1
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Zheng T, Tang Q, Wan L, Zhao Y, Xu R, Xu X, Li H, Han D. Controlled Self-Assembly of the Catalytic Core of Hydrolases Using DNA Scaffolds. NANO LETTERS 2023; 23:2081-2086. [PMID: 36854101 DOI: 10.1021/acs.nanolett.2c03387] [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: 06/18/2023]
Abstract
Precisely organizing functional molecules of the catalytic cores in natural enzymes to promote catalytic performance is a challenging goal in respect to artificial enzyme construction. In this work, we report a DNA-scaffolded mimicry of the catalytic cores of hydrolases, which showed a controllable and hierarchical acceleration of the hydrolysis of fluorescein diacetate (FDA). The results revealed that the efficiency of hydrolysis was greatly increased by the DNA-scaffold-induced proximity of catalytic amino acid residues (histidine and arginine) with up to 4-fold improvement relative to the free amino acids. In addition, DNA-scaffolded one-dimensional and two-dimensional assemblies of multiple catalytic cores could further accelerate the hydrolysis. This work demonstrated that the DNA-guided assembly could be used as a promising platform to build enzyme mimics in a programmable and hierarchical way.
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Affiliation(s)
- Tingting Zheng
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qian Tang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liqi Wan
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yumeng Zhao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Rui Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xuemei Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Haowen Li
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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2
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Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
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Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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3
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Snider DM, Pandit S, Coffin ML, Ebrahimi SB, Samanta D. DNA-Mediated Control of Protein Function in Semi-Synthetic Systems. Chembiochem 2022; 23:e202200464. [PMID: 36058885 DOI: 10.1002/cbic.202200464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/02/2022] [Indexed: 01/25/2023]
Abstract
The development of strategies for controlling protein function in a precise and predictable manner has the potential to revolutionize catalysis, diagnostics, and medicine. In this regard, the use of DNA has emerged as a powerful approach for modulating protein activity. The programmable nature of DNA allows for constructing sophisticated architectures wherein proteins can be placed with control over position, orientation, and stoichiometry. This ability is especially useful considering that the properties of proteins can be influenced by their local environment or their proximity to other functional molecules. Here, we chronicle the different strategies that have been developed to interface DNA with proteins in semi-synthetic systems. We further delineate the unique applications unlocked by the unprecedented level of structural control that DNA affords. We end by outlining outstanding challenges in the area and discuss future research directions towards potential solutions.
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Affiliation(s)
- Dylan M Snider
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Subrata Pandit
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Mackenzie L Coffin
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Sasha B Ebrahimi
- Drug Product Development - Steriles, GlaxoSmithKline 1250 S Collegeville Rd, Collegeville, PA 19426, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
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4
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Winegar PH, Figg CA, Teplensky MH, Ramani N, Mirkin CA. Modular Nucleic Acid Scaffolds for Synthesizing Monodisperse and Sequence-Encoded Antibody Oligomers. Chem 2022; 8:3018-3030. [PMID: 36405374 PMCID: PMC9674055 DOI: 10.1016/j.chempr.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesizing protein oligomers that contain exact numbers of multiple different proteins in defined architectures is challenging. DNA-DNA interactions can be used to program protein assembly into oligomers; however, existing methods require changes to DNA design to achieve different numbers and oligomeric sequences of proteins. Herein, we develop a modular DNA scaffold that uses only six synthetic oligonucleotides to organize proteins into defined oligomers. As a proof-of-concept, model proteins (antibodies) are oligomerized into dimers and trimers, where antibody function is retained. Illustrating the modularity of this technique, dimer and trimer building blocks are then assembled into pentamers containing three different antibodies in an exact stoichiometry and oligomeric sequence. In sum, this report describes a generalizable method for organizing proteins into monodisperse, sequence-encoded oligomers using DNA. This advance will enable studies into how oligomeric protein sequences affect material properties in areas spanning pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.
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Affiliation(s)
- Peter H. Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - C. Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - Michelle H. Teplensky
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Namrata Ramani
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Lead contact
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5
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Zhu X, Yan X, Yang S, Wang Y, Wang S, Tian Y. DNA-Mediated Assembly of Carbon Nanomaterials. Chempluschem 2022; 87:e202200089. [PMID: 35589623 DOI: 10.1002/cplu.202200089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/26/2022] [Indexed: 02/18/2024]
Abstract
Carbon nanomaterials (CNMs) have attracted extensive attentions on account of their superior electrical, mechanical, optical, and biological properties. However, the dimensional limit and irregular arrangement have hampered their further application. It is necessary to find an easy, efficient and controllable way to assemble CNMs into well-ordered array. DNA nanotechnology, owning to the advantages of precise programmability, highly structural predictability and spatial addressability, has been widely applied in the assembly of CNMs. Summarizing the progress and achievements in this field will be of great value to related studies. Herein, based on the different dimensions of CNMs containing 0-dimensional (0D) carbon dots (CDs), fullerenes, 1-dimensional (1D) carbon nanotubes (CNTs) and 2-dimensional (2D) graphene, we introduced the conjugation strategies between DNA and CNMs, their different assembly methods and their applications. In addition, we also discuss the existing challenges and future opportunities in the field.
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Affiliation(s)
- Xurong Zhu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Xuehui Yan
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Sichang Yang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Yong Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Shuang Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, 518055, Shenzhen, P. R. China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
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6
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Kahn J, Xiong Y, Huang J, Gang O. Cascaded Enzyme Reactions over a Three-Dimensional, Wireframe DNA Origami Scaffold. JACS AU 2022; 2:357-366. [PMID: 35252986 PMCID: PMC8889550 DOI: 10.1021/jacsau.1c00387] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 05/31/2023]
Abstract
DNA nanotechnology has increasingly been used as a platform to scaffold enzymes based on its unmatched ability to structure enzymes in a desired format. The capability to organize enzymes has taken many forms from more traditional 2D pairings on individual scaffolds to recent works introducing enzyme organizations in 3D lattices. As the ability to define nanoscale structure has grown, it is critical to fully deconstruct the impact of enzyme organization at the single-scaffold level. Here, we present an open, three-dimensional (3D) DNA wireframe octahedron which is used to create a library of spatially arranged organizations of glucose oxidase and horseradish peroxidase. We explore the contribution of enzyme spacing, arrangement, and location on the 3D scaffold to cascade activity. The experiments provide insight into enzyme scaffold design, including the insignificance of scaffold sequence makeup on activity, an increase in activity at small enzyme spacings of <10 nm, and activity changes that arise from discontinuities in scaffold architecture. Most notably, the experiments allow us to determine that enzyme colocalization itself on the DNA scaffold dominates over any specific enzyme arrangement.
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Affiliation(s)
- Jason
S. Kahn
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York 11973, United States
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Yan Xiong
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - James Huang
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York 11973, United States
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York New York 10027, United States
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7
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Li D, Xiong Q, Liang L, Duan H. Multienzyme nanoassemblies: from rational design to biomedical applications. Biomater Sci 2021; 9:7323-7342. [PMID: 34647942 DOI: 10.1039/d1bm01106e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multienzyme nanoassemblies (MENAs) that combine the functions of several enzymes into one entity have attracted widespread research interest due to their improved enzymatic performance and great potential for multiple applications. Considerable progress has been made to design and fabricate MENAs in recent years. This review begins with an introduction of the up-to-date strategies in designing MENAs, mainly including substrate channeling, compartmentalization and control of enzyme stoichiometry. The desirable properties that endow MENAs with important applications are also discussed in detail. Then, the recent advances in utilizing MENAs in the biomedical field are reviewed, with a particular focus on biosensing, tumor therapy, antioxidant and drug delivery. Finally, the challenges and perspectives for development of versatile MENAs are summarized.
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Affiliation(s)
- Di Li
- State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. .,School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qirong Xiong
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
| | - Li Liang
- State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hongwei Duan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
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8
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Kubota R, Tanaka W, Hamachi I. Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies. Chem Rev 2021; 121:14281-14347. [DOI: 10.1021/acs.chemrev.0c01334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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9
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Xu X, Han D. DNA-Guided Programmable Protein Assemblies for Biomedical Applications. Chempluschem 2021; 86:284-290. [PMID: 33605561 DOI: 10.1002/cplu.202100001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/13/2021] [Indexed: 12/22/2022]
Abstract
While the protein assemblies have been found widely existing and playing significant roles in biological systems, their imitation and re-construction is further boosting more applications in biomedical research, such as enzymatic reaction regulation, sensing, and biomedicine. DNA nanotechnology provides a programmable strategy for the fabrication of nanostructures with unprecedented accuracy on the nanoscale. By linking the DNA nanotechnology with proteins of different functions, the precise construction of DNA-guided protein assemblies can be achieved for various biomedical applications. This minireview summarizes the recent advances in the programmable protein assemblies on DNA nanoplatforms and discusses the outlook of DNA-guided protein assemblies in the biomedical research.
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Affiliation(s)
- Xuemei Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Da Han
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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10
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Dong Y, Mao Y. DNA Origami as Scaffolds for Self‐Assembly of Lipids and Proteins. Chembiochem 2019; 20:2422-2431. [DOI: 10.1002/cbic.201900073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/22/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteDepartment of MicrobiologyHarvard Medical School 450 Brookline Avenue Boston MA 02215 USA
- Intel Parallel Computing Center for Structural BiologyDana-Farber Cancer Institute 450 Brookline Avenue Boston MA 02215 USA
- Present address: CAS Key Laboratory of Colloid Interfaces and Chemical ThermodynamicsInstitute of ChemistryChinese Academy of Sciences No. 2 Zhongguancun Beiyijie Beijing 100190 P.R. China
| | - Youdong Mao
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteDepartment of MicrobiologyHarvard Medical School 450 Brookline Avenue Boston MA 02215 USA
- Intel Parallel Computing Center for Structural BiologyDana-Farber Cancer Institute 450 Brookline Avenue Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic PhysicsSchool of PhysicsCenter for Quantitative BiologyPeking University Beijing 100871 P.R. China
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11
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Yang Y, Zhang S, Yao S, Pan R, Hidaka K, Emura T, Fan C, Sugiyama H, Xu Y, Endo M, Qian X. Programming Rotary Motions with a Hexagonal DNA Nanomachine. Chemistry 2019; 25:5158-5162. [PMID: 30791173 DOI: 10.1002/chem.201900221] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/21/2019] [Indexed: 12/22/2022]
Abstract
Biological macromolecular machines perform impressive mechanical movements. F-adenosine triphosphate (ATP) synthase uses a proton gradient to generate ATP through mechanical rotations. Here, a programmed hexagonal DNA nanomachine, in which a three-armed DNA nanostructure (TAN) can perform stepwise rotations in the confined nanospace powered by DNA fuels, is demonstrated. The movement of TAN can precisely go through a 60° rotation, which is confirmed by atomic force microscopy, and each stepwise directional rotating is monitored by fluorescent measurements. Moreover, the rotary nanomachine is used to spatially organize cascade enzymes: glucose oxidase (GOx) and horseradish peroxidase (HRP) in four different arrangements. The multistep regulations of the biocatalytic activities are achieved by employing TAN rotations. This work presents a new prototype of rotary nanodevice with both angular and directional control, and provides a nanoscale mechanical engineering platform for the reactive molecular components, demonstrating that DNA-based framework may have significant roles in futuristic nanofactory construction.
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Affiliation(s)
- Yangyang Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Shiwei Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Shengtao Yao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Rizhao Pan
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of, Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, P. R. China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
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12
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Liu L, Rong Q, Ke G, Zhang M, Li J, Li Y, Liu Y, Chen M, Zhang XB. Efficient and Reliable MicroRNA Imaging in Living Cells via a FRET-Based Localized Hairpin-DNA Cascade Amplifier. Anal Chem 2019; 91:3675-3680. [PMID: 30714362 DOI: 10.1021/acs.analchem.8b05778] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) play critical roles in many biological processes and are vital biomarkers for disease diagnostics. Hence, it is of significance to develop miRNA biosensors with fast responses, high sensitivity, and excellent reliability in living cells. As one kind of DNA molecular machine, DNA amplifiers are very promising for intracellular miRNA imaging due to their nonenzymatic, isothermal working principle and excellent signal-amplification ability. However, the practical application of current DNA amplifiers is still an issue because of their slow kinetics, unsatisfactory efficiency, and false-positive signals. Herein, taking advantage of the spatial-confinement effect on a three-dimensional (3D) finite DNA nanostructure, a FRET-based localized hairpin-DNA cascade amplifier (termed as localized-HDCA) is developed for the rapid, efficient, and reliable imaging of intracellular tumor-related miRNA. The localized-HDCA system consists of two metastable hairpin DNAs (H1 and H2) localized on a DNA nanocube. Benefiting from the spatial-confinement effect in the confined space of DNA nanocubes, not only was the speed of the miRNA-triggered HDCA reaction significantly accelerated (7 times faster), but also the reaction efficiency was greatly improved (2.6 times higher). In addition, the FRET-based 3D finite DNA nanocubes provide this localized-HDCA with improved cell permeability and better nuclease resistance as well as the ability to avoid false-positive signals, which guarantee reliable miRNA imaging in living cells. With these advantages, this strategy is expected to be widely applied to the development of more efficient and robust DNA molecular machines for biomedical research and clinical diagnosis.
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Affiliation(s)
- Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Qiming Rong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Meng Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Jin Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Yingqian Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Yongchun Liu
- College of Materials Science and Engineering , Hunan University , Changsha 410082 , China
| | - Mei Chen
- College of Materials Science and Engineering , Hunan University , Changsha 410082 , China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
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13
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Ma Y, Lv Z, Li T, Tian T, Lu L, Liu W, Zhu Z, Yang C. Design and synthesis of ortho-phthalaldehyde phosphoramidite for single-step, rapid, efficient and chemoselective coupling of DNA with proteins under physiological conditions. Chem Commun (Camb) 2018; 54:9434-9437. [PMID: 30079422 DOI: 10.1039/c8cc05037f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
ortho-Phthalaldehyde (OPA) phosphoramidite with high reaction activity was designed and synthesized for labelling oligodeoxynucleotides (DNA). The DNA modified with OPA (OPA-DNA) can covalently couple with native proteins rapidly and efficiently via a condensation reaction with the formation of phthalimidines, which provides a highly efficient method for bioconjugation of DNA and native proteins under physiological conditions.
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Affiliation(s)
- Yanli Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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14
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Zhou L, Liu Y, Shi H, Yang X, Huang J, Liu S, Chen Q, Liu J, Wang K. Flexible Assembly of an Enzyme Cascade on a DNA Triangle Prism Nanostructure for the Controlled Biomimetic Generation of Nitric Oxide. Chembiochem 2018; 19:2099-2106. [DOI: 10.1002/cbic.201800337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Li Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Yu Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Songyang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Qiaoshu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
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15
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Cascades in Compartments: En Route to Machine-Assisted Biotechnology. Angew Chem Int Ed Engl 2017; 56:13574-13589. [DOI: 10.1002/anie.201703806] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
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16
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Kaskaden in Kompartimenten: auf dem Weg zu maschinengestützter Biotechnologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703806] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
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17
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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18
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Rajendran A, Nakata E, Nakano S, Morii T. Nucleic-Acid-Templated Enzyme Cascades. Chembiochem 2017; 18:696-716. [DOI: 10.1002/cbic.201600703] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Indexed: 11/08/2022]
Affiliation(s)
| | - Eiji Nakata
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Shun Nakano
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Takashi Morii
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
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