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Equilibrium and Non-equilibrium Reaction Schemes for Prebiotic Polymerization of Ribonucleotides 核糖核苷酸前生物聚合的平衡和非平衡反应方案
ChemSystemsChem Pub Date : 2023-09-21 DOI: 10.1002/syst.202300033
Varun Kitson, Quentin Sanders, Dr. Avinash V. Dass, Prof. Paul G. Higgs
{"title":"Equilibrium and Non-equilibrium Reaction Schemes for Prebiotic Polymerization of Ribonucleotides","authors":"Varun Kitson,&nbsp;Quentin Sanders,&nbsp;Dr. Avinash V. Dass,&nbsp;Prof. Paul G. Higgs","doi":"10.1002/syst.202300033","DOIUrl":"10.1002/syst.202300033","url":null,"abstract":"<p>The RNA World theory for the origin of life requires polymers to be generated initially by abiotic reactions. Experiments have studied polymerization of 5′-monophosphates, 2′,3′-cyclic phosphates, and 5′-triphosphates. We consider theoretical models of polymerization in solution illustrating the differences between these cases. We consider (i) a basic model where all monomers undergo reversible joining and breaking; (ii) a model where 2′,3′-cyclic phosphates can join, and breaking regenerates the cyclic phosphate; (iii) a model where 5′-triphosphates can join irreversibly, in addition to the joining and breaking of 2′,3′-cyclic phosphates. In cases (i) and (ii) there is an equilibrium steady state with balance between making and breaking bonds. In case (iii) there is a circular reaction flux in which monomers are activated by an external phosphate source, activated monomers form polymers, and polymers break to release non-activated monomers. The mean length can be calculated as a function of concentration. In case (iii), the mean length switches from a low-concentration regime controlled by the 5′-triphosphates to a high-concentration regime controlled by the 2′,3′-cyclic phosphates. The circular reaction flux is reminiscent of a metabolism. If formation of 5’-triphosphates was already in place for RNA synthesis, ATP could subsequently been coopted for metabolism.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135944293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assembly of Multi-Compartment Cell Mimics by Droplet-Based Microfluidics 基于微流控的多室细胞模拟装配
ChemSystemsChem Pub Date : 2023-09-08 DOI: 10.1002/syst.202300034
Tsvetomir Ivanov, Dr. Shoupeng Cao, Dr. Thao P. Doan-Nguyen, Heloísa Bremm Madalosso, Dr. Lucas Caire da Silva, Prof. Dr. Katharina Landfester
{"title":"Assembly of Multi-Compartment Cell Mimics by Droplet-Based Microfluidics","authors":"Tsvetomir Ivanov,&nbsp;Dr. Shoupeng Cao,&nbsp;Dr. Thao P. Doan-Nguyen,&nbsp;Heloísa Bremm Madalosso,&nbsp;Dr. Lucas Caire da Silva,&nbsp;Prof. Dr. Katharina Landfester","doi":"10.1002/syst.202300034","DOIUrl":"https://doi.org/10.1002/syst.202300034","url":null,"abstract":"<p>In recent years, there has been a growing interest in multi-compartment systems as a means of developing materials that mimic the structure and function of biological cells. These hierarchical systems, including artificial cells and cell-like reactors, can efficiently perform biochemical tasks by exploiting compartmentalization inspired by biological systems. However, the bottom-up design of cell mimics presents significant challenges due to the need for precise and efficient assembly of components. This short review examines recent advances in droplet-based microfluidics (DBM), which has emerged as a powerful technique for creating cell-like systems with multi-compartment architectures, precise composition, and biomimetic functionality. DBM has proven to be a reliable method for generating populations of cell-mimics with a compartment-in-compartment structure, some of which have adaptable properties that resemble the dynamic properties of natural cells. Notable examples will be discussed to illustrate how droplet-based microfluidics provides a versatile approach to create, manipulate, and study cell-mimics.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"109165941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Front Cover: Elucidating the Mechanism of Freeze-Thaw Driven Content Mixing between Protocells (ChemSystemsChem 5/2023) 封面：阐明冻融驱动的原细胞之间内容物混合的机制（ChemSystemsChem5/2023）
ChemSystemsChem Pub Date : 2023-07-25 DOI: 10.1002/syst.202300036
Benedikt Peter, Prof. Dr. Petra Schwille
{"title":"Front Cover: Elucidating the Mechanism of Freeze-Thaw Driven Content Mixing between Protocells (ChemSystemsChem 5/2023)","authors":"Benedikt Peter,&nbsp;Prof. Dr. Petra Schwille","doi":"10.1002/syst.202300036","DOIUrl":"https://doi.org/10.1002/syst.202300036","url":null,"abstract":"<p><b>The Front Cover</b> illustrates the exchange of genetic material between model protocells through cycles of freezing and thawing. Freeze-thaw cycles as prebiotic environmental driver induce a transient increase in membrane permeability enabling the lateral transfer of genetic information in a population of primitive protocells. More information can be found in the Research Article by Benedikt Peter and Petra Schwille.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50143919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Elucidating the Mechanism of Freeze-Thaw Driven Content Mixing between Protocells 阐明冻融驱动的原细胞间内容物混合的机制
ChemSystemsChem Pub Date : 2023-07-25 DOI: 10.1002/syst.202300035
Benedikt Peter, Prof. Dr. Petra Schwille
{"title":"Elucidating the Mechanism of Freeze-Thaw Driven Content Mixing between Protocells","authors":"Benedikt Peter,&nbsp;Prof. Dr. Petra Schwille","doi":"10.1002/syst.202300035","DOIUrl":"https://doi.org/10.1002/syst.202300035","url":null,"abstract":"<p>The front cover artwork is provided by the Schwille group from the Max Planck Institute of Biochemistry in Martinsried. The image shows the dissemination of genetic material in a population of primitive protocells during freeze-thaw induced periods of membrane permeability. Read the full text of the Research Article at 10.1002/syst.202300008.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50143918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bidirectional Communication between Droplet Interface Bilayers Driven by Cell-Free Quorum Sensing Gene Circuits** 由无细胞群体感应基因电路驱动的液滴界面双层之间的双向通信
ChemSystemsChem Pub Date : 2023-07-17 DOI: 10.1002/syst.202300029
Dr. David T. Gonzales, Surased Suraritdechachai, Dr. Christoph Zechner, Dr. T.-Y. Dora Tang
{"title":"Bidirectional Communication between Droplet Interface Bilayers Driven by Cell-Free Quorum Sensing Gene Circuits**","authors":"Dr. David T. Gonzales,&nbsp;Surased Suraritdechachai,&nbsp;Dr. Christoph Zechner,&nbsp;Dr. T.-Y. Dora Tang","doi":"10.1002/syst.202300029","DOIUrl":"10.1002/syst.202300029","url":null,"abstract":"<p>Building synthetic multicellular systems using non-living molecular components is a grand challenge in the field of bottom-up synthetic biology. Towards this goal, a diverse range of chemistries have been developed to provide mechanisms of intercellular communication and methods to assemble multicellular compartments. However, building bottom-up synthetic multicellular systems is still challenging because it requires the integration of intercellular reaction networks with compatible cellular compartment properties. In this study, we encapsulated cell-free expression systems (CFES) expressing two quorum sensing genetic circuits into droplet interface bilayer (DIB) synthetic cells to demonstrate bidirectional communication. We further develop a method of generating custom DIB multicellular structures by acoustic liquid handling to automatically dispense the CFES droplets and show the potential for multiplexing compartmentalized gene circuits for generating heterogeneous populations of cells. Our work provides a step towards building more complex multicellular systems with intercellular communication from the bottom-up to study and experimentally model biological multiscalar processes.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42919189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Peptide and Peptidomimetic Assemblies in Dynamic Combinatorial Chemistry 动态组合化学中的肽和拟肽组装体
ChemSystemsChem Pub Date : 2023-07-07 DOI: 10.1002/syst.202300011
Ashmi Rodrigues, Dr. Lou Rocard, Dr. Roba Moumné
{"title":"Peptide and Peptidomimetic Assemblies in Dynamic Combinatorial Chemistry","authors":"Ashmi Rodrigues,&nbsp;Dr. Lou Rocard,&nbsp;Dr. Roba Moumné","doi":"10.1002/syst.202300011","DOIUrl":"10.1002/syst.202300011","url":null,"abstract":"<p>A strong revival of interest has been dedicated to peptides over the last few years, in different fields including drug discovery, biosensing and material sciences. The use of dynamic covalent chemistry has allowed the development of self-adaptative peptides or peptidomimetics, responsive to their environment. The development of methods allowing the building, screening or deconvolution of libraries of peptides is a highly active research area and dynamic combinatorial chemistry represents an innovative and underexploited method in this field. This Review gives an overview of the use of dynamic covalent chemistry as a tool to produce peptides or peptidomimetics, with particular attention to applications in dynamic combinatorial chemistry.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41504341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Constitutionally Dynamic Cage Acts as a Convertible and Adaptable Information Manager in Supramolecular Logic 构造动态笼是超分子逻辑中可转换自适应的信息管理器
ChemSystemsChem Pub Date : 2023-07-05 DOI: 10.1002/syst.202300009
Vishnu Verman Rajasekaran, Sohom Kundu, Debabrata Mondal, Prof. Dr. Michael Schmittel
{"title":"A Constitutionally Dynamic Cage Acts as a Convertible and Adaptable Information Manager in Supramolecular Logic","authors":"Vishnu Verman Rajasekaran,&nbsp;Sohom Kundu,&nbsp;Debabrata Mondal,&nbsp;Prof. Dr. Michael Schmittel","doi":"10.1002/syst.202300009","DOIUrl":"10.1002/syst.202300009","url":null,"abstract":"<p>A three-component molecular ensemble consisting of the constitutionally dynamic cage <b>1</b>, rotaxane <b>2</b> and luminophore <b>3</b> acts as a signal transducer which assimilates three input signals, i. e., Zn<sup>2+</sup>, H<sup>+</sup>, and Cu<sup>+</sup>, to perform individual logic operations (e. g. a 3-input NOR gate with catalytic output, 3-input AND gate with optical output) and operates as an unconventional 3-input demultiplexer.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41823549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Emergence of ATP- and GTP-Binding Aptamers from Single RNA Sequences by Error-Prone Replication and Selection** 通过易错复制和选择从单个RNA序列中产生ATP和GTP结合适体
ChemSystemsChem Pub Date : 2023-06-05 DOI: 10.1002/syst.202300006
Dr. Falk Wachowius, Dr. Benjamin T. Porebski, Dr. Christopher M. Johnson, Dr. Philipp Holliger
{"title":"Emergence of ATP- and GTP-Binding Aptamers from Single RNA Sequences by Error-Prone Replication and Selection**","authors":"Dr. Falk Wachowius,&nbsp;Dr. Benjamin T. Porebski,&nbsp;Dr. Christopher M. Johnson,&nbsp;Dr. Philipp Holliger","doi":"10.1002/syst.202300006","DOIUrl":"10.1002/syst.202300006","url":null,"abstract":"<p>The spontaneous emergence of function from diverse RNA sequence pools is widely considered an important transition in the origin of life. Here we show that diverse sequence pools are not a prerequisite for the emergence of function. Starting five independent selection experiments each from a single RNA seed sequence - comprising a central homopolymeric poly-A (or poly-U) segment flanked by different conserved primer binding sites - we observe transformation (continuous drift) of the seeds into low diversity sequence pools by mutation, truncation and recombination without ever reaching that of a random pool even after 24 rounds. Upon continuous error prone replication and selection for ATP binding we isolate specific ATP- or GTP-binding aptamers with low micromolar affinities. Our results have implications for early RNA evolution in the light of the high mutation rates associated with both non-enzymatic and enzymatic prebiotic RNA replication.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46517822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Influence of Silicate Rock Glass Compositions on the Efficacy of Prebiotic RNA Polymerization Reactions: The Case of 3’,5’ Cyclic Guanosine Monophosphate 硅酸盐岩石玻璃组分对益生元RNA聚合反应效能的影响:以3′，5′环单磷酸鸟苷为例
ChemSystemsChem Pub Date : 2023-05-22 DOI: 10.1002/syst.202300016
Dr. Judit E. Šponer, Dr. Jaroslav Kloužek, Dr. Jakub Výravský, Sreekar Wunnava, Prof. Dr. Bettina Scheu, Prof. Dr. Dieter Braun, Prof. Dr. Stephen J. Mojzsis, Dr. Jan Palacký, Prof. Michaela Vorlíčková, Prof. Jiří Šponer, Dr. Roman Matyášek, Dr. Aleš Kovařík
{"title":"Influence of Silicate Rock Glass Compositions on the Efficacy of Prebiotic RNA Polymerization Reactions: The Case of 3’,5’ Cyclic Guanosine Monophosphate","authors":"Dr. Judit E. Šponer,&nbsp;Dr. Jaroslav Kloužek,&nbsp;Dr. Jakub Výravský,&nbsp;Sreekar Wunnava,&nbsp;Prof. Dr. Bettina Scheu,&nbsp;Prof. Dr. Dieter Braun,&nbsp;Prof. Dr. Stephen J. Mojzsis,&nbsp;Dr. Jan Palacký,&nbsp;Prof. Michaela Vorlíčková,&nbsp;Prof. Jiří Šponer,&nbsp;Dr. Roman Matyášek,&nbsp;Dr. Aleš Kovařík","doi":"10.1002/syst.202300016","DOIUrl":"10.1002/syst.202300016","url":null,"abstract":"<p>Silicate glasses are ubiquitous on terrestrial planets wherever molten rock – generated by volcanism or impacts – is quenched by air or water. Hence, they provided ready and abundant reactive solid surfaces for prebiotic chemistry on the early Earth. Here, we show that rock glass composition determines basicity, which in turn modulates the outcome of prebiotic synthetic processes such as the polymerization of 3’, 5’ cyclic guanosine monophosphate.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46268418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Front Cover: Carbodiimide-Fueled Assembly of π-Conjugated Peptides Regulated by Electrostatic Interactions (ChemSystemsChem 4/2023) 封面：静电相互作用调节的π-共轭肽的碳二亚胺燃料组装（ChemSystemsChem4/2023）
ChemSystemsChem Pub Date : 2023-05-16 DOI: 10.1002/syst.202300025
Dr. Ze-Fan Yao, Yuyao Kuang, Phillip Kohl, Dr. Youli Li, Prof. Dr. Herdeline Ann M. Ardoña
{"title":"Front Cover: Carbodiimide-Fueled Assembly of π-Conjugated Peptides Regulated by Electrostatic Interactions (ChemSystemsChem 4/2023)","authors":"Dr. Ze-Fan Yao,&nbsp;Yuyao Kuang,&nbsp;Phillip Kohl,&nbsp;Dr. Youli Li,&nbsp;Prof. Dr. Herdeline Ann M. Ardoña","doi":"10.1002/syst.202300025","DOIUrl":"https://doi.org/10.1002/syst.202300025","url":null,"abstract":"<p><b>The Front Cover</b> depicts a workflow for the supramolecular assembly-disassembly cycle of peptidic monomers bearing π-conjugated units. Through a carbodiimide-fueled approach, transformation of the peptide moieties instructs the monomers to self-assemble, yet still be responsive to thermal-assisted and hydrolysis-induced disassembly. Cover design by ScienceBrush. More information can be found in the Research Article by Herdeline Ann M. Ardoña and co-workers.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202300025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50135355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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