1
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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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2
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Yang Y, Zhou Z, Guo Y, Chen R, Tian D, Ren S, Zhou H, Gao Z. Programmable DNA tweezers-SDA for ultra-sensitive signal amplification fluorescence sensing strategy. Anal Chim Acta 2024; 1292:342245. [PMID: 38309853 DOI: 10.1016/j.aca.2024.342245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND DNA tweezers, classified as DNA nanomachines, have gained prominence as multifunctional biosensors due to their advantages, including a straightforward structure, response mechanism, and high programmability. While the DNA tweezers demonstrate simultaneous, rapid, and stable responses to different targets, their detection sensitivity requires enhancement. Some small molecules, such as mycotoxins, often require more sensitive detection due to their extremely high toxicity. Therefore, more effective signal amplification strategies are needed to further enhance the sensitivity of DNA tweezers in biosensing. RESULTS We designed programmable DNA tweezers that detect small-molecule mycotoxins and miRNAs through simple sequence substitution. While the DNA tweezers demonstrate simultaneous, rapid, and stable responses to different targets, their detection sensitivity requires enhancement. We introduced the Strand Displacement Amplification (SDA) technique to address this limitation, proposing a strategy of novel programmable DNA tweezers-SDA ultrasensitive signal amplification fluorescence sensing. We specifically investigate the effectiveness of this approach concerning signal amplification for two critical mycotoxins: aflatoxin B1 (AFB1) and zearalenone (ZEN). Results indicate that the detection ranges of AFB1 and ZEN via this strategy were 1-10,000 pg mL -1 and 10-100,000 pg mL -1, respectively, with corresponding detection limits of 0.933 pg mL -1 and 1.07 pg mL -1. Compared with the DNA tweezers direct detection method for mycotoxins, the newly constructed programmable DNA tweezers-SDA fluorescence sensing strategy achieved a remarkable 104-fold increase in the detection sensitivity for AFB1 and ZEN. SIGNIFICANCE The constructed programmable DNA tweezers-SDA ultrasensitive signal-amplified fluorescence sensing strategy exhibits excellent detection performance for mycotoxins. The superb versatility of this strategy allows the developed method to be easily used for detecting other analytes by simply replacing the aptamer and cDNA, which has incredible potential in various fields such as food safety screening, clinical diagnostics, and environmental analysis.
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Affiliation(s)
- Yingao Yang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zixuan Zhou
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yifen Guo
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China; Department of Family Planning, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Ruipeng Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Daoming Tian
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
| | - Huanying Zhou
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
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3
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Wang J, Zhang X, Shi P, Cao B, Wang B. A DNA Finite-State Machine Based on the Programmable Allosteric Strategy of DNAzyme. Int J Mol Sci 2023; 24:ijms24043588. [PMID: 36834996 PMCID: PMC9963683 DOI: 10.3390/ijms24043588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 02/16/2023] Open
Abstract
Living organisms can produce corresponding functions by responding to external and internal stimuli, and this irritability plays a pivotal role in nature. Inspired by such natural temporal responses, the development and design of nanodevices with the ability to process time-related information could facilitate the development of molecular information processing systems. Here, we proposed a DNA finite-state machine that can dynamically respond to sequential stimuli signals. To build this state machine, a programmable allosteric strategy of DNAzyme was developed. This strategy performs the programmable control of DNAzyme conformation using a reconfigurable DNA hairpin. Based on this strategy, we first implemented a finite-state machine with two states. Through the modular design of the strategy, we further realized the finite-state machine with five states. The DNA finite-state machine endows molecular information systems with the ability of reversible logic control and order detection, which can be extended to more complex DNA computing and nanomachines to promote the development of dynamic nanotechnology.
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Affiliation(s)
- Jun Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Xiaokang 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
| | - Ben Cao
- 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
- Correspondence: ; Tel.: +86-0411-87402106
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4
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Zhao L, He X, Liu Y, Wei M, Jin H. Development of a simple and rapid fluorescent aptasensor based on
DNA
tweezer. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luyang Zhao
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control Henan University of Technology Zhengzhou People's Republic of China
| | - Xing He
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control Henan University of Technology Zhengzhou People's Republic of China
| | - Yong Liu
- College of Chemistry and Chemical Engineering Henan University Kaifeng People's Republic of China
| | - Min Wei
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control Henan University of Technology Zhengzhou People's Republic of China
| | - Huali Jin
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control Henan University of Technology Zhengzhou People's Republic of China
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5
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Ouyang Y, Zhang P, Willner I. Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures. Bioconjug Chem 2022; 34:51-69. [PMID: 35973134 PMCID: PMC9853509 DOI: 10.1021/acs.bioconjchem.2c00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.
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6
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Bachurin SS, Kletskii ME, Burov ON, Bibov MY, Dobaeva NM, Berezovskiy DP. Oligonucleotides-transformers for molecular biology and nanoengineering. Gene X 2022; 820:146277. [PMID: 35149154 DOI: 10.1016/j.gene.2022.146277] [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: 08/02/2021] [Revised: 01/14/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022] Open
Abstract
In the present review, numerous experimental and theoretical data describing the properties of non-canonical DNA structures (NSs) are analyzed. NSs (G-quadruplex, i-motif, hairpin, and triplex) play an important role in epigenetic processes (including the genetic variability of viruses), are prone to energetically low-cost conformational transformations and can very effectively be used in the design of nanoscale devices. Numerous experimental data have been analyzed in connection with the so-called oligonucleotides-transformers (nucleotide sequences that able to fold not only into one, but also into several NSs). These sequences were recently predicted by our calculations using automata and graph theories ("Dafna" algorithm). Possible applications of the oligonucleotides-transformers in nanoengineering and genetic editing of organisms are considered.
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Affiliation(s)
- Stanislav S Bachurin
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation.
| | - Mikhail E Kletskii
- Chemical Department of Southern Federal University, 7 Zorge Str, Rostov-on-Don 344090, Russian Federation
| | - Oleg N Burov
- Chemical Department of Southern Federal University, 7 Zorge Str, Rostov-on-Don 344090, Russian Federation
| | - Mikhail Yu Bibov
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation
| | - Natalya M Dobaeva
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation
| | - Dmitriy P Berezovskiy
- I.M. Sechenov First Moscow State Medical University (Sechenov University), build. 4, 2 Bolshaya Pirogovskaya Str, Moscow 119435, Russian Federation
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7
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Dong J, Ouyang Y, Wang J, O’Hagan MP, Willner I. Assembly of Dynamic Gated and Cascaded Transient DNAzyme Networks. ACS NANO 2022; 16:6153-6164. [PMID: 35294174 PMCID: PMC9047661 DOI: 10.1021/acsnano.1c11631] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules revealing dynamic, transient assembly and disassembly of G-quadruplex structures and G-quadruplex-based DNAzymes, gated transient processes, and cascaded dynamic transient reactions that involve G-quadruplex and DNAzyme structures. The dynamic transient processes are driven by functional DNA reaction modules activated by a fuel strand and guided toward dissipative operation by a nicking enzyme (Nt.BbvCI). The dynamic networks were further characterized by computational simulation of the experiments using kinetic models, allowing us to predict the dynamic performance of the networks under different auxiliary conditions applied to the systems. The systems reported herein could provide functional DNA machineries for the spatiotemporal control of G-quadruplex structures perturbing gene expression and thus provide a therapeutic means for related emergent diseases.
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8
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Zhao LD, Yang X, Zhong X, zhuo Y. Advances in Electrochemiluminescence Biosensors Based on DNA Walkers. Chempluschem 2022; 87:e202200070. [DOI: 10.1002/cplu.202200070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/19/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Li-Dan Zhao
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - Xia Yang
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - Xia Zhong
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - ying zhuo
- Southwest University College of Chemistry and Chemical Engineering No.2 Tiansheng RoadBeiBei District 400715 Chongqing CHINA
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9
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Tian R, Wang S, Qiu Y, Zong Z, Han T, Zhang Y. DNA tweezers-controlled direct electrical contact of horseradish peroxidase on porous carbon nanotube substrate. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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10
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Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
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Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
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11
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Xu M, Tang D. Recent advances in DNA walker machines and their applications coupled with signal amplification strategies: A critical review. Anal Chim Acta 2021; 1171:338523. [PMID: 34112433 DOI: 10.1016/j.aca.2021.338523] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023]
Abstract
DNA walkers, a type of dynamic nanomachines, have become the subject of burgeoning research in the field of biology. These walkers are powered by driving forces based on strand displacement reactions, protein enzyme/DNAzyme reactions and conformational transitions. With the unique properties of high directionality, flexibility and efficiency, DNA walkers move progressively and autonomously along multiple dimensional tracks, offering abundant and promising applications in biosensing, material assembly and synthesis, and early cancer diagnosis. Notably, DNA walkers identified as signal amplifiers can be combined with various amplification approaches to enhance signal transduction and amplify biosensor sensing signals. Herein, we systematically and comprehensively review the walking principles of various DNA walkers and the recent progress on multiple dimensional tracks by presenting representative examples and an insightful discussion. We also summarized and categorized the diverse signal amplification strategies with which DNA walkers have coupled. Finally, we outline the challenges and future trends of DNA walker machines in emerging analytical fields.
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Affiliation(s)
- Mingdi Xu
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350108, People's Republic of China; Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
| | - Dianping Tang
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
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12
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Zhao S, Yu L, Yang S, Tang X, Chang K, Chen M. Boolean logic gate based on DNA strand displacement for biosensing: current and emerging strategies. NANOSCALE HORIZONS 2021; 6:298-310. [PMID: 33877218 DOI: 10.1039/d0nh00587h] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA computers are considered one of the most prominent next-generation molecular computers that perform Boolean logic using DNA elements. DNA-based Boolean logic gates, especially DNA strand displacement-based logic gates (SDLGs), have shown tremendous potential in biosensing since they can perform the logic analysis of multi-targets simultaneously. Moreover, SDLG biosensors generate a unique output in the form of YES/NO, which is contrary to the quantitative measurement used in common biosensors. In this review, the recent achievements of SDLG biosensing strategies are summarized. Initially, the development and mechanisms of Boolean logic gates, strand-displacement reaction, and SDLGs are introduced. Afterwards, the diversified input and output of SDLG biosensors are elaborated. Then, the state-of-the-art SDLG biosensors are reviewed in the classification of different signal-amplification methods, such as rolling circle amplification, catalytic hairpin assembly, strand-displacement amplification, DNA molecular machines, and DNAzymes. Most importantly, limitations and future trends are discussed. The technology reviewed here is a promising tool for multi-input analysis and lays a foundation for intelligent diagnostics.
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Affiliation(s)
- Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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13
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Chen J, Lin HY, Ji X, Zhao H, Sun B, Wang CL, Zhu M. Host-guest chemistry of giant molecular shape amphiphiles based on POSS-PDI conjugates. NANOSCALE 2021; 13:4295-4300. [PMID: 33595571 DOI: 10.1039/d0nr08934f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Giant shape amphiphiles (GSA) are giant molecules made with nano-building blocks that have distinct shapes. The incompatible packing behaviors of the nano-building blocks of GSA could create cavities within certain conformers of the GSA, but the host-guest chemistry of GSA has not been explored yet. In this study, POSS-PDI-POSS (PPP), which is made by connecting two nano-cubes, isobutyl-polyhedral oligomeric silsesquioxanes (POSS), to a conjugated π-conjugated core, perylene diimide (PDI), is demonstrated as a novel acyclic synthetic host. In its bent conformer, PPP shows a cavity next to its PDI core. Via forming host-guest complexes with π-conjugated guests such as pyrene and perylene, PPP is found to transform from the bent-conformer into the extended-conformer, creating the steric features to accommodate guest molecules. Subsequent thermal annealing of the host-guest complexes removes the π-conjugated guests and restores the bent conformation and photophysical properties of PPP, which verifies that PPP, as a novel acyclic host, is capable of dynamic host-guest assembly. Moreover, the results prove that cavities at the molecular level can be created by connecting nano-building blocks with distinct shapes. This finding may inspire developments in the host-guest chemistry of GSA and nanomaterial innovation.
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Affiliation(s)
- Jia Chen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Center for Advanced Low-Dimension Materials, Donghua University, 201620, Shanghai, P. R. China.
| | - Heng-Yi Lin
- Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsueh Road, Hsin-Chu, 30010, Taiwan.
| | - Xiaohuan Ji
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Center for Advanced Low-Dimension Materials, Donghua University, 201620, Shanghai, P. R. China.
| | - Haoru Zhao
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Center for Advanced Low-Dimension Materials, Donghua University, 201620, Shanghai, P. R. China.
| | - Bin Sun
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Center for Advanced Low-Dimension Materials, Donghua University, 201620, Shanghai, P. R. China.
| | - Chien-Lung Wang
- Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsueh Road, Hsin-Chu, 30010, Taiwan.
| | - Meifang Zhu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Center for Advanced Low-Dimension Materials, Donghua University, 201620, Shanghai, P. R. China.
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14
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Pan J, He Y, Liu Z, Chen J. Dual recognition element-controlled logic DNA circuit for COVID-19 detection based on exonuclease III and DNAzyme. Chem Commun (Camb) 2021; 57:1125-1128. [PMID: 33410447 DOI: 10.1039/d0cc06799g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two fragments of the COVID-19 genome (specific and homologous) were used as two inputs to construct an AND logic gate for COVID-19 detection based on exonuclease III and DNAzyme. The detection sensitivity of the assay can reach fM levels. Satisfactory recovery values were obtained in real sample analysis.
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Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - Ying He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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15
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Zhou Z, Fan D, Wang J, Sohn YS, Nechushtai R, Willner I. Triggered Dimerization and Trimerization of DNA Tetrahedra for Multiplexed miRNA Detection and Imaging of Cancer Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007355. [PMID: 33470517 DOI: 10.1002/smll.202007355] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/06/2020] [Indexed: 05/21/2023]
Abstract
The reversible and switchable triggered reconfiguration of tetrahedra nanostructures from monomer tetrahedra structures into dimer or trimer structures is introduced. The triggered bridging of monomer tetrahedra by K+ -ion-stabilized G-quadruplexes or T-A•T triplexes leads to dimer or trimer tetrahedra structures that are separated by crown ether or basic pH conditions, respectively. The signal-triggered dimerization/trimerization of DNA tetrahedra structures is used to develop multiplexed miRNA-sensing platforms, and the tetrahedra mixture is used for intracellular sensing and imaging of miRNAs.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Daoqing Fan
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Jianbang Wang
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yang Sung Sohn
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Rachel Nechushtai
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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17
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Xu M, Lin L, Li N, Jiang X, Li J, Gong L, Zhuang J. Nanoscale assembly line composed of dual DNA-machines enabling sensitive microRNA detection using upconversion nanoparticles probes. J Pharm Biomed Anal 2020; 195:113842. [PMID: 33358621 DOI: 10.1016/j.jpba.2020.113842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022]
Abstract
DNA machines are smart artificial devices that perform well-organized DNA hybridization reactions or nanoscale mechanical movements. Herein, a nanoscale assembly line composing of dual DNA machines is meticulously designed by coupling a catalytic hairpin assembly (CHA)-based machine with a 3D DNA walker machine. Equipped with upconversion nanoparticles (UCNPs) as signal tags, the dual DNA machines-based assembly line (DDMAL) can efficiently amplify the fluorescent signal of target recognition event, enabling sensitive detection of microRNA (miRNA). In detail, once activated by target miRNA-21, the CHA machine is initiated to constantly produce a single-stranded DNA (named binding DNA) via the strand displacement reaction. The binding DNA as a trigger factor can initiate the DNA walker machine by linking a walking strand DNA with an anchor strand DNA immobilized on the surface of magnetic beads (MBs). The movement of walking strand on the surface of MBs is then driven by Mn2+-dependent DNAzyme formed through the hybridization of walking strand with a UCNPs-linked substrate strand. The DNAzyme-catalyzed cleavage of substrate strand is accompanied by the release of numerous UCNPs from MBs. By measuring the fluorescent signal of released UCNPs after the magnetic separation, target miRNA-21 can be detected by the DDMAL system in a linear range from 1.0 fM to 10 nM, with a limit of detection (LOD) of 0.62 fM (3σ). Moreover, the practicability of DDMAL system was demonstrated by using it to evaluate the expression levels of miRNA-21 in cell lines and assay miRNA-21 in human serum.
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Affiliation(s)
- Mingdi Xu
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China.
| | - Lang Lin
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China
| | - Ning Li
- The Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, School of Pharmacy, Fujian Medical University, Fuzhou, 350122, PR China
| | - Xiaoyu Jiang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China
| | - Jingling Li
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China
| | - Lingzhu Gong
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China
| | - Junyang Zhuang
- The Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, School of Pharmacy, Fujian Medical University, Fuzhou, 350122, PR China.
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18
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Yue L, Wang S, Zhou Z, Willner I. Nucleic Acid Based Constitutional Dynamic Networks: From Basic Principles to Applications. J Am Chem Soc 2020; 142:21577-21594. [DOI: 10.1021/jacs.0c09891] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liang Yue
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhixin Zhou
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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19
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Yue L, Wang S, Willner I. Functional Constitutional Dynamic Networks Revealing Evolutionary Reproduction/Variation/Selection Principles. J Am Chem Soc 2020; 142:14437-14442. [PMID: 32787246 PMCID: PMC7498142 DOI: 10.1021/jacs.0c05669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Indexed: 12/27/2022]
Abstract
Within the broad research efforts to engineer chemical pathways to yield high-throughput evolutionary synthesis of genes and their screening for dictated functionalities, we introduce the evolution of nucleic-acid-based constitutional dynamic networks (CDNs) that follow reproduction/variation/selection principles. These fundamental principles are demonstrated by assembling a library of nucleic-acid strands and hairpins as functional modules for evolving networks. Primary T1-initiated selection of components from the library assembles a parent CDN X, where the evolved constituents exhibit catalytic properties to cleave the hairpins in the library. Cleavage of the hairpins yields fragments, which reproduces T1 to replicate CDN X, whereas the other fragments T2 and T3 select other components to evolve two other CDNs, Y and Z (variation). By applying appropriate counter triggers, we demonstrate the guided selection of networks from the evolved CDNs. By integrating additional hairpin substrates into the system, CDN-dictated emergent catalytic transformations are accomplished. The study provides pathways to construct evolutionary dynamic networks revealing enhanced gated and cascaded functions.
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Affiliation(s)
- Liang Yue
- Institute of Chemistry, The Center
for Nanoscience and Nanotechnology, The
Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, The Center
for Nanoscience and Nanotechnology, The
Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Center
for Nanoscience and Nanotechnology, The
Hebrew University of Jerusalem, Jerusalem 91904, Israel
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20
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Yang P, Zhang KW, Peng X, Chai YQ, Yuan R, Liang WB. An orbitron-like 3D DNA clip-based nanomachine and its application for sensitive fluorescent bioassay of MicroRNA. Anal Chim Acta 2020; 1126:24-30. [PMID: 32736721 DOI: 10.1016/j.aca.2020.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/07/2020] [Accepted: 06/01/2020] [Indexed: 11/19/2022]
Abstract
Herein, an orbitron-like three-dimensional (3D) DNA clip-based nanomachine was proposed for ultrasensitive fluorescent bioassay of microRNA, which was constructed by mechanically interlocking double-DNA-ring with two single-stranded DNAs, performing an orbitron-like 3D structure with double freely rotated DNA rings as the open state. In the presence of target microRNA, the proposed orbitron-like 3D DNA clip can alter its structure from open to closed state in identification of the target microRNA, generating the closure between the previously modified fluorescent dyes and the quenchers to perform a "signal off" fluorescent signal correlated with the concentration of target microRNA. Compared with the normal DNA nanomachines, such as DNA tweezers constructed by self-assembly of three single-stranded DNAs which regulated the open and closed states on the basis of linear conformational changes, the proposed 3D DNA clip-based nanomachine with high mechanical rigidity realized the conformational changes in 3D space with the assistance of target microRNA, which could effectively increase the adjustable distance range and reduce the background signal. Furthermore, the 3D DNA clip-based nanomachine was applied in the fluorescent detection of microRNA-21 with favorable performances for the sensitive detection of microRNA in cells, providing a new avenue for early clinical diagnoses of disease.
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Affiliation(s)
- Peng Yang
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Kai-Wei Zhang
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Xin Peng
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ya-Qin Chai
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wen-Bin Liang
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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21
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Rossetti M, Bertucci A, Patiño T, Baranda L, Porchetta A. Programming DNA-Based Systems through Effective Molarity Enforced by Biomolecular Confinement. Chemistry 2020; 26:9826-9834. [PMID: 32428310 DOI: 10.1002/chem.202001660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
The fundamental concept of effective molarity is observed in a variety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To control molecular encountering and promote effective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of a number of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Lorena Baranda
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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22
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He M, Lehn JM. Time-Dependent Switching of Constitutional Dynamic Libraries and Networks from Kinetic to Thermodynamic Distributions. J Am Chem Soc 2019; 141:18560-18569. [DOI: 10.1021/jacs.9b09395] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Meixia He
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
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23
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Yue L, Wang S, Wulf V, Willner I. Stiffness-switchable DNA-based constitutional dynamic network hydrogels for self-healing and matrix-guided controlled chemical processes. Nat Commun 2019; 10:4774. [PMID: 31636256 PMCID: PMC6803638 DOI: 10.1038/s41467-019-12697-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/26/2019] [Indexed: 12/31/2022] Open
Abstract
Constitutional dynamic networks (CDNs) attract interest as signal-triggered reconfigurable systems mimicking natural networks. The application of CDNs to control material properties is, however, a major challenge. Here we report on the design of a CDN consisting of four toehold-modified constituents, two of which act as bidentate units for chain-elongating, while the other two form a tetradentate structure acting as a crosslinking unit. Their hybridization yields a hydrogel of medium stiffness controlled by the balance between bidentate and tetradentate units. Stabilization of the tetradentate constituent by an auxiliary effector up-regulates the crosslinking unit, yielding a high-stiffness hydrogel. Conversely, stabilization of one of the bidentate constituents by an orthogonal effector enriches the chain-elongation units leading to a low-stiffness hydrogel. Using appropriate counter effectors, the hydrogels are reversibly switched across low-, medium- and high-stiffness states. The hydrogels are used to develop self-healing and controlled drug-release matrices and functional materials for operating biocatalytic cascades. Dynamic hydrogels with controllable properties are of interest for a range of applications. Here, the authors report on a DNA hydrogel system which can be tailored to have reversible mechanical changes, reversible shape changes, is self-healing and can be used for controlled release applications.
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Affiliation(s)
- Liang Yue
- Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Shan Wang
- Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Verena Wulf
- Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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24
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Zhou Z, Zhang P, Yue L, Willner I. Triggered Interconversion of Dynamic Networks Composed of DNA-Tetrahedra Nanostructures. NANO LETTERS 2019; 19:7540-7547. [PMID: 31549514 DOI: 10.1021/acs.nanolett.9b03606] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Constitutional dynamic networks (CDNs) consisting of DNA tetrahedra allow the dynamically triggered adaptive control over the compositions and structures of the constituents. In one system, a CDN consisting of four tetrahedra constituents is orthogonally triggered by two alternative triggers, T1 or T2, to reconfigure into two different CDNs, revealing adaptive control-over the tetrahedra compositions in the two CDNs. In the presence of the counter triggers T1' or T2', the parent CDN is regenerated. In the second system, the assembly of a CDN consisting of four dimeric tetrahedra exhibiting variable sizes and shapes is described. The orthogonal triggering of the CDN by two different triggers T3 or T4, leads to the adaptive reconfiguration of the CDN into new equilibrated CDNs exhibiting control-over the compositions and shapes of the dimeric tetrahedra comprising the CDNs. Mg2+-ion-dependent DNAzyme units conjugated to the tetrahedra nanostructures and complementary electrophoretic experiments provide means to quantitatively evaluate the compositions of the different CDN systems. By the functionalization of the four-tetrahedra-based CDN system with two fluorophor donor-acceptor pairs and the orthogonal reconfiguration of the CDN in the presence of two alternative triggers, the control-over the FRET functions of the CDN systems is demonstrated.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Pu Zhang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Liang Yue
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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25
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Yue L, Wulf V, Wang S, Willner I. Evolution of Nucleic‐Acid‐Based Constitutional Dynamic Networks Revealing Adaptive and Emergent Functions. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Liang Yue
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Verena Wulf
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Shan Wang
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Itamar Willner
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
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26
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Yue L, Wulf V, Wang S, Willner I. Evolution of Nucleic-Acid-Based Constitutional Dynamic Networks Revealing Adaptive and Emergent Functions. Angew Chem Int Ed Engl 2019; 58:12238-12245. [PMID: 31243855 DOI: 10.1002/anie.201905235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Indexed: 12/12/2022]
Abstract
The evolution of networks is a fundamental unresolved issue in developing the area of systems chemistry. We introduce a versatile rewiring mechanism that leads to the emergence of nucleic-acid-based constitutional dynamic networks (CDNs). A two-component constituent AA' functionalized with a Mg2+ -ion-dependent DNAzyme activator unit forms a complex with an intact hairpin HBB' composed of B and B' sequences. Cleavage of HBB' leads to the two-component constituent BB', and its rewiring with AA' yields CDN X composed of the equilibrated constituents AA', AB', BA', and BB'. In analogy, subjecting AA' to an intact hairpin HCC' leads to the formation of CDN Y consisting of AA', AC', CA', and CC'. Subjecting AA' to the mixture of HBB' and HCC' evolves the [3×3] CDN Z, composed of nine constituents, thus demonstrating hierarchical adaptive properties. Furthermore, the DNAzyme units associated with the constituents are applied to tailor emerging catalytic functions from the different CDNs.
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Affiliation(s)
- Liang Yue
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Verena Wulf
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Shan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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27
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Yue L, Wang S, Willner I. Triggered reversible substitution of adaptive constitutional dynamic networks dictates programmed catalytic functions. SCIENCE ADVANCES 2019; 5:eaav5564. [PMID: 31093526 PMCID: PMC6510552 DOI: 10.1126/sciadv.aav5564] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/26/2019] [Indexed: 05/22/2023]
Abstract
The triggered substitution of networks and their resulting functions play an important mechanism in biological transformations, such as intracellular metabolic pathways and cell differentiation. We describe the triggered, cyclic, reversible intersubstitution of three nucleic acid-based constitutional dynamic networks (CDNs) and the programmed catalytic functions guided by the interconverting CDNs. The transitions between the CDNs are activated by nucleic acid strand displacement processes acting as triggers and counter triggers, leading to the adaptive substitution of the constituents and to emerging catalytic functions dictated by the compositions of the different networks. The quantitative evaluation of the compositions of the different CDNs is achieved by DNAzyme reporters and complementary electrophoresis experiments. By coupling a library of six hairpins to the interconverting CDNs, the CDN-guided, emerging, programmed activities of three different biocatalysts are demonstrated. The study has important future applications in the development of sensor systems, finite-state logic devices, and selective switchable catalytic assemblies.
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28
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Li F, Xiao M, Pei H. DNA‐Based Chemical Reaction Networks. Chembiochem 2019; 20:1105-1114. [DOI: 10.1002/cbic.201800721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Fan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound ImagingLaboratory of Evolutionary TheranosticsSchool of Biomedical EngineeringHealth Science CenterShenzhen University Nanhai Avenue 3688 518060 Shenzhen Guangzhou P.R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
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29
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Yang F, Zhong X, Jiang X, Zhuo Y, Yuan R, Wei S. An ultrasensitive aptasensor based on self-enhanced Au nanoclusters as highly efficient electrochemiluminescence indicator and multi-site landing DNA walker as signal amplification. Biosens Bioelectron 2019; 130:262-268. [PMID: 30771715 DOI: 10.1016/j.bios.2019.01.057] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/03/2019] [Accepted: 01/21/2019] [Indexed: 12/16/2022]
Abstract
Gold nanoclusters (Au NCs) have been shown to be prospective nanoscale electrochemiluminescence (ECL) materials that are being extensively explored in bioanalysis. However, the low ECL efficiency of Au NCs has been a bottleneck barrier for their better bioapplications. To overcome this disadvantage, a low oxidation potential co-reactant N,N-diisopropylethylenediamine (DPEA) was first used to prepare self-enhanced Au NCs (Au-DPEA NCs) for drastically enhancing the ECL efficiency of Au NCs in this study. In addition, an efficient multi-site landing DNA walker with multidirectional motion track and rapid payloads release compared to directional DNA walker was constructed for converting target mucin 1 (MUC1) to intermediate DNA and achieving significant signal amplification. On the basis of the Au-DPEA NCs as efficient ECL signal labels and multi-site landing DNA walker as signal amplification strategy, an ECL aptasensor was established for the ultrasensitive detection of MUC1 in the range from 1 fg mL-1 to 1 ng mL-1 with a limit of detection down to 0.54 fg mL-1. The results demonstrated that the present study opened a new research direction for the development of high-efficiency Au NCs indicator as well as ultrasensitive ECL sensing platform for applications in clinical and bioanalysis.
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Affiliation(s)
- Fang Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xia Zhong
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xinya Jiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing 408100, PR China
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Shaping Wei
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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30
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Yu Y, Zhou Y, Zhu M, Su G, Deng H, Chen W, Peng H. Dynamic split G-quadruplex programmed reversible nanodevice. Chem Commun (Camb) 2019; 55:389-392. [PMID: 30540300 DOI: 10.1039/c8cc08744j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We propose a dynamic nanodevice based on a split G-quadruplex (G4). By splitting it apart, we can successfully decouple the G-tetrad formation from external stimuli, greatly expanding the stimulus for G4 based devices. Taking advantage of the rigid force from a DNA duplex, the nanodevice can be switched reversibly through the conformational transformation.
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Affiliation(s)
- Yanyan Yu
- School of pharmacy, Nantong University, Nantong 226001, Jiangsu Province, China.
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31
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Men G, Lehn JM. Multiple adaptation of constitutional dynamic networks and information storage in constitutional distributions of acylhydrazones. Chem Sci 2019; 10:90-98. [PMID: 30713621 PMCID: PMC6333171 DOI: 10.1039/c8sc03858a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/25/2018] [Indexed: 01/07/2023] Open
Abstract
We report a study of the behavior of four dynamic covalent libraries (DCLs) based on acylhydrazones aAbB and of the corresponding square constitutional dynamic networks (CDNs) NA-ND under the effect of three agents, namely, metal cations, base + metal cations and light irradiation; in particular, the successful switching of the CDN NB between two orthogonal distributions results, respectively, from metallo-selection and photo-selection. The four DCLs undergo triple adaptation when subjected to the three agents with the generation of specific CDN distributions characteristic of each of the four DCLs. The ternary outputs displayed by the DCLs present three states (-1, 0 and 1) related to three different constitutional distributions expressed in response to the triple inputs applied. This latter process amounts to the storage of molecular information in dynamic distributions rather than in selective interactions between complementary entities undergoing molecular recognition.
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Affiliation(s)
- Guangwen Men
- Laboratoire de Chimie Supramoléculaire , Institut de Science et d'Ingénierie Supramoléculaires , Université de Strasbourg , 8 allée Gaspard Monge , 67000 Strasbourg , France . ; ; Tel: +33 3 68 85 51 44
- State Key Laboratory of Supramolecular Structure and Materials , Jilin University , 2699 Qianjin Avenue , Changchun , 130012 , P. R. China
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire , Institut de Science et d'Ingénierie Supramoléculaires , Université de Strasbourg , 8 allée Gaspard Monge , 67000 Strasbourg , France . ; ; Tel: +33 3 68 85 51 44
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32
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Zhou Z, Liu X, Yue L, Willner I. Controlling the Catalytic and Optical Properties of Aggregated Nanoparticles or Semiconductor Quantum Dots Using DNA-Based Constitutional Dynamic Networks. ACS NANO 2018; 12:10725-10735. [PMID: 30256615 DOI: 10.1021/acsnano.8b05452] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nucleic acid-based constitutional dynamic networks (CDNs) attract growing interest as a means to mimic complex biological networks. The triggered stabilization of the CDNs allows the dictated guided reversible reconfiguration and re-equilibration of the CDNs to other CDN configurations, where some of the constituents are up-regulated, while other constituents are down-regulated. Although substantial progress in controlling the adaptive dynamic control of the compositions of networks by means of auxiliary triggers was demonstrated, the use of CDNs as active ensembles for controlling chemical functionalities is still a challenge. We report on the assembly of signal-triggered CDN systems that guide the switchable aggregation of Au nanoparticles (NPs), thereby controlling their plasmonic properties and their catalytic functions (Au NPs-catalyzed oxidation of l-DOPA to dopachrome). In addition, we demonstrate that the triggered and orthogonal up-regulation and down-regulation of the constituents of the CDNs leads to the dictated aggregation of different-sized CdSe/ZnS quantum dots (QDs), cross-linked by K+-ion-stabilized G-quadruplex units. The incorporation of hemin into the G-quadruplex cross-linking units yields horseradish peroxidase-mimicking DNAzyme units that catalyze the generation of chemiluminescence via the oxidation of luminol by H2O2. The resulting chemiluminescence stimulates the chemiluminescence resonance energy transfer (CRET) process to the QDs, resulting in the luminescence of the two-sized QDs. By the application of appropriate triggers, the CDN-dictated up-regulation and down-regulation of the different-sized QDs aggregates are demonstrated, and the control over the photophysical functions of the different-sized QDs, by means of the CDNs, is highlighted.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Xia Liu
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Liang Yue
- 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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33
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Zhou Z, Yue L, Wang S, Lehn JM, Willner I. DNA-Based Multiconstituent Dynamic Networks: Hierarchical Adaptive Control over the Composition and Cooperative Catalytic Functions of the Systems. J Am Chem Soc 2018; 140:12077-12089. [DOI: 10.1021/jacs.8b06546] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liang Yue
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jean-Marie Lehn
- Institut de Science et d’Ingénierie Supramoléculaires (ISIS), University of Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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34
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Wang S, Yue L, Li Z, Zhang J, Tian H, Willner I. Light‐Induced Reversible Reconfiguration of DNA‐Based Constitutional Dynamic Networks: Application to Switchable Catalysis. Angew Chem Int Ed Engl 2018; 57:8105-8109. [DOI: 10.1002/anie.201803371] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Shan Wang
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Liang Yue
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Zi‐Yuan Li
- Key Laboratory for Advanced MaterialsSchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai China
| | - Junji Zhang
- Key Laboratory for Advanced MaterialsSchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai China
| | - He Tian
- Key Laboratory for Advanced MaterialsSchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai China
| | - Itamar Willner
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
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35
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Wang S, Yue L, Li Z, Zhang J, Tian H, Willner I. Light‐Induced Reversible Reconfiguration of DNA‐Based Constitutional Dynamic Networks: Application to Switchable Catalysis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803371] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shan Wang
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Liang Yue
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Zi‐Yuan Li
- Key Laboratory for Advanced MaterialsSchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai China
| | - Junji Zhang
- Key Laboratory for Advanced MaterialsSchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai China
| | - He Tian
- Key Laboratory for Advanced MaterialsSchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai China
| | - Itamar Willner
- Institute of ChemistryThe Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
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36
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Yue L, Wang S, Lilienthal S, Wulf V, Remacle F, Levine RD, Willner I. Intercommunication of DNA-Based Constitutional Dynamic Networks. J Am Chem Soc 2018; 140:8721-8731. [DOI: 10.1021/jacs.8b03450] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Liang Yue
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Sivan Lilienthal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Verena Wulf
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Françoise Remacle
- Department of Chemistry, University of Liege, B6c, 4000 Liege, Belgium
| | - R. D. Levine
- 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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37
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Harroun SG, Prévost-Tremblay C, Lauzon D, Desrosiers A, Wang X, Pedro L, Vallée-Bélisle A. Programmable DNA switches and their applications. NANOSCALE 2018; 10:4607-4641. [PMID: 29465723 DOI: 10.1039/c7nr07348h] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.
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Affiliation(s)
- Scott G Harroun
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada.
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