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Bekkouche I, Kuznetsova MN, Rejepov DT, Vetcher AA, Shishonin AY. Recent Advances in DNA Nanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2449. [PMID: 37686956 PMCID: PMC10490369 DOI: 10.3390/nano13172449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Maria N. Kuznetsova
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Dovlet T. Rejepov
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
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Shirt-Ediss B, Connolly J, Elezgaray J, Torelli E, Navarro SA, Bacardit J, Krasnogor N. Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists. Comput Struct Biotechnol J 2023; 21:3615-3626. [PMID: 37520280 PMCID: PMC10371787 DOI: 10.1016/j.csbj.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto 'raw sequence' exchange format allows published origami designs to be re-attempted in the laboratory by other groups, but effectively stops designs from being significantly modified or re-purposed for new future applications. To make the raw sequence exchange format more accessible to further design and engineering, in this work we propose the first algorithmic solution to the inverse problem of converting staple/scaffold sequences back to a 'guide schematic' resembling the original origami schematic. The guide schematic can be used to aid the manual re-input of an origami into a CAD tool like caDNAno, hence recovering a high-level editable design file. Creation of a guide schematic can also be used to double check that a list of staple strand sequences does not have errors and indeed does assemble into a desired origami nanostructure prior to costly laboratory experimentation. We tested our reverse algorithm on 36 diverse origami designs from the literature and found that 29 origamis (81 %) had a good quality guide schematic recovered from raw sequences. Our software is made available at https://revnano.readthedocs.io.
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Affiliation(s)
- Ben Shirt-Ediss
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Jordan Connolly
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Juan Elezgaray
- Centre de Recherche Paul Pascal, CNRS, UMR503, Pessac 33600, France
| | - Emanuela Torelli
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Silvia Adriana Navarro
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Jaume Bacardit
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
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Udono H, Gong J, Sato Y, Takinoue M. DNA Droplets: Intelligent, Dynamic Fluid. Adv Biol (Weinh) 2023; 7:e2200180. [PMID: 36470673 DOI: 10.1002/adbi.202200180] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.
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Affiliation(s)
- Hirotake Udono
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Jing Gong
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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4
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Liang L, Jia S, Barman I. DNA-POINT: DNA Patterning of Optical Imprint for Nanomaterials Topography. ACS APPLIED MATERIALS & INTERFACES 2022; 14:38388-38397. [PMID: 35969693 DOI: 10.1021/acsami.2c10908] [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: 06/15/2023]
Abstract
Engineering well-defined scale-spanning structures through transfer of diverse biomolecules and materials to a surface is of tremendous interest in life sciences research yet remains profoundly challenging. Here, we report a novel method, termed as DNA patterning of optical imprint for nanomaterials topography (DNA-POINT), for rapid photopatterning of large area, geometrically complex surfaces via light-responsive DNA. Our method employs top-down multiphoton-driven patterning of azobenzene-modified DNA strands, offering precise position control of molecules and nanoparticles along the axial plane and a template for bottom-up self-assembly of multiple layers of different chemical composition along the vertical plane. We demonstrate the surface patterning of plasmonic gold nanoparticles, fluorophore-labeled oligonucleotides, and multiple layers consisting of molecule-nanoparticle hybrid patterns into preconceived shapes without compromising on the functionality of the biomolecules. Furthermore, we exhibit scanning mode operation of DNA-POINT, thereby paving the way for maskless and cleanroom-free fast fabrication of biochips for high-throughput diagnostics and biosensing applications.
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Affiliation(s)
- Le Liang
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, The Institute for Advanced Studies, Wuhan University, Wuhan 430071, China
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sisi Jia
- Zhangjiang Laboratory, Shanghai 201210, China
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Department of Radiology & Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
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Surface Assembly of DNA Origami on a Lipid Bilayer Observed Using High-Speed Atomic Force Microscopy. Molecules 2022; 27:molecules27134224. [PMID: 35807467 PMCID: PMC9268156 DOI: 10.3390/molecules27134224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
The micrometer-scale assembly of various DNA nanostructures is one of the major challenges for further progress in DNA nanotechnology. Programmed patterns of 1D and 2D DNA origami assembly using specific DNA strands and micrometer-sized lattice assembly using cross-shaped DNA origami were performed on a lipid bilayer surface. During the diffusion of DNA origami on the membrane surface, the formation of lattices and their rearrangement in real-time were observed using high-speed atomic force microscopy (HS-AFM). The formed lattices were used to further assemble DNA origami tiles into their cavities. Various patterns of lattice–tile complexes were created by changing the interactions between the lattice and tiles. For the control of the nanostructure formation, the photo-controlled assembly and disassembly of DNA origami were performed reversibly, and dynamic assembly and disassembly were observed on a lipid bilayer surface using HS-AFM. Using a lipid bilayer for DNA origami assembly, it is possible to perform a hierarchical assembly of multiple DNA origami nanostructures, such as the integration of functional components into a frame architecture.
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- 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.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- 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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Yu Y, Yoshimura SH. Investigating the morphological dynamics of the plasma membrane by high-speed atomic force microscopy. J Cell Sci 2021; 134:272010. [PMID: 34468000 DOI: 10.1242/jcs.243584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite numerous recent developments in bioimaging techniques, nanoscale and live-cell imaging of the plasma membrane has been challenging because of the insufficient z-resolution of optical microscopes, as well as the lack of fluorescent probes to specifically label small membrane structures. High-speed atomic force microscopy (HS-AFM) is a powerful tool for visualising the dynamics of a specimen surface and is therefore suitable for observing plasma membrane dynamics. Recent developments in HS-AFM for live-cell imaging have enabled the visualisation of the plasma membrane and the network of cortical actin underneath the membrane in a living cell. Furthermore, correlative imaging with fluorescence microscopy allows for the direct visualisation of morphological changes of the plasma membrane together with the dynamic assembly or disassembly of proteins during the entire course of endocytosis in a living cell. Here, we review these recent advances in HS-AFM in order to analyse various cellular events occurring at the cell surface.
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Affiliation(s)
- Yiming Yu
- Graduate School of Biostudies, Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto 606-8501, Japan
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Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
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Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
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Liu Y, Cheng J, Fan S, Ge H, Luo T, Tang L, Ji B, Zhang C, Cui D, Ke Y, Song J. Modular Reconfigurable DNA Origami: From Two-Dimensional to Three-Dimensional Structures. Angew Chem Int Ed Engl 2020; 59:23277-23282. [PMID: 32894584 DOI: 10.1002/anie.202010433] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Indexed: 12/12/2022]
Abstract
DNA origami enables the manipulation of objects at nanoscale, and demonstrates unprecedented versatility for fabricating both static and dynamic nanostructures. In this work, we introduce a new strategy for transferring modular reconfigurable DNA nanostructures from two-dimensional to three-dimensional. A 2D DNA sheet could be modularized into connected parts (e.g., two, three, and four parts in this work), which can be independently transformed between two conformations with a few DNA "trigger" strands. More interestingly, the transformation of the connected 2D modules can lead to the controlled, resettable structural conversion of a 2D sheet to a 3D architecture, due to the constraints induced by the connections between the 2D modules. This new approach can provide an efficient mean for constructing programmable, higher-order, and complex DNA objects, as well as sophisticated dynamic substrates for various applications.
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Affiliation(s)
- Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huan Ge
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linlin Tang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bin Ji
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 30322, Atlanta, GA, USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
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11
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Liu Y, Cheng J, Fan S, Ge H, Luo T, Tang L, Ji B, Zhang C, Cui D, Ke Y, Song J. Modular Reconfigurable DNA Origami: From Two‐Dimensional to Three‐Dimensional Structures. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yan Liu
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Sisi Fan
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Huan Ge
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong University Shanghai 200240 China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Linlin Tang
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Bin Ji
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong University Shanghai 200240 China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University 30322 Atlanta GA USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
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Jaekel A, Stegemann P, Saccà B. Manipulating Enzymes Properties with DNA Nanostructures. Molecules 2019; 24:molecules24203694. [PMID: 31615123 PMCID: PMC6832416 DOI: 10.3390/molecules24203694] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.
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Affiliation(s)
- Andreas Jaekel
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Pierre Stegemann
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Barbara Saccà
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
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Tam DY, Zhuang X, Wong SW, Lo PK. Photoresponsive Self-Assembled DNA Nanomaterials: Design, Working Principles, and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805481. [PMID: 30861628 DOI: 10.1002/smll.201805481] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/30/2019] [Indexed: 05/23/2023]
Abstract
Photoresponsive DNA nanomaterials represent a new class of remarkable functional materials. By adjusting the irradiation wavelength, light intensity, and exposure time, various photocontrolled DNA-based systems can be reversibly or irreversibly regulated in respect of their size, shape, conformation, movement, and dissociation/association. This Review introduces the most updated progress in the development of photoresponsive DNA-based system and emphasizes their advantages over other stimuli-responsive systems. Their design and mechanisms to trigger the photoresponses are shown and discussed. The potential application of these photon-responsive DNA nanomaterials in biology, biomedicine, materials science, nanophotonic and nanoelectronic are also covered and described. The challenges faced and further directions of the development of photocontrolled DNA-based systems are also highlighted.
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Affiliation(s)
- Dick Yan Tam
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Xinyu Zhuang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Sze Wing Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
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Direct Observation of Dynamic Movement of DNA Molecules in DNA Origami Imaged Using High-Speed AFM. Methods Mol Biol 2019; 1814:213-224. [PMID: 29956235 DOI: 10.1007/978-1-4939-8591-3_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The visualization of biomolecules is a straightforward way to elucidate the physical properties of molecules and their reaction processes. Atomic force microscopy (AFM) enables the direct imaging of biomolecules under physiological conditions at nanometer-scale spatial resolution. Because AFM visualizes all molecules in a scanning area, an observation scaffold is required for the target-specific imaging of molecules in the dynamic state. The DNA origami technology allows the precise placement of target molecules in a designed nanostructure, and the detection of the molecules at the single-molecule level. DNA origami is applied for visualizing the detailed motions of molecules using high-speed AFM (HS-AFM), which enables the analysis of the dynamic movement of biomolecules in a subsecond time resolution. Here, we describe the combination of the DNA origami system with HS-AFM for the imaging of DNA structural changes controlled by photoresponsive molecules. The hybridization and dehybridization of photoresponsive oligonucleotides were visualized directly using this observation system. These target-oriented observation systems should contribute to the detailed analysis of biomolecules in real time with molecular resolution.
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15
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Dudek M, Deiana M, Pokladek Z, Pawlik K, Matczyszyn K. Reversible Photocontrol of DNA Melting by Visible-Light-Responsive F4-Coordinated Azobenzene Compounds. Chemistry 2018; 24:18963-18970. [PMID: 30198626 DOI: 10.1002/chem.201803529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 12/23/2022]
Abstract
Spatiotemporal control over the regulation of intra- and intermolecular motions in naturally occurring systems is systematically studied to expand the toolbox of mechanical operations in multicomponent nanoarchitectures. DNA is ideally suited for programming light-powered processes that are based on a minimalist molecular design. Here, the noncovalent incorporation of bistable photoswitches into B-like DNA moieties is shown to trigger the thermal transition midpoint of the duplexes by converting visible light into directed mechanical work by orchestrating the collective actions of the photoresponsive chromophores and the host DNA nanostructures. Besides its practical applications, the resulting hybrid nanosystem bears unique features of modulability, biocompatibility, reversibility, and addressability, which are key components for developing molecular photon-controlled programmed materials.
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Affiliation(s)
- Marta Dudek
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Ziemowit Pokladek
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Krzysztof Pawlik
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wroclaw, Poland
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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16
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刘 林, 魏 余, 刘 文, 孙 彤, 王 凯, 汪 颖, 李 宾. [Progress in the applications of high-speed atomic force microscopy in cell biology]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:931-937. [PMID: 30187879 PMCID: PMC6744042 DOI: 10.3969/j.issn.1673-4254.2018.08.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Indexed: 12/24/2022]
Abstract
Without losing its high resolution, high-speed atomic force microscope (HS-AFM) represents a perfect combinationof scanning speed and precision and allows real-time and in situ observation of the dynamic processes in a biological system atboth the cellular and molecular levels. By combining the extremely high temporal resolution with the spatial resolution andcoupling with other advanced technologies, HS-AFM shows promising prospects for applications in life sciences such as cellbiology. In this review, we summarize the latest progress of HS-AFM in the field of cell biology, and discuss the impact ofenvironmental factors on conformation dynamics of DNA, the binding processes between DNA and protein, the domainchanges of membrane proteins, motility of myosin, and surface structure changes of living cells.
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Affiliation(s)
- 林 刘
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 余辉 魏
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - 文静 刘
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 彤 孙
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 凯喆 王
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 颖 汪
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - 宾 李
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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17
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Lubbe AS, Szymanski W, Feringa BL. Recent developments in reversible photoregulation of oligonucleotide structure and function. Chem Soc Rev 2018; 46:1052-1079. [PMID: 28128377 DOI: 10.1039/c6cs00461j] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.
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Affiliation(s)
- Anouk S Lubbe
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. and Department of Radiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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18
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew Chem Int Ed Engl 2017; 56:15210-15233. [PMID: 28444822 DOI: 10.1002/anie.201701868] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/16/2022]
Abstract
Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
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Affiliation(s)
- Yuwei Hu
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Andrea Idili
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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19
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex-DNA-Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701868] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | | | - Andrea Idili
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Francesco Ricci
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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20
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Willner EM, Kamada Y, Suzuki Y, Emura T, Hidaka K, Dietz H, Sugiyama H, Endo M. Single-Molecule Observation of the Photoregulated Conformational Dynamics of DNA Origami Nanoscissors. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Elena M. Willner
- Physik Department and Institute for Advanced Study; Technische Universität München; Am Coulombwall 4a 85748 Garching near Munich Germany
| | - Yuu Kamada
- Department of Chemistry, Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
- Current address: Frontier Research Institute for Interdisciplinary Sciences; Tohoku University; Aramaki aza Aoba 6-3 Aoba-ku Sendai 980-8578 Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Hendrik Dietz
- Physik Department and Institute for Advanced Study; Technische Universität München; Am Coulombwall 4a 85748 Garching near Munich Germany
| | - Hiroshi Sugiyama
- Institute for Integrated Cell Material Sciences; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
- Department of Chemistry, Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Masayuki Endo
- Institute for Integrated Cell Material Sciences; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
- Department of Chemistry, Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
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21
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Willner EM, Kamada Y, Suzuki Y, Emura T, Hidaka K, Dietz H, Sugiyama H, Endo M. Single-Molecule Observation of the Photoregulated Conformational Dynamics of DNA Origami Nanoscissors. Angew Chem Int Ed Engl 2017; 56:15324-15328. [PMID: 29044955 DOI: 10.1002/anie.201708722] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/04/2017] [Indexed: 12/31/2022]
Abstract
We demonstrate direct observation of the dynamic opening and closing behavior of photocontrollable DNA origami nanoscissors using high-speed atomic force microscopy (HS-AFM). First the conformational change between the open and closed state controlled by adjustment of surrounding salt concentration could be directly observed during AFM scanning. Then light-responsive moieties were incorporated into the nanoscissors to control these structural changes by photoirradiation. Using photoswitchable DNA strands, we created a photoresponsive nanoscissors variant and were able to distinguish between the open and closed conformations after respective irradiation with ultraviolet (UV) and visible (Vis) light by gel electrophoresis and AFM imaging. Additionally, these reversible changes in shape during photoirradiation were directly visualized using HS-AFM. Moreover, four photoswitchable nanoscissors were assembled into a scissor-actuator-like higher-order object, the configuration of which could be controlled by the open and closed switching induced by irradiation with UV and Vis light.
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Affiliation(s)
- Elena M Willner
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching near Munich, Germany
| | - Yuu Kamada
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Current address: Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramaki aza Aoba 6-3, Aoba-ku, Sendai, 980-8578, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hendrik Dietz
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching near Munich, Germany
| | - Hiroshi Sugiyama
- Institute for Integrated Cell Material Sciences, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell Material Sciences, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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22
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Shibata M, Watanabe H, Uchihashi T, Ando T, Yasuda R. High-speed atomic force microscopy imaging of live mammalian cells. Biophys Physicobiol 2017; 14:127-135. [PMID: 28900590 PMCID: PMC5590786 DOI: 10.2142/biophysico.14.0_127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/26/2017] [Indexed: 01/17/2023] Open
Abstract
Direct imaging of morphological dynamics of live mammalian cells with nanometer resolution under physiological conditions is highly expected, but yet challenging. High-speed atomic force microscopy (HS-AFM) is a unique technique for capturing biomolecules at work under near physiological conditions. However, application of HS-AFM for imaging of live mammalian cells was hard to be accomplished because of collision between a huge mammalian cell and a cantilever during AFM scanning. Here, we review our recent improvements of HS-AFM for imaging of activities of live mammalian cells without significant damage to the cell. The improvement of an extremely long (~3 μm) AFM tip attached to a cantilever enables us to reduce severe damage to soft mammalian cells. In addition, a combination of HS-AFM with simple fluorescence microscopy allows us to quickly locate the cell in the AFM scanning area. After these improvements, we demonstrate that developed HS-AFM for live mammalian cells is possible to image morphogenesis of filopodia, membrane ruffles, pits open-close formations, and endocytosis in COS-7, HeLa cells as well as hippocampal neurons.
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Affiliation(s)
- Mikihiro Shibata
- High-speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.,Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Hiroki Watanabe
- Research Institute of Biomolecule Metrology Co., Ltd., Tsukuba, Ibaraki 305-0853, Japan
| | - Takayuki Uchihashi
- Department of Physics and Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Toshio Ando
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, Florida 33458, USA
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23
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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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24
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Mathur D, Medintz IL. Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community. Anal Chem 2017; 89:2646-2663. [DOI: 10.1021/acs.analchem.6b04033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
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25
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Yang Y, Tashiro R, Suzuki Y, Emura T, Hidaka K, Sugiyama H, Endo M. A Photoregulated DNA-Based Rotary System and Direct Observation of Its Rotational Movement. Chemistry 2017; 23:3979-3985. [PMID: 28199775 DOI: 10.1002/chem.201605616] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Indexed: 12/15/2022]
Abstract
Various DNA-based nanodevices have been developed on the nanometer scale using light as regulation input. However, the programmed controllability is still a major challenge for these artificial nanodevices. Herein, we demonstrate a rotary DNA nanostructure in which the rotations are controlled by light. A bar-shaped DNA rotor, fabricated as a stiff double-crossover molecule, was placed on the top of a rectangular DNA tile. The photoresponsive oligonucleotides modified with azobenzenes were employed as switching motifs to release/trap the rotor at specific angular position on DNA tile by switching photoirradiations between ultraviolet and visible light. As a result, two reconfigurable states (perpendicular and parallel) of rotor were obtained, in which the angular changes were characterized by AFM and fluorescence quenching assays. Moreover, the reversible rotary motions during the photoirradiation were directly visualized on the DNA tile surface in a nanometer-scale precision using a second-scale scanning of the high-speed AFM.
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Affiliation(s)
- Yangyang Yang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Present address: Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minanitamagakicho, Suzuka-shi, Mie, 513-8670, Japan
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Present address: Frontier Research Institute, for Interdisciplinary Sciences, Tohoku University, Aramaki aza Aoba 6-3, Aoba-ku, Sendai, 980-8578, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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26
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Dai Z, Leung HM, Lo PK. Stimuli-Responsive Self-Assembled DNA Nanomaterials for Biomedical Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602881. [PMID: 28005298 DOI: 10.1002/smll.201602881] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/31/2016] [Indexed: 05/23/2023]
Abstract
Stimuli-responsive DNA-based materials represent a major class of remarkable functional nanomaterials for nano-biotechnological applications. In this review, recent progress in the development of stimuli-responsive systems based on self-assembled DNA nanostructures is introduced and classified. Representative examples are presented in terms of their design, working principles and mechanisms to trigger the response of the stimuli-responsive DNA system upon expose to a large variety of stimuli including pH, metal ions, oligonucleotides, small molecules, enzymes, heat, and light. Substantial in vitro studies have clearly revealed the advantages of the use of stimuli-responsive DNA nanomaterials in different biomedical applications, particularly for biosensing, drug delivery, therapy and diagnostic purposes in addition to bio-computing. Some of the challenges faced and suggestions for further development are also highlighted.
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Affiliation(s)
- Ziwen Dai
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Hoi Man Leung
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
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27
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Takeuchi Y, Endo M, Suzuki Y, Hidaka K, Durand G, Dausse E, Toulmé JJ, Sugiyama H. Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure. Biomater Sci 2017; 4:130-5. [PMID: 26438892 DOI: 10.1039/c5bm00274e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.
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Affiliation(s)
- Yosuke Takeuchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Guillaume Durand
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Jean-Jacques Toulmé
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.
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28
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Peng P, Shi L, Wang H, Li T. A DNA nanoswitch-controlled reversible nanosensor. Nucleic Acids Res 2016; 45:541-546. [PMID: 27899631 PMCID: PMC5314764 DOI: 10.1093/nar/gkw1146] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/14/2016] [Accepted: 11/02/2016] [Indexed: 02/07/2023] Open
Abstract
We present a conceptually new reversible nanosensor regulated by a DNA nanoswitch. This system is not only responsive to external stimuli (e.g. ATP) but also can be reversibly switched between ‘OFF’ and ‘ON’ states via toehold mediated strand displacement reactions. It functions like a molecular net woven by DNA to capture or release the target molecules. As a proof-of-principle experiment, ATP is here chosen as the model to demonstrate our new strategy, which holds great promise for applications such as switchable DNA nanomachines and nanocarriers for drug delivery.
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Affiliation(s)
- Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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29
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Liao WC, Riutin M, Parak WJ, Willner I. Programmed pH-Responsive Microcapsules for the Controlled Release of CdSe/ZnS Quantum Dots. ACS NANO 2016; 10:8683-8689. [PMID: 27526081 DOI: 10.1021/acsnano.6b04056] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Two methods for the preparation of pH-responsive all-DNA microcapsules loaded with CdSe/ZnS quantum dots (QDs) are discussed. One approach involves the construction of DNA microcapsules composed of nucleic acid layers that include, at pH 7.2, "dormant" C-G·C(+) triplex sequences. The formation of the C-G·C(+) triplex structures at pH 5.0 leads to the cleavage of the microcapsules and to the release of the QDs. A second approach involves the synthesis of CdSe/ZnS QD-loaded DNA microcapsules, stabilized at pH 7.2 by T-A·T interlayer triplex bridges. The dissociation of the bridges at pH 9.0 separates the bridging triplex units, resulting in the degradation of the microcapsules and to the release of the QDs. The programmed pH-stimulated release of luminescent QDs, emitting at 620 and 560 nm, from the C-G·C(+) or T-A·T triplex-responsive microcapsules is demonstrated by subjecting the QD-loaded microcapsule mixtures to pH 5.0 or pH 9.0, respectively.
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Affiliation(s)
- Wei-Ching Liao
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Marianna Riutin
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Wolfgang J Parak
- Fachbereich Physik, Philipps-Universität Marburg , Renthof 7, 35037 Marburg, Germany
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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30
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Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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31
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Nakasone Y, Ooi H, Kamiya Y, Asanuma H, Terazima M. Dynamics of Inter-DNA Chain Interaction of Photoresponsive DNA. J Am Chem Soc 2016; 138:9001-4. [DOI: 10.1021/jacs.6b02525] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusuke Nakasone
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | | | | - Masahide Terazima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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32
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Abstract
Dimers of origami tiles are bridged by the Pb(2+)-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1-T2 and T3-T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb(2+)-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb(2+)-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1-T5-T4. In the presence of Pb(2+)-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb(2+) or histidine as trigger cleaves the trimer to yield T5-T4 and T1 or the dimer T1-T5 and T4, respectively. In the presence of Pb(2+)-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging.
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Affiliation(s)
- Na Wu
- 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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33
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A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function. Nat Commun 2016; 7:10591. [PMID: 26830310 PMCID: PMC4740900 DOI: 10.1038/ncomms10591] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/02/2016] [Indexed: 12/23/2022] Open
Abstract
Nature has developed striking light-powered proteins such as bacteriorhodopsin, which can convert light energy into conformational changes for biological functions. Such natural machines are a great source of inspiration for creation of their synthetic analogues. However, synthetic molecular machines typically operate at the nanometre scale or below. Translating controlled operation of individual molecular machines to a larger dimension, for example, to 10-100 nm, which features many practical applications, is highly important but remains challenging. Here we demonstrate a light-driven plasmonic nanosystem that can amplify the molecular motion of azobenzene through the host nanostructure and consequently translate it into reversible chiroptical function with large amplitude modulation. Light is exploited as both energy source and information probe. Our plasmonic nanosystem bears unique features of optical addressability, reversibility and modulability, which are crucial for developing all-optical molecular devices with desired functionalities.
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34
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Endo M, Xing X, Zhou X, Emura T, Hidaka K, Tuesuwan B, Sugiyama H. Single-Molecule Manipulation of the Duplex Formation and Dissociation at the G-Quadruplex/i-Motif Site in the DNA Nanostructure. ACS NANO 2015; 9:9922-9929. [PMID: 26371377 DOI: 10.1021/acsnano.5b03413] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We demonstrate the single-molecule operation and observation of the formation and resolution of double-stranded DNA (dsDNA) containing a G-quadruplex (GQ) forming and counterpart i-motif forming sequence in the DNA nanostructure. Sequential manipulation of DNA strands in the DNA frame was performed to prepare a topologically controlled GQ/i-motif dsDNA. Using strand displacement and the addition and removal of K(+), the topologically controlled GQ/i-motif dsDNA in the DNA frame was obtained in high yield. The dsDNA was resolved into the single-stranded DNA, GQ, and i-motif by the addition of K(+) and operation in acidic conditions. The dissociation of the dsDNA under the GQ and i-motif formation condition was monitored by high-speed atomic force microscopy. The results indicate that the dsDNA containing the GQ- and i-motif sequence is effectively dissolved when the duplex is helically loosened in the DNA nanoscaffold.
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Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST , Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Xiwen Xing
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan, Hubei 430072, People's Republic of China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan, Hubei 430072, People's Republic of China
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Bodin Tuesuwan
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University , Bangkok 10330, Thailand
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- CREST , Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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35
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Goldau T, Murayama K, Brieke C, Asanuma H, Heckel A. Azobenzene C-Nucleosides for Photocontrolled Hybridization of DNA at Room Temperature. Chemistry 2015; 21:17870-6. [DOI: 10.1002/chem.201503303] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Indexed: 12/26/2022]
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36
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Yang Y, Goetzfried MA, Hidaka K, You M, Tan W, Sugiyama H, Endo M. Direct Visualization of Walking Motions of Photocontrolled Nanomachine on the DNA Nanostructure. NANO LETTERS 2015; 15:6672-6. [PMID: 26302358 PMCID: PMC5507700 DOI: 10.1021/acs.nanolett.5b02502] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A light-driven artificial molecular nanomachine was constructed based on DNA scaffolding. Pyrene-modified walking strands and disulfide bond-connected stator strands, employed as anchorage sites to support walker movement, were assembled into a 2D DNA tile. Pyrene molecules excited by photoirradiation at 350 nm induced cleavage of disulfide bond-connected stator strands, enabling the DNA walker to migrate from one cleaved stator to the next on the DNA tile. The time-dependent movement of the walker was observed and the entire walking process of the walker was characterized by distribution of the walker-stator duplex at four anchorage sites on the tile under different irradiation times. Importantly, the light-fuelled mechanical movements on DNA tile were first visualized in real time during UV irradiation using high-speed atomic force microscopy (HS-AFM).
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Affiliation(s)
- Yangyang Yang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Marisa A. Goetzfried
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mingxu You
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
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37
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Endo M, Takeuchi Y, Suzuki Y, Emura T, Hidaka K, Wang F, Willner I, Sugiyama H. Single-Molecule Visualization of the Activity of a Zn2+
-Dependent DNAzyme. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504656] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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38
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Endo M, Takeuchi Y, Suzuki Y, Emura T, Hidaka K, Wang F, Willner I, Sugiyama H. Single-Molecule Visualization of the Activity of a Zn(2+)-Dependent DNAzyme. Angew Chem Int Ed Engl 2015. [PMID: 26195344 DOI: 10.1002/anie.201504656] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We demonstrate the single-molecule imaging of the catalytic reaction of a Zn(2+)-dependent DNAzyme in a DNA origami nanostructure. The single-molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high-speed atomic force microscopy (AFM). This nanostructure-based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single-molecule level.
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Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan).
- CREST (Japan) Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075 (Japan).
| | - Yosuke Takeuchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Fuan Wang
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel)
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel).
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan).
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan).
- CREST (Japan) Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075 (Japan).
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39
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Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells. Sci Rep 2015; 5:8724. [PMID: 25735540 PMCID: PMC4348644 DOI: 10.1038/srep08724] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 02/02/2015] [Indexed: 01/06/2023] Open
Abstract
Visualization of morphological dynamics of live cells with nanometer resolution under physiological conditions is highly desired, but challenging. It has been demonstrated that high-speed atomic force microscopy is a powerful technique for visualizing dynamics of biomolecules under physiological conditions. However, application of high-speed atomic force microscopy for imaging larger objects such as live mammalian cells has been complicated because of the collision between the cantilever and samples. Here, we demonstrate that attaching an extremely long (~3 μm) and thin (~5 nm) tip by amorphous carbon to the cantilever allows us to image the surface structure of live cells with the spatiotemporal resolution of nanometers and seconds. We demonstrate that long-tip high-speed atomic force microscopy is capable of imaging morphogenesis of filopodia, membrane ruffles, pit formation, and endocytosis in COS-7, HeLa cells and hippocampal neurons.
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40
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Wang F, Liu X, Willner I. DNA switches: from principles to applications. Angew Chem Int Ed Engl 2014; 54:1098-129. [PMID: 25521588 DOI: 10.1002/anie.201404652] [Citation(s) in RCA: 356] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/25/2014] [Indexed: 12/13/2022]
Abstract
The base sequence of nucleic acid encodes structural and functional properties into the biopolymer. Structural information includes the formation of duplexes, G-quadruplexes, i-motif, and cooperatively stabilized assemblies. Functional information encoded in the base sequence involves the strand-displacement process, the recognition properties by aptamers, and the catalytic functions of DNAzymes. This Review addresses the implementation of the information encoded in nucleic acids to develop DNA switches. A DNA switch is a supramolecular nucleic acid assembly that undergoes cyclic, switchable, transitions between two distinct states in the presence of appropriate triggers and counter triggers, such as pH value, metal ions/ligands, photonic and electrical stimuli. Applications of switchable DNA systems to tailor switchable DNA hydrogels, for the controlled drug-release and for the activation of switchable enzyme cascades, are described, and future perspectives of the systems are addressed.
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Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel) http://chem.ch.huji.ac.il/willner/
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41
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42
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Li J, Wang X, Liang X. Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology. Chem Asian J 2014; 9:3344-58. [DOI: 10.1002/asia.201402758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 01/29/2023]
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43
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Takenaka T, Endo M, Suzuki Y, Yang Y, Emura T, Hidaka K, Kato T, Miyata T, Namba K, Sugiyama H. Photoresponsive DNA nanocapsule having an open/close system for capture and release of nanomaterials. Chemistry 2014; 20:14951-4. [PMID: 25223393 DOI: 10.1002/chem.201404757] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Indexed: 11/10/2022]
Abstract
A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system and toehold system were introduced into the NC for the inclusion and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy (AFM), and the open behavior was directly observed by high-speed AFM. The encapsulation of the DNA-modified AuNP within the NC was carried out by hybridization of a specific DNA strand (capture strand), and the release of the AuNP was examined by addition of toehold-containing complementary DNA strand (release strand). The release of the AuNP from the NC was achieved by the opening of the NC and subsequent strand displacement.
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Affiliation(s)
- Tomohiro Takenaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
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44
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Zhang F, Nangreave J, Liu Y, Yan H. Structural DNA nanotechnology: state of the art and future perspective. J Am Chem Soc 2014; 136:11198-211. [PMID: 25029570 PMCID: PMC4140475 DOI: 10.1021/ja505101a] [Citation(s) in RCA: 393] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 12/12/2022]
Abstract
Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson-Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming.
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Affiliation(s)
- Fei Zhang
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Jeanette Nangreave
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Yan Liu
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Hao Yan
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
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45
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Endo M, Sugiyama H. Single-molecule imaging of dynamic motions of biomolecules in DNA origami nanostructures using high-speed atomic force microscopy. Acc Chem Res 2014; 47:1645-53. [PMID: 24601497 DOI: 10.1021/ar400299m] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CONSPECTUS: Direct imaging of molecular motions is one of the most fundamental issues for elucidating the physical properties of individual molecules and their reaction mechanisms. Atomic force microscopy (AFM) enables direct molecular imaging, especially for biomolecules in the physiological environment. Because AFM can visualize the molecules at nanometer-scale spatial resolution, a versatile observation scaffold is needed for the precise imaging of molecule interactions in the reactions. The emergence of DNA origami technology allows the precise placement of desired molecules in the designed nanostructures and enables molecules to be detected at the single-molecule level. In our study, the DNA origami system was applied to visualize the detailed motions of target molecules in reactions using high-speed AFM (HS-AFM), which enables the analysis of dynamic motions of biomolecules in a subsecond time resolution. In this system, biochemical properties such as the placement of various double-stranded DNAs (dsDNAs) containing unrestricted DNA sequences, modified nucleosides, and chemical functions can be incorporated. From a physical point of view, the tension and rotation of dsDNAs can be controlled by placement into the DNA nanostructures. From a topological point of view, the orientations of dsDNAs and various shapes of dsDNAs including Holliday junctions can be incorporated for studies on reaction mechanisms. In this Account, we describe the combination of the DNA origami system and HS-AFM for imaging various biochemical reactions including enzymatic reactions and DNA structural changes. To observe the behaviors and reactions of DNA methyltransferase and DNA repair enzymes, the substrate dsDNAs were incorporated into the cavity of the DNA frame, and the enzymes that bound to the target dsDNA were observed using HS-AFM. DNA recombination was also observed using the recombination substrates and Holliday junction intermediates placed in the DNA frame, and the direction of the reactions was controlled by introducing structural stress to the substrates. In addition, the movement of RNA polymerase and its reaction were visualized using a template dsDNA attached to the origami structure. To observe DNA structural changes, G-quadruplex formation and disruption, the switching behaviors of photoresponsive oligonucleotides, and B-Z transition were visualized using the DNA frame observation system. For the formation and disruption of G-quadruplex and double-helix DNA, the two dsDNA chains incorporated into the DNA frame could amplify the small structural change to the global structural change, which enabled the visualization of their association and dissociation by HS-AFM. The dynamic motion of the helical rotation induced by the B-Z transition was also directly imaged in the DNA frame. Furthermore, the stepwise motions of mobile DNA along the DNA track were visualized on the DNA origami surface. These target-orientated observation systems should contribute to the detailed analysis of biomolecule motions in real time and at molecular resolution.
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Affiliation(s)
- Masayuki Endo
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Hiroshi Sugiyama
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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Kamiya Y, Asanuma H. Light-driven DNA nanomachine with a photoresponsive molecular engine. Acc Chem Res 2014; 47:1663-72. [PMID: 24617966 DOI: 10.1021/ar400308f] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONSPECTUS: DNA is regarded as an excellent nanomaterial due to its supramolecular property of duplex formation through A-T and G-C complementary pairs. By simply designing sequences, we can create any desired 2D or 3D nanoarchitecture with DNA. Based on these nanoarchitectures, motional DNA-based nanomachines have also been developed. Most of the nanomachines require molecular fuels to drive them. Typically, a toehold exchange reaction is applied with a complementary DNA strand as a fuel. However, repetitive operation of the machines accumulates waste DNA duplexes in the solution that gradually deteriorate the motional efficiency. Hence, we are facing an "environmental problem" even in the nanoworld. One of the direct solutions to this problem is to use clean energy, such as light. Since light does not contaminate the reaction system, a DNA nanomachine run by a photon engine can overcome the drawback of waste that is a problem with molecular-fueled engines. There are several photoresponsive molecules that convert light energy to mechanical motion through the change of geometry of the molecules; these include spiropyran, diarylethene, stilbene, and azobenzene. Although each molecule has both advantages and drawbacks, azobenzene derivatives are widely used as "molecular photon engines". In this Account, we review light-driven DNA nanomachines mainly focusing on the photoresponsive DNAs that we have developed for the past decade. The basis of our method is installation of an azobenzene into a DNA sequence through a d-threoninol scaffold. Reversible hybridization of the DNA duplex, triggered by trans-cis isomerization of azobenzene in the DNA sequences by irradiation with light, induces mechanical motion of the DNA nanomachine. Moreover we have successfully developed azobenzene derivatives that improve its photoisomerizaition properties. Use of these derivatives and techniques have allowed us to design various DNA machines that demonstrate sophisticated motion in response to lights of different wavelengths without a drop in photoregulatory efficiency. In this Account, we emphasize the advantages of our methods including (1) ease of preparation, (2) comprehensive sequence design of azobenzene-tethered DNA, (3) efficient photoisomerization, and (4) reversible photocontrol of hybridization by irradiation with appropriate wavelengths of light. We believe that photon-fueled DNA nanomachines driven by azobenzene-derivative molecular photon-fueled engines will be soon science rather than "science fiction".
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Affiliation(s)
- Yukiko Kamiya
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
- Ecotopia
Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
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Suzuki Y, Endo M, Cañas C, Ayora S, Alonso JC, Sugiyama H, Takeyasu K. Direct analysis of Holliday junction resolving enzyme in a DNA origami nanostructure. Nucleic Acids Res 2014; 42:7421-8. [PMID: 24792171 PMCID: PMC4066755 DOI: 10.1093/nar/gku320] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Holliday junction (HJ) resolution is a fundamental step for completion of homologous recombination. HJ resolving enzymes (resolvases) distort the junction structure upon binding and prior cleavage, raising the possibility that the reactivity of the enzyme can be affected by a particular geometry and topology at the junction. Here, we employed a DNA origami nano-scaffold in which each arm of a HJ was tethered through the base-pair hybridization, allowing us to make the junction core either flexible or inflexible by adjusting the length of the DNA arms. Both flexible and inflexible junctions bound to Bacillus subtilis RecU HJ resolvase, while only the flexible junction was efficiently resolved into two duplexes by this enzyme. This result indicates the importance of the structural malleability of the junction core for the reaction to proceed. Moreover, cleavage preferences of RecU-mediated reaction were addressed by analyzing morphology of the reaction products.
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Affiliation(s)
- Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masayuki Endo
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Cristina Cañas
- Centro Nacional de Biotecnología, CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - Silvia Ayora
- Centro Nacional de Biotecnología, CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - Juan C Alonso
- Centro Nacional de Biotecnología, CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kunio Takeyasu
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University Yoshida-konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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48
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List J, Weber M, Simmel FC. Hydrophobes Schalten einer doppellagigen DNA-Origami-Struktur. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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List J, Weber M, Simmel FC. Hydrophobic actuation of a DNA origami bilayer structure. Angew Chem Int Ed Engl 2014; 53:4236-9. [PMID: 24616083 DOI: 10.1002/anie.201310259] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Indexed: 01/07/2023]
Abstract
Amphiphilic compounds have a strong tendency to form aggregates in aqueous solutions. It is shown that such aggregation can be utilized to fold cholesterol-modified, single-layered DNA origami structures into sandwich-like bilayer structures, which hide the cholesterol modifications in their interior. The DNA bilayer structures unfold after addition of the surfactant Tween 80, and also in the presence of lipid bilayer membranes, with opening kinetics well described by stretched exponentials. It is also demonstrated that by combination with an appropriate lock and key mechanism, hydrophobic actuation of DNA sandwiches can be made conditional on the presence of an additional molecular input such as a specific DNA sequence.
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Affiliation(s)
- Jonathan List
- Lehrstuhl für Systembiophysik, Physik-Department - E14 und ZNN-WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching (Germany) http://www.e14.ph.tum.de
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50
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Suzuki Y, Endo M, Yang Y, Sugiyama H. Dynamic Assembly/Disassembly Processes of Photoresponsive DNA Origami Nanostructures Directly Visualized on a Lipid Membrane Surface. J Am Chem Soc 2014; 136:1714-7. [DOI: 10.1021/ja4109819] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yuki Suzuki
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masayuki Endo
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yangyang Yang
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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