Light‐Induced Peptide Replication Controls Logic Operations in Small Networks

Dadon, Zehavit; Samiappan, Manickasundaram; Safranchik, Eliya Y.; Ashkenasy, Gonen

doi:10.1002/chem.201001488

Cited by 51 publications

(41 citation statements)

References 46 publications

(38 reference statements)

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“…The light-induced replication process was further studied as a means to affect competition experiments within ternary networks (Figure 2.8) [74]. We expanded this system to a network by synthesizing two new nucleophilic fragments, N aa and N z , which compete together with N for ligation to E as a common reactant.…”

Section: Light-induced Logic Operationsmentioning

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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Section: Light-induced Logic Operationsmentioning

confidence: 99%

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

Dadon

Samiappan

Wagner

et al. 2012

Biomolecular Information Processing

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“…[1][2][3][4][5] The programmable hybridization of nucleic acid provides a framework to design nanoscale assemblies. [6][7][8][9][10][11][12][13][14][15] Peptide nucleic acid (PNA) provides excellent control properties over a self-assembled system including better stability than DNA duplexes, even for short sequences, and higher mismatch sensitivity. Moreover, its neutral net charge allows for tuning the structural and electrostatic characteristics through using other amino acids instead of glycine.…”

Section: Introductionmentioning

confidence: 99%

Controlled Assembly of SNAP–PNA–Fluorophore Systems on DNA Templates To Produce Fluorescence Resonance Energy Transfer

Gholami

Hanley

2014

Bioconjugate Chem.

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The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (

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“…These peptides were made of 25-40 amino acids and served as templates for substrate binding and enhanced condensation. We have shown recently that the utility of these molecules can be expanded within small molecular networks, in which replication is also a product of template-assisted cross-catalysis (Ashkenasy et al 2004;Dadon et al 2008), and furthermore that the network connectivity is sensitive to chemical and light changes in the environment (Dadon et al 2010;Samiappan et al 2011). Since the formation of long coiled coil peptides under prebiotic conditions is rather unlikely, it has been postulated that shorter peptides with simpler sequences may serve as templates for self-replication, provided that they arrange into unique well defined structures.…”

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confidence: 99%

Self-assembly and Self-replication of Short Amphiphilic β-sheet Peptides

Bourbo

Matmor

Shtelman

et al. 2011

Orig Life Evol Biosph

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Most self-replicating peptide systems are made of α-helix forming sequences. However, it has been postulated that shorter and simpler peptides may also serve as templates for replication when arranged into well-defined structures. We describe here the design and characterization of new peptides that form soluble β-sheet aggregates that serve to significantly accelerate their ligation and self-replication. We then discuss the relevance of these phenomena to early molecular evolution, in light of additional functionality associated with β-sheet assemblies.

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Light‐Induced Peptide Replication Controls Logic Operations in Small Networks

Cited by 51 publications

References 46 publications

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

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

Controlled Assembly of SNAP–PNA–Fluorophore Systems on DNA Templates To Produce Fluorescence Resonance Energy Transfer

Self-assembly and Self-replication of Short Amphiphilic β-sheet Peptides

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