1
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Wu R, Chen Y, Zhang Y, Liu R, Zhang Q, Zhang C. Catalytic Gold Nanoparticle Assembly Programmed by DNAzyme Circuits. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307107. [PMID: 38191832 DOI: 10.1002/smll.202307107] [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: 08/17/2023] [Revised: 12/19/2023] [Indexed: 01/10/2024]
Abstract
Assembled gold nanoparticle (AuNP) superstructures can generate unique physicochemical characteristics and be used in various applications, thus becoming an attractive research field. Recently, several DNA-assisted gold nanoparticle assembly methods have been rigorously developed that typically require a non-catalytic equimolar molecular assembly to guarantee the designed assembly. Although efficient and accurate, exploring such non-catalytic nanoparticle assemblies in the complex cellular milieu under low trigger concentrations remains challenging. Therefore, developing a catalytic method that facilitates gold nanoparticle assemblies with relatively low DNA trigger concentrations is desirable. In this report, a catalytic method to program gold nanoparticle assemblies by DNAzyme circuits is presented, where only a small number of DNA triggers are able to induce the production of a large number of the desired nanoparticle assemblies. The feasibility of using logic DNAzyme circuits to control catalytic nanoparticle assemblies is experimentally verified. Additionally, catalytic AuNP assembly systems are established with cascading and feedback functions. The work provides an alternative research direction to enrich the tool library of nanoparticle assembly and their application in biosensing and nanomedicine.
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Affiliation(s)
- Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yiming Chen
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
| | - Yongpeng Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 100096, China
| | - Rongming Liu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Cheng Zhang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
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2
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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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3
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Zhang Y, Yang C, He J, Li M, Yuan R, Xu W. Ratiometric Fluorescence Biosensing of Tandem Biemissive Ag Clusters Boosted by Confined Catalytic DNA Assembly. Anal Chem 2023; 95:17928-17936. [PMID: 37971735 DOI: 10.1021/acs.analchem.3c04388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The reaction kinetics and yield of traditional DNA assembly with a low local concentration in homogeneous solution remain challenging. Exploring confined catalytic DNA assembly (CCDA) is intriguing to boost the reaction rate and efficacy for creating rapid and sensitive biosensing platforms. A rolling circle amplification (RCA) product containing multiple tandem repeats is a natural scaffold capable of guiding the periodic assembly of customized functional probes at precise sites. Here, we present a RCA-confined CCDA strategy to speed up amplifiable conversion for ratiometric fluorescent sensing of a sequence-specific inducer (I*) by using string green-/red-Ag clusters (sgAgCs and srAgCs) as two counterbalance emitters. Upon recognition of I*, CCDA events are operated by two toehold-mediated strand displacements and localized in repetitive units, thereby releasing I* for recycled signal amplification in the as-grown RCA concatemer. The local concentration of reactive species is increased to facilitate rapider dsDNA complex assembly and more efficient input-output conversion, on which the clustering template sequences of sgAgCs and srAgCs are blocked and opened, enabling srAgCs synthesis but opposite to sgAgCs. Thus, the fluorescence emission of srAgCs goes up, while sgAgCs go down. With the resultant ratio featuring inherent built-in correction, rapid, sensitive, and accurate quantification of I* at the picomolar level is achieved. Benefiting from efficient RCA confinement to enhance reaction kinetics and conversion yield, this CCDA-based strategy provides a new paradigm for developing simple and diverse biosensing methodologies.
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Affiliation(s)
- Yuqing Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chunli Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Mengdie Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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4
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Ouyang Y, Dong J, Willner I. Dynamic DNA Networks-Guided Directional and Orthogonal Transient Biocatalytic Cascades. J Am Chem Soc 2023; 145:22135-22149. [PMID: 37773962 PMCID: PMC10571085 DOI: 10.1021/jacs.3c08020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Indexed: 10/01/2023]
Abstract
DNA frameworks, consisting of constitutional dynamic networks (CDNs) undergoing fuel-driven reconfiguration, are coupled to a dissipative reaction module that triggers the reconfigured CDNs into a transient intermediate CDNs recovering the parent CDN state. Biocatalytic cascades consisting of the glucose oxidase (GOx)/horseradish peroxidase (HRP) couple or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) couple are tethered to the constituents of two different CDNs, allowing the CDNs-guided operation of the spatially confined GOx/HRP or LDH/NAD+ biocatalytic cascades. By applying two different fuel triggers, the directional transient CDN-guided upregulation/downregulation of the two biocatalytic cascades are demonstrated. By mixing the GOx/HRP-biocatalyst-modified CDN with the LDH/NAD+-biocatalyst-functionalized CDN, a composite CDN is assembled. Triggering the composite CDN with two different fuel strands results in orthogonal transient upregulation of the GOx/HRP cascade and transient downregulation of the LDH/NAD+ cascade or vice versa. The transient CDNs-guided biocatalytic cascades are computationally simulated by kinetic models, and the computational analyses allow the prediction of the performance of transient biocatalytic cascades under different auxiliary conditions. The concept of orthogonally triggered temporal, transient, biocatalytic cascades by means of CDN frameworks is applied to design an orthogonally operating CDN for the temporal upregulated or downregulated transient thrombin-induced coagulation of fibrinogen to fibrin.
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Affiliation(s)
- Yu Ouyang
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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5
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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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6
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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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7
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Li Z, Wang J, Willner I. Alternate Strategies to Induce Dynamically Modulated Transient Transcription Machineries. ACS NANO 2023; 17:18266-18279. [PMID: 37669432 PMCID: PMC10540262 DOI: 10.1021/acsnano.3c05336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023]
Abstract
Emulating native transient transcription machineries modulating temporal gene expression by synthetic circuits is a major challenge in the area of systems chemistry. Three different methods to operate transient transcription machineries and to modulate the gated transcription processes of target RNAs are introduced. One method involves the design of a reaction module consisting of transcription templates being triggered by promoter fuel strands transcribing target RNAs and in parallel generating functional DNAzymes in the transcription templates, modulating the dissipative depletion of the active templates and the transient operation of transcription circuits. The second approach involves the application of a reaction module consisting of two transcription templates being activated by a common fuel promoter strand. While one transcription template triggers the transcription of the target RNA, the second transcription template transcribes the anti-fuel strand, displacing the promoter strand associated with the transcription templates, leading to the depletion of the transcription templates and to the dynamic transient modulation of the transcription process. The third strategy involves the assembly of a reaction module consisting of a reaction template triggered by a fuel promoter strand transcribing the target RNA. The concomitant nickase-stimulated depletion of the promoter strand guides the transient modulation of the transcription process. Via integration of two parallel fuel-triggered transcription templates in the three transcription reaction modules and application of template-specific blocker units, the parallel and gated transiently modulated transcription of two different RNA aptamers is demonstrated. The nickase-stimulated transiently modulated transcription reaction module is applied as a functional circuit guiding the dynamic expression of gated, transiently operating, catalytic DNAzymes.
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Affiliation(s)
| | | | - Itamar Willner
- The Institute of Chemistry, The Center
for Nanoscience and Nanotechnology, The
Hebrew University of Jerusalem, Jerusalem 91904, Israel
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8
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Rao A, Roy S, Jain V, Pillai PP. Nanoparticle Self-Assembly: From Design Principles to Complex Matter to Functional Materials. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25248-25274. [PMID: 35715224 DOI: 10.1021/acsami.2c05378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The creation of matter with varying degrees of complexities and desired functions is one of the ultimate targets of self-assembly. The ability to regulate the complex interactions between the individual components is essential in achieving this target. In this direction, the initial success of controlling the pathways and final thermodynamic states of a self-assembly process is promising. Despite the progress made in the field, there has been a growing interest in pushing the limits of self-assembly processes. The main inception of this interest is that the intended self-assembled state, with varying complexities, may not be "at equilibrium (or at global minimum)", rendering free energy minimization unsuitable to form the desired product. Thus, we believe that a thorough understanding of the design principles as well as the ability to predict the outcome of a self-assembly process is essential to form a collection of the next generation of complex matter. The present review highlights the potent role of finely tuned interparticle interactions in nanomaterials to achieve the preferred self-assembled structures with the desired properties. We believe that bringing the design and prediction to nanoparticle self-assembly processes will have a similar effect as retrosynthesis had on the logic of chemical synthesis. Along with the guiding principles, the review gives a summary of the different types of products created from nanoparticle assemblies and the functional properties emerging from them. Finally, we highlight the reasonable expectations from the field and the challenges lying ahead in the creation of complex and evolvable matter.
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Affiliation(s)
- Anish Rao
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Sumit Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Vanshika Jain
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Pramod P Pillai
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
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9
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O’Hagan M, Duan Z, Huang F, Laps S, Dong J, Xia F, Willner I. Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications. Chem Rev 2023; 123:6839-6887. [PMID: 37078690 PMCID: PMC10214457 DOI: 10.1021/acs.chemrev.3c00016] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Indexed: 04/21/2023]
Abstract
This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.
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Affiliation(s)
- Michael
P. O’Hagan
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Shay Laps
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fan Xia
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Itamar Willner
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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10
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Li Z, Wang J, Willner B, Willner I. Topologically Triggered Dynamic DNA Frameworks. Isr J Chem 2023. [DOI: 10.1002/ijch.202300013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Zhenzhen Li
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Jianbang Wang
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Bilha Willner
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Itamar Willner
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
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11
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Xiang L, Liu LL, Yuan R, Chai YQ. Aggregation-Induced Electrochemiluminescence of Copper Nanoclusters by Regulating Valence State Ratio of Cu(I)/Cu(0) for Ultrasensitive Detection of MicroRNA. Anal Chem 2023; 95:4454-4460. [PMID: 36880263 DOI: 10.1021/acs.analchem.2c05029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
In this work, Cu nanoclusters (Cu NCs) with strong aggregation-induced electrochemiluminescence (AIECL) as emitters were used to construct an ECL biosensor for ultrasensitive detection of microRNA-141 (miR-141). Impressively, the ECL signals enhanced with the increased content of Cu(I) in the aggregative Cu NCs. When the ratio of Cu(I)/Cu(0) in aggregative Cu NCs was 3.2, Cu NCs aggregates showed the highest ECL intensity, in which Cu(I) could enhance the cuprophilic Cu(I)···Cu(I) interaction to form rod-shaped aggregates for restricting nonradiative transitions to obviously improve the ECL response. As a result, the ECL intensity of the aggregative Cu NCs was 3.5 times higher than that of the monodispersed Cu NCs. With the aid of the cascade strand displacement amplification (SDA) strategy, an outstanding ECL biosensor was developed to achieve the ultrasensitive detection of miR-141, whose linear range varied from 10 aM to 1 nM with a detection limit of 1.2 aM. This approach opened an avenue to prepare non-noble metal nanomaterials as robust ECL emitters and provided a new idea for detection of biomolecules for diagnosis of disease.
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Affiliation(s)
- Lian Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Lin-Lei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
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12
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Marchetti A, Gori A, Ferretti AM, Esteban DA, Bals S, Pigliacelli C, Metrangolo P. Templated Out-of-Equilibrium Self-Assembly of Branched Au Nanoshells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206712. [PMID: 36650930 DOI: 10.1002/smll.202206712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Out-of-equilibrium self-assembly of metal nanoparticles (NPs) has been devised using different types of strategies and fuels, but achieving finite 3D structures with a controlled morphology through this assembly mode is still rare. Here, a spherical peptide-gold superstructure (PAuSS) is used as a template to control the out-of-equilibrium self-assembly of Au NPs, obtaining a transient 3D-branched Au-nanoshell (BAuNS) stabilized by sodium dodecyl sulphate (SDS). The BAuNS dismantles upon SDS concentration gradient equilibration over time in the sample solution, leading to NPs disassembly and regression to PAuSS. Notably, BAuNS assembly and disassembly promotes temporary interparticle plasmonic coupling, leading to reversible and tunable changes of their plasmonic properties, a highly desirable behavior in the development of optoelectronic nanodevices.
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Affiliation(s)
- Alessandro Marchetti
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milano, 20131, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche, National Research Council of Italy, Via M. Bianco 9, 20131 and Via G. Fantoli 16/15, Milano, 20138, Italy
| | - Anna Maria Ferretti
- Istituto di Scienze e Tecnologie Chimiche, National Research Council of Italy, Via M. Bianco 9, 20131 and Via G. Fantoli 16/15, Milano, 20138, Italy
| | - Daniel Arenas Esteban
- Department of Physics, Electron microscopy for Materials research (EMAT), University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
| | - Sara Bals
- Department of Physics, Electron microscopy for Materials research (EMAT), University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
| | - Claudia Pigliacelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milano, 20131, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milano, 20131, Italy
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13
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Zhang P, Ouyang Y, Zhuo Y, Chai Y, Yuan R. Recent Advances in DNA Nanostructures Applied in Sensing Interfaces and Cellular Imaging. Anal Chem 2023; 95:407-419. [PMID: 36625113 DOI: 10.1021/acs.analchem.2c04540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pu Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yu Ouyang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China.,Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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14
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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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15
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Kruse J, Sanromán‐Iglesias M, Marauri A, Rivilla I, Grzelczak M. Coupling Reversible Clustering of DNA‐Coated Gold Nanoparticles with Chemothermal Cycloaddition Reaction. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Joscha Kruse
- Donostia International Physics Center (DIPC) Paseo Manuel de Lardizabal 4 20018 Donostia-San Sebastián Spain
- CIC nanoGUNE BRTA Tolosa Hiribidea 76 20018 Donostia-Sebastián Spain
| | - Maria Sanromán‐Iglesias
- Centro de Física de Materiales CSIC-UPV/EHU Paseo Manuel de Lardizabal 5 20018 Donostia San-Sebastián Spain
| | - Aimar Marauri
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) Lardizabal Pasealekua 3 20018 Donostia-San Sebastián Spain
| | - Ivan Rivilla
- Donostia International Physics Center (DIPC) Paseo Manuel de Lardizabal 4 20018 Donostia-San Sebastián Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
| | - Marek Grzelczak
- Donostia International Physics Center (DIPC) Paseo Manuel de Lardizabal 4 20018 Donostia-San Sebastián Spain
- Centro de Física de Materiales CSIC-UPV/EHU Paseo Manuel de Lardizabal 5 20018 Donostia San-Sebastián Spain
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16
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Yi Y, Han Y, Cheng X, Zhang Z, Sun Y, Zhang K, Xu JJ. Three-Dimensional Surface-Enhanced Raman Scattering Platform with Hotspots Built by a Nano-mower for Rapid Detection of MRSA. Anal Chem 2022; 94:17205-17211. [PMID: 36446023 DOI: 10.1021/acs.analchem.2c03834] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the greatest threats to human health due to its strong drug resistance, wide distribution range, and high infection rate. Rapid identification of MRSA strains is very important for accurate diagnosis and early treatment of MRSA infections. Here, we introduced an Exo III-assisted nanomotor mower to build 3D hotspots for rapid detection of MRSA by surface-enhanced Raman scattering (SERS). As the bacteria bound to the aptamer, two trigger chains were released from the double-stranded structure, and the nano-mowers were activated by opening a hairpin probe on gold nanoparticles (AuNPs). With the continued cleavage of Exo III and cyclic release of the trigger chain, multiple hairpin DNAs on the AuNPs were cleaved to increase the motor power. The resulting nano-mower continued slicing protective DNA from larger AuNPs, exposing the AuNPs. Without the protection of DNA, Mg2+ in the buffer induced spontaneous aggregation of the AuNPs, and a large number of hotspots were formed for SERS measurements. Under optimal conditions, MRSA can be detected within 40 min, and the concentration of MRSA showed a good linear relationship with the SERS intensity at 1342 cm-1, with a limit of detection as low as 1 CFU/mL and a wide linear range (100 to 107 CFU/mL). This strategy creates a rapid bacterial detection method that performs well on actual samples utilizing portable Raman spectroscopy instruments, with potential applications in food detection, water detection, clinical treatment, and diagnosis.
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Affiliation(s)
- Yang Yi
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Yunxiang Han
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Xi Cheng
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Zhe Zhang
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Yudie Sun
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Kui Zhang
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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17
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Dong J, O'Hagan MP, Willner I. Switchable and dynamic G-quadruplexes and their applications. Chem Soc Rev 2022; 51:7631-7661. [PMID: 35975685 DOI: 10.1039/d2cs00317a] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO2 nanoparticles or metal-organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.
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Affiliation(s)
- Jiantong Dong
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- 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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18
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Li Z, Wang J, Willner I. Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs. SCIENCE ADVANCES 2022; 8:eabq5947. [PMID: 35977022 PMCID: PMC9385147 DOI: 10.1126/sciadv.abq5947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Following transient spatiotemporal misregulation of gene expression programs by native transcription machineries, we introduce a versatile biomimetic concept to design transient dynamic transcription machineries, revealing gated and cascaded temporal transcription of RNAs. The concept is based on the engineering of the reaction module consisting of malachite green (MG) and/or DFHBI {(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylene]-3,5-dihydro-2,3-dimethyl-4H-imidazol-4-one} DNA scaffolds, T7 RNA polymerase (RNAP) aptamer transcription scaffold, and the inhibited T7 RNAP-aptamer complex. In the presence of the counter RNAP aptamer strand and ribonucleoside triphosphates, the triggered activation of the three transcription scaffolds are activated, leading to the transcription of the MG and/or DFHBI RNA aptamer and to the transcription of the RNAP aptamer acting as an autoinhibitor that leads to the transient temporal, dissipative, and blockage of all transcription. By appropriate design of the transcription scaffolds and the inhibitors/coupler, transient gated and cascaded transcription processes are demonstrated, and a bimodal transcription module synthesizing a transient operating ribozyme is introduced.
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19
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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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20
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Liyana Gunawardana VW, Finnegan TJ, Ward CE, Moore CE, Badjić JD. Dissipative Formation of Covalent Basket Cages. Angew Chem Int Ed Engl 2022; 61:e202207418. [PMID: 35723284 PMCID: PMC9544755 DOI: 10.1002/anie.202207418] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 11/23/2022]
Abstract
Living systems use chemical fuels to transiently assemble functional structures. As a step toward constructing abiotic mimics of such structures, we herein describe dissipative formation of covalent basket cage CBC 5 by reversible imine condensation of cup-shaped aldehyde 2 (i.e., basket) with trivalent aromatic amine 4. This nanosized [4+4] cage (V=5 nm3 , Mw =6150 Da) has shape of a truncated tetrahedron with four baskets at its vertices and four aromatic amines forming the faces. Importantly, tris-aldehyde basket 2 and aliphatic tris-amine 7 undergo condensation to give small [1+1] cage 6. The imine metathesis of 6 and aromatic tris-amine 4 into CBC 5 was optimized to bias the equilibrium favouring 6. Addition of tribromoacetic acid (TBA) as a chemical fuel perturbs this equilibrium to result in the transient formation of CBC 5, with subsequent consumption of TBA via decarboxylation driving the system back to the starting state.
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Affiliation(s)
| | - Tyler J. Finnegan
- Department of Chemistry & BiochemistryThe Ohio State University100 West 18th AvenueColumbusOH 43210USA
| | - Carson E. Ward
- Department of Chemistry & BiochemistryThe Ohio State University100 West 18th AvenueColumbusOH 43210USA
| | - Curtis E. Moore
- Department of Chemistry & BiochemistryThe Ohio State University100 West 18th AvenueColumbusOH 43210USA
| | - Jovica D. Badjić
- Department of Chemistry & BiochemistryThe Ohio State University100 West 18th AvenueColumbusOH 43210USA
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21
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Sharko A, Livitz D, De Piccoli S, Bishop KJM, Hermans TM. Insights into Chemically Fueled Supramolecular Polymers. Chem Rev 2022; 122:11759-11777. [PMID: 35674495 DOI: 10.1021/acs.chemrev.1c00958] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Supramolecular polymerization can be controlled in space and time by chemical fuels. A nonassembled monomer is activated by the fuel and subsequently self-assembles into a polymer. Deactivation of the molecule either in solution or inside the polymer leads to disassembly. Whereas biology has already mastered this approach, fully artificial examples have only appeared in the past decade. Here, we map the available literature examples into four distinct regimes depending on their activation/deactivation rates and the equivalents of deactivating fuel. We present increasingly complex mathematical models, first considering only the chemical activation/deactivation rates (i.e., transient activation) and later including the full details of the isodesmic or cooperative supramolecular processes (i.e., transient self-assembly). We finish by showing that sustained oscillations are possible in chemically fueled cooperative supramolecular polymerization and provide mechanistic insights. We hope our models encourage the quantification of activation, deactivation, assembly, and disassembly kinetics in future studies.
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Affiliation(s)
| | - Dimitri Livitz
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | | | - Kyle J M Bishop
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Thomas M Hermans
- University of Strasbourg & CNRS, UMR7140, Strasbourg 67000, France
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22
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Badjic JD, Liyana Gunawardana VW, Finnegan TJ, Ward CE, Moore CE. Dissipative Formation of Covalent Basket Cages. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jovica D Badjic
- Ohio State University Department of Chemistry 100 W. 18th Avenue 43210 Columbus UNITED STATES
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23
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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: 67] [Impact Index Per Article: 33.5] [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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24
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Polymer-assisted Au@PDA nanoparticles lyophilized powder with high stability and low adsorption and its application in colorimetric biosensing. Anal Chim Acta 2022; 1220:339995. [DOI: 10.1016/j.aca.2022.339995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/27/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022]
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25
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He JY, Deng HL, Shang X, Yang CL, Zuo SY, Yuan R, Liu HY, Xu WJ. Modulating the Fluorescence of Silver Nanoclusters Wrapped in DNA Hairpin Loops via Confined Strand Displacement and Transient Concatenate Ligation for Amplifiable Biosensing. Anal Chem 2022; 94:8041-8049. [PMID: 35617342 DOI: 10.1021/acs.analchem.2c01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
It is intriguing to modulate the fluorescence emission of DNA-scaffolded silver nanoclusters (AgNCs) via confined strand displacement and transient concatenate ligation for amplifiable biosensing of a DNA segment related to SARS-CoV-2 (s2DNA). Herein, three stem-loop structural hairpins for signaling, recognizing, and assisting are designed to assemble a variant three-way DNA device (3WDD) with the aid of two linkers, in which orange-emitting AgNC (oAgNC) is stably clustered and populated in the closed loop of a hairpin reporter. The presence of s2DNA initiates the toehold-mediated strand displacement that is confined in this 3WDD for repeatable recycling amplification, outputting numerous hybrid DNA-duplex conformers that are implemented for a transient "head-tail-head" tandem ligation one by one. As a result, the oAgNC-hosted hairpin loops are quickly opened in loose coil motifs, bringing a significant fluorescence decay of multiple clusters dependent on s2DNA. Demonstrations and understanding of the tunable spectral performance of a hairpin loop-wrapped AgNC via switching 3WDD conformation would be highly beneficial to open a new avenue for applicable biosensing, bioanalysis, or clinical diagnostics.
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Affiliation(s)
- Jia-Yang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hui-Lin Deng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xin Shang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chun-Li Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Si-Yu Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hong-Yan Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wen-Ju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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26
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Hu O, Li Z, He Q, Tong Y, Tan Y, Chen Z. Fluorescence Biosensor for One-Step Simultaneous Detection of Mycobacterium tuberculosis Multidrug-Resistant Genes Using nanoCoTPyP and Double Quantum Dots. Anal Chem 2022; 94:7918-7927. [PMID: 35594337 DOI: 10.1021/acs.analchem.2c00723] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The diagnosis of multidrug-resistant tuberculosis (MDR-TB) is crucial for the subsequent drug guidance to improve therapy and control the spread of this infectious disease. Herein, we developed a novel florescence biosensor for simultaneous detection of Mycobacterium tuberculosis (Mtb) multidrug-resistant genes (rpoB531 for rifampicin and katG315 for isoniazid) by using our synthesized nanocobalt 5,10,15,20-tetra(4-pyridyl)-21H,23H-porphine (nanoCoTPyP) and double quantum dots (QDs). Several nanoCoTPyPs with different charges and morphology were successfully prepared via the surfactant-assisted method and their quenching ability and restoring efficiency for DNA detection were systematically analyzed. It was found that spherical nanoCoTPyP with positive charge exhibited excellent quenching effect and sensing performance for the two DNAs' detection due to its affinity differences towards single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). ssDNA attached on QDs (QDs-ssDNA) was specifically hybridized with targets to form QDs-dsDNA, resulting in fluorescence recovery due to the disruption of the interactions between nanoCoTPyP and ssDNA. Two drug-resistant genes could be simultaneously quantified in a single run and relatively low limits of detection (LODs) were obtained (24 pM for T1 and 20 pM for T2). Furthermore, the accuracy and reliability of our method were verified by testing clinical samples. This simple and low-cost approach had great potential to be applied in clinical diagnosis of MDR-TB.
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Affiliation(s)
- Ou Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Zeyu Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Qidi He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Yanli Tong
- Guangdong Second Provincial General Hospital, Guangzhou 510317, P. R. China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, P. R. China
| | - Zuanguang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
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27
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Ouyang Y, Zhang P, Willner I. Dissipative biocatalytic cascades and gated transient biocatalytic cascades driven by nucleic acid networks. SCIENCE ADVANCES 2022; 8:eabn3534. [PMID: 35522744 PMCID: PMC9075803 DOI: 10.1126/sciadv.abn3534] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Living systems consist of complex transient cellular networks guiding structural, catalytic, and switchable functions driven by auxiliary triggers, such as chemical or light energy inputs. We introduce two different transient, dissipative, biocatalytic cascades, the coupled glucose oxidase (GOx)/horseradish peroxidase (HRP) glucose-driven oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS2-) to the radical anion (ABTS•-) and the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) lactate-driven reduction of NAD+ to NADH. The transient biocatalytic systems are driven by nucleic acid reaction modules using a nucleic acid fuel strand L1' and a nicking enzyme, Nt.BbvCI, as fuel-degrading catalyst, leading to the dynamic spatiotemporal transient formation of structurally proximate biocatalysts activating the biocatalytic cascades and transient coupled processes, including the generation of chemiluminescence and the synthesis of alanine. Subjecting the mixture of biocatalysts to selective inhibitors allows the gated transient operation of the biocatalysts. The kinetics of transient biocatalytic cascades are accompanied by kinetic models and computational simulations.
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28
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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: 21] [Impact Index Per Article: 10.5] [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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Affiliation(s)
- Jiantong Dong
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Yu Ouyang
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Michael P. O’Hagan
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
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