1
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Matsubayashi HT, Mountain J, Takahashi N, Deb Roy A, Yao T, Peterson AF, Saez Gonzalez C, Kawamata I, Inoue T. Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85β/AP2-mediated endocytosis. Nat Commun 2024; 15:2612. [PMID: 38521786 PMCID: PMC10960865 DOI: 10.1038/s41467-024-46855-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
Class IA phosphoinositide 3-kinase (PI3K) galvanizes fundamental cellular processes such as migration, proliferation, and differentiation. To enable these multifaceted roles, the catalytic subunit p110 utilizes the multi-domain, regulatory subunit p85 through its inter SH2 domain (iSH2). In cell migration, its product PI(3,4,5)P3 generates locomotive activity. While non-catalytic roles are also implicated, underlying mechanisms and their relationship to PI(3,4,5)P3 signaling remain elusive. Here, we report that a disordered region of iSH2 contains AP2 binding motifs which can trigger clathrin and dynamin-mediated endocytosis independent of PI3K catalytic activity. The AP2 binding motif mutants of p85 aberrantly accumulate at focal adhesions and increase both velocity and persistency in fibroblast migration. We thus propose the dual functionality of PI3K in the control of cell motility, catalytic and non-catalytic, arising distinctly from juxtaposed regions within iSH2.
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Affiliation(s)
- Hideaki T Matsubayashi
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University, Baltimore, MD, USA.
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Tohoku, Japan.
| | - Jack Mountain
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Nozomi Takahashi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Tohoku, Japan
| | - Abhijit Deb Roy
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Tony Yao
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Amy F Peterson
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Cristian Saez Gonzalez
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Ibuki Kawamata
- Department of Robotics, Tohoku University, Tohoku, Japan
- Natural Science Division, Ochanomizu University, Kyoto, Japan
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takanari Inoue
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University, Baltimore, MD, USA.
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2
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Karna D, Mano E, Ji J, Kawamata I, Suzuki Y, Mao H. Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies. Nat Commun 2023; 14:6459. [PMID: 37833326 PMCID: PMC10575982 DOI: 10.1038/s41467-023-41604-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/06/2023] [Indexed: 10/15/2023] Open
Abstract
The intrinsic complexity of many mesoscale (10-100 nm) cellular machineries makes it challenging to elucidate their topological arrangement and transition dynamics. Here, we exploit DNA origami nanospring as a model system to demonstrate that tens of piconewton linear force can modulate higher-order conformation dynamics of mesoscale molecular assemblies. By switching between two chemical structures (i.e., duplex and tetraplex DNA) in the junctions of adjacent origami modules, the corresponding stretching or compressing chemo-mechanical stress reversibly flips the backbone orientations of the DNA nanosprings. Both coarse-grained molecular dynamics simulations and atomic force microscopy measurements reveal that such a backbone conformational switch does not alter the right-handed chirality of the nanospring helix. This result suggests that mesoscale helical handedness may be governed by the torque, rather than the achiral orientation, of nanospring backbones. It offers a topology-based caging/uncaging concept to present chemicals in response to environmental cues in solution.
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Affiliation(s)
- Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Eriko Mano
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8579, Japan.
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan.
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, 1577 Kurimamachiya-Cho, Tsu, 514-8507, Japan.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA.
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3
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Watanabe K, Kawamata I, Murata S, Suzuki Y. Multi-Reconfigurable DNA Origami Nanolattice Driven by the Combination of Orthogonal Signals. JACS Au 2023; 3:1435-1442. [PMID: 37234113 PMCID: PMC10206592 DOI: 10.1021/jacsau.3c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/01/2023] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
The progress of the scaffolded DNA origami technology has enabled the construction of various dynamic nanodevices imitating the shapes and motions of mechanical elements. To further expand the achievable configurational changes, the incorporation of multiple movable joints into a single DNA origami structure and their precise control are desired. Here, we propose a multi-reconfigurable 3 × 3 lattice structure consisting of nine frames with rigid four-helix struts connected with flexible 10-nucleotide joints. The configuration of each frame is determined by the arbitrarily selected orthogonal pair of signal DNAs, resulting in the transformation of the lattice into various shapes. We also demonstrated sequential reconfiguration of the nanolattice and its assemblies from one into another via an isothermal strand displacement reaction at physiological temperatures. Our modular and scalable design approach could serve as a versatile platform for a variety of applications that require reversible and continuous shape control with nanoscale precision.
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Affiliation(s)
- Kotaro Watanabe
- Department
of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Ibuki Kawamata
- Department
of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Satoshi Murata
- Department
of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Yuki Suzuki
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8578, Japan
- Department
of Chemistry for Materials, Graduate School of Engineering, Mie University, 1577 Kurimamachiya-Cho, Tsu 514-8507, Mie, Japan
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4
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Elonen A, Natarajan AK, Kawamata I, Oesinghaus L, Mohammed A, Seitsonen J, Suzuki Y, Simmel FC, Kuzyk A, Orponen P. Algorithmic Design of 3D Wireframe RNA Polyhedra. ACS Nano 2022; 16:16608-16616. [PMID: 36178116 PMCID: PMC9620399 DOI: 10.1021/acsnano.2c06035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/26/2022] [Indexed: 06/01/2023]
Abstract
We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism. The design software is openly available and also provides an export of the targeted 3D structure into the oxDNA molecular dynamics simulator for easy simulation and visualization.
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Affiliation(s)
- Antti Elonen
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
| | | | - Ibuki Kawamata
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8577, Japan
- Natural
Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan
| | - Lukas Oesinghaus
- Physics
Department E14, Technical University Munich, 85748 Garching, Germany
| | - Abdulmelik Mohammed
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
- Department
of Biomedical Engineering, San José
State University, San José, California 95192, United States
| | - Jani Seitsonen
- Department
of Applied Physics and Nanomicroscopy Center, Aalto University, 00076 Aalto, Finland
| | - Yuki Suzuki
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8577, Japan
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8577, Japan
- Division
of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu 514-8507, Japan
| | - Friedrich C. Simmel
- Physics
Department E14, Technical University Munich, 85748 Garching, Germany
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Pekka Orponen
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
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5
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Suzuki Y, Kawamata I, Watanabe K, Mano E. Lipid bilayer-assisted dynamic self-assembly of hexagonal DNA origami blocks into monolayer crystalline structures with designed geometries. iScience 2022; 25:104292. [PMID: 35573202 PMCID: PMC9097702 DOI: 10.1016/j.isci.2022.104292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/18/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
The DNA origami technique is used to construct custom-shaped nanostructures that can be used as components of two-dimensional crystalline structures with user-defined structural patterns. Here, we designed an Mg2+-responsive hexagonal 3D DNA origami block with self-shape-complementary ruggedness on the sides. Hexagonal DNA origami blocks were electrostatically adsorbed onto a fluidic lipid bilayer membrane surface to ensure lateral diffusion. A subsequent increase in the Mg2+ concentration in the surrounding environment induced the self-assembly of the origami blocks into lattices with prescribed geometries based on a self-complementary shape fit. High-speed atomic force microscopy (HS-AFM) images revealed dynamic events involved in the self-assembly process, including edge reorganization, defect splitting, diffusion, and filling, which provide a glimpse into how the lattice structures are self-improved. Lipid bilayer-assisted self-assembly of 3D DNA origami blocks was achieved Time-lapse AFM imaging of the self-assembly processes was performed Different assembly patterns were achieved from a single DNA origami design
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Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8578, Japan
- Corresponding author
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kotaro Watanabe
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Eriko Mano
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8578, Japan
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6
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Abstract
Reaction-diffusion systems are one of the models of the formation process with various patterns found in nature. Inspired by natural pattern formation, several methods for designing artificial chemical reaction-diffusion systems have been proposed. DNA is a suitable building block to build such artificial systems owing to its programmability. Previously, we reported a line pattern formed due to the reaction and diffusion of synthetic DNA; however, the width of the line was too wide to be used for further applications such as parallel and multi-stage pattern formations. Here, we propose a novel method to programme a reaction-diffusion system in a hydrogel medium to realise a sharp line capable of forming superimposed and cascaded patterns. The mechanism of this system utilises a two-segment polymerisation of DNA caused by hybridisation. To superimpose the system, we designed orthogonal DNA sequences that formed two lines in different locations on the hydrogel. Additionally, we designed a reaction to release DNA and form a cascade pattern, in which the third line appears between the two lines. To explain the mechanism of our system, we modelled the system as partial differential equations, whose simulation results agreed well with the experimental data. Our method to fabricate cascaded patterns may inspire combinations of DNA-based technologies and expand the applications of artificial reaction-diffusion systems.
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Affiliation(s)
- Keita Abe
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan.
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan.
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan. and Natural Science Division, Faculty of Core Research, Ochanomizu University, Japan
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7
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Affiliation(s)
- Yudai Yamashita
- Department of Robotics, Graduate School of Engineering, Tohoku University
| | - Kotaro Watanabe
- Department of Robotics, Graduate School of Engineering, Tohoku University
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University
- Natural Science Division, Faculty of Core Research, Ochanomizu University
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8
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Karna D, Stilgenbauer M, Jonchhe S, Ankai K, Kawamata I, Cui Y, Zheng YR, Suzuki Y, Mao H. Chemo-Mechanical Modulation of Cell Motions Using DNA Nanosprings. Bioconjug Chem 2021; 32:311-317. [PMID: 33475341 PMCID: PMC8199798 DOI: 10.1021/acs.bioconjchem.0c00674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell motions such as migration and change in cellular morphology are essential activities for multicellular organism in response to environmental stimuli. These activities are a result of coordinated clustering/declustering of integrin molecules at the cell membrane. Here, we prepared DNA origami nanosprings to modulate cell motions by targeting the clustering of integrin molecules. Each nanospring was modified with arginyl-glycyl-aspartic acid (RGD) domains with a spacing such that when the nanospring is coiled, the RGD ligands trigger the clustering of integrin molecules, which changes cell motions. The coiling or uncoiling of the nanospring is controlled, respectively, by the formation or dissolution of an i-motif structure between neighboring piers in the DNA origami nanodevice. At slightly acidic pH (<6.5), the folding of the i-motif leads to the coiling of the nanospring, which inhibits the motion of HeLa cells. At neutrality (pH 7.4), the unfolding of the i-motif allows cells to resume mechanical movement as the nanospring becomes uncoiled. We anticipate that this pH-responsive DNA nanoassembly is valuable to inhibit the migration of metastatic cancer cells in acidic extracellular environment. Such a chemo-mechanical modulation provides a new mechanism for cells to mechanically respond to endogenous chemical cues.
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Affiliation(s)
- Deepak Karna
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Morgan Stilgenbauer
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sagun Jonchhe
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Kazuya Ankai
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8579, Japan
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Yunxi Cui
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
- College of Life Sciences, Nankai University, Tianjin, China, 300071
| | - Yao-Rong Zheng
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
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9
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Iwabuchi S, Kawamata I, Murata S, Nomura SIM. A large, square-shaped, DNA origami nanopore with sealing function on a giant vesicle membrane. Chem Commun (Camb) 2021; 57:2990-2993. [PMID: 33587063 DOI: 10.1039/d0cc07412h] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intaking molecular information from the external environment is essential for the normal functioning of artificial cells/molecular robots. Herein, we report the design and function of a membrane nanopore using a DNA origami square tube with a cross-section of 100 nm2. When the nanopore is added to a giant vesicle that mimics a cell membrane, the permeation of large external hydrophilic fluorescent molecules is observed. Furthermore, the addition of up to four ssDNA strands enables size-based selective transport of molecules. A controllable artificial nanopore should facilitate the communication between the vesicle components and their environment.
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Affiliation(s)
- Shoji Iwabuchi
- Department of Robotics, Tohoku University, Miyagi 980-8579, Japan.
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10
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Liu S, Murata S, Kawamata I. DNA Ring Motif with Flexible Joints. Micromachines (Basel) 2020; 11:mi11110987. [PMID: 33142895 PMCID: PMC7693582 DOI: 10.3390/mi11110987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022]
Abstract
The invention of DNA origami has expanded the geometric complexity and functionality of DNA nanostructures. Using DNA origami technology, we develop a flexible multi-joint ring motif as a novel self-assembling module. The motif can connect with each other through self-complementary sequences on its segments. The flexible joints can be fixed in a straightened position as desired, thereby allowing the motif to take various shapes. We can adjust the number of flexible joints and the number of connectable segments, thereby enabling programmable self-assembly of the motif. We successfully produced the motif and evaluated several self-assembly patterns. The proposed multi-joint ring motif can provide a novel method for creating functional molecular devices.
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Affiliation(s)
- Shiyun Liu
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (S.L.); (S.M.)
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (S.L.); (S.M.)
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (S.L.); (S.M.)
- Natural Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan
- Correspondence:
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11
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Suzuki Y, Kawamata I, Mizuno K, Murata S. Large Deformation of a DNA‐Origami Nanoarm Induced by the Cumulative Actuation of Tension‐Adjustable Modules. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary SciencesTohoku University 6-3 Aramaki-aza Aoba, Aoba-ku Sendai 980-8578 Japan
- Department of RoboticsGraduate School of EngineeringTohoku University 6-6-01 Aramaki-Aza Aoba, Aoba-ku Sendai 980-8579 Japan
| | - Ibuki Kawamata
- Department of RoboticsGraduate School of EngineeringTohoku University 6-6-01 Aramaki-Aza Aoba, Aoba-ku Sendai 980-8579 Japan
| | - Kohei Mizuno
- Department of RoboticsGraduate School of EngineeringTohoku University 6-6-01 Aramaki-Aza Aoba, Aoba-ku Sendai 980-8579 Japan
| | - Satoshi Murata
- Department of RoboticsGraduate School of EngineeringTohoku University 6-6-01 Aramaki-Aza Aoba, Aoba-ku Sendai 980-8579 Japan
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12
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Suzuki Y, Kawamata I, Mizuno K, Murata S. Large Deformation of a DNA-Origami Nanoarm Induced by the Cumulative Actuation of Tension-Adjustable Modules. Angew Chem Int Ed Engl 2020; 59:6230-6234. [PMID: 31944509 DOI: 10.1002/anie.201916233] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 01/03/2023]
Abstract
Making use of the programmability and structural flexibility of the DNA molecule, a DNA-origami nanoarm capable of undergoing large deformation is constructed. This DNA-origami nanoarm comprised serially repeated tension-adjustable modules, the cumulative actuation of which resulted in a large deformation of the arm structure, which transformed from a linear shape into an arched shape. Combining atomic force microscopy and theoretical analyses based on the mechanics of materials, we demonstrate that the degree of deformation can be systematically controlled by merely replacing a set of strands that is required for the actuation of the module. Moreover, by employing a G-quadruplex-forming sequence for the actuation, we could achieve reversible ion-induced contraction and relaxation of the nanoarm. The adjustability and scalability of this design could enable the production of DNA nanodevices that exhibit large deformation in response to external stimuli.
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Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan.,Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Kohei Mizuno
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, 980-8579, Japan
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13
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Watanabe T, Sato Y, Otaka H, Kawamata I, Murata S, Nomura SIM. DNA Origami "Quick" Refolding Inside of a Micron-Sized Compartment. Molecules 2019; 25:E8. [PMID: 31861399 PMCID: PMC6983259 DOI: 10.3390/molecules25010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Investigations into the refolding of DNA origami leads to the creation of reconstructable nanostructures and deepens our understanding of the sustainability of life. Here, we report the refolding of the DNA origami structure inside a micron-sized compartment. In our experiments, conventional DNA origami and truss-type DNA origami were annealed and purified to remove the excess staples in a test tube. The DNA origami was then encapsulated inside of a micron-sized compartment of water-in-oil droplets, composed of neutral surfactants. The re-annealing process was then performed to initiate refolding in the compartment. The resulting 100-nm-sized DNA nanostructures were observed using atomic force microscopy (AFM), and the qualities of their structures were evaluated based on their shape. We found that the refolding of the DNA origami structure was favored inside the droplets compared with refolding in bulk solution. The refolded structures were able to fold even under "quick" one-minute annealing conditions. In addition, the smaller droplets (average diameter: 1.2 µm) appeared to be more advantageous for the refolding of the origamis than larger droplets. These results are expected to contribute to understanding the principles of life phenomena based on multimolecular polymer self-assembly in a micron-sized compartment, and for the production and maintenance of artificially designed molecules.
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Affiliation(s)
- Taiki Watanabe
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
| | - Yusuke Sato
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
| | - Hayato Otaka
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
| | - Shin-Ichiro M. Nomura
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
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14
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Sato Y, Komiya K, Kawamata I, Murata S, Nomura SIM. Isothermal amplification of specific DNA molecules inside giant unilamellar vesicles. Chem Commun (Camb) 2019; 55:9084-9087. [PMID: 31287464 DOI: 10.1039/c9cc03277k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An isothermal amplification circuit for specific DNA molecules was implemented in giant unilamellar vesicles. Using this circuit, over 5000-fold amplification of output DNAs was achieved, and the amplification behaviour depended on the concentration of input signal DNAs in a cell-sized compartment. Moreover, initiation of the amplification by photo-stimulation was demonstrated.
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Affiliation(s)
- Yusuke Sato
- Department of Robotics, Tohoku University, Miyagi 980-8579, Japan.
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15
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Matsumoto Y, Kabuki S, Sugawara A, Kitahara T, Akiba T, Fujita Y, Kawamata I, Yamada K, Amino K, Sasaki Y, Nishida M, Murakami K, Sugahara K, Saito N, Kunieda E. Basic evaluation of a novel 4D target and human body phantom. Phys Med Biol 2019; 64:145002. [PMID: 31146274 DOI: 10.1088/1361-6560/ab259c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Stereotactic body radiation therapy (SBRT) is usually verified with a dynamic phantom or solid phantom, but there is a demand for phantoms that can accurately simulate tumor dynamics within an individual that would allow customized validation in every patient. We developed a new 4D dynamic target phantom (multi-cell 4D phantom) that allows simulation of tumor movement in patients. The basic quality and dynamic reproducibility of this new phantom was verified in this investigation. The newly developed multi-cell 4D phantom comprises four main components: soft tissue, bones, lungs, and tumor (target). The phantom structure was based on computed tomography (CT) data of a male. In this study, we investigated the basic performance of a multi-cell 4D phantom. All the CT numbers of the phantom were very close to those of human data. The geometric maximum amplitudes were 4.57 mm in the lateral direction, 4.59 mm in the ventrodorsal direction, and 3.68 mm in the cranio-caudal direction. Geometric errors were 0.84, 0.58, and 0.40 mm, respectively. Movements of the abdominal surface were stable for 60 s. Repeated measurements show no actual differences in target movements between multiple measurements and indicated high reproducibility (r > 0.97). End-to-end tests using Gafchromic film revealed a gamma pass rate of 98% or above (2 mm/3%). Although our phantom performed limited reproducibility in the movement of the patient tumor at present, a satisfactory level of precision was confirmed in general. This is a very promising device for use in the verification of radiation therapy for moving targets.
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Affiliation(s)
- Y Matsumoto
- Department of Radiation Oncology, Tokai University Hachioji Hospital, Hachioji, Tokyo, 192-0032, Japan. Author to whom correspondence should be addressed
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16
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Abstract
We propose a method to control the diffusion speed of DNA molecules with a target sequence in a polymer solution. The interaction between solute DNA and diffusion-suppressing DNA that has been anchored to a polymer matrix is modulated by the concentration of the third DNA molecule called the competitor by a mechanism called toehold exchange. Experimental results show that the sequence-specific modulation of the diffusion coefficient is successfully achieved. The diffusion coefficient can be modulated up to sixfold by changing the concentration of the competitor. The specificity of the modulation is also verified under the coexistence of a set of DNA with noninteracting base sequences. With this mechanism, we are able to control the diffusion coefficient of individual DNA species by the concentration of another DNA species. This methodology introduces a programmability to a DNA-based reaction-diffusion system.
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Affiliation(s)
| | - Fumi Takabatake
- Department of Physics, Chiba University, Chiba 263-8522, Japan
| | - Keita Abe
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
| | - Ibuki Kawamata
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
| | | | - Satoshi Murata
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
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17
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Abstract
We constructed a rotary DNA origami device and tested its stepping operation on a mica substrate by sequential strand displacement with four different sets of signal DNA strands. This work paves the way for building a variety of dynamic rotary DNA nanodevices which respond to multiple signals.
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Affiliation(s)
- Takahiro Tomaru
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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18
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Kageyama R, Kawamata I, Tanabe K, Suzuki Y, Nomura SIM, Murata S. Construction of T-Motif-Based DNA Nanostructures through Enzymatic Reactions. Chembiochem 2018; 19:873-876. [PMID: 29399977 DOI: 10.1002/cbic.201700682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 11/06/2022]
Abstract
The most common way to fabricate DNA nanostructures is to mix individually synthesized DNA oligomers in one pot. However, if DNA nanostructures could be produced through enzymatic reactions, they could be applied in various environments, including in vivo. Herein, an enzymatic method developed to construct a DNA nanostructure from a simple motif called a T-motif is reported. A long, repeated structure was replicated from a circular template by rolling circle amplification and then cleaved into T-motif segments by restriction enzymes. These motifs have been successfully assembled into a ladder-like nanostructure without purification or controlled annealing. This approach is widely applicable to constructing a variety of DNA nanostructures through enzymatic reactions.
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Affiliation(s)
- Ryo Kageyama
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Ibuki Kawamata
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Kaori Tanabe
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Yuki Suzuki
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Shin-Ichiro M Nomura
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Satoshi Murata
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
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19
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Uchida T, Abe K, Endo Y, Ichiseki S, Akita S, Liu S, Aradachi S, Saito M, Fukuchi A, Kikkawa T, Dammaretz T, Kawamata I, Suzuki Y, Nomura SIM, Murata S. Revolving Vernier Mechanism Controls Size of Linear Homomultimer. Small 2017; 13:1702158. [PMID: 28895291 DOI: 10.1002/smll.201702158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/01/2017] [Indexed: 06/07/2023]
Abstract
A new kind of the Vernier mechanism that is able to control the size of linear assembly of DNA origami nanostructures is proposed. The mechanism is realized by mechanical design of DNA origami, which consists of a hollow cylinder and a rotatable shaft in it connected through the same scaffold. This nanostructure stacks with each other by the shape complementarity at its top and bottom surfaces of the cylinder, while the number of stacking is limited by twisting angle of the shaft. Experiments have shown that the size distribution of multimeric assembly of the origami depends on the twisting angle of the shaft; the average lengths of the multimer are decamer, hexamer, and tetramer for 0°, 10°, and 20° twist, respectively. In summary, it is possible to affect the number of polymerization by adjusting the precise shape and movability of a molecular structure.
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Affiliation(s)
- Takeo Uchida
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Keita Abe
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Yuma Endo
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Shosei Ichiseki
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Satoru Akita
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Shiyun Liu
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Sho Aradachi
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Masataka Saito
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Akihiko Fukuchi
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Taiyo Kikkawa
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Theo Dammaretz
- BIOMOD 2015, Team Sendai, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Yuki Suzuki
- Department of Robotics, Graduate School of Engineering, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
- Frontier Research Institute for Interdisciplinary Science, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Shin-Ichiro M Nomura
- Department of Robotics, Graduate School of Engineering, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Aoba-yama, Sendai, Miyagi, 980-8579, Japan
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20
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Kurokawa C, Fujiwara K, Morita M, Kawamata I, Kawagishi Y, Sakai A, Murayama Y, Nomura SIM, Murata S, Takinoue M, Yanagisawa M. DNA cytoskeleton for stabilizing artificial cells. Proc Natl Acad Sci U S A 2017; 114:7228-7233. [PMID: 28652345 PMCID: PMC5514726 DOI: 10.1073/pnas.1702208114] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Cell-sized liposomes and droplets coated with lipid layers have been used as platforms for understanding live cells, constructing artificial cells, and implementing functional biomedical tools such as biosensing platforms and drug delivery systems. However, these systems are very fragile, which results from the absence of cytoskeletons in these systems. Here, we construct an artificial cytoskeleton using DNA nanostructures. The designed DNA oligomers form a Y-shaped nanostructure and connect to each other with their complementary sticky ends to form networks. To undercoat lipid membranes with this DNA network, we used cationic lipids that attract negatively charged DNA. By encapsulating the DNA into the droplets, we successfully created a DNA shell underneath the membrane. The DNA shells increased interfacial tension, elastic modulus, and shear modulus of the droplet surface, consequently stabilizing the lipid droplets. Such drastic changes in stability were detected only when the DNA shell was in the gel phase. Furthermore, we demonstrate that liposomes with the DNA gel shell are substantially tolerant against outer osmotic shock. These results clearly show the DNA gel shell is a stabilizer of the lipid membrane akin to the cytoskeleton in live cells.
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Affiliation(s)
- Chikako Kurokawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588 Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Kanagawa 223-8522, Japan
| | - Masamune Morita
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
| | - Ibuki Kawamata
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
| | - Yui Kawagishi
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
| | - Atsushi Sakai
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588 Japan
| | - Yoshihiro Murayama
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588 Japan
| | | | - Satoshi Murata
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan;
| | - Miho Yanagisawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588 Japan;
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21
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Cervantes-Salguero K, Kawamata I, Nomura SIM, Murata S. Unzipping and shearing DNA with electrophoresed nanoparticles in hydrogels. Phys Chem Chem Phys 2017; 19:13414-13418. [PMID: 28513698 DOI: 10.1039/c7cp02214j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show electric control of unzipping and shearing dehybridization of a DNA duplex anchored to a hydrogel. Tensile force is applied by electrophoresing (25 V cm-1) gold nanoparticles pulling the DNA duplex. The pulled DNA strand is gradually released from the hydrogel. The unzipping release rate is faster than shearing; for example, 3-fold for a 15 base pair duplex, which helps to design electrically driven DNA devices.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-1 Aobayama, Sendai 980-8579, Japan.
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22
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Sato Y, Hiratsuka Y, Kawamata I, Murata S, Nomura SIM. Micrometer-sized molecular robot changes its shape in response to signal molecules. Sci Robot 2017; 2:2/4/eaal3735. [DOI: 10.1126/scirobotics.aal3735] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/03/2017] [Indexed: 11/02/2022]
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23
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Yonamine Y, Cervantes-Salguero K, Nakanishi W, Kawamata I, Minami K, Komatsu H, Murata S, Hill JP, Ariga K. In situ 2D-extraction of DNA wheels by 3D through-solution transport. Phys Chem Chem Phys 2016; 17:32122-5. [PMID: 26583486 DOI: 10.1039/c5cp05765e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controlled transfer of DNA nanowheels from a hydrophilic to a hydrophobic surface was achieved by complexation of the nanowheels with a cationic lipid (2C12N(+)). 2D surface-assisted extraction, '2D-extraction', enabled structure-persistent transfer of DNA wheels, which could not be achieved by simple drop-casting.
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Affiliation(s)
- Yusuke Yonamine
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Keitel Cervantes-Salguero
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Waka Nakanishi
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Ibuki Kawamata
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Kosuke Minami
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Hirokazu Komatsu
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Satoshi Murata
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Jonathan P Hill
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - 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, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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24
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Kandatsu D, Cervantes-Salguero K, Kawamata I, Hamada S, Nomura SIM, Fujimoto K, Murata S. Reversible Gel-Sol Transition of a Photo-Responsive DNA Gel. Chembiochem 2016; 17:1118-21. [PMID: 27123549 DOI: 10.1002/cbic.201600088] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 12/13/2022]
Abstract
Stimuli-responsive DNA gels that can undergo a sol-gel transition in response to photo-irradiation provide a way to engineer functional gel material with fully designed DNA base sequences. We propose an X-shaped DNA motif that turns into a gel by hybridization of self-complementary sticky ends. By embedding a photo-crosslinking artificial base in the sticky-end sequence, repetitive gel-sol transitions are achieved through UV irradiation at different wavelengths. The concentration of the DNA motif necessary for gelation is as low as 40 μm after modification of the geometrical properties of the motif. The physical properties, such as swelling degree and diffusion coefficient, were assessed experimentally.
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Affiliation(s)
- Daisuke Kandatsu
- Department of Robotics, Tohoku University, Aoba, Sendai, Miyagi, 980-8579, Japan
| | | | - Ibuki Kawamata
- Department of Robotics, Tohoku University, Aoba, Sendai, Miyagi, 980-8579, Japan
| | - Shogo Hamada
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, 14853, USA
| | - Shin-Ichiro M Nomura
- Department of Robotics, Tohoku University, Aoba, Sendai, Miyagi, 980-8579, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, 923-1292, Japan
| | - Satoshi Murata
- Department of Robotics, Tohoku University, Aoba, Sendai, Miyagi, 980-8579, Japan.
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25
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Yonamine Y, Cervantes-Salguero K, Minami K, Kawamata I, Nakanishi W, Hill JP, Murata S, Ariga K. Supramolecular 1-D polymerization of DNA origami through a dynamic process at the 2-dimensionally confined air-water interface. Phys Chem Chem Phys 2016; 18:12576-81. [PMID: 27091668 DOI: 10.1039/c6cp01586g] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, a Langmuir-Blodgett (LB) system has been utilized for the regulation of polymerization of a DNA origami structure at the air-water interface as a two-dimensionally confined medium, which enables dynamic condensation of DNA origami units through variation of the film area at the macroscopic level (ca. 10-100 cm(2)). DNA origami sheets were conjugated with a cationic lipid (dioctadecyldimethylammonium bromide, 2C18N(+)) by electrostatic interaction and the corresponding LB-film was prepared. By applying dynamic pressure variation through compression-expansion processes, the lipid-modified DNA origami sheets underwent anisotropic polymerization forming a one-dimensionally assembled belt-shaped structure of a high aspect ratio although the thickness of the polymerized DNA origami was maintained at the unimolecular level. This approach opens up a new field of mechanical induction of the self-assembly of DNA origami structures.
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Affiliation(s)
- Yusuke Yonamine
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
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26
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Tanaka Y, Ikeda A, Yamada S, Yamamoto I, Sato O, Ohsuga H, Shinohara Y, Kawamata I. [Surgical treatment of orbital dysplasia associated with von Recklinghausen's disease. Case report]. Neurol Med Chir (Tokyo) 1988; 28:293-7. [PMID: 2457833 DOI: 10.2176/nmc.28.293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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27
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Takashima Y, Tanaka S, Hosono S, Kawamata I, Murayama H. [Distribution of isothipendyl in O/W type creams and its release]. YAKUGAKU ZASSHI 1985; 105:166-70. [PMID: 2861270 DOI: 10.1248/yakushi1947.105.2_166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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28
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Takashima Y, Kawamata I, Tsunoda K, Kimura M, Murayama H. [The foretell method of the observation of crystal growth of dequalinium chloride in short time in oil in water type ointments]. YAKUGAKU ZASSHI 1984; 104:1263-7. [PMID: 6533286 DOI: 10.1248/yakushi1947.104.12_1263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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29
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Abstract
Since gamma-hydroxybutyric acid (GHB) is known to be an effective anesthetic adjuvant in animal and a natural metabolite of succinic semialdehyde (SSA), the effect of SSA and GHB on the convulsive action of vitamin B6 antagonists was studied using the onset of seizure as a parameter. The administration of SSA and GHB to mice protected them against the convulsive action of B6 antagonist, such as castrix (2-chloro-4-dimethyl-6-methylpyrimidine), thiosemicarbazide, or penicillamine. The anticonvulsant effect of SSA seems to be due to an increase in brain levels of GHB converted in vivo from SSA.
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