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Goetzfried MA, Vogele K, Mückl A, Kaiser M, Holland NB, Simmel FC, Pirzer T. Periodic Operation of a Dynamic DNA Origami Structure Utilizing the Hydrophilic-Hydrophobic Phase-Transition of Stimulus-Sensitive Polypeptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1903541. [PMID: 31531953 DOI: 10.1002/smll.201903541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Dynamic DNA nanodevices are designed to perform structure-encoded motion actuated by a variety of different physicochemical stimuli. In this context, hybrid devices utilizing other components than DNA have the potential to considerably expand the library of functionalities. Here, the reversible reconfiguration of a DNA origami structure using the stimulus sensitivity of elastin-like polypeptides is reported. To this end, a rectangular sheet made using the DNA origami technique is functionalized with these peptides and by applying changes in salt concentration the hydrophilic-hydrophobic phase transition of these peptides actuate the folding of the structure. The on-demand and reversible switching of the rectangle is driven by externally imposed temperature oscillations and appears at specific transition temperatures. Using transmission electron microscopy, it is shown that the structure exhibits distinct conformational states with different occupation probabilities, which are dependent on structure-intrinsic parameters such as the local number and the arrangement of the peptides on the rectangle. It is also shown through ensemble fluorescence resonance energy transfer spectroscopy that the transition temperature and thus the thermodynamics of the rectangle-peptide system depends on the stimuli salt concentration and temperature, as well as on the intrinsic parameters.
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Affiliation(s)
- Marisa A Goetzfried
- Physics of Synthetic Biological Systems-E14, Physics Department and ZNN, Technische Universität München, 85748, Garching, Germany
| | - Kilian Vogele
- Physics of Synthetic Biological Systems-E14, Physics Department and ZNN, Technische Universität München, 85748, Garching, Germany
| | - Andrea Mückl
- Physics of Synthetic Biological Systems-E14, Physics Department and ZNN, Technische Universität München, 85748, Garching, Germany
| | - Marcus Kaiser
- Operations Research, Department of Mathematics, Technische Universität München, 80333, München, Germany
| | - Nolan B Holland
- Department of Chemical and Biomedical Engineering, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems-E14, Physics Department and ZNN, Technische Universität München, 85748, Garching, Germany
| | - Tobias Pirzer
- Physics of Synthetic Biological Systems-E14, Physics Department and ZNN, Technische Universität München, 85748, Garching, Germany
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2
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Ishikawa D, Suzuki Y, Kurokawa C, Ohara M, Tsuchiya M, Morita M, Yanagisawa M, Endo M, Kawano R, Takinoue M. DNA Origami Nanoplate‐Based Emulsion with Nanopore Function. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Daisuke Ishikawa
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences Tohoku University 6-3 Aramaki aza Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Chikako Kurokawa
- Department of Applied Physics Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Masayuki Ohara
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Misato Tsuchiya
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Masamune Morita
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Miho Yanagisawa
- Department of Applied Physics Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
- Komaba Institute for Science Graduate School of Arts and Sciences The University of Tokyo 3-8-1 Komaba, Meguro Tokyo 153-8902 Japan
| | - Masayuki Endo
- Department of Chemistry Graduate School of Science Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Masahiro Takinoue
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
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Ishikawa D, Suzuki Y, Kurokawa C, Ohara M, Tsuchiya M, Morita M, Yanagisawa M, Endo M, Kawano R, Takinoue M. DNA Origami Nanoplate-Based Emulsion with Nanopore Function. Angew Chem Int Ed Engl 2019; 58:15299-15303. [PMID: 31411794 DOI: 10.1002/anie.201908392] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Indexed: 11/10/2022]
Abstract
Bio-inspired functional microcapsules have attracted increasing attention in many fields from physical/chemical science to artificial-cell engineering. Although particle-stabilised microcapsules are advantageous for their stability and functionalisation potential, versatile methods for their functionalisation are desired to expand their possibilities. This study reports a water-in-oil microdroplet stabilised with amphiphilic DNA origami nanoplates. By utilising DNA nanotechnology, DNA nanoplates were designed as a nanopore device for ion transportation and to stabilise the oil-water interface. Microscopic examination revealed the microcapsule formed by the accumulation of amphiphilic DNA nanoplates at the oil-water interface. Ion current measurements revealed the nanoplate pores functioned as channel to transport ions. These findings provide a general strategy for the programmable design of microcapsules to engineer artificial cells and molecular robots.
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Affiliation(s)
- Daisuke Ishikawa
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Chikako Kurokawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Masayuki Ohara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Misato Tsuchiya
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Masamune Morita
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Miho Yanagisawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan.,Komaba Institute for Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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4
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Agarwal NP, Matthies M, Gür FN, Osada K, Schmidt TL. Block Copolymer Micellization as a Protection Strategy for DNA Origami. Angew Chem Int Ed Engl 2017; 56:5460-5464. [DOI: 10.1002/anie.201608873] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 01/01/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Nayan P. Agarwal
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Michael Matthies
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Fatih N. Gür
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Kensuke Osada
- Department of Bioengineering; University of Tokyo; Japan
| | - Thorsten L. Schmidt
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
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Agarwal NP, Matthies M, Gür FN, Osada K, Schmidt TL. Block Copolymer Micellization as a Protection Strategy for DNA Origami. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201608873] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nayan P. Agarwal
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Michael Matthies
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Fatih N. Gür
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Kensuke Osada
- Department of Bioengineering; University of Tokyo; Japan
| | - Thorsten L. Schmidt
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
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Nickels PC, Høiberg HC, Simmel SS, Holzmeister P, Tinnefeld P, Liedl T. DNA Origami Seesaws as Comparative Binding Assay. Chembiochem 2016; 17:1093-6. [PMID: 27038073 PMCID: PMC5084756 DOI: 10.1002/cbic.201600059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Indexed: 11/28/2022]
Abstract
The application of commonly used force spectroscopy in biological systems is often limited by the need for an invasive tether connecting the molecules of interest to a bead or cantilever tip. Here we present a DNA origami-based prototype in a comparative binding assay. It has the advantage of in situ readout without any physical connection to the macroscopic world. The seesaw-like structure has a lever that is able to move freely relative to its base. Binding partners on each side force the structure into discrete and distinguishable conformations. Model experiments with competing DNA hybridisation reactions yielded a drastic shift towards the conformation with the stronger binding interaction. With reference DNA duplexes of tuneable length on one side, this device can be used to measure ligand interactions in comparative assays.
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Affiliation(s)
- Philipp C Nickels
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Hans C Høiberg
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Stephanie S Simmel
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Phil Holzmeister
- Institut für physikalische und theoretische Chemie, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106, Braunschweig, Germany
| | - Philip Tinnefeld
- Institut für physikalische und theoretische Chemie, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106, Braunschweig, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
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Vyborna Y, Vybornyi M, Rudnev AV, Häner R. DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers. Angew Chem Int Ed Engl 2015; 54:7934-8. [DOI: 10.1002/anie.201502066] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 03/31/2015] [Indexed: 12/31/2022]
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8
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Vyborna Y, Vybornyi M, Rudnev AV, Häner R. DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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9
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Burns JR, Al-Juffali N, Janes SM, Howorka S. Membrane-Spanning DNA Nanopores with Cytotoxic Effect. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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