1
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Cui S, Liu X, Zhang X, Shi P, Zheng Y, Wang B, Zhang Q. Engineering Modular DNA Reaction Networks for Signal Processing. Chemistry 2024; 30:e202400740. [PMID: 38623910 DOI: 10.1002/chem.202400740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/26/2024] [Accepted: 04/16/2024] [Indexed: 04/17/2024]
Abstract
Diversified molecular information-processing methods have significant implications for nanoscale manipulation and control, monitoring and disease diagnosis of organisms, and direct intervention in biological activities. However, as an effective approach for implementing multifunctional molecular information processing, DNA reaction networks (DRNs) with numerous functionally specialized molecular structures have challenged them on scale design, leading to increased network complexity, further causing problems such as signal leakage, attenuation, and cross-talk in network reactions. Our study developed a strategy for performing various signal-processing tasks through engineering modular DRNs. This strategy is based on a universal core unit with signal selection capability, and a time-adjustable signal self-resetting module is achieved by combing the core unit and self-resetting unit, which improves the time controllability of modular DRNs. In addition, multi-input and -output signal cross-catalytic and continuously adjustable signal delay modules were realized by combining core and threshold units, providing a flexible, precise method for modular DRNs to process the signal. The strategy simplifies the design of DRNs, helps generate design ideas for large-scale integrated DRNs with multiple functions, and provides prospects in biocomputing, gene regulation, and biosensing.
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Affiliation(s)
- Shuang Cui
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Bin Wang
- School of Software Engineering, Dalian University, Dalian, 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
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2
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Wang J, Han X, Yu H, Xie G. AND Logic-Gate-Based Dual-Locking Probe System for the Sensitive Detection of microRNA and APE1. Anal Chem 2024; 96:9570-9575. [PMID: 38822787 DOI: 10.1021/acs.analchem.4c01080] [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: 06/03/2024]
Abstract
MicroRNA (miRNA) and apurinic/apyrimidinic endonuclease 1 (APE1) have been reported to be closely associated with cancers, making them potential crucial biomarkers and therapeutic targets. However, focusing on the detection of a single target is not conducive to the diagnosis and prognosis assessment of diseases. In this study, an AND logic-gate-based dual-locking hairpin-mediated catalytic hairpin assembly (DL-CHA) was developed for sensitive and specific detection of microRNA and APE1. By addition of a lock to each of the hairpins, with APE1 and microRNA serving as keys, fluorescence signals could only be detected in the presence of simultaneous stimulation by APE1 and miRNA-224. This indicated that the biosensor could operate as an AND logic gate. DL-CHA exhibited advantages such as a low background, rapid response, and high logic capability. Therefore, the biosensor serves as a novel approach to cancer diagnosis with significant potential applications.
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Affiliation(s)
- Jiani Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
- Sichuan Nursing Vocational College,Chengdu 610100, People's Republic of China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
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3
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Wang L, Luo W, Weng Z, Wang Z, Wu Y, Zhao R, Han X, Liu X, Zhang J, Yang Y, Xie G. Building a stable and robust anti-interference DNA dissipation system by eliminating the accumulation of systemic specified errors. Anal Chim Acta 2024; 1302:342493. [PMID: 38580407 DOI: 10.1016/j.aca.2024.342493] [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: 10/10/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND The emergence of DNA nanotechnology has enabled the systematic design of diverse bionic dissipative behaviors under the precise control of nucleic acid nanodevices. Nevertheless, when compared to the dissipation observed in robust living systems, it is highly desirable to enhance the anti-interference for artificial DNA dissipation to withstand perturbations and facilitate repairs within the complex biological environments. RESULTS In this study, we introduce strategically designed "trash cans" to facilitate kinetic control over interferences, transforming the stochastic binding of individual components within a homogeneous solution into a competitive binding process. This approach effectively eliminates incorrect binding and the accumulation of systemic interferences while ensuring a consistent pattern of energy fluctuation from response to silence. Remarkably, even in the presence of numerous interferences differing by only one base, we successfully achieve complete system reset through multiple cycles, effectively restoring the energy level to a minimum. SIGNIFICANCE The system was able to operate stably without any adverse effect under conditions of irregular interference, high-abundance interference, and even multiplex interferences including DNA and RNA crosstalk. This work not only provides an effective paradigm for constructing robust DNA dissipation systems but also greatly broadens the potential of DNA dissipation for applications in high-precision molecular recognition and complex biological reaction networks.
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Affiliation(s)
- Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - You Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xin Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Jianhong Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yujun Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China.
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4
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Liu X, Zhang X, Cui S, Xu S, Liu R, Wang B, Wei X, Zhang Q. A signal transmission strategy driven by gap-regulated exonuclease hydrolysis for hierarchical molecular networks. Commun Biol 2024; 7:335. [PMID: 38493265 PMCID: PMC10944543 DOI: 10.1038/s42003-024-06036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Exonucleases serve as efficient tools for signal processing and play an important role in biochemical reactions. Here, we identify the mechanism of cooperative exonuclease hydrolysis, offering a method to regulate the cooperative hydrolysis driven by exonucleases through the modulation of the number of bases in gap region. A signal transmission strategy capable of producing amplified orthogonal DNA signal is proposed to resolve the polarity of signals and byproducts, which provides a solution to overcome the signal attenuation. The gap-regulated mechanism combined with DNA strand displacement (DSD) reduces the unpredictable secondary structures, allowing for the coexistence of similar structures in hierarchical molecular networks. For the application of the strategy, a molecular computing model is constructed to solve the maximum weight clique problems (MWCP). This work enhances for our knowledge of these important enzymes and promises application prospects in molecular computing, signal detection, and nanomachines.
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Affiliation(s)
- Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Shujuan Xu
- Key Lab of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China
| | - Rongming Liu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian, 116622, Liaoning, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.
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5
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Fu J, Zhang L, Long Y, Liu Z, Meng G, Zhao H, Su X, Shi S. Multiplexed CRISPR-Based Nucleic Acid Detection Using a Single Cas Protein. Anal Chem 2023; 95:16089-16097. [PMID: 37883656 DOI: 10.1021/acs.analchem.3c01861] [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: 10/28/2023]
Abstract
Thanks to its ease, speed, and sensitivity, CRISPR-based nucleic acid detection has been increasingly explored for molecular diagnostics. However, one of its major limitations is lack of multiplexing capability because the detection relies on the trans-cleavage activity of the Cas protein, which necessitates the use of multiple orthogonal Cas proteins for multiplex detection. Here we report the development of a multiplexed CRISPR-based nucleic acid detection system with single-nucleotide resolution using a single Cas protein (Cas12a). This method, termed as CRISPR-TMSD, integrates the toehold-mediated strand displacement (TMSD) reaction, and the cis-cleavage activity of the Cas protein and multiplexed detection are achieved using a single Cas protein owing to the use of target-specific reporters. A set of computational simulation toolkits was used to design the TMSD reporter, allowing for highly sensitive and specific identification of target sequences. In combination with the recombinase polymerase amplification (RPA), the detection limit can reach as low as 1 copy/μL. As proof of concept, CRISPR-TMSD was subsequently used to detect an oncogenic gene and SARS-CoV-2 RNA with a single-nucleotide resolution. This work represents a conceptually new strategy for designing a CRISPR-based diagnostic system and has great potential to expand the application of CRISPR-based diagnostics.
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Affiliation(s)
- Jinyu Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Linghao Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yanlin Long
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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6
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Kou Q, Yang J, Wang L, Zhao H, Zhang L, Su X. Enhanced DNA Entropy-Driven Circuit by Locked Nucleic Acids and Simulation-Guided Localization. ACS APPLIED MATERIALS & INTERFACES 2023; 15:47415-47424. [PMID: 37773989 DOI: 10.1021/acsami.3c11189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Signal amplification methods based on DNA molecular interactions are promising tools for detecting various biomarkers in low abundance. The entropy-driven circuit (EDC), as an enzyme-free signal amplification method, has been used in detecting and imaging a variety of biomarkers. The localization strategy can effectively increase the local concentration of the DNA reaction modules to improve the signal amplification effect. However, the localization strategy may also amplify the leak reaction of the EDC, and effective signal amplification can be limited by the unclear structure-function relationship. Herein, we utilized locked nucleic acid (LNA) modification to enhance the stability of the localized entropy-driven circuit (LEDC), which suppressed a 94.6% leak signal. The coarse-grained model molecular simulation was used to guide the structure design of the LEDC, and the influence of critical factors such as the localized distance and spacer length was analyzed at the molecular level to obtain the best reaction performance. The sensitivities of miR-21 and miR-141 detected by a simulation-guided optimal LEDC probe were 17.45 and 65 pM, 1345 and 521 times higher than free-EDC, respectively. The LEDC was further employed for the fluorescence imaging of miRNA in cancer cells, showing excellent specificity and sensitivity. This work utilizes LNA and molecular simulations to comprehensively improve the performance of a localized DNA signal amplification circuit, providing an advanced DNA probe design strategy for biosensing and imaging as well as valuable information for the designers of DNA-based probes.
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Affiliation(s)
- Qiaoni Kou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiarui Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Lei Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hongyang Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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7
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Zeng C, Liu X, Wang B, Qin R, Zhang Q. Multifunctional Exo III-assisted scalability strategy for constructing DNA molecular logic circuits. Analyst 2023; 148:1954-1960. [PMID: 36994799 DOI: 10.1039/d3an00086a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The construction of logic circuits is critical to DNA computing. Simple and effective scalability methods have been the focus of attention in various fields related to constructing logic circuits. We propose a double-stranded separation (DSS) strategy to facilitate the construction of complex circuits. The strategy combines toehold-mediated strand displacement with exonuclease III (Exo III), which is a multifunctional nuclease. Exo III can quickly recognize an apurinic/apyrimidinic (AP) site. DNA oligos with an AP site can generate an output signal by the strand displacement reaction. However, in contrast to traditional strand displacement reactions, the double-stranded waste from the strand displacement can be further hydrolysed by the endonuclease function of Exo III, thus generating an additional output signal. The DSS strategy allows for the effective scalability of molecular logic circuits, enabling multiple logic computing capabilities simultaneously. In addition, we succeeded in constructing a logic circuit with dual logic functions that provides foundations for more complex circuits in the future and has a broad scope for development in logic computing, biosensing, and nanomachines.
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Affiliation(s)
- Chenyi Zeng
- Key Laboratory of Advanced Design and Intelligent Computing, School of Software Engineering, Dalian University, Dalian 116622, China.
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, School of Software Engineering, Dalian University, Dalian 116622, China.
| | - Rui Qin
- Key Laboratory of Advanced Design and Intelligent Computing, School of Software Engineering, Dalian University, Dalian 116622, China.
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, School of Software Engineering, Dalian University, Dalian 116622, China.
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8
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Kou Q, Wang L, Zhang L, Ma L, Fu S, Su X. Simulation-Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2205191. [PMID: 36287076 DOI: 10.1002/smll.202205191] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/30/2022] [Indexed: 06/16/2023]
Abstract
DNA-based nanodevices equipped with localized modules have been promising probes for biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction. However, there is a lack of mechanistic insights into this reaction that limits the sensing speed and sensitivity. A coarse-grained model is utilized to simulate the intramolecular hybridization of localized DNA circuits (LDCs) not only optimizing the performance, but also providing mechanistic insights into the hybridization reaction. The simulation guided-LDCs enable the detection of multiple biomarkers with high sensitivity and rapid speed showing good consistency with the simulation. Fluorescence assays demonstrate that the simulation-guided LDC shows an enhanced sensitivity up to 9.3 times higher than that of the same probes without localization. The detection limits of ATP, miRNA, and APE1 reach 0.14 mM, 0.68 pM, and 0.0074 U mL-1 , respectively. The selected LDC is operated in live cells with good success in simultaneously detecting the biomarkers and discriminating between cancer cells and normal cells. LDC is successfully applied to detect the biomarkers in cancer tissues from patients, allowing the discrimination of cancer/adjacent/normal tissues. This work herein presents a design workflow for DNA nanodevices holding great potential for expanding the applications of DNA nanotechnology in diagnostics and therapeutics.
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Affiliation(s)
- Qiaoni Kou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Lei Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Liang Ma
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing, 100029, P. R. China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
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9
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Wang D, Zhang M, Zhang Y, Qiu G, Chen J, Zhu X, Kong C, Lu X, Liang X, Duan L, Fang C, Liu J, Zhang K, Luo T. Intraparticle Double-Scattering-Decoded Sonogenetics for Augmenting Immune Checkpoint Blockade and CAR-T Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203106. [PMID: 36156442 PMCID: PMC9661857 DOI: 10.1002/advs.202203106] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/02/2022] [Indexed: 05/29/2023]
Abstract
Genetically arming new chimeric antigen receptors (CARs) on T cells is a prevalent method to fulfill CAR-T immunotherapy. However, this approach fails to completely address the poor infiltration, complex immunosuppressive tumor microenvironment (ITM), and insufficient immune cells, which are recognized as the three dominant hurdles to discouraging the trafficking and persistence of CAR-T and immune checkpoint blockade (ICB) immunotherapies against solid tumors. To address the three hurdles, a sonoimmunity-engineered nanoplatform is designed in which a rattle-type-structured carrier enables intraparticle-double-scattering to generate massive reactive oxygen species (ROS) during the sonodynamic process. Abundant ROS accumulation can directly kill tumor cells, release antigens, and activate systematic immune responses for expanding effector T or CAR-T cells, while alleviating ITM via immunosuppressive macrophage polarization and reduction in pro-tumorigenic cytokine secretion. Furthermore, the co-loaded phosphodiesterase-5 inhibitors release nitric oxide (NO) to impel vascular normalization and open the infiltration barrier (IB) for allowing more T cells to enter into the tumor. Systematic experiments demonstrate the feasibility of such intraparticle-double-scattering-decoded sonogenetics in the sonoimmunity-engineered nanoplatforms for expanding effector T or CAR-T cells, thereby promoting their infiltration into tumors and alleviating ITM. These compelling actions lead to excellent CAR-T and ICB immunotherapies against solid tumors with repressed tumor metastasis.
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Affiliation(s)
- Duo Wang
- Department of Medical UltrasoundDepartment of Interventional Therapy and Department of Gastrointestinal SurgeryGuangxi Medical University Cancer HospitalGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Mengqi Zhang
- Department of Medical UltrasoundDepartment of Interventional Therapy and Department of Gastrointestinal SurgeryGuangxi Medical University Cancer HospitalGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Yan Zhang
- Central Laboratory and Ultrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Guanhua Qiu
- Department of Medical UltrasoundDepartment of Interventional Therapy and Department of Gastrointestinal SurgeryGuangxi Medical University Cancer HospitalGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Jie Chen
- Central Laboratory and Ultrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Xiaoqi Zhu
- Department of Medical UltrasoundDepartment of Interventional Therapy and Department of Gastrointestinal SurgeryGuangxi Medical University Cancer HospitalGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Cunqing Kong
- Department of Medical UltrasoundDepartment of Interventional Therapy and Department of Gastrointestinal SurgeryGuangxi Medical University Cancer HospitalGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Xiuxin Lu
- Department of Medical UltrasoundDepartment of Interventional Therapy and Department of Gastrointestinal SurgeryGuangxi Medical University Cancer HospitalGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Xiayi Liang
- Central Laboratory and Ultrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Lixia Duan
- Central Laboratory and Ultrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Chao Fang
- Central Laboratory and Ultrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
- National Center for International Research of Bio‐targeting TheranosticsGuangxi Key Laboratory of Bio‐targeting TheranosticsCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Medical UniversityNo. 22 Shuangyong RoadNanning530021P. R. China
| | - Junjie Liu
- Department of Medical UltrasoundDepartment of Interventional Therapy and Department of Gastrointestinal SurgeryGuangxi Medical University Cancer HospitalGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Kun Zhang
- Central Laboratory and Ultrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
- National Center for International Research of Bio‐targeting TheranosticsGuangxi Key Laboratory of Bio‐targeting TheranosticsCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Medical UniversityNo. 22 Shuangyong RoadNanning530021P. R. China
| | - Tao Luo
- Department of Medical UltrasoundDepartment of Interventional Therapy and Department of Gastrointestinal SurgeryGuangxi Medical University Cancer HospitalGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
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10
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Photoacoustic detection of SARS-CoV-2 spike N501Y single-nucleotide polymorphism based on branched rolling circle amplification. Talanta 2022. [PMCID: PMC9630300 DOI: 10.1016/j.talanta.2022.124047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Rapid and accurate diagnosis of SARS-CoV-2 single-nucleotide variations is an urgent need for the initial detection of local circulation and monitoring the alternation of dominant variant. In this proof-of-concept study, a homogeneous and isothermal photoacoustic biosensor is demonstrated for rapid molecular amplification and detection of a synthetic DNA corresponding to SARS-CoV-2 spike N501Y. Branched rolling circle amplification produces single-stranded amplicons that can aggregate detection probe-modified AuNPs, which induces a strong photoacoustic signal at 640 nm due to both the surface plasmon resonance shift and the size-dependent effect of laser-induced nanobubbles, achieving a sub-femtomolar detection limit within a total assay time of 80 min. The limit of detection can be kept when measuring 5% serum samples. Moreover, the proposed biosensor is highly specific for single-nucleotide polymorphism discrimination and robust against background DNA.
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11
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Liu Q, Zhang W, Jiao R, Lv Z, Lin X, Xiao Y, Zhang K. Rational Nanomedicine Design Enhances Clinically Physical Treatment-Inspired or Combined Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203921. [PMID: 36002305 PMCID: PMC9561875 DOI: 10.1002/advs.202203921] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/03/2022] [Indexed: 05/19/2023]
Abstract
Independent of tumor type and non-invasive or minimally-invasive feature, current physical treatments including ultrasound therapy, microwave ablation (MWA), and radiofrequency ablation (RFA) are widely used as the local treatment methods in clinics for directly killing tumors and activating systematic immune responses. However, the activated immune responses are inadequate and incompetent for tumor recession, and the incomplete thermal ablation even aggravates the immunosuppressive tumor microenvironment (ITM), resulting in the intractable tumor recurrence and metastasis. Intriguingly, nanomedicine provides a powerful platform as they can elevate energy utilization efficiency and augment oncolytic effects for mitigating ITM and potentiating the systematic immune responses. Especially after combining with clinical immunotherapy, the anti-tumor killing effect by activating or enhancing the human anti-tumor immune system is reached, enabling the effective prevention against tumor recurrence and metastasis. This review systematically introduces the cutting-edge progress and direction of nanobiotechnologies and their corresponding nanomaterials. Moreover, the enhanced physical treatment efficiency against tumor progression, relapse, and metastasis via activating or potentiating the autologous immunity or combining with exogenous immunotherapeutic agents is exemplified, and their rationales are analyzed. This review offers general guidance or directions to enhance clinical physical treatment from the perspectives of immunity activation or magnification.
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Affiliation(s)
- Qiaoqiao Liu
- Department of RadiologyLiuzhou People's Hospital Affiliated to Guangxi Medical UniversityNo. 8 Wenchang RoadLiuzhou545006P. R. China
- Central LaboratoryShanghai Tenth People's HospitalTongji University School of MedicineShanghai200072P. R. China
- National Center for International Research of Bio‐targeting TheranosticsGuangxi Key Laboratory of Bio‐targeting TheranosticsGuangxi Medical UniversityNo. 22 Shuangyong Road 22Nanning530021P. R. China
| | - Wei Zhang
- Department of RadiologyLiuzhou People's Hospital Affiliated to Guangxi Medical UniversityNo. 8 Wenchang RoadLiuzhou545006P. R. China
| | - Rong Jiao
- National Center for International Research of Bio‐targeting TheranosticsGuangxi Key Laboratory of Bio‐targeting TheranosticsGuangxi Medical UniversityNo. 22 Shuangyong Road 22Nanning530021P. R. China
| | - Zheng Lv
- Department of RadiologyLiuzhou People's Hospital Affiliated to Guangxi Medical UniversityNo. 8 Wenchang RoadLiuzhou545006P. R. China
- Central LaboratoryShanghai Tenth People's HospitalTongji University School of MedicineShanghai200072P. R. China
| | - Xia Lin
- National Center for International Research of Bio‐targeting TheranosticsGuangxi Key Laboratory of Bio‐targeting TheranosticsGuangxi Medical UniversityNo. 22 Shuangyong Road 22Nanning530021P. R. China
| | - Yunping Xiao
- Department of RadiologyLiuzhou People's Hospital Affiliated to Guangxi Medical UniversityNo. 8 Wenchang RoadLiuzhou545006P. R. China
| | - Kun Zhang
- Department of RadiologyLiuzhou People's Hospital Affiliated to Guangxi Medical UniversityNo. 8 Wenchang RoadLiuzhou545006P. R. China
- Central LaboratoryShanghai Tenth People's HospitalTongji University School of MedicineShanghai200072P. R. China
- National Center for International Research of Bio‐targeting TheranosticsGuangxi Key Laboratory of Bio‐targeting TheranosticsGuangxi Medical UniversityNo. 22 Shuangyong Road 22Nanning530021P. R. China
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12
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Qin Z, Liu Y, Zhang L, Liu J, Su X. Programming Dissipation Systems by DNA Timer for Temporally Regulating Enzyme Catalysis and Nanostructure Assembly. ACS NANO 2022; 16:14274-14283. [PMID: 36102909 DOI: 10.1021/acsnano.2c04405] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Live cells precisely control their temporal pattern in energy dissipative processes such as catalysis and assembly. Here, we demonstrate a DNA-based artificial dissipative nonequilibrium system where the transient state is controlled by the processive digestion of λ-exonuclease (λ Exo). This enzyme reaction serves as an orthogonal and independent molecular timer allowing for the programmable regulation of the transient-state lifetime. This dissipation system is concatenated to enzyme catalysis and nanostructure assembly networks. Dynamic activation of enzyme catalysis and dynamic disassembly of DNA nanotubes (DNT) are realized, and the state lifetimes of these systems are accurately encoded by the DNA timer. This work demonstrates nontrivial dissipation systems with built-in molecular timers, which can be a useful tool for developing artificial reaction networks and nanostructures with enhanced complexities and intelligence.
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Affiliation(s)
- Zhaohui Qin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Yu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Jiajia Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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13
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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: 61] [Impact Index Per Article: 30.5] [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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14
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Fan X, Walther A. 1D Colloidal chains: recent progress from formation to emergent properties and applications. Chem Soc Rev 2022; 51:4023-4074. [PMID: 35502721 DOI: 10.1039/d2cs00112h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrating nanoscale building blocks of low dimensionality (0D; i.e., spheres) into higher dimensional structures endows them and their corresponding materials with emergent properties non-existent or only weakly existent in the individual building blocks. Constructing 1D chains, 2D arrays and 3D superlattices using nanoparticles and colloids therefore continues to be one of the grand goals in colloid and nanomaterial science. Amongst these higher order structures, 1D colloidal chains are of particular interest, as they possess unique anisotropic properties. In recent years, the most relevant advances in 1D colloidal chain research have been made in novel synthetic methodologies and applications. In this review, we first address a comprehensive description of the research progress concerning various synthetic strategies developed to construct 1D colloidal chains. Following this, we highlight the amplified and emergent properties of the resulting materials, originating from the assembly of the individual building blocks and their collective behavior, and discuss relevant applications in advanced materials. In the discussion of synthetic strategies, properties, and applications, particular attention will be paid to overarching concepts, fresh trends, and potential areas of future research. We believe that this comprehensive review will be a driver to guide the interdisciplinary field of 1D colloidal chains, where nanomaterial synthesis, self-assembly, physical property studies, and material applications meet, to a higher level, and open up new research opportunities at the interface of classical disciplines.
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Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular Chemistry, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 31, 79104, Freiburg, Germany.
| | - Andreas Walther
- A3BMS Lab, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
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15
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Chen J, Fu S, Zhang C, Liu H, Su X. DNA Logic Circuits for Cancer Theranostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2108008. [PMID: 35254723 DOI: 10.1002/smll.202108008] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Cancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self-assembly of DNA molecules at the nanometer scale to construct intelligent DNA chemical reaction systems. The DNA logic circuit is a particularly emerging approach for computing within the DNA chemical systems. DNA logic circuits can sensitively respond to tumor-specific markers and the TME through logic operations and signal amplification, to generate detectable signals or to release anti-cancer agents. In this review, the fundamental concepts of DNA logic circuits are clarified, the basic modules in the circuit are summarized, and how this advanced nano-assembly circuit responds to tumor-related molecules, how to perform logic operations, to realize signal amplification, and selectively release drugs through discussing over 30 application examples, are demonstrated. This review shows that DNA logic circuits have powerful logic judgment and signal amplification functions in improving the specificity and sensitivity of cancer diagnosis and making cancer treatment controllable. In the future, researchers are expected to overcome the existing shortcomings of DNA logic circuits and design smarter DNA devices with better biocompatibility and stability, which will further promote the development of cancer theranostics.
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Affiliation(s)
- Jing Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chunyi Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huiyu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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16
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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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