1
|
Ranganath VA, Maity I. Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises. Angew Chem Int Ed Engl 2024; 63:e202318134. [PMID: 38226567 DOI: 10.1002/anie.202318134] [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: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.
Collapse
Affiliation(s)
- Vinay Ambekar Ranganath
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
| | - Indrajit Maity
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
| |
Collapse
|
2
|
Sahu S, Parthasarathy V, Mishra AK. Phenylethynylanthracene based push-pull molecular systems: tuning the photophysics through para-substituents on the phenyl ring. Phys Chem Chem Phys 2023; 25:1957-1969. [PMID: 36541448 DOI: 10.1039/d2cp05074a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Organic push-pull molecules contain donor and acceptor moieties connected via π-linkages through which intramolecular electron charge transfer (ICT) can occur in the ground and excited states; giving these molecules interesting photophysical properties. The molecules chosen in this work are some basic phenylethynylanthracene derivatives to show that with just a change of substituents this class of small molecules can show dramatic changes in their photophysical properties. The emission properties and ICT abilities of these molecules are compared with regards to various electron donating and withdrawing substituents. Substituents such as cyano and methoxycarbonyl groups do not induce any ICT character whereas substituents like aldehyde, N,N-dimethylamino and nitro groups cause appreciable ICT character in this class of molecules and their emission spectra extend almost throughout the whole visible region. The comparative ICT character was correlated with the results of electron density difference calculations. Computational studies show that the molecules are planar in their ground as well as excited states; except the nitro group containing molecule, which has an orthogonally twisted structure in the excited state. The emission properties of this molecule led to its inclusion into a class of nitroaromatics which shows maximum emission intensity in moderately polar solvents and the emission is quenched drastically by either decreasing or increasing solvent polarity. Fluorescence anisotropy studies show very good sensitivity of these compounds towards microviscosity of their immediate molecular environment. A white light emitting (WLE) gel was prepared using 4-(anthracen-9-ylethynyl)benzonitrile (AnPCN) and 4-(anthracen-9-ylethynyl)-N,N-dimethylaniline (AnPNMe2) by taking polyvinyl alcohol (PVA) as the gelator and the resulting gel exhibited very good CIE (0.31, 0.33) with CCT (6598 K) and CRI (87). As an example, the use of the gel was also demonstrated by applying it to a commercial UV LED which showed satisfactory results. AnPNMe2 was used to sense polar solvent vapors in TLC plates and Whatman paper due to its good solvatochromic behavior.
Collapse
Affiliation(s)
- Sonali Sahu
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.
| | | | - Ashok Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.
| |
Collapse
|
3
|
Liang J, Zhang P, Yang H, Zhang Y, Yao T, Liu K, Wang Y, Zhang X, Qin X. Design, synthesis and biological evaluation of novel nitric oxide donors with antioxidative activity. Eur J Med Chem 2022; 236:114331. [PMID: 35421659 DOI: 10.1016/j.ejmech.2022.114331] [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: 01/19/2022] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 11/04/2022]
Abstract
Reactive oxygen species (ROS) are the primary cause of organic nitrate drug tolerance and endothelial dysfunction. In order to scavenge the ROS and maintain the therapeutic effect of nitrates, we designed and synthesized ten new types of dual-acting nitrate molecules by combining NIT-type nitroxides and 5-ISMN. These included two types of novel epimeric nitroxide-nitrate conjugates (15(S) and 15(R)), which had pharmacophore connections. We also synthesized 8 NIT radicals without 5-ISMN in order to compare the activities of these novel nitric oxide donors. Several dual-acting nitroxide-based nitrate conjugates showed the ability to release NO and cause anti-oxidant effects in human umbilical vein endothelial cells. Among these conjugates, 15(S) showed the most prominent pro-vasodilative effect. In angiotensin II infusion-induced hypertensive mice, 15(S) treatment for 4 weeks decreased both the systolic and diastolic blood pressures and ameliorated the vascular endothelial and smooth muscle functions of isolated thoracic aortas. In addition, the vascular structure of the mice was restored and their vascular oxidative stress was decreased. The results suggest that these novel nitric oxide donors can be used as potential drugs in the treatment of vascular diseases. Therefore, the strategy of using a combination of antioxidants and NO-donors can be a promising way to develop novel organic nitrate drugs for future use in combating disease.
Collapse
Affiliation(s)
- Jing Liang
- Department of Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China; Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi, 710021, China
| | - Pengfei Zhang
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Hongyan Yang
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Ying Zhang
- Department of Endocrinology and Metabolism, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Tuanli Yao
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi, 710021, China
| | - Keke Liu
- Department of Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Yukun Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China; Southern University of Science and Technology Hospital, Shenzhen, 518055, China.
| | - Xing Zhang
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
| | - Xiangyang Qin
- Department of Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- İlhan Sevim
- Lehrstuhl für Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
| |
Collapse
|
6
|
Mai AQ, Bánsági T, Taylor AF, Pojman JA. Reaction-diffusion hydrogels from urease enzyme particles for patterned coatings. Commun Chem 2021; 4:101. [PMID: 36697546 PMCID: PMC9814597 DOI: 10.1038/s42004-021-00538-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/07/2021] [Indexed: 01/28/2023] Open
Abstract
The reaction and diffusion of small molecules is used to initiate the formation of protective polymeric layers, or biofilms, that attach cells to surfaces. Here, inspired by biofilm formation, we present a general method for the growth of hydrogels from urease enzyme-particles by combining production of ammonia with a pH-regulated polymerization reaction in solution. We show through experiments and simulations how the propagating basic front and thiol-acrylate polymerization were continuously maintained by the localized urease reaction in the presence of urea, resulting in hydrogel layers around the enzyme particles at surfaces, interfaces or in motion. The hydrogels adhere the enzyme-particles to surfaces and have a tunable growth rate of the order of 10 µm min-1 that depends on the size and spatial distribution of particles. This approach can be exploited to create enzyme-hydrogels or chemically patterned coatings for applications in biocatalytic flow reactors.
Collapse
Affiliation(s)
- Anthony Q. Mai
- grid.64337.350000 0001 0662 7451Department of Chemistry & The Macromolecular Studies Group, Louisiana State University, Baton Rouge, LA USA
| | - Tamás Bánsági
- grid.11835.3e0000 0004 1936 9262Chemical and Biological Engineering, University of Sheffield, Sheffield, UK ,grid.6572.60000 0004 1936 7486Department of Chemistry, University of Birmingham, Birmingham, UK
| | - Annette F. Taylor
- grid.11835.3e0000 0004 1936 9262Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - John A. Pojman
- grid.64337.350000 0001 0662 7451Department of Chemistry & The Macromolecular Studies Group, Louisiana State University, Baton Rouge, LA USA
| |
Collapse
|
7
|
Chen B, Qin F, Su M, Zhang Z, Pan Q, Zou M, Yang X, Chen S, Derome D, Carmeliet J, Song Y. Self-Driven Multiplex Reaction: Reactant and Product Diffusion via a Transpiration-Inspired Capillary. ACS APPLIED MATERIALS & INTERFACES 2021; 13:22031-22039. [PMID: 33939416 DOI: 10.1021/acsami.1c03614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
When dealing with reactions of a liquid reactant and a solid catalyst, macroreactors with vigorous stirring equipment may be dangerous and cause wastage of energy. Reducing the diffusion distance and promoting reactants to reach the catalyst surface for efficient reaction remain the key challenges. Here, inspired by capillary-driven water motion in plants, we propose to implement a self-driven multiplex reaction (SMR) in nanocatalyst-loaded microchannels. Unlike the classical capillary rise, the droplet in SMR has variable pressure difference, leading to tunable flow velocity for controlling the reaction rate without any auxiliary equipment. The SMR in microchannels contributes to an increase in the reaction rate by more than 2 orders of magnitude compared to that in macroreactors. Specifically, this strategy reduces the reaction volume by 170 times, the catalyst usage by about 12 times, and the energy consumption by 50 times. This apparatus with a small volume and less catalyst content promises to provide an efficient strategy for the precise manipulation of chemical reactions.
Collapse
Affiliation(s)
- Bingda Chen
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Zhongguancun North First Street 2, 100190 Beijing, P. R. China
- University of Chinese Academy of Sciences, Yuquan Road No. 19A, 100049 Beijing, P. R. China
| | - Feifei Qin
- Chair of Building Physics, Department of Mechanical and Process Engineering, ETH Zürich (Swiss Federal Institute of Technology in Zürich), Zürich 8092, Switzerland
| | - Meng Su
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Zhongguancun North First Street 2, 100190 Beijing, P. R. China
- University of Chinese Academy of Sciences, Yuquan Road No. 19A, 100049 Beijing, P. R. China
| | - Zeying Zhang
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Zhongguancun North First Street 2, 100190 Beijing, P. R. China
- University of Chinese Academy of Sciences, Yuquan Road No. 19A, 100049 Beijing, P. R. China
| | - Qi Pan
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Zhongguancun North First Street 2, 100190 Beijing, P. R. China
| | - Miaomiao Zou
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Zhongguancun North First Street 2, 100190 Beijing, P. R. China
- University of Chinese Academy of Sciences, Yuquan Road No. 19A, 100049 Beijing, P. R. China
| | - Xu Yang
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Zhongguancun North First Street 2, 100190 Beijing, P. R. China
| | - Sisi Chen
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Zhongguancun North First Street 2, 100190 Beijing, P. R. China
| | - Dominique Derome
- Department of Civil and Building Engineering, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Jan Carmeliet
- Chair of Building Physics, Department of Mechanical and Process Engineering, ETH Zürich (Swiss Federal Institute of Technology in Zürich), Zürich 8092, Switzerland
| | - Yanlin Song
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Zhongguancun North First Street 2, 100190 Beijing, P. R. China
- University of Chinese Academy of Sciences, Yuquan Road No. 19A, 100049 Beijing, P. R. China
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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
| |
Collapse
|
10
|
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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: 76] [Impact Index Per Article: 19.0] [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.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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: 33] [Impact Index Per Article: 8.3] [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.
Collapse
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
| |
Collapse
|
15
|
Abstract
One of the grand challenges in contemporary systems chemistry research is to mimic life-like functions using simple synthetic molecular networks. This is particularly true for systems that are out of chemical equilibrium and show complex dynamic behaviour, such as multi-stability, oscillations and chaos. We report here on thiodepsipeptide-based non-enzymatic networks propelled by reversible replication processes out of equilibrium, displaying bistability. Accordingly, we present quantitative analyses of the bistable behaviour, featuring a phase transition from the simple equilibration processes taking place in reversible dynamic chemistry into the bistable region. This behaviour is observed only when the system is continuously fueled by a reducing agent that keeps it far from equilibrium, and only when operating within a specifically defined parameter space. We propose that the development of biomimetic bistable systems will pave the way towards the study of more elaborate functions, such as information transfer and signalling.
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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: 17] [Impact Index Per Article: 3.4] [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.
Collapse
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
| |
Collapse
|
18
|
Affiliation(s)
- Meniz Altay
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Yigit Altay
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| |
Collapse
|
19
|
Semenov SN, Belding L, Cafferty BJ, Mousavi MP, Finogenova AM, Cruz RS, Skorb EV, Whitesides GM. Autocatalytic Cycles in a Copper-Catalyzed Azide–Alkyne Cycloaddition Reaction. J Am Chem Soc 2018; 140:10221-10232. [DOI: 10.1021/jacs.8b05048] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sergey N. Semenov
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Lee Belding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Brian J. Cafferty
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Maral P.S. Mousavi
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Anastasiia M. Finogenova
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Ricardo S. Cruz
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Ekaterina V. Skorb
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Kavli Institute for Bionano Inspired Science and Technology, School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
20
|
Altay M, Altay Y, Otto S. Parasitic Behavior of Self-Replicating Molecules. Angew Chem Int Ed Engl 2018; 57:10564-10568. [PMID: 29856109 DOI: 10.1002/anie.201804706] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/16/2022]
Abstract
Self-replication plays a central role in the origin of life and in strategies to synthesize life de novo. Studies on self-replication have focused mostly on isolated systems, while the dynamics of systems containing multiple replicators have received comparatively little attention. Yet most evolutionary scenarios involve the interplay between different replicators. Here we report the emergence of parasitic behavior in a system containing self-replicators derived from two subtly different building blocks 1 and 2. Replicators from 2 form readily through cross-catalysis by pre-existing replicators made from 1. Once formed, the new replicators consume the original replicators to which they owe their existence. These results resemble parasitic and predatory behavior that is normally associated with living systems and show how such lifelike behavior has its roots in relatively simple systems of self-replicating molecules.
Collapse
Affiliation(s)
- Meniz Altay
- 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
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| |
Collapse
|
21
|
Robertson CC, Mackenzie HW, Kosikova T, Philp D. An Environmentally Responsive Reciprocal Replicating Network. J Am Chem Soc 2018; 140:6832-6841. [DOI: 10.1021/jacs.7b13576] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Craig C. Robertson
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh St Andrews, Fife KY16 9ST, United Kingdom
| | - Harold W. Mackenzie
- 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
| | - Douglas Philp
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh St Andrews, Fife KY16 9ST, United Kingdom
| |
Collapse
|
22
|
Bánsági T, Taylor AF. Switches induced by quorum sensing in a model of enzyme-loaded microparticles. J R Soc Interface 2018. [PMID: 29514986 DOI: 10.1098/rsif.2017.0945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Quorum sensing refers to the ability of bacteria and other single-celled organisms to respond to changes in cell density or number with population-wide changes in behaviour. Here, simulations were performed to investigate quorum sensing in groups of diffusively coupled enzyme microparticles using a well-characterized autocatalytic reaction which raises the pH of the medium: hydrolysis of urea by urease. The enzyme urease is found in both plants and microorganisms, and has been widely exploited in engineering processes. We demonstrate how increases in group size can be used to achieve a sigmoidal switch in pH at high enzyme loading, oscillations in pH at intermediate enzyme loading and a bistable, hysteretic switch at low enzyme loading. Thus, quorum sensing can be exploited to obtain different types of response in the same system, depending on the enzyme concentration. The implications for microorganisms in colonies are discussed, and the results could help in the design of synthetic quorum sensing for biotechnology applications such as drug delivery.
Collapse
Affiliation(s)
- Tamás Bánsági
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Annette F Taylor
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| |
Collapse
|
23
|
Kosikova T, Philp D. Exploring the emergence of complexity using synthetic replicators. Chem Soc Rev 2018; 46:7274-7305. [PMID: 29099123 DOI: 10.1039/c7cs00123a] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.
Collapse
Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
| | | |
Collapse
|
24
|
Grzybowski BA, Fitzner K, Paczesny J, Granick S. From dynamic self-assembly to networked chemical systems. Chem Soc Rev 2018; 46:5647-5678. [PMID: 28703815 DOI: 10.1039/c7cs00089h] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although dynamic self-assembly, DySA, is a relatively new area of research, the past decade has brought numerous demonstrations of how various types of components - on scales from (macro)molecular to macroscopic - can be arranged into ordered structures thriving in non-equilibrium, steady states. At the same time, none of these dynamic assemblies has so far proven practically relevant, prompting questions about the field's prospects and ultimate objectives. The main thesis of this Review is that formation of dynamic assemblies cannot be an end in itself - instead, we should think more ambitiously of using such assemblies as control elements (reconfigurable catalysts, nanomachines, etc.) of larger, networked systems directing sequences of chemical reactions or assembly tasks. Such networked systems would be inspired by biology but intended to operate in environments and conditions incompatible with living matter (e.g., in organic solvents, elevated temperatures, etc.). To realize this vision, we need to start considering not only the interactions mediating dynamic self-assembly of individual components, but also how components of different types could coexist and communicate within larger, multicomponent ensembles. Along these lines, the review starts with the discussion of the conceptual foundations of self-assembly in equilibrium and non-equilibrium regimes. It discusses key examples of interactions and phenomena that can provide the basis for various DySA modalities (e.g., those driven by light, magnetic fields, flows, etc.). It then focuses on the recent examples where organization of components in steady states is coupled to other processes taking place in the system (catalysis, formation of dynamic supramolecular materials, control of chirality, etc.). With these examples of functional DySA, we then look forward and consider conditions that must be fulfilled to allow components of multiple types to coexist, function, and communicate with one another within the networked DySA systems of the future. As the closing examples show, such systems are already appearing heralding new opportunities - and, to be sure, new challenges - for DySA research.
Collapse
Affiliation(s)
- Bartosz A Grzybowski
- IBS Center for Soft and Living Matter, UNIST, UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 689-798, Republic of Korea.
| | | | | | | |
Collapse
|
25
|
Cullen W, Metherell AJ, Wragg AB, Taylor CGP, Williams NH, Ward MD. Catalysis in a Cationic Coordination Cage Using a Cavity-Bound Guest and Surface-Bound Anions: Inhibition, Activation, and Autocatalysis. J Am Chem Soc 2018; 140:2821-2828. [PMID: 29412665 DOI: 10.1021/jacs.7b11334] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Kemp elimination (reaction of benzisoxazole with base to give 2-cyanophenolate) is catalyzed in the cavity of a cubic M8L12 coordination cage because of a combination of (i) benzisoxazole binding in the cage cavity driven by the hydrophobic effect, and (ii) accumulation of hydroxide ions around the 16+ cage surface driven by ion-pairing. Here we show how reaction of the cavity-bound guest is modified by the presence of other anions which can also accumulate around the cage surface and displace hydroxide, inhibiting catalysis of the cage-based reaction. Addition of chloride or fluoride inhibits the reaction with hydroxide to the extent that a new autocatalytic pathway becomes apparent, resulting in a sigmoidal reaction profile. In this pathway the product 2-cyanophenolate itself accumulates around the cationic cage surface, acting as the base for the next reaction cycle. The affinity of different anions for the cage surface is therefore 2-cyanophenolate (generating autocatalysis) > chloride > fluoride (which both inhibit the reaction with hydroxide but cannot deprotonate the benzisoxazole guest) > hydroxide (default reaction pathway). The presence of this autocatalytic pathway demonstrates that a reaction of a cavity-bound guest can be induced with different anions around the cage surface in a controllable way; this was confirmed by adding different phenolates to the reaction, which accelerate the Kemp elimination to different extents depending on their basicity. This represents a significant step toward the goal of using the cage as a catalyst for bimolecular reactions between a cavity-bound guest and anions accumulated around the surface.
Collapse
Affiliation(s)
- William Cullen
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, U.K
| | | | - Ashley B Wragg
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, U.K
| | | | | | - Michael D Ward
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, U.K.,Department of Chemistry, University of Warwick , Coventry CV4 7AL, U.K
| |
Collapse
|
26
|
Artificial intelligence exploration of unstable protocells leads to predictable properties and discovery of collective behavior. Proc Natl Acad Sci U S A 2018; 115:885-890. [PMID: 29339510 DOI: 10.1073/pnas.1711089115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protocell models are used to investigate how cells might have first assembled on Earth. Some, like oil-in-water droplets, can be seemingly simple models, while able to exhibit complex and unpredictable behaviors. How such simple oil-in-water systems can come together to yield complex and life-like behaviors remains a key question. Herein, we illustrate how the combination of automated experimentation and image processing, physicochemical analysis, and machine learning allows significant advances to be made in understanding the driving forces behind oil-in-water droplet behaviors. Utilizing >7,000 experiments collected using an autonomous robotic platform, we illustrate how smart automation cannot only help with exploration, optimization, and discovery of new behaviors, but can also be core to developing fundamental understanding of such systems. Using this process, we were able to relate droplet formulation to behavior via predicted physical properties, and to identify and predict more occurrences of a rare collective droplet behavior, droplet swarming. Proton NMR spectroscopic and qualitative pH methods enabled us to better understand oil dissolution, chemical change, phase transitions, and droplet and aqueous phase flows, illustrating the utility of the combination of smart-automation and traditional analytical chemistry techniques. We further extended our study for the simultaneous exploration of both the oil and aqueous phases using a robotic platform. Overall, this work shows that the combination of chemistry, robotics, and artificial intelligence enables discovery, prediction, and mechanistic understanding in ways that no one approach could achieve alone.
Collapse
|
27
|
Sadownik JW, Kosikova T, Philp D. Generating System-Level Responses from a Network of Simple Synthetic Replicators. J Am Chem Soc 2017; 139:17565-17573. [PMID: 29087701 DOI: 10.1021/jacs.7b09735] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The creation of reaction networks capable of exhibiting responses that are properties of entire systems represents a significant challenge for the chemical sciences. The system-level behavior of a reaction network is linked intrinsically to its topology and the functional connections between its nodes. A simple network of chemical reactions constructed from four reagents, in which each reagent reacts with exactly two others, can exhibit up-regulation of two products even when only a single chemical reaction is addressed catalytically. We implement a system with this topology using two maleimides and two nitrones of different sizes-either short or long and each bearing complementary recognition sites-that react pairwise through 1,3-dipolar cycloaddition reactions to create a network of four length-segregated replicating templates. Comprehensive 1H NMR spectroscopy experiments unravel the network topology, confirming that, in isolation, three out of four templates self-replicate, with the shortest template exhibiting the highest efficiency. The strongest template effects within the network are the mutually cross-catalytic relationships between the two templates of intermediate size. The network topology is such that the addition of different preformed templates as instructions to a mixture of all starting materials elicits system-level behavior. Instruction with a single template up-regulates the formation of two templates in a predictable manner. These results demonstrate that the rules governing system-level behavior can be unraveled through the application of wholly synthetic networks with well-defined chemistries and interactions.
Collapse
Affiliation(s)
- Jan W Sadownik
- 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
| | - Douglas Philp
- School of Chemistry and EaStCHEM, University of St Andrews , North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| |
Collapse
|
28
|
Pogodaev AA, Wong ASY, Huck WTS. Photochemical Control over Oscillations in Chemical Reaction Networks. J Am Chem Soc 2017; 139:15296-15299. [PMID: 29040807 PMCID: PMC5668888 DOI: 10.1021/jacs.7b08109] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Systems chemistry
aims to emulate the functional behavior observed
in living systems by constructing chemical reaction networks (CRNs)
with well-defined dynamic properties. Future expansion of the complexity
of these systems would require external control to tune behavior and
temporal organization of such CRNs. In this work, we design and implement
a photolabile probe, which upon irradiation strengthens the negative
feedback loop of a CRN that produces oscillations of trypsin under
out-of-equilibrium conditions. By changing the timing and duration
of irradiation, we can tailor the temporal response of the network.
Collapse
Affiliation(s)
- Aleksandr A Pogodaev
- Institute for Molecules and Materials, Radboud University, Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Albert S Y Wong
- Institute for Molecules and Materials, Radboud University, Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
29
|
Altay Y, Tezcan M, Otto S. Emergence of a New Self-Replicator from a Dynamic Combinatorial Library Requires a Specific Pre-Existing Replicator. J Am Chem Soc 2017; 139:13612-13615. [PMID: 28910535 PMCID: PMC5632813 DOI: 10.1021/jacs.7b07346] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Our
knowledge regarding the early steps in the formation of evolvable
life and what constitutes the minimal molecular basis of life remains
far from complete. The recent emergence of systems chemistry reinvigorated
the investigation of systems of self-replicating molecules to address
these questions. Most of these studies focus on single replicators
and the effects of replicators on the emergence of other replicators
remains under-investigated. Here we show the cross-catalyzed emergence
of a novel self-replicator from a dynamic combinatorial library made
from a threonine containing peptide building block, which, by itself,
only forms trimers and tetramers that do not replicate. Upon seeding
of this library with different replicators of different macrocycle
size (hexamers and octamers), we observed the emergence of hexamer
replicator consisting of six units of the threonine peptide only when
it is seeded with an octamer replicator containing eight units of
a serine building block. These results reveal for the first time how
a new replicator can emerge in a process that relies critically on
the assistance by another replicator through cross-catalysis and that
replicator composition is history dependent.
Collapse
Affiliation(s)
- Yigit Altay
- Centre for Systems Chemistry, Stratingh Institute , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Meniz Tezcan
- Centre for Systems Chemistry, Stratingh Institute , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
30
|
Kosikova T, Philp D. A Critical Cross-Catalytic Relationship Determines the Outcome of Competition in a Replicator Network. J Am Chem Soc 2017; 139:12579-12590. [DOI: 10.1021/jacs.7b06270] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Douglas Philp
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| |
Collapse
|
31
|
Autonomous model protocell division driven by molecular replication. Nat Commun 2017; 8:237. [PMID: 28798300 PMCID: PMC5552811 DOI: 10.1038/s41467-017-00177-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/07/2017] [Indexed: 11/08/2022] Open
Abstract
The coupling of compartmentalisation with molecular replication is thought to be crucial for the emergence of the first evolvable chemical systems. Minimal artificial replicators have been designed based on molecular recognition, inspired by the template copying of DNA, but none yet have been coupled to compartmentalisation. Here, we present an oil-in-water droplet system comprising an amphiphilic imine dissolved in chloroform that catalyses its own formation by bringing together a hydrophilic and a hydrophobic precursor, which leads to repeated droplet division. We demonstrate that the presence of the amphiphilic replicator, by lowering the interfacial tension between droplets of the reaction mixture and the aqueous phase, causes them to divide. Periodic sampling by a droplet-robot demonstrates that the extent of fission is increased as the reaction progresses, producing more compartments with increased self-replication. This bridges a divide, showing how replication at the molecular level can be used to drive macroscale droplet fission.Coupling compartmentalisation and molecular replication is essential for the development of evolving chemical systems. Here the authors show an oil-in-water droplet containing a self-replicating amphiphilic imine that can undergo repeated droplet division.
Collapse
|
32
|
Duim H, Otto S. Towards open-ended evolution in self-replicating molecular systems. Beilstein J Org Chem 2017; 13:1189-1203. [PMID: 28694865 PMCID: PMC5496545 DOI: 10.3762/bjoc.13.118] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/18/2017] [Indexed: 01/24/2023] Open
Abstract
In this review we discuss systems of self-replicating molecules in the context of the origin of life and the synthesis of de novo life. One of the important aspects of life is the ability to reproduce and evolve continuously. In this review we consider some of the prerequisites for obtaining unbounded evolution of self-replicating molecules and describe some recent advances in this field. While evolution experiments involving self-replicating molecules have shown promising results, true open-ended evolution has not been realized so far. A full understanding of the requirements for open-ended evolution would provide a better understanding of how life could have emerged from molecular building blocks and what is needed to create a minimal form of life in the laboratory.
Collapse
Affiliation(s)
- Herman Duim
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
33
|
|
34
|
Kamonsutthipaijit N, Anderson HL. Template-directed synthesis of linear porphyrin oligomers: classical, Vernier and mutual Vernier. Chem Sci 2017; 8:2729-2740. [PMID: 28553508 PMCID: PMC5426366 DOI: 10.1039/c6sc05355f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/20/2017] [Indexed: 12/22/2022] Open
Abstract
We demonstrate a variety of template-directed strategies for preparing linear monodisperse butadiyne-linked porphyrin oligomers by Glaser–Hay coupling, based on the coordination of pyridine-substituted nickel(ii) porphyrins to zinc(ii) porphyrins.
Three different types of template-directed syntheses of linear porphyrin oligomers are presented. In the classical approach the product has the same number of binding sites as the template, whereas in Vernier reactions the product has the lowest common multiple of the numbers of binding sites in the template and the building block. Mutual Vernier templating is like Vernier templating except that both strands of the Vernier complex undergo coupling simultaneously, so that it becomes impossible to say which is the ‘template’ and which is the ‘building block’. The template-directed synthesis of monodisperse linear oligomers is more difficult than that of cyclic oligomers, because the products of linear templating have reactive ends. All three types of templating are demonstrated here, and used to prepare a nickel(ii) porphyrin dodecamer with 4-pyridyl substituents on all twelve porphyrin units. The stabilities and cooperativities of the double-strand complexes involved in these reactions were investigated by UV-vis-NIR titration. The four-rung ladder duplex has a stability constant of about 2 × 1018 M–1 in dichloromethane at 298 K.
Collapse
Affiliation(s)
| | - Harry L Anderson
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , Oxford OX1 3TA , UK .
| |
Collapse
|
35
|
Abstract
A series of exciting phenomena that can occur in supramolecular systems away from equilibrium are reviewed.
Collapse
Affiliation(s)
- Gonen Ashkenasy
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer Sheva
- Israel
| | | | - Sijbren Otto
- Centre for Systems Chemistry
- Stratingh Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Annette F. Taylor
- Chemical and Biological Engineering
- University of Sheffield
- Sheffield S1 3JD
- UK
| |
Collapse
|
36
|
Tanaka H, Zeravcic Z, Brenner MP. Mutation at Expanding Front of Self-Replicating Colloidal Clusters. PHYSICAL REVIEW LETTERS 2016; 117:238004. [PMID: 27982625 DOI: 10.1103/physrevlett.117.238004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 06/06/2023]
Abstract
We construct a scheme for self-replicating square clusters of particles in two spatial dimensions, and validate it with computer simulations in a finite-temperature heat bath. We find that the self-replication reactions propagate through the bath in the form of Fisher waves. Our model reflects existing colloidal systems, but is simple enough to allow simulation of many generations and thereby the first study of evolutionary dynamics in an artificial system. By introducing spatially localized mutations in the replication rules, we show that the mutated cluster population can survive and spread with the expanding front in circular sectors of the colony.
Collapse
Affiliation(s)
- Hidenori Tanaka
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Zorana Zeravcic
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Soft matter and chemistry laboratory, ESPCI PSL Research University, 75005 Paris, France
| | - Michael P Brenner
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|