydrogel whereas for proteins deposited on a surface, the gel growth is initiated exclusively from the surface.
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Affiliation(s)
- Jennifer Rodon Fores
- Université de Strasbourg , CNRS , Institut Charles Sadron (UPR22) , 23 rue du Loess , 67034 Strasbourg Cedex 2 , BP 84047 , France . ;
| | - Miryam Criado-Gonzalez
- Université de Strasbourg , CNRS , Institut Charles Sadron (UPR22) , 23 rue du Loess , 67034 Strasbourg Cedex 2 , BP 84047 , France . ;
- Institut National de la Santé et de la Recherche Médicale , INSERM Unité 1121 , 11 rue Humann , 67085 Strasbourg Cedex , France
- Université de Strasbourg , Faculté de Chirurgie Dentaire , 8 rue Sainte Elisabeth , 67000 Strasbourg , France
| | - Marc Schmutz
- Université de Strasbourg , CNRS , Institut Charles Sadron (UPR22) , 23 rue du Loess , 67034 Strasbourg Cedex 2 , BP 84047 , France . ;
| | - Christian Blanck
- Université de Strasbourg , CNRS , Institut Charles Sadron (UPR22) , 23 rue du Loess , 67034 Strasbourg Cedex 2 , BP 84047 , France . ;
| | - Pierre Schaaf
- Université de Strasbourg , CNRS , Institut Charles Sadron (UPR22) , 23 rue du Loess , 67034 Strasbourg Cedex 2 , BP 84047 , France . ;
- Institut National de la Santé et de la Recherche Médicale , INSERM Unité 1121 , 11 rue Humann , 67085 Strasbourg Cedex , France
- Université de Strasbourg , Faculté de Chirurgie Dentaire , 8 rue Sainte Elisabeth , 67000 Strasbourg , France
| | - Fouzia Boulmedais
- Université de Strasbourg , CNRS , Institut Charles Sadron (UPR22) , 23 rue du Loess , 67034 Strasbourg Cedex 2 , BP 84047 , France . ;
| | - Loïc Jierry
- Université de Strasbourg , CNRS , Institut Charles Sadron (UPR22) , 23 rue du Loess , 67034 Strasbourg Cedex 2 , BP 84047 , France . ;
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17
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Kosikova T, Philp D. Two Synthetic Replicators Compete To Process a Dynamic Reagent Pool. J Am Chem Soc 2019; 141:3059-3072. [PMID: 30668914 DOI: 10.1021/jacs.8b12077] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Complementary building blocks, comprising a set of four aromatic aldehydes and a set of four nucleophiles-three anilines and one hydroxylamine-combine through condensation reactions to afford a dynamic covalent library (DCL) consisting of the eight starting materials and 16 condensation products. One of the aldehydes and, consequently, all of the DCL members derived from this compound bear an amidopyridine recognition site. Exposure of this DCL to two maleimides, Mp and Mm, each equipped with a carboxylic acid recognition site, results in the formation of a series of products through irreversible 1,3-dipolar cycloaddition reactions with the four nitrones present in the DCL. However, only the two cycloadducts in the product pool that incorporate both recognition sites, Tp and Tm, are self-replicators that can harness the DCL as feedstock for their own formation, facilitating their own synthesis via autocatalytic and cross-catalytic pathways. The ability of these replicators to direct their own formation from the components present in the dynamic reagent pool in response to the input of instructions in the form of preformed replicators is demonstrated through a series of quantitative 19F{1H} NMR spectroscopy experiments. Simulations establish the critical relationships between the kinetic and thermodynamic parameters of the replicators, the initial reagent concentrations, and the presence or absence of the DCL and their influence on the competition between Tp and Tm. Thus, we establish the rules that govern the behavior of the competing replicators under conditions where their formation is coupled tightly to the processing of a DCL.
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Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , KY16 9ST Fife , United Kingdom
| | - Douglas Philp
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , KY16 9ST Fife , United Kingdom
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