1
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Liu K, Blokhuis A, van Ewijk C, Kiani A, Wu J, Roos WH, Otto S. Light-driven eco-evolutionary dynamics in a synthetic replicator system. Nat Chem 2024; 16:79-88. [PMID: 37653230 DOI: 10.1038/s41557-023-01301-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Darwinian evolution involves the inheritance and selection of variations in reproducing entities. Selection can be based on, among others, interactions with the environment. Conversely, the replicating entities can also affect their environment generating a reciprocal feedback on evolutionary dynamics. The onset of such eco-evolutionary dynamics marks a stepping stone in the transition from chemistry to biology. Yet the bottom-up creation of a molecular system that exhibits eco-evolutionary dynamics has remained elusive. Here we describe the onset of such dynamics in a minimal system containing two synthetic self-replicators. The replicators are capable of binding and activating a co-factor, enabling them to change the oxidation state of their environment through photoredox catalysis. The replicator distribution adapts to this change and, depending on light intensity, one or the other replicator becomes dominant. This study shows how behaviour analogous to eco-evolutionary dynamics-which until now has been restricted to biology-can be created using an artificial minimal replicator system.
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Affiliation(s)
- Kai Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Alex Blokhuis
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Chris van Ewijk
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Armin Kiani
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Juntian Wu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands.
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2
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Dev D, Wagner N, Pramanik B, Sharma B, Maity I, Cohen-Luria R, Peacock-Lopez E, Ashkenasy G. A Peptide-Based Oscillator. J Am Chem Soc 2023; 145:26279-26286. [PMID: 37984498 DOI: 10.1021/jacs.3c09377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Living organisms are replete with rhythmic and oscillatory behavior at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recent studies of synthetic oscillators that mimic such functions have shown decayed cycles in batch-mode reactions or sustained oscillatory kinetics under flow conditions. Considering the hypothesized functionality of peptides in early chemical evolution and their central role in current bio-nanotechnology, we now reveal a peptide-based oscillator. Oscillatory behavior was achieved by coupling coiled-coil-based replication processes as positive feedback to controlled initiation and inhibition pathways in a continuously stirred tank reactor (CSTR). Our results stress that assembly into the supramolecular structure and specific interactions with the replication substrates are crucial for oscillations. The replication-inhibition processes were first studied in batch mode, which produced a single damped cycle. Thereafter, combined experimental and theoretical characterization of the replication process in a CSTR under different flow and environmental (pH, redox) conditions demonstrated reasonably sustained oscillations. We propose that studies in this direction might pave the way to the design of robust oscillation networks that mimic the autonomous behavior of proteins in cells (e.g., in the cyanobacterial circadian clock) and hence hint at feasible pathways that accelerated the transition from simple peptides to extant enzymes.
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Affiliation(s)
- Dharm Dev
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bapan Pramanik
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bhawna Sharma
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Centre for Nano and Material Sciences, Jain Global Campus, Bangalore, Karnataka 560070, India
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Enrique Peacock-Lopez
- Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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3
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Glionna C, Kumar V, Le Saux G, Pramanik B, Wagner N, Cohen-Luria R, Ashkenasy G, Ashkenasy N. Dynamic Surface Layer Coiled Coil Proteins Processing Analog-to-Digital Information. J Am Chem Soc 2021; 143:17441-17451. [PMID: 34652148 DOI: 10.1021/jacs.1c06356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Surface layer proteins perform multiple functions in prokaryotic cells, including cellular defense, cell-shape maintenance, and regulation of import and export of materials. However, mimicking the complex and dynamic behavior of such two-dimensional biochemical systems is challenging, and hence research has so far focused mainly on the design and manipulation of the structure and functionality of protein assemblies in solution. Motivated by the new opportunities that dynamic surface layer proteins may offer for modern technology, we herein demonstrate that immobilization of coiled coil proteins onto an inorganic surface facilitates complex behavior, manifested by reversible chemical reactions that can be rapidly monitored as digital surface readouts. Using multiple chemical triggers as inputs and several surface characteristics as outputs, we can realize reversible switching and logic gate operations that are read in parallel. Moreover, using the same coiled coil protein monolayers for derivatization of nanopores drilled into silicon nitride membranes facilitates control over ion and mass transport through the pores, thereby expanding the applicability of the dynamic coiled coil system for contemporary stochastic biosensing applications.
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Affiliation(s)
- Chiara Glionna
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Vinod Kumar
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Guillaume Le Saux
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bapan Pramanik
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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4
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Walther A. Viewpoint: From Responsive to Adaptive and Interactive Materials and Materials Systems: A Roadmap. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905111. [PMID: 31762134 PMCID: PMC7612550 DOI: 10.1002/adma.201905111] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/13/2019] [Indexed: 05/17/2023]
Abstract
Soft matter systems and materials are moving toward adaptive and interactive behavior, which holds outstanding promise to make the next generation of intelligent soft materials systems inspired from the dynamics and behavior of living systems. But what is an adaptive material? What is an interactive material? How should classical responsiveness or smart materials be delineated? At present, the literature lacks a comprehensive discussion on these topics, which is however of profound importance in order to identify landmark advances, keep a correct and noninflating terminology, and most importantly educate young scientists going into this direction. By comparing different levels of complex behavior in biological systems, this Viewpoint strives to give some definition of the various different materials systems characteristics. In particular, the importance of thinking in the direction of training and learning materials, and metabolic or behavioral materials is highlighted, as well as communication and information-processing systems. This Viewpoint aims to also serve as a switchboard to further connect the important fields of systems chemistry, synthetic biology, supramolecular chemistry and nano- and microfabrication/3D printing with advanced soft materials research. A convergence of these disciplines will be at the heart of empowering future adaptive and interactive materials systems with increasingly complex and emergent life-like behavior.
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Affiliation(s)
- Andreas Walther
- A3BMS Lab-Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104, Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Albertstr. 19, 79104, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110, Freiburg, Germany
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5
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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6
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Wagner N, Hochberg D, Peacock-Lopez E, Maity I, Ashkenasy G. Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior. Life (Basel) 2019; 9:life9020045. [PMID: 31163645 PMCID: PMC6617095 DOI: 10.3390/life9020045] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 12/05/2022] Open
Abstract
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent to a steady state. In this paper we review the properties of these simple replicating networks, and show, via four working models, how even though closed systems exhibit a wide range of emergent phenomena, many of the more interesting phenomena leading to complexification and emergence indeed require open systems.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra Ajalvir Km. 4, 28850 Torrejón de Ardoz, Madrid, Spain.
| | | | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
- Present address: Institute for Macromolecular Chemistry, Albert Ludwigs University of Freiburg, D-79104 Freiburg, Germany.
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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7
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Zhang X, Chen L, Lim KH, Gonuguntla S, Lim KW, Pranantyo D, Yong WP, Yam WJT, Low Z, Teo WJ, Nien HP, Loh QW, Soh S. The Pathway to Intelligence: Using Stimuli-Responsive Materials as Building Blocks for Constructing Smart and Functional Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1804540. [PMID: 30624820 DOI: 10.1002/adma.201804540] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/09/2018] [Indexed: 05/22/2023]
Abstract
Systems that are intelligent have the ability to sense their surroundings, analyze, and respond accordingly. In nature, many biological systems are considered intelligent (e.g., humans, animals, and cells). For man-made systems, artificial intelligence is achieved by massively sophisticated electronic machines (e.g., computers and robots operated by advanced algorithms). On the other hand, freestanding materials (i.e., not tethered to a power supply) are usually passive and static. Hence, herein, the question is asked: can materials be fabricated so that they are intelligent? One promising approach is to use stimuli-responsive materials; these "smart" materials use the energy supplied by a stimulus available from the surrounding for performing a corresponding action. After decades of research, many interesting stimuli-responsive materials that can sense and perform smart functions have been developed. Classes of functions discussed include practical functions (e.g., targeting and motion), regulatory functions (e.g., self-regulation and amplification), and analytical processing functions (e.g., memory and computing). The pathway toward creating truly intelligent materials can involve incorporating a combination of these different types of functions into a single integrated system by using stimuli-responsive materials as the basic building blocks.
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Affiliation(s)
- Xuan Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Linfeng Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Kang Hui Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Spandhana Gonuguntla
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Kang Wen Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Dicky Pranantyo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wai Pong Yong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wei Jian Tyler Yam
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Zhida Low
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wee Joon Teo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Hao Ping Nien
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Qiao Wen Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Siowling Soh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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8
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Kosikova T, Philp D. Two Synthetic Replicators Compete To Process a Dynamic Reagent Pool. J Am Chem Soc 2019; 141:3059-3072. [PMID: 30668914 DOI: 10.1021/jacs.8b12077] [Citation(s) in RCA: 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.
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Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , KY16 9ST Fife , United Kingdom
| | - Douglas Philp
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , KY16 9ST Fife , United Kingdom
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9
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Wang LJ, Wang HX, Jiang L, Zhang CY. Development of an in Vitro Autocatalytic Self-Replication System for Biosensing Application. ACS Sens 2018; 3:2675-2683. [PMID: 30460848 DOI: 10.1021/acssensors.8b01171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular self-replication is a fundamental function of all living organisms with the capability of templating and catalyzing its own synthesis, and it plays important roles in prebiotic chemical evolution and effective synthetic machineries. However, the construction of the self-replication system in vitro remains a great challenge and its application for biosensing is rare. Here, we demonstrate for the first time the construction of an in vitro enzymatic nucleic acid self-replication system and its application for amplified sensing of human 8-oxoguanine DNA glycosylase (hOGG1) based on autocatalytic self-replication-driven cascaded recycling amplification. In this strategy, hOGG1 excises 8-oxoguanine (8-oxoG) to unfold the hairpin substrate, activating the autonomous biocatalytic process with molecular beacons (MBs) as both the fuels for producing nucleic acid templates and the generators for signal output, leading to the continuous replication of biocatalytic nucleic acid templates and the repeated cleavage of MBs for an enhanced fluorescence signal. This strategy exhibits an extremely low detection limit of 4.3 × 10-7 U/μL and a large dynamic range of 5 orders of magnitude from 1 × 10-6 to 0.05 U/μL. Importantly, it can be applied for the detection of enzyme kinetic parameters, the screening of hOGG1 inhibitors, and the quantification of hOGG1 activity in even 1 single lung cancer cell, providing a new approach for biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Hou-xiu Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Longhe Jiang
- Wendeng Orthopaedic Hospital of Shandong, Wendeng 264400, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
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10
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Rink WM, Thomas F. De Novo Designed α-Helical Coiled-Coil Peptides as Scaffolds for Chemical Reactions. Chemistry 2018; 25:1665-1677. [DOI: 10.1002/chem.201802849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Indexed: 01/31/2023]
Affiliation(s)
- W. Mathis Rink
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Straße 3a 37075 Göttingen Germany
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11
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Hordijk W, Shichor S, Ashkenasy G. The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics. Chemphyschem 2018; 19:2437-2444. [PMID: 29813174 DOI: 10.1002/cphc.201800101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Indexed: 11/09/2022]
Abstract
Chemical networks often exhibit emergent, systems-level properties that cannot be simply derived from the linear sum of the individual components. The design and analysis of increasingly complex chemical networks thus constitute a major area of research in Systems Chemistry. In particular, much research is focused on the emergence of functional properties in prebiotic chemical networks relevant to the origin and early evolution of life. Here, we apply a formal framework known as RAF theory to study the dynamics of a complex network of mutually catalytic peptides. We investigate in detail the influence of network modularity, initial template seeding, and product inhibition on the network dynamics. We show that these results can be useful for designing new experiments, and further argue how they are relevant to origin of life studies.
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Affiliation(s)
- Wim Hordijk
- Institute for Advanced Study, University of Amsterdam, The Netherlands
| | - Shira Shichor
- Ben-Gurion University of the Negev, Be'er Sheva, Israel
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12
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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
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13
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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: 65] [Impact Index Per Article: 10.8] [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.
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Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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14
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Komáromy D, Tezcan M, Schaeffer G, Marić I, Otto S. Effector-Triggered Self-Replication in Coupled Subsystems. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dávid Komáromy
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Meniz Tezcan
- 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
| | - Ivana Marić
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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15
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Komáromy D, Tezcan M, Schaeffer G, Marić I, Otto S. Effector-Triggered Self-Replication in Coupled Subsystems. Angew Chem Int Ed Engl 2017; 56:14658-14662. [DOI: 10.1002/anie.201707191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dávid Komáromy
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Meniz Tezcan
- 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
| | - Ivana Marić
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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16
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Wagner N, Mukherjee R, Maity I, Peacock-Lopez E, Ashkenasy G. Bistability and Bifurcation in Minimal Self-Replication and Nonenzymatic Catalytic Networks. Chemphyschem 2017; 18:1842-1850. [PMID: 28112462 DOI: 10.1002/cphc.201601293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/23/2017] [Indexed: 11/08/2022]
Abstract
Bistability and bifurcation, found in a wide range of biochemical networks, are central to the proper function of living systems. We investigate herein recent model systems that show bistable behavior based on nonenzymatic self-replication reactions. Such models were used before to investigate catalytic growth, chemical logic operations, and additional processes of self-organization leading to complexification. By solving for their steady-state solutions by using various analytical and numerical methods, we analyze how and when these systems yield bistability and bifurcation and discover specific cases and conditions producing bistability. We demonstrate that the onset of bistability requires at least second-order catalysis and results from a mismatch between the various forward and reverse processes. Our findings may have far-reaching implications in understanding early evolutionary processes of complexification, emergence, and potentially the origin of life.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Rakesh Mukherjee
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | | | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
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17
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Wagner N, Ashkenasy G. How Catalytic Order Drives the Complexification of Molecular Replication Networks. Isr J Chem 2015. [DOI: 10.1002/ijch.201400198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Gurevich L, Cohen-Luria R, Wagner N, Ashkenasy G. Robustness of synthetic circadian clocks to multiple environmental changes. Chem Commun (Camb) 2015; 51:5672-5. [PMID: 25714790 DOI: 10.1039/c5cc00098j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A molecular network that mimics circadian clocks from cyanobacteria is constructed in silico. Simulating its oscillatory behaviour under variable conditions reveals its robustness relative to networks of alternative topologies. The principles for synthetic chemical circadian networks to work properly are consequently highlighted.
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Affiliation(s)
- Lilia Gurevich
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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19
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Yang Y, Yang Y, Xie X, Cai X, Wang Z, Gong W, Zhang H, Li Y, Mei X. A near-infrared two-photon-sensitive peptide-mediated liposomal delivery system. Colloids Surf B Biointerfaces 2015; 128:427-438. [DOI: 10.1016/j.colsurfb.2015.02.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 02/07/2015] [Accepted: 02/19/2015] [Indexed: 01/30/2023]
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20
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Pavlov VA, Klabunovskii EI. The origin of homochirality in nature: a possible version. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Xie X, Yang Y, Yang Y, Zhang H, Li Y, Mei X. A photo-responsive peptide- and asparagine-glycine-arginine (NGR) peptide-mediated liposomal delivery system. Drug Deliv 2015; 23:2445-2456. [PMID: 25693640 DOI: 10.3109/10717544.2015.1008707] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The conjugation of tunable peptides or materials with nanocarriers represents a promising approach for drug delivery to tumor cells. In this study, we report the development of a novel liposomal carrier system that exploits the cell surface binding synergism between photo-sensitive peptides (PSPs) and targeting ligands. The positive charges of the lysine residues on the cell-penetrating peptides (CPPs) were temporarily caged by the photolabile-protective groups (PG), thereby forming a PSP. Furthermore, this PSP enhances specific uptake into cancer cells after rapidly uncaging the PG via near-infrared (NIR) light illumination. In the circulatory system, the cell penetrability of PSP was hindered. In contrast, the asparagine-glycine-arginine (NGR) peptide moieties, selectively bind to CD13-positive tumors, were attached to the nanocarrier to facilitate the active accumulation of this liposomal carrier in tumor tissue. The dual-modified liposomes (PSP/NGR-L) were prepared by emulsification method, and the concentrations of DSPE-PEG2000-psCPP and DSPE-PEG5000-NGR in the liposomes were chosen to be 4% and 1% (molar ratio), respectively. The mean particle size of the PSP/NGR-L was about 95 nm, and the drug entrapment efficiency was more than 90%. Cellular uptake results demonstrated that the proposed PSP/NGR-L had an enhancement of cancer cell recognition and specific uptake. Furthermore, the PSP/NGR-L demonstrated a stronger antitumor efficacy in the HT-1080 tumor model in nude mice with the aid of NIR illumination.
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Affiliation(s)
- Xiangyang Xie
- a Beijing Institute of Pharmacology and Toxicology , Beijing , China.,b Wuhan General Hospital of Guangzhou Military Command , Wuhan , China , and
| | - Yanfang Yang
- a Beijing Institute of Pharmacology and Toxicology , Beijing , China.,c Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation , Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , China
| | - Yang Yang
- a Beijing Institute of Pharmacology and Toxicology , Beijing , China
| | - Hui Zhang
- a Beijing Institute of Pharmacology and Toxicology , Beijing , China
| | - Ying Li
- a Beijing Institute of Pharmacology and Toxicology , Beijing , China
| | - Xingguo Mei
- a Beijing Institute of Pharmacology and Toxicology , Beijing , China
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22
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Wagner N, Alasibi S, Peacock-Lopez E, Ashkenasy G. Coupled Oscillations and Circadian Rhythms in Molecular Replication Networks. J Phys Chem Lett 2015; 6:60-65. [PMID: 26263092 DOI: 10.1021/jz502350u] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Living organisms often display rhythmic and oscillatory behavior. We investigate here a challenge in contemporary Systems Chemistry, that is, to construct "bottom-up" molecular networks that display such complex behavior. We first describe oscillations during self-replication by applying kinetic parameters relevant to peptide replication in an open environment. Small networks of coupled oscillators are then constructed in silico, producing various functions such as logic gates, integrators, counters, triggers, and detectors. These networks are finally utilized to simulate the connectivity and network topology of the Kai proteins circadian clocks from the S. elongatus cyanobacteria, thus producing rhythms whose constant frequency is independent of the input intake rate and robust toward concentration fluctuations. We suggest that this study helps further reveal the underlying principles of biological clocks and may provide clues into their emergence in early molecular evolution.
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Affiliation(s)
- Nathaniel Wagner
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
| | - Samaa Alasibi
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
| | - Enrique Peacock-Lopez
- ‡Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States
| | - Gonen Ashkenasy
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
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23
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Wolf A, Moulin E, Cid JJ, Goujon A, Du G, Busseron E, Fuks G, Giuseppone N. pH and light-controlled self-assembly of bistable [c2] daisy chain rotaxanes. Chem Commun (Camb) 2015; 51:4212-5. [DOI: 10.1039/c4cc10331a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Triarylamine – [c2] daisy chain rotaxane conjugates behave as logic-gates controlled by pH and light modulations to self-assemble in supramolecular fibers.
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Affiliation(s)
- Adrian Wolf
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2
- France
| | - Emilie Moulin
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2
- France
| | - Juan-José Cid
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2
- France
| | - Antoine Goujon
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2
- France
| | - Guangyan Du
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2
- France
| | - Eric Busseron
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2
- France
| | - Gad Fuks
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2
- France
| | - Nicolas Giuseppone
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2
- France
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24
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Thapaliya ER, Captain B, Raymo FM. Plasmonic Acceleration of a Photochemical Replicator. ASIAN J ORG CHEM 2014. [DOI: 10.1002/ajoc.201402211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Dadon Z, Wagner N, Alasibi S, Samiappan M, Mukherjee R, Ashkenasy G. Competition and Cooperation in Dynamic Replication Networks. Chemistry 2014; 21:648-54. [DOI: 10.1002/chem.201405195] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Indexed: 11/09/2022]
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26
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Gholami Z, Hanley Q. Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer. Bioconjug Chem 2014; 25:1820-8. [PMID: 25191824 DOI: 10.1021/bc500319p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
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 (PNA) with the O(6)-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA-directed assembly of homo- and heterodimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template-directed assembly of PNA-modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels, which may find use in the study of assembly processes in cells.
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Affiliation(s)
- Zahra Gholami
- School of Science and Technology, Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS, United Kingdom
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27
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Thapaliya ER, Swaminathan S, Captain B, Raymo FM. Autocatalytic Fluorescence Photoactivation. J Am Chem Soc 2014; 136:13798-804. [DOI: 10.1021/ja5068383] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Ek Raj Thapaliya
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Subramani Swaminathan
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Burjor Captain
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Françisco M. Raymo
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
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28
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Yang Y, Yang Y, Xie X, Cai X, Mei X. Preparation and characterization of photo-responsive cell-penetrating peptide-mediated nanostructured lipid carrier. J Drug Target 2014; 22:891-900. [DOI: 10.3109/1061186x.2014.940589] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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29
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30
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Bissette AJ, Fletcher SP. Mechanisms of Autocatalysis. Angew Chem Int Ed Engl 2013; 52:12800-26. [DOI: 10.1002/anie.201303822] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Indexed: 12/17/2022]
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31
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Busseron E, Ruff Y, Moulin E, Giuseppone N. Supramolecular self-assemblies as functional nanomaterials. NANOSCALE 2013; 5:7098-140. [PMID: 23832165 DOI: 10.1039/c3nr02176a] [Citation(s) in RCA: 496] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In this review, we survey the diversity of structures and functions which are encountered in advanced self-assembled nanomaterials. We highlight their flourishing implementations in three active domains of applications: biomedical sciences, information technologies, and environmental sciences. Our main objective is to provide the reader with a concise and straightforward entry to this broad field by selecting the most recent and important research articles, supported by some more comprehensive reviews to introduce each topic. Overall, this compilation illustrates how, based on the rules of supramolecular chemistry, the bottom-up approach to design functional objects at the nanoscale is currently producing highly sophisticated materials oriented towards a growing number of applications with high societal impact.
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Affiliation(s)
- Eric Busseron
- SAMS Research Group, University of Strasbourg, Institut Charles Sadron, CNRS, 23 rue du Loess, BP 84087, 67034 Strasbourg Cedex 2, France
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32
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Dadon Z, Samiappan M, Shahar A, Zarivach R, Ashkenasy G. A High-Resolution Structure that Provides Insight into Coiled-Coil Thiodepsipeptide Dynamic Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303900] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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33
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Dadon Z, Samiappan M, Shahar A, Zarivach R, Ashkenasy G. A high-resolution structure that provides insight into coiled-coil thiodepsipeptide dynamic chemistry. Angew Chem Int Ed Engl 2013; 52:9944-7. [PMID: 23929823 DOI: 10.1002/anie.201303900] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/16/2013] [Indexed: 01/29/2023]
Abstract
Stable and reactive: A crystal structure at 1.35 Å of a thioester coiled-coil protein reveals high similarity to all-peptide-bond proteins. In these assemblies, the thioester bonds are kept reactive towards thiol molecules in the mixture. This enables efficient domain exchange between proteins in response to changes in folding conditions or introduction of external templates.
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Affiliation(s)
- Zehavit Dadon
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 84105 (Israel)
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34
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Dieckmann A, Houk KN. Analysis of supramolecular complex energetics in artificial replicators. Chem Sci 2013. [DOI: 10.1039/c3sc51192h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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35
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Rubinov B, Wagner N, Matmor M, Regev O, Ashkenasy N, Ashkenasy G. Transient fibril structures facilitating nonenzymatic self-replication. ACS NANO 2012; 6:7893-901. [PMID: 22856322 DOI: 10.1021/nn302223v] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An emerging new direction of research focuses on developing "self-synthesizing materials", those supramolecular structures that can promote their own formation by accelerating the synthesis of building blocks and/or an entire assembly. It was postulated recently that practical design of such systems can benefit from the ability to control the assembly of amphiphilic molecules into nanostructures. We describe here the self-assembly pathway of short amphiphilic peptides into various forms of soluble β-sheet structures--β-plates, fibrils, and hollow nanotubes--and their consequent activity as autocatalysts for the synthesis of monomeric peptides from simpler building blocks. A detailed kinetic analysis of both the self-assembly and self-replication processes allows us to suggest a full model and simulate the replication process, revealing that only specific structures, primarily fibrils that are stable within the solution for a time shorter than a few hours, can be active as catalysts. Interestingly, we have found that such a process also induces fibril reproduction, in a mechanism very similar to the propagation of prion proteins by transmission of misfolded states.
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Affiliation(s)
- Boris Rubinov
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
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36
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37
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Samiappan M, Alasibi S, Cohen-Luria R, Shanzer A, Ashkenasy G. Allosteric effects in coiled-coil proteins folding and lanthanide-ion binding. Chem Commun (Camb) 2012; 48:9577-9. [DOI: 10.1039/c2cc35166h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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38
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Dadon Z, Samiappan M, Wagner N, Ashkenasy G. Chemical and light triggering of peptide networks under partial thermodynamic control. Chem Commun (Camb) 2012; 48:1419-21. [DOI: 10.1039/c1cc14301h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Bourbo V, Matmor M, Shtelman E, Rubinov B, Ashkenasy N, Ashkenasy G. Self-assembly and self-replication of short amphiphilic β-sheet peptides. ORIGINS LIFE EVOL B 2011; 41:563-7. [PMID: 22139518 DOI: 10.1007/s11084-011-9257-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 08/28/2011] [Indexed: 12/01/2022]
Abstract
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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Affiliation(s)
- Valery Bourbo
- Department of Chemistry, Ben Gurion University of Negev, Beer Sheva, Israel
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40
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Röthlingshöfer M, Gorska K, Winssinger N. Nucleic Acid-Templated Energy Transfer Leading to a Photorelease Reaction and its Application to a System Displaying a Nonlinear Response. J Am Chem Soc 2011; 133:18110-3. [DOI: 10.1021/ja2086504] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Manuel Röthlingshöfer
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg − CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
| | - Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg − CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
| | - Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg − CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
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41
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Ashkenasy G, Dadon Z, Alesebi S, Wagner N, Ashkenasy N. Building Logic into Peptide Networks: Bottom-Up and Top-Down. Isr J Chem 2011. [DOI: 10.1002/ijch.201000071] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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42
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Samiappan M, Dadon Z, Ashkenasy G. Replication NAND gate with light as input and output. Chem Commun (Camb) 2011; 47:710-2. [DOI: 10.1039/c0cc04098c] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Shamay Y, Adar L, Ashkenasy G, David A. Light induced drug delivery into cancer cells. Biomaterials 2010; 32:1377-86. [PMID: 21074848 DOI: 10.1016/j.biomaterials.2010.10.029] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 10/15/2010] [Indexed: 01/18/2023]
Abstract
Cell-penetrating peptides (CPPs) can be used for intracellular delivery of a broad variety of cargoes, including various nanoparticulate pharmaceutical carriers. However, the cationic nature of all CPP sequences, and thus lack of cell specificity, limits their in vivo use for drug delivery applications. Here, we have devised and tested a strategy for site-specific delivery of dyes and drugs into cancer cells by using polymers bearing a light activated caged CPP (cCPP). The positive charge of Lys residues on the minimum sequence of the CPP penetratin ((52)RRMKWKK(58)) was masked with photo-cleavable groups to minimize non-specific adsorption and cellular uptake. Once illuminated by UV light, these protecting groups were cleaved, the positively charged CPP regained its activity and facilitated rapid intracellular delivery of the polymer-dye or polymer-drug conjugates into cancer cells. We have found that a 10-min light illumination time was sufficient to enhance the penetration of the polymer-CPP conjugates bearing the proapoptotic peptide, (D)(KLAKLAK)(2), into 80% of the target cells, and to promote a 'switch' like cytotoxic activity resulting a shift from 100% to 10% in cell viability after 2 h. This report provides an example for tumor targeting by means of light activation of cell-penetrating peptides for intracellular drug delivery.
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Affiliation(s)
- Yosi Shamay
- Department of Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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