Autocatalysis and the Generation of Self-Replicating Systems.

Wintner, Edward A.; Rebek, Julius; Pilawa, B.; Jensen, Georg W.; Møller, Inge L.; Nielsen, Ruby I.; Olsen, Carl Erik; Rosendahl, Connie N.; Haugg, Monika; Trabesinger-Rüf, Nathalie; Weinhold, Elmar G.

doi:10.3891/acta.chem.scand.50-0469

Cited by 66 publications

(34 citation statements)

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“…Over the years chemists have designed and characterized minimal self-replication systems made of nucleic acids (DNA [17][18][19][20] and RNA [21] ), peptides, [22][23][24][25] mixed protein-nucleic acids, [26] and small organic molecules. [27][28][29][30] The catalytic principles of Abstract: A mixture of molecules can be regarded as a network if all the molecular components participate in some kind of interaction with other molecules-either physical or functional interactions. Template-assisted ligation reactions that direct replication processes can serve as the functional elements that connect two members of a chemical network.…”

Section: Introductionmentioning

confidence: 99%

Systems Chemistry: Logic Gates, Arithmetic Units, and Network Motifs in Small Networks

Wagner

Ashkenasy

2009

Chemistry A European J

104

106

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A mixture of molecules can be regarded as a network if all the molecular components participate in some kind of interaction with other molecules--either physical or functional interactions. Template-assisted ligation reactions that direct replication processes can serve as the functional elements that connect two members of a chemical network. In such a process, the template does not necessarily catalyze its own formation, but rather the formation of another molecule, which in turn can operate as a template for reactions within the network medium. It was postulated that even networks made up of small numbers of molecules possess a wealth of molecular information sufficient to perform rather complex behavior. To probe this assumption, we have constructed virtual arrays consisting of three replicating molecules, in which dimer templates are capable of catalyzing reactants to form additional templates. By using realistic parameters from peptides or DNA replication experiments, we simulate the construction of various functional motifs within the networks. Specifically, we have designed and implemented each of the three-element Boolean logic gates, and show how these networks are assembled from four basic "building blocks". We also show how the catalytic pathways can be wired together to perform more complex arithmetic units and network motifs, such as the half adder and half subtractor computational modules, and the coherent feed-forward loop network motifs under different sets of parameters. As in previous studies of chemical networks, some of the systems described display behavior that would be difficult to predict without the numerical simulations. Furthermore, the simulations reveal trends and characteristics that should be useful as "recipes" for future design of experimental functional motifs and for potential integration into modular circuits and molecular computation devices.

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Section: Introductionmentioning

confidence: 99%

Systems Chemistry: Logic Gates, Arithmetic Units, and Network Motifs in Small Networks

Wagner

Ashkenasy

2009

Chemistry A European J

104

106

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“…On the other hand, it has been recognized by some that the template-directing function is actually a special kind of catalysis (Inoue and Orgel 1983;Bag and Von Kiedrowski 1996;Wintner and Rebek 1996;Robertson et al 2000), though there was little discussion as to where the specialty lies. This may cause confusion.…”

Section: Template-directing Function: a Type Of Direction-favoring Camentioning

confidence: 99%

“…And what is the earliest form of self-replication in the origin of life? To address such questions, much effort has been focused on molecular self-replication (Joyce 1987;Orgel 1992;Bag and Von Kiedrowski 1996;Wintner and Rebek 1996;Robertson et al 2000), compartment-associated self-replication (Bachmann et al 1992;Szostak et al 2001;Oberholzer and Luisi 2002;Hanczyc et al 2003;Rasmussen et al 2004), and the role of metabolism (Shapiro 2000;Pross 2004;Anet 2004).…”

Section: Introductionmentioning

confidence: 99%

Self-replication: spelling it out in a chemical background

Chen

Zhang

et al. 2010

Theory Biosci.

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Self-replication, an important concept abstracted from reproduction, the key feature of life, remains vague in definition and lacking in clear interpretation in terms of its chemical mechanism. Mentioned frequently in discussions concerning the essence of life and its origin, the vague concept has caused a lot of uncertain statements, confusable references, and malposed debates, and has seriously held back efforts in this field. In this article, we try to improve the situation by a conceptual analysis in a more fundamental and clearer background. Self-replication in the substantial world could not mean anything but that "an entity favors the production of its own." The major chemical mechanism for such favoring is catalysis, which can be classified into speed- and direction-favoring types (the template-directing function is actually a type of direction-favoring catalysis). Molecular self-replication could be based on autocatalysis or self-metabolism; the self-replication of a complex entity could be based on autocatalytic and/or self-metabolic sets, and should involve a mechanism of self-division. This conceptual clarification sheds light on the dim areas concerning the essence of life and its origin.

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“…These can potentially be used as controllable tools for studying systems behavior. Toward this aim, different research groups have designed and characterized dynamic combinatorial libraries [32][33][34][35][36][37][38] and replication networks made of nucleic acids (DNA and RNA) [39][40][41][42], peptides [43][44][45][46], and small organic molecules [47][48][49][50]. …”

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confidence: 99%

Peptide‐Based Computation: Switches, Gates, and Simple Arithmetic

Dadon

Samiappan

Wagner

et al. 2012

Biomolecular Information Processing

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IntroductionBoolean algebra deals with the ''0'' and ''1'' values, utilized as presentations of false and true statements, respectively. The Boolean logic thus provides simple and concise means to describe the output of chemical processes that depend on more than one factor. Historically, the study of chemical logic gates has started with the design of small organic molecules that perform the desired functions when triggered by simple entities such as protons, hydroxyls, or metal ions [1,2]. Since the first demonstration by de Silva, many different chemical logic systems were developed, including metal-organic complexes, peptides, and DNA. The response of these systems to additional chemical triggers, as well as to electrochemical and light triggers, has been demonstrated quite frequently [3][4][5][6][7]. Interestingly, many of the recently described logic operations, and also the more complex arithmetic units, were designed based on pursuing dynamic processes instead of simple binding to one operating molecule [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]. Beyond the basic demonstrations, scientists were able to exploit their new gates as smart devices that control various applications such as catalysis, sensing analytes, drug delivery, and even in vivo transcription. In a related line of research, modules of large biochemical systems have also been described to function as Boolean entities, in studies that used the ''top-down'' screening for such operations [25][26][27][28][29][30][31]. This chapter describes primarily our own research, in which we use synthetic networks made of small proteins as tools for performing chemical computations. We do so by practicing both the bottom-up approach, using individual molecules as gates, and the top-down approach, for which the entire molecular network is used to perform the desired functionality.Biology can serve as inspiration and can provide chemists with the design principles for engineering networks of interacting and replicating molecules. These can potentially be used as controllable tools for studying systems behavior. Toward this aim, different research groups have designed and characterized dynamic combinatorial libraries [32][33][34][35][36][37][38] and replication networks made of nucleic acids (DNA and RNA) [39][40][41][42], peptides [43][44][45][46], and small organic molecules [47][48][49][50].

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Autocatalysis and the Generation of Self-Replicating Systems.

Cited by 66 publications

References 0 publications

Systems Chemistry: Logic Gates, Arithmetic Units, and Network Motifs in Small Networks

Systems Chemistry: Logic Gates, Arithmetic Units, and Network Motifs in Small Networks

Self-replication: spelling it out in a chemical background

Peptide‐Based Computation: Switches, Gates, and Simple Arithmetic

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