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Komiyama M, Yoshimoto K, Sisido M, Ariga K. Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170156] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
| | - Masahiko Sisido
- Professor Emeritus, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827
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Hou C, Guan S, Wang R, Zhang W, Meng F, Zhao L, Xu J, Liu J. Supramolecular Protein Assemblies Based on DNA Templates. J Phys Chem Lett 2017; 8:3970-3979. [PMID: 28792224 DOI: 10.1021/acs.jpclett.7b01564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA plays an important role in the process of protein assembly. DNA viruses such as the M13 virus are typical examples in which single DNA genomes behave as templates to induce the assembly of multiple major coat protein (PVIII) monomers. Thus, the design of protein assemblies based on DNA templates attracts much interest in the construction of supramolecular structures and materials. With the development of DNA nanotechnology, precise 1D and 3D protein nanostructures have been designed and constructed by using DNA templates through DNA-protein interactions, protein-ligand interactions, and protein-adapter interactions. These DNA-templated protein assemblies show great potential in catalysis, medicine, light-responsive systems, drug delivery, and signal transduction. Herein, we review the progress on DNA-based protein nanostructures that possess sophisticated nanometer-sized structures with programmable shapes and stimuli-responsive parameters, and we present their great potential in the design of biomaterials and biodevices in the future.
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Affiliation(s)
| | | | - Ruidi Wang
- Department of Chemistry, University of British Columbia , Vancouver, British Columbia V6T 1Z1, Canada
| | - Wei Zhang
- Zhuhai United Laboratories Co., Ltd. , Nation High & New Technology Industry Development Zone, Zhuhai 519040, China
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Kuzuya A, Sakai Y, Yamazaki T, Xu Y, Yamanaka Y, Ohya Y, Komiyama M. Allosteric control of nanomechanical DNA origami pinching devices for enhanced target binding. Chem Commun (Camb) 2017; 53:8276-8279. [DOI: 10.1039/c7cc03991c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Significant enhancement of single-molecular binding of specific targets was achieved by allosterically controlling nanomechanical DNA origami pinching devices.
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Affiliation(s)
- Akinori Kuzuya
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Yusuke Sakai
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
| | - Takahiro Yamazaki
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
| | - Yan Xu
- Department of Medical Sciences
- University of Miyazaki
- Miyazaki 889-1692
- Japan
| | - Yusei Yamanaka
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Yuichi Ohya
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Makoto Komiyama
- International Center for Materials Nanoarchitectonics
- National Institute for Materials Science
- Tsukuba
- Japan
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Yamazaki T, Heddle JG, Kuzuya A, Komiyama M. Orthogonal enzyme arrays on a DNA origami scaffold bearing size-tunable wells. NANOSCALE 2014; 6:9122-6. [PMID: 24974892 DOI: 10.1039/c4nr01598c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A new waffle-like DNA origami assembly (DNA waffle) with nine nanometer-scale wells in a 3 × 3 matrix pattern has been successfully constructed and used as a scaffold for selective nano-patterning of individual protein molecules. The folding pattern of the scaffold was specially designed so that the dimensions of each well could be independently tuned according to the dimensions of the guest nanoparticles. We demonstrated that two distinct proteins, streptavidin (SA) tetramer (d = 5 nm) and anti-fluorescein antibody (IgG) (inter-paratope distance ∼ 14.0 nm), could be selectively captured in size-variable wells of dimensions 6.8 × 12 × 2.0 nm for SA and 6.8 × 12 × 2.0 nm or 10.2 × 12 × 2.0 nm for IgG, respectively, through the attachment of two biotins or two fluoresceins at the two edges of each well. This allowed the formation of a heterogeneous protein nanoarray of individual molecules. The position of SA or IgG capture can be fully controlled by placement of biotins or fluoresceins in the nanoarray well. Moreover, a hetero-nanoarray consisting of two kinds of enzyme: horseradish peroxidase-labeled streptavidin (HRP-SA) and alkaline phosphatase-labeled anti-FITC antibody (AP-IgG) was successfully constructed through selective attachment of biotin or fluorescein in any desired wells. Successful enzyme-heteroarray formation was confirmed by enzymatic activity analyses after purification of mixtures of enzymes and DNA waffles.
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Affiliation(s)
- Takahiro Yamazaki
- RCAST, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Zhang C, Tian C, Guo F, Liu Z, Jiang W, Mao C. DNA-Directed Three-Dimensional Protein Organization. Angew Chem Int Ed Engl 2012; 51:3382-5. [DOI: 10.1002/anie.201108710] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Indexed: 11/12/2022]
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Zhang C, Tian C, Guo F, Liu Z, Jiang W, Mao C. DNA-Directed Three-Dimensional Protein Organization. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108710] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Zhao H, Huang W, Wu X, Xing Z, He Y, Chen Q. Different superstructures formed by Janus-type nucleosides. Chem Commun (Camb) 2012; 48:6097-9. [DOI: 10.1039/c2cc31036h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Pan MY, Hang W, Zhao XJ, Zhao H, Deng PC, Xing ZH, Qing Y, He Y. Janus-type AT nucleosides: synthesis, solid and solution state structures. Org Biomol Chem 2011; 9:5692-702. [DOI: 10.1039/c1ob05577a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kuzuya A, Koshi N, Kimura M, Numajiri K, Yamazaki T, Ohnishi T, Okada F, Komiyama M. Programmed nanopatterning of organic/inorganic nanoparticles using nanometer-scale wells embedded in a DNA origami scaffold. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:2664-2667. [PMID: 21072871 DOI: 10.1002/smll.201001484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo 4 -6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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Yang D, Campolongo MJ, Nhi Tran TN, Ruiz RCH, Kahn JS, Luo D. Novel DNA materials and their applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2010; 2:648-69. [PMID: 20730873 PMCID: PMC7169675 DOI: 10.1002/wnan.111] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials.
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Affiliation(s)
- Dayong Yang
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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Numajiri K, Yamazaki T, Kimura M, Kuzuya A, Komiyama M. Discrete and Active Enzyme Nanoarrays on DNA Origami Scaffolds Purified by Affinity Tag Separation. J Am Chem Soc 2010; 132:9937-9. [DOI: 10.1021/ja104702q] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kentaro Numajiri
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takahiro Yamazaki
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Mayumi Kimura
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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Numajiri K, Kimura M, Kuzuya A, Komiyama M. Stepwise and reversible nanopatterning of proteins on a DNA origami scaffold. Chem Commun (Camb) 2010; 46:5127-9. [DOI: 10.1039/c0cc00044b] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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