1
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Cui S, Liu X, Zhang X, Shi P, Zheng Y, Wang B, Zhang Q. Engineering Modular DNA Reaction Networks for Signal Processing. Chemistry 2024; 30:e202400740. [PMID: 38623910 DOI: 10.1002/chem.202400740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/26/2024] [Accepted: 04/16/2024] [Indexed: 04/17/2024]
Abstract
Diversified molecular information-processing methods have significant implications for nanoscale manipulation and control, monitoring and disease diagnosis of organisms, and direct intervention in biological activities. However, as an effective approach for implementing multifunctional molecular information processing, DNA reaction networks (DRNs) with numerous functionally specialized molecular structures have challenged them on scale design, leading to increased network complexity, further causing problems such as signal leakage, attenuation, and cross-talk in network reactions. Our study developed a strategy for performing various signal-processing tasks through engineering modular DRNs. This strategy is based on a universal core unit with signal selection capability, and a time-adjustable signal self-resetting module is achieved by combing the core unit and self-resetting unit, which improves the time controllability of modular DRNs. In addition, multi-input and -output signal cross-catalytic and continuously adjustable signal delay modules were realized by combining core and threshold units, providing a flexible, precise method for modular DRNs to process the signal. The strategy simplifies the design of DRNs, helps generate design ideas for large-scale integrated DRNs with multiple functions, and provides prospects in biocomputing, gene regulation, and biosensing.
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Affiliation(s)
- Shuang Cui
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Bin Wang
- School of Software Engineering, Dalian University, Dalian, 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
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2
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Liu X, Shi Q, Qi P, Wang Z, Zhang T, Zhang S, Wu J, Guo Z, Chen J, Zhang Q. Recent advances in living cell nucleic acid probes based on nanomaterials for early cancer diagnosis. Asian J Pharm Sci 2024; 19:100910. [PMID: 38948397 PMCID: PMC11214190 DOI: 10.1016/j.ajps.2024.100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 07/02/2024] Open
Abstract
The early diagnosis of cancer is vital for effective treatment and improved prognosis. Tumor biomarkers, which can be used for the early diagnosis, treatment, and prognostic evaluation of cancer, have emerged as a topic of intense research interest in recent years. Nucleic acid, as a type of tumor biomarker, contains vital genetic information, which is of great significance for the occurrence and development of cancer. Currently, living cell nucleic acid probes, which enable the in situ imaging and dynamic monitoring of nucleic acids, have become a rapidly developing field. This review focuses on living cell nucleic acid probes that can be used for the early diagnosis of tumors. We describe the fundamental design of the probe in terms of three units and focus on the roles of different nanomaterials in probe delivery.
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Affiliation(s)
- Xuyao Liu
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Qi Shi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Peng Qi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Ziming Wang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Tongyue Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Sijia Zhang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jiayan Wu
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhaopei Guo
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jie Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Qiang Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
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3
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Gong X, Li R, Zhang J, Zhang P, Jiang Z, Hu L, Liu X, Wang Y, Wang F. Scaling up of a Self-Confined Catalytic Hybridization Circuit for Robust microRNA Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400517. [PMID: 38613838 PMCID: PMC11165520 DOI: 10.1002/advs.202400517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/27/2024] [Indexed: 04/15/2024]
Abstract
The precise regulation of cellular behaviors within a confined, crowded intracellular environment is highly amenable in diagnostics and therapeutics. While synthetic circuitry system through a concatenated chemical reaction network has rarely been reported to mimic dynamic self-assembly system. Herein, a catalytic self-defined circuit (CSC) for the hierarchically concatenated assembly of DNA domino nanostructures is engineered. By incorporating pre-sealed symmetrical fragments into the preying hairpin reactants, the CSC system allows the hierarchical DNA self-assembly via a microRNA (miRNA)-powered self-sorting catalytic hybridization reaction. With minimal strand complexity, this self-sustainable CSC system streamlined the circuit component and achieved localization-intensified cascaded signal amplification. Profiting from the self-adaptively concatenated hybridization reaction, a reliable and robust method has been achieved for discriminating carcinoma tissues from the corresponding para-carcinoma tissues. The CSC-sustained self-assembly strategy provides a comprehensive and smart toolbox for organizing various hierarchical DNA nanostructures, which may facilitate more insights for clinical diagnosis and therapeutic assessment.
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Affiliation(s)
- Xue Gong
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityCollege of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Ruomeng Li
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityCollege of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Jiajia Zhang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Pu Zhang
- College of PharmacyChongqing Medical UniversityChongqing400016P. R. China
| | - Zhongwei Jiang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Lianzhe Hu
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Xiaoqing Liu
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityCollege of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Yi Wang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education)Chongqing Key Laboratory of Green Catalysis Materials and TechnologyCollege of ChemistryChongqing Normal UniversityChongqing401331P. R. China
| | - Fuan Wang
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityCollege of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
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4
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Samanta A, Baranda Pellejero L, Masukawa M, Walther A. DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 2024; 8:454-470. [PMID: 38750171 DOI: 10.1038/s41570-024-00606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.
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Affiliation(s)
- Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India.
| | | | - Marcos Masukawa
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
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5
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Ouyang Y, Willner I. Phototriggered Equilibrated and Transient Orthogonally Operating Constitutional Dynamic Networks Guiding Biocatalytic Cascades. J Am Chem Soc 2024; 146:6806-6816. [PMID: 38422481 PMCID: PMC10941189 DOI: 10.1021/jacs.3c13562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
The photochemical deprotection of structurally engineered o-nitrobenzylphosphate-caged hairpin nucleic acids is introduced as a versatile method to evolve constitutional dynamic networks, CDNs. The photogenerated CDNs, in the presence of fuel strands, interact with auxiliary CDNs, resulting in their dynamically equilibrated reconfiguration. By modification of the constituents associated with the auxiliary CDNs with glucose oxidase (GOx)/horseradish peroxidase (HRP) or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) cofactor, the photogenerated CDN drives the orthogonal operation upregulated/downregulated operation of the GOx/HRP and LDH/NAD+ biocatalytic cascade in the conjugate mixture of auxiliary CDNs. Also, the photogenerated CDN was applied to control the reconfiguration of coupled CDNs, leading to upregulated/downregulated formation of the antithrombin aptamer units, resulting in the dictated inhibition of thrombin activity (fibrinogen coagulation). Moreover, a reaction module consisting of GOx/HRP-modified o-nitrobenzyl phosphate-caged DNA hairpins, photoresponsive caged auxiliary duplexes, and nickase leads upon irradiation to the emergence of a transient, dissipative CDN activating in the presence of two alternate auxiliary triggers, achieving transient operation of up- and downregulated GOx/HRP biocatalytic cascades.
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Affiliation(s)
- Yu Ouyang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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6
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Yang S, Bögels BWA, Wang F, Xu C, Dou H, Mann S, Fan C, de Greef TFA. DNA as a universal chemical substrate for computing and data storage. Nat Rev Chem 2024; 8:179-194. [PMID: 38337008 DOI: 10.1038/s41570-024-00576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.
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Affiliation(s)
- Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Can Xu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, UK.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
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7
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Sharma C, Sarkar A, Walther A. Transient co-assemblies of micron-scale colloids regulated by ATP-fueled reaction networks. Chem Sci 2023; 14:12299-12307. [PMID: 37969603 PMCID: PMC10631234 DOI: 10.1039/d3sc04017h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/15/2023] [Indexed: 11/17/2023] Open
Abstract
Self-assembly of colloidal particles offers an attractive bottom-up approach to functional materials. Current design strategies for colloidal assemblies are mostly based on thermodynamically controlled principles and lack autonomous behavior. The next advance in the properties of colloidal assemblies will come from coupling these structures to out-of-equilibrium chemical reaction networks furnishing them with autonomous and dynamic behavior. This, however, constitutes a major challenge of carefully modulating the interparticle potentials on a temporal circuit program and avoiding kinetic trapping and irreversible aggregation. Herein, we report the coupling of a fuel-driven DNA-based enzymatic reaction network (ERN) to micron-sized colloidal particles to achieve their transient co-assembly. The ERN operating on the molecular level transiently releases an Output strand which links two DNA functionalized microgel particles together into co-assemblies with a programmable assembly lifetime. The system generates minimal waste and recovers all components of the ERN after the consumption of the ATP fuel. The system can be reactivated by addition of new fuel as shown for up to three cycles. The design can be applied to organize other building blocks into hierarchical structures and materials with advanced biomimetic properties.
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Affiliation(s)
- Charu Sharma
- Department of Chemistry, Life-Like Materials and Systems, University of Mainz Duesbergweg 10-14 55128 Mainz Germany
| | - Aritra Sarkar
- Department of Chemistry, Life-Like Materials and Systems, University of Mainz Duesbergweg 10-14 55128 Mainz Germany
| | - Andreas Walther
- Department of Chemistry, Life-Like Materials and Systems, University of Mainz Duesbergweg 10-14 55128 Mainz Germany
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8
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Yang J, Liang Y, Li X, Zhang Y, Qian L, Ke Y, Zhang C. A Spatially Programmable DNA Nanorobot Arm to Modulate Anisotropic Gold Nanoparticle Assembly by Enzymatic Excision. Angew Chem Int Ed Engl 2023; 62:e202308797. [PMID: 37691009 DOI: 10.1002/anie.202308797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has drawn much attention for their unique characteristics in plasmonics and biomedicine. Bio-inspired methods have already provided programmable, molecular approaches to direct AuNP assemblies using biopolymers. The existing methods, however, predominantly use DNA as scaffolds to directly guide the AuNP interactions to produce intended superstructures. New paradigms for regulating AuNP assembly will greatly enrich the toolbox for DNA-directed AuNP manipulation and fabrication. Here, we developed a strategy of using a spatially programmable enzymatic nanorobot arm to modulate anisotropic DNA surface modifications and assembly of AuNPs. Through spatial controls of the proximity of the reactants, the locations of the modifications were precisely regulated. We demonstrated the control of the modifications on a single 15 nm AuNP, as well as on a rectangular DNA origami platform, to direct unique anisotropic AuNP assemblies. This method adds an alternative enzymatic manipulation to DNA-directed AuNP superstructure assembly.
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Affiliation(s)
- Jing Yang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yuan Liang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Xiang Li
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yongpeng Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Long Qian
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Cheng Zhang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
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9
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Pattloch S, Dzubiella J. Mean-field models for the chemical fueling of transient soft matter states. SOFT MATTER 2023; 19:7804-7814. [PMID: 37795797 DOI: 10.1039/d3sm00742a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
The chemical fueling of transient states (CFTS) is a powerful process to control the nonequilibrium structuring and the homeostatic function of adaptive soft matter systems. Here, we introduce a simple mean-field model of CFTS based on the activation of metastable equilibrium states in a tilted 'Landau' bistable energy landscape along a coarse-grained reaction coordinate (or 'order parameter') triggered by a nonmonotonic two-step chemical fueling reaction. Evaluation of the model in the quasi-static (QS) limit-valid for fast system relaxation-allows us to extract useful analytical laws for the critical activation concentration and duration of the transient states in dependence of physical parameters, such as rate constants, fuel concentrations, and the system's distance to its equilibrium transition point. We apply our model in the QS limit explicitly to recent experiments of CFTS of collapsing responsive microgels and find a very good performance with only a few global and physically interpretable fitting parameters, which can be employed for programmable material design. Moreover, our model framework also allows a thermodynamic analysis of the energy and performed work in the system. Finally, we go beyond the QS limit, where the system's response is slow and retarded versus the chemical reaction, using an overdamped Smoluchowski approach. The latter demonstrates how internal system time scales can be used to tune the time-dependent behavior and programmed delay of the transient states in full nonequilibrium.
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Affiliation(s)
- Sven Pattloch
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany.
- Cluster of Excellence livMatS@FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, D-79110 Freiburg, Germany
| | - Joachim Dzubiella
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany.
- Cluster of Excellence livMatS@FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, D-79110 Freiburg, Germany
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10
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Jahnke K, Göpfrich K. Engineering DNA-based cytoskeletons for synthetic cells. Interface Focus 2023; 13:20230028. [PMID: 37577007 PMCID: PMC10415745 DOI: 10.1098/rsfs.2023.0028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/30/2023] [Indexed: 08/15/2023] Open
Abstract
The development and bottom-up assembly of synthetic cells with a functional cytoskeleton sets a major milestone to understand cell mechanics and to develop man-made machines on the nano- and microscale. However, natural cytoskeletal components can be difficult to purify, deliberately engineer and reconstitute within synthetic cells which therefore limits the realization of multifaceted functions of modern cytoskeletons in synthetic cells. Here, we review recent progress in the development of synthetic cytoskeletons made from deoxyribonucleic acid (DNA) as a complementary strategy. In particular, we explore the capabilities and limitations of DNA cytoskeletons to mimic functions of natural cystoskeletons like reversible assembly, cargo transport, force generation, mechanical support and guided polymerization. With recent examples, we showcase the power of rationally designed DNA cytoskeletons for bottom-up assembled synthetic cells as fully engineerable entities. Nevertheless, the realization of dynamic instability, self-replication and genetic encoding as well as contractile force generating motors remains a fruitful challenge for the complete integration of multifunctional DNA-based cytoskeletons into synthetic cells.
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Affiliation(s)
- Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Center for Molecular Biology (ZMBH), Heidelberg University, Im Neuenheimer Feld 329, 69120 Heidelberg, Germany
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11
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Qin Y, Ouyang Y, Wang J, Chen X, Sohn YS, Willner I. Transient Dynamic Operation of G-Quadruplex-Gated Glucose Oxidase-Loaded ZIF-90 Metal-Organic Framework Nanoparticle Bioreactors. NANO LETTERS 2023; 23:8664-8673. [PMID: 37669541 PMCID: PMC10540265 DOI: 10.1021/acs.nanolett.3c02542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/27/2023] [Indexed: 09/07/2023]
Abstract
Glucose oxidase-loaded ZIF-90 metal-organic framework nanoparticles conjugated to hemin-G-quadruplexes act as functional bioreactor hybrids operating transient dissipative biocatalytic cascaded transformations consisting of the glucose-driven H2O2-mediated oxidation of Amplex-Red to resorufin or the glucose-driven generation of chemiluminescence by the H2O2-mediated oxidation of luminol. One system involves the fueled activation of a reaction module leading to the temporal formation and depletion of the bioreactor conjugate operating the nickase-guided transient biocatalytic cascades. The second system demonstrates the fueled activation of a reaction module yielding a bioreactor conjugate operating the exonuclease III-dictated transient operation of the two biocatalytic cascades. The temporal operations of the bioreactor circuits are accompanied by kinetic models and computational simulations enabling us to predict the dynamic behavior of the systems subjected to different auxiliary conditions.
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Affiliation(s)
- Yunlong Qin
- The
Institute of Chemistry, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Yu Ouyang
- The
Institute of Chemistry, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- The
Institute of Chemistry, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Xinghua Chen
- The
Institute of Chemistry, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- The
Institute of Life Science, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The
Institute of Chemistry, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
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12
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Bucci J, Irmisch P, Del Grosso E, Seidel R, Ricci F. Timed Pulses in DNA Strand Displacement Reactions. J Am Chem Soc 2023; 145:20968-20974. [PMID: 37710955 PMCID: PMC10540199 DOI: 10.1021/jacs.3c06664] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Indexed: 09/16/2023]
Abstract
Inspired by naturally occurring regulatory mechanisms that allow complex temporal pulse features with programmable delays, we demonstrate here a strategy to achieve temporally programmed pulse output signals in DNA-based strand displacement reactions (SDRs). To achieve this, we rationally designed input strands that, once bound to their target duplex, can be gradually degraded, resulting in a pulse output signal. We also designed blocker strands that suppress strand displacement and determine the time at which the pulse reaction is generated. We show that by controlling the degradation rate of blocker and input strands, we can finely control the delayed pulse output over a range of 10 h. We also prove that it is possible to orthogonally delay two different pulse reactions in the same solution by taking advantage of the specificity of the degradation reactions for the input and blocker strands. Finally, we show here two possible applications of such delayed pulse SDRs: the time-programmed pulse decoration of DNA nanostructures and the sequentially appearing and self-erasing formation of DNA-based patterns.
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Affiliation(s)
- Juliette Bucci
- Department
of Chemical Sciences and Technologies, University
of Rome, Tor Vergata,
Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Patrick Irmisch
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - Erica Del Grosso
- Department
of Chemical Sciences and Technologies, University
of Rome, Tor Vergata,
Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Ralf Seidel
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - Francesco Ricci
- Department
of Chemical Sciences and Technologies, University
of Rome, Tor Vergata,
Via della Ricerca Scientifica, 00133 Rome, Italy
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13
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Zhang X, Liu Y, Wang B, Zhou S, Shi P, Cao B, Zheng Y, Zhang Q, Kirilov Kasabov N. Biomolecule-Driven Two-Factor Authentication Strategy for Access Control of Molecular Devices. ACS NANO 2023; 17:18178-18189. [PMID: 37703447 DOI: 10.1021/acsnano.3c05070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The rise of DNA nanotechnology is promoting the development of molecular security devices and marking an essential change in information security technology, to one that can resist the threats resulting from the increase in computing power, brute force attempts, and quantum computing. However, developing a secure and reliable access control strategy to guarantee the confidentiality of molecular security devices is still a challenge. Here, a biomolecule-driven two-factor authentication strategy for access control of molecular devices is developed. Importantly, the two-factor is realized by applying the specificity and nicking properties of the nicking enzyme and the programmable design of the DNA sequence, endowing it with the characteristic of a one-time password. To demonstrate the feasibility of this strategy, an access control module is designed and integrated to further construct a role-based molecular access control device. By constructing a command library composed of three commands (Ca, Cb, Ca and Cb), the authorized access of three roles in the molecular device is realized, in which the command Ca corresponds to the authorization of role A, Cb corresponds to the authorization of role B, and Ca and Cb corresponds to the authorization of role C. In this way, when users access the device, they not only need the correct factor but also need to apply for role authorization in advance to obtain secret information. This strategy provides a highly robust method for the research on access control of molecular devices and lays the foundation for research on the next generation of information security.
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Affiliation(s)
- Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Nikola Kirilov Kasabov
- Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland 1010, New Zealand
- Intelligent Systems Research Center, Ulster University, Londonderry BT48, United Kingdom
- IICT, Bulgarian Academy of Sciences, Sofia 1040, Bulgaria
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14
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Sharma C, Samanta A, Schmidt RS, Walther A. DNA-Based Signaling Networks for Transient Colloidal Co-Assemblies. J Am Chem Soc 2023; 145:17819-17830. [PMID: 37543962 DOI: 10.1021/jacs.3c04807] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Programmable chemical circuits inspired by signaling networks in living cells are a promising approach for the development of adaptive and autonomous self-assembling molecular systems and material functions. Progress has been made at the molecular level, but connecting molecular control circuits to self-assembling larger elements such as colloids that enable real-space studies and access to functional materials is sparse and can suffer from kinetic traps, flocculation, or difficult system integration protocols. Herein, we report a toehold-mediated DNA strand displacement reaction network capable of autonomously directing two different microgels into transient and self-regulating co-assemblies. The microgels are functionalized with DNA and become elemental components of the network. The flexibility of the circuit design allows the installation of delay phases or accelerators by chaining additional circuit modules upstream or downstream of the core circuit. The design provides an adaptable and robust route to regulate other building blocks for advanced biomimetic functions.
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Affiliation(s)
- Charu Sharma
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Ricarda Sophia Schmidt
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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15
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Lang X, Huang Y, He L, Wang Y, Thumu U, Chu Z, Huck WTS, Zhao H. Mechanosensitive non-equilibrium supramolecular polymerization in closed chemical systems. Nat Commun 2023; 14:3084. [PMID: 37248275 DOI: 10.1038/s41467-023-38948-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/23/2023] [Indexed: 05/31/2023] Open
Abstract
Chemical fuel-driven supramolecular systems have been developed showing out-of-equilibrium functions such as transient gelation and oscillations. However, these systems suffer from undesired waste accumulation and they function only in open systems. Herein, we report non-equilibrium supramolecular polymerizations in a closed system, which is built by viologens and pyranine in the presence of hydrazine hydrate. On shaking, the viologens are quickly oxidated by air followed by self-assembly of pyranine into micrometer-sized nanotubes. The self-assembled nanotubes disassemble spontaneously over time by the reduced agent, with nitrogen as the only waste product. Our mechanosensitive dissipative system can be extended to fabricate a chiral transient supramolecular helix by introducing chiral-charged small molecules. Moreover, we show that shaking induces transient fluorescence enhancement or quenching depending on substitution of viologens. Ultrasound is introduced as a specific shaking way to generate template-free reproducible patterns. Additionally, the shake-driven transient polymerization of amphiphilic naphthalenetetracarboxylic diimide serves as further evidence of the versatility of our mechanosensitive non-equilibrium system.
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Affiliation(s)
- Xianhua Lang
- School of Chemical Engineering, State Key Lab of Polymer Materials Engineering, Sichuan University, 610065, Chengdu, China
| | - Yingjie Huang
- School of Chemical Engineering, State Key Lab of Polymer Materials Engineering, Sichuan University, 610065, Chengdu, China
| | - Lirong He
- School of Chemical Engineering, State Key Lab of Polymer Materials Engineering, Sichuan University, 610065, Chengdu, China
| | - Yixi Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Udayabhaskararao Thumu
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Zonglin Chu
- College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, China
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Hui Zhao
- School of Chemical Engineering, State Key Lab of Polymer Materials Engineering, Sichuan University, 610065, Chengdu, China.
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16
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Dong J, Willner I. Dynamic Transcription Machineries Guide the Synthesis of Temporally Operating DNAzymes, Gated and Cascaded DNAzyme Catalysis. ACS NANO 2023; 17:687-696. [PMID: 36576858 PMCID: PMC9836355 DOI: 10.1021/acsnano.2c10108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Transient transcription machineries play important roles in the dynamic modulation of gene expression and the sequestered regulation of cellular networks. The present study emulates such processes by designing artificial reaction modules consisting of transcription machineries that guide the transient synthesis of catalytic DNAzymes, the transient operation of gated DNAzymes, and the temporal activation of an intercommunicated DNAzyme cascade. The reaction modules rely on functional constituents that lead to the triggered activation of transcription machineries in the presence of the nucleoside triphosphates oligonucleotide fuel, yielding the transient formation and dissipative depletion of the intermediate DNAzyme(s) products. The kinetics of the transient DNAzyme networks are computationally simulated, allowing to predict and experimentally validate the performance of the systems under different auxiliary conditions. The study advances the field of systems chemistry by introducing transcription machinery-based networks for the dynamic control over transient catalysis─a primary step toward life-like cellular assemblies.
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17
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Zhang QL, Wang Y, Wang LL, Xie F, Wu RY, Ma XY, Li H, Liu Y, Yao S, Xu L. Programming Non-Nucleic Acid Molecules into Computational Nucleic Acid Systems. Angew Chem Int Ed Engl 2023; 62:e202214698. [PMID: 36373715 DOI: 10.1002/anie.202214698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Indexed: 11/16/2022]
Abstract
Nucleic acid (NA) computation has been widely developed in the past years to solve kinds of logic and mathematic issues in both information technologies and biomedical analysis. However, the difficulty to integrate non-NA molecules limits its power as a universal platform for molecular computation. Here, we report a versatile prototype of hybridized computation integrated with both nucleic acids and non-NA molecules. Employing the conformationally controlled ligand converters, we demonstrate that non-NA molecules, including both small molecules and proteins, can be computed as nucleic acid strands to construct the circuitry with increased complexity and scalability, and can be even programmed to solve arithmetical calculations within the computational nucleic acid system. This study opens a new door for molecular computation in which all-NA circuits can be expanded with integration of various ligands, and meanwhile, ligands can be precisely programmed by the nuclei acid computation.
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Affiliation(s)
- Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Fan Xie
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xu-Yang Ma
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Han Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shunchun Yao
- School of Electric Power Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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18
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Sun M, Deng J, Walther A. Communication and Cross-Regulation between Chemically Fueled Sender and Receiver Reaction Networks. Angew Chem Int Ed Engl 2023; 62:e202214499. [PMID: 36354214 PMCID: PMC10107503 DOI: 10.1002/anie.202214499] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Indexed: 11/11/2022]
Abstract
Nature connects multiple fuel-driven chemical/enzymatic reaction networks (CRNs/ERNs) via cross-regulation to hierarchically control biofunctions for a tailored adaption in complex sensory landscapes. Herein, we introduce a facile example of communication and cross-regulation among two fuel-driven DNA-based ERNs regulated by a concatenated RNA transcription regulator. ERN1 ("sender") is designed for the fuel-driven promoter formation for T7 RNA polymerase, which activates RNA transcription. The produced RNA can deactivate or activate DNA in ERN2 ("receiver") by toehold-mediated strand displacement, leading to a communication between two ERNs. The RNA from ERN1 can repress or promote the fuel-driven state of ERN2; ERN2 in turn feedbacks to regulate the lifetime of ERN1. Furthermore, the incorporation of RNase H allows for RNA degradation and enables the autonomous recovery of ERN2. We believe that concatenation of multiple CRNs/ERNs provides a basis for the design of more elaborate autonomous regulatory mechanisms in systems chemistry and synthetic biology.
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Affiliation(s)
- Mo Sun
- Department of Chemistry, Fudan University, Shanghai, 200438, China.,Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
| | - Jie Deng
- Life Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Dana-Farber Cancer Institute, Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
| | - Andreas Walther
- Life Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
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19
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Stasi M, Monferrer A, Babl L, Wunnava S, Dirscherl CF, Braun D, Schwille P, Dietz H, Boekhoven J. Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle. J Am Chem Soc 2022; 144:21939-21947. [PMID: 36442850 PMCID: PMC9732876 DOI: 10.1021/jacs.2c08463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to synthesize a nanomachine with similar functions, precision, and speed. The field of DNA nanotechnology has given rise to the engineering precision required for such a device. Simultaneously, the field of systems chemistry developed fast chemical reaction cycles that convert fuel to change the function of molecules. In this work, we thus combined a chemical reaction cycle with the precision of DNA nanotechnology to yield kinetic control over the conformational state of a DNA hairpin. Future work on such systems will result in out-of-equilibrium DNA nanodevices with precise functions.
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Affiliation(s)
- Michele Stasi
- School
of Natural Sciences, Department of Chemistry, Technical University of Munich, Garching85748, Germany
| | - Alba Monferrer
- School
of Natural Sciences, Department of Physics, Technical University of Munich, Am Coulombwall 4, Garching85748, Germany,Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, Garching85748, Germany
| | - Leon Babl
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried82152,Germany
| | - Sreekar Wunnava
- Center
for NanoScience (CeNS) and Systems Biophysics, Ludwig-Maximilian University Munich, Munich80799, Germany
| | | | - Dieter Braun
- Center
for NanoScience (CeNS) and Systems Biophysics, Ludwig-Maximilian University Munich, Munich80799, Germany
| | - Petra Schwille
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried82152,Germany
| | - Hendrik Dietz
- School
of Natural Sciences, Department of Physics, Technical University of Munich, Am Coulombwall 4, Garching85748, Germany,Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, Garching85748, Germany
| | - Job Boekhoven
- School
of Natural Sciences, Department of Chemistry, Technical University of Munich, Garching85748, Germany,
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20
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Abstract
Over the past 40 years, structural and dynamic DNA nanotechnologies have undoubtedly demonstrated to be effective means for organizing matter at the nanoscale and reconfiguring equilibrium structures, in a predictable fashion and with an accuracy of a few nanometers. Recently, novel concepts and methodologies have been developed to integrate nonequilibrium dynamics into DNA nanostructures, opening the way to the construction of synthetic materials that can adapt to environmental changes and thus acquire new properties. In this Review, we summarize the strategies currently applied for the construction of synthetic DNA filaments and conclude by reporting some recent and most relevant examples of DNA filaments that can emulate typical structural and dynamic features of the cytoskeleton, such as compartmentalization in cell-like vesicles, support for active transport of cargos, sustained or transient growth, and responsiveness to external stimuli.
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21
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Qin Z, Liu Y, Zhang L, Liu J, Su X. Programming Dissipation Systems by DNA Timer for Temporally Regulating Enzyme Catalysis and Nanostructure Assembly. ACS NANO 2022; 16:14274-14283. [PMID: 36102909 DOI: 10.1021/acsnano.2c04405] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Live cells precisely control their temporal pattern in energy dissipative processes such as catalysis and assembly. Here, we demonstrate a DNA-based artificial dissipative nonequilibrium system where the transient state is controlled by the processive digestion of λ-exonuclease (λ Exo). This enzyme reaction serves as an orthogonal and independent molecular timer allowing for the programmable regulation of the transient-state lifetime. This dissipation system is concatenated to enzyme catalysis and nanostructure assembly networks. Dynamic activation of enzyme catalysis and dynamic disassembly of DNA nanotubes (DNT) are realized, and the state lifetimes of these systems are accurately encoded by the DNA timer. This work demonstrates nontrivial dissipation systems with built-in molecular timers, which can be a useful tool for developing artificial reaction networks and nanostructures with enhanced complexities and intelligence.
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Affiliation(s)
- Zhaohui Qin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Yu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Jiajia Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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22
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Del Grosso E, Franco E, Prins LJ, Ricci F. Dissipative DNA nanotechnology. Nat Chem 2022; 14:600-613. [PMID: 35668213 DOI: 10.1038/s41557-022-00957-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 04/13/2022] [Indexed: 12/11/2022]
Abstract
DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature.
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Affiliation(s)
- Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Rome, Italy
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, USA.
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padua, Padua, Italy.
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Rome, Italy.
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23
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Fan X, Walther A. 1D Colloidal chains: recent progress from formation to emergent properties and applications. Chem Soc Rev 2022; 51:4023-4074. [PMID: 35502721 DOI: 10.1039/d2cs00112h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrating nanoscale building blocks of low dimensionality (0D; i.e., spheres) into higher dimensional structures endows them and their corresponding materials with emergent properties non-existent or only weakly existent in the individual building blocks. Constructing 1D chains, 2D arrays and 3D superlattices using nanoparticles and colloids therefore continues to be one of the grand goals in colloid and nanomaterial science. Amongst these higher order structures, 1D colloidal chains are of particular interest, as they possess unique anisotropic properties. In recent years, the most relevant advances in 1D colloidal chain research have been made in novel synthetic methodologies and applications. In this review, we first address a comprehensive description of the research progress concerning various synthetic strategies developed to construct 1D colloidal chains. Following this, we highlight the amplified and emergent properties of the resulting materials, originating from the assembly of the individual building blocks and their collective behavior, and discuss relevant applications in advanced materials. In the discussion of synthetic strategies, properties, and applications, particular attention will be paid to overarching concepts, fresh trends, and potential areas of future research. We believe that this comprehensive review will be a driver to guide the interdisciplinary field of 1D colloidal chains, where nanomaterial synthesis, self-assembly, physical property studies, and material applications meet, to a higher level, and open up new research opportunities at the interface of classical disciplines.
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Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular Chemistry, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 31, 79104, Freiburg, Germany.
| | - Andreas Walther
- A3BMS Lab, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
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24
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Sharma C, Walther A. Self-Regulating Colloidal Co-Assemblies That Accelerate Their Own Destruction via Chemo-Structural Feedback. Angew Chem Int Ed Engl 2022; 61:e202201573. [PMID: 35235231 PMCID: PMC9311650 DOI: 10.1002/anie.202201573] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 11/13/2022]
Abstract
Biological self‐assemblies self‐ and cross‐regulate each other via chemical reaction networks (CRNs) and feedback. Although artificial transient self‐assemblies have been realized via activation/deactivation CRNs, the transient structures themselves do mostly not engage in the CRN. We introduce a rational design approach for chemo‐structural feedback, and present a transient colloidal co‐assembly system, where the formed co‐assemblies accelerate their destruction autonomously. We achieve this by immobilizing enzymes of a deactivating acid‐producing enzymatic cascade on pH‐switchable microgels that can form co‐assemblies at high pH. Since the enzyme partners are immobilized on individual microgels, the co‐assembled state brings them close enough for enhanced acid generation. The amplified deactivator production (acid) leads to an almost two‐fold reduction in the lifetime of the transiently formed pH‐state. Our study thus introduces versatile mechanisms for chemo‐structural feedback.
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Affiliation(s)
- Charu Sharma
- A3BMS Lab, Department of Chemistry, University of Mainz, 55128, Mainz, Germany
| | - Andreas Walther
- A3BMS Lab, Department of Chemistry, University of Mainz, 55128, Mainz, Germany.,Cluster of Excellence livMats @ FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79098, Freiburg, Germany
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25
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Sharma C, Walther A. Self‐Regulating Colloidal Co‐Assemblies That Accelerate Their Own Destruction via Chemo‐Structural Feedback. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Charu Sharma
- A3BMS Lab Department of Chemistry University of Mainz 55128 Mainz Germany
| | - Andreas Walther
- A3BMS Lab Department of Chemistry University of Mainz 55128 Mainz Germany
- Cluster of Excellence livMats @ FIT Freiburg Center for Interactive Materials and Bioinspired Technologies University of Freiburg 79098 Freiburg Germany
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26
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Deng J, Liu W, Sun M, Walther A. Dissipative Organization of DNA Oligomers for Transient Catalytic Function. Angew Chem Int Ed Engl 2022; 61:e202113477. [PMID: 35026052 PMCID: PMC9306540 DOI: 10.1002/anie.202113477] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 12/31/2022]
Abstract
The development of synthetic non-equilibrium systems opens doors for man-made life-like materials. Yet, creating distinct transient functions from artificial fuel-driven structures remains a challenge. Building on our ATP-driven dynamic covalent DNA assembly in an enzymatic reaction network of concurrent ATP-powered ligation and restriction, we introduce ATP-fueled transient organization of functional subunits for various functions. The programmability of the ligation/restriction site allows to precisely organize multiple sticky-end-encoded oligo segments into double-stranded (ds) DNA complexes. We demonstrate principles of ATP-driven organization into sequence-defined oligomers by sensing barcode-embedded targets with different defects. Furthermore, ATP-fueled DNAzymes for substrate cleavage are achieved by transiently ligating two DNAzyme subunits into a dsDNA complex, rendering ATP-fueled transient catalytic function.
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Affiliation(s)
- Jie Deng
- A3BMS Lab, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Department of Cancer Biology, Dana-Farber Cancer Institute and Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Liu
- A3BMS Lab, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Mo Sun
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.,Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Andreas Walther
- A3BMS Lab, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
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27
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Huang L, Shen S, Zhong Y, Zhang Y, Zhang L, Wang X, Xia X, Tong X, Zhou J, Tu J. Multifunctional Hyphae Carbon Powering Lithium-Sulfur Batteries. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107415. [PMID: 34741475 DOI: 10.1002/adma.202107415] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Biotechnology can bring new breakthroughs on design and fabrication of energy materials and devices. In this work, a novel and facile biological self-assembly technology to fabricate multifunctional Rhizopus hyphae carbon fiber (RHCF) and its derivatives on a large scale for electrochemical energy storage is proposed. Crosslinked hollow carbon fibers are successfully prepared by conversion of Rhizopus hyphae, and macroscopic production of centimeter-level carbon balls consisting of hollow RHCFs is further realized. Moreover, the self-assembled RHCF balls show strong adsorption characteristics on metal ions and can be converted into a series of derivatives such as RHCF/metal oxides. Notably, the designed RHCF derivatives are demonstrated with powerful multifunctionability as cathode, anode, and separator for lithium-sulfur batteries (LSBs). The RHCF can act as the host material to combine with metal oxide (CoO) and S, Li metal, and a polypropylene (PP) separator to form a new RHCF/CoO-S cathode, an RHCF/Li anode, and an RHCF/PP separator, respectively. Consequently, the optimized LSB full cell presents excellent cycling performance and superior high-rate capacity (881.3 mA h g-1 at 1 C). This work provides a new method for large-scale preparation of hollow carbon fibers and derivatives for advanced energy storage and conversion.
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Affiliation(s)
- Lei Huang
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
- State Key Laboratory of Silicon Materials, Key Laboratory of Advanced Materials and Applications for Batteries of Zhejiang Province, School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Shenghui Shen
- State Key Laboratory of Silicon Materials, Key Laboratory of Advanced Materials and Applications for Batteries of Zhejiang Province, School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Yu Zhong
- State Key Laboratory of Silicon Materials, Key Laboratory of Advanced Materials and Applications for Batteries of Zhejiang Province, School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Yongqi Zhang
- Yangtze Delta Region Institute (Huzhou) & Institute of Fundamental and Frontier Science, University of Electronic Science and Technology of China, Huzhou, 313000, China
| | - Lingjie Zhang
- State Key Laboratory of Silicon Materials, Key Laboratory of Advanced Materials and Applications for Batteries of Zhejiang Province, School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xiuli Wang
- State Key Laboratory of Silicon Materials, Key Laboratory of Advanced Materials and Applications for Batteries of Zhejiang Province, School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xinhui Xia
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
- State Key Laboratory of Silicon Materials, Key Laboratory of Advanced Materials and Applications for Batteries of Zhejiang Province, School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xili Tong
- State Key Laboratory of Coal Conversation, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, 030001, P. R. China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Jiangping Tu
- State Key Laboratory of Silicon Materials, Key Laboratory of Advanced Materials and Applications for Batteries of Zhejiang Province, School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China
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28
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Deng J, Liu W, Sun M, Walther A. Dissipative Organization of DNA Oligomers for Transient Catalytic Function. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jie Deng
- A3BMS Lab, Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
- Department of Cancer Biology Dana-Farber Cancer Institute and Wyss Institute for Biologically Inspired Engineering Harvard Medical School Boston MA 02115 USA
| | - Wei Liu
- A3BMS Lab, Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Mo Sun
- Cluster of Excellence livMatS @ FIT – Freiburg Center for Interactive Materials and Bioinspired Technologies University of Freiburg Georges-Köhler-Allee 105 79110 Freiburg Germany
- Department of Chemistry Fudan University Shanghai 200438 China
| | - Andreas Walther
- A3BMS Lab, Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
- Cluster of Excellence livMatS @ FIT – Freiburg Center for Interactive Materials and Bioinspired Technologies University of Freiburg Georges-Köhler-Allee 105 79110 Freiburg Germany
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29
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pH-responsive aggregate consisted of oligodeoxynucleotides bearing nitrophenol group that deliver drugs into acidic cells. Bioorg Med Chem Lett 2021; 58:128519. [PMID: 34952176 DOI: 10.1016/j.bmcl.2021.128519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 11/21/2022]
Abstract
A decrease in pH is observed in most solid tumors, thus, the development of drug delivery systems that respond to slightly acidic extracellular pH environment is important in providing tumor-targeted therapies. DNA aggregates can act as useful drug delivery agents, and therefore, we designed an artificial oligodeoxynucleotides (ODNs) that form an aggregate only under acidic conditions in this study. In other words, we expected that if we could make DNA aggregates that form only in an acidic environment and that encapsulate drugs, it would be possible to transport drugs to tumor tissues selectively. Nitrophenol derivatives, which undergo protonation and deprotonation in response to pH changes, was introduced into ODNs. The ODNs formed aggregates under weakly acidic conditions because of expression of amphiphilicity, which was induced by protonation of nitrophenol unit, and were smoothly taken up into cells. We also found that the aggregates transport anticancer drug, 5FU, into acidified cells to show cytotoxic effects.
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30
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Gentile S, Del Grosso E, Pungchai PE, Franco E, Prins LJ, Ricci F. Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA. J Am Chem Soc 2021; 143:20296-20301. [PMID: 34843256 PMCID: PMC8662731 DOI: 10.1021/jacs.1c09503] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We demonstrate a strategy that allows
for the spontaneous reconfiguration
of self-assembled DNA polymers exploiting RNA as chemical fuel. To
do this, we have rationally designed orthogonally addressable DNA
building blocks that can be transiently deactivated by RNA fuels and
subtracted temporarily from participation in the self-assembly process.
Through a fine modulation of the rate at which the building blocks
are reactivated we can carefully control the final composition of
the polymer and convert a disordered polymer in a higher order polymer,
which is disfavored from a thermodynamic point of view. We measure
the dynamic reconfiguration via fluorescent signals and confocal microscopy,
and we derive a kinetic model that captures the experimental results.
Our approach suggests a novel route toward the development of biomolecular
materials in which engineered chemical reactions support the autonomous
spatial reorganization of multiple components.
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Affiliation(s)
- Serena Gentile
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Passa E Pungchai
- Department of Bioengineering, University of California at Los Angeles, 410 Westwood Plaza, Los Angeles, California 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padua, Via Marzolo 1, 35131 Padua, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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