1
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Geng Q, Keya JJ, Hotta T, Verhey KJ. KIF1C, an RNA transporting kinesin-3, undergoes liquid-liquid phase separation through its C-terminal disordered domain. bioRxiv 2023:2023.10.23.563538. [PMID: 37961614 PMCID: PMC10634753 DOI: 10.1101/2023.10.23.563538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The spatial distribution of mRNA is critical for local control of protein production. Recent studies have identified the kinesin-3 family member KIF1C as an RNA transporter. However, it is not clear how KIF1C interacts with RNA molecules. Here, we show that KIF1C's C-terminal tail domain is an intrinsically disordered region (IDR) containing a prion-like domain (PLD) that is unique compared to the C-terminal tails of other kinesin family members. In cells, KIF1C constructs undergo reversible formation of dynamic puncta that display physical properties of liquid condensates and incorporate RNA molecules in a sequence-selective manner. The IDR is necessary and sufficient for driving liquid-liquid phase separation (LLPS) but the condensate properties can be modulated by adjacent coiled-coil segments. The purified KIF1C IDR domain undergoes LLPS in vitro at near-endogenous nM concentrations in a salt-dependent manner. Deletion of the IDR abolished the ability of KIF1C to undergo LLPS and disrupted the distribution of mRNA cargoes to the cell periphery. Our work thus uncovers an intrinsic correlation between the LLPS activity of KIF1C and its role as an RNA transporter. In addition, as the first kinesin motor reported to undergo LLPS, our work reveals a previously uncharacterized mode of motor-cargo interaction that extends our understanding of the behavior of cytoskeletal motor proteins.
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Affiliation(s)
- Qi Geng
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jakia Jannat Keya
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
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2
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Ishii S, Akter M, Keya JJ, Rashid MR, Afroze F, Nasrin SR, Kakugo A. Purification of Tubulin from Porcine Brain and its Fluorescence Dye Modification. Methods Mol Biol 2022; 2430:3-16. [PMID: 35476322 DOI: 10.1007/978-1-0716-1983-4_1] [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] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Filamentous microtubules, polymers of the heterodimeric protein tubulins play one of the major roles in the emergent nano-biotechnological devices. To develop the feature of those devices, it is important to understand the function of microtubule in in vitro, hence, the availability of purified αβ-tubulin is required. Additionally, fluorescently labeled tubulin has become a powerful approach for extensively studying the dynamics of these components. In this chapter, the process of purifying the heterodimeric αβ-tubulin from porcine brain will be described, as well as the process of labeling of the purified tubulin with fluorescence dye.
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Affiliation(s)
- Satsuki Ishii
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Mst Rubaya Rashid
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Farhana Afroze
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | | | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan. .,Faculty of Science, Hokkaido University, Sapporo, Japan.
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3
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Akter M, Keya JJ, Kayano K, Kabir AMR, Inoue D, Hess H, Sada K, Kuzuya A, Asanuma H, Kakugo A. Cooperative cargo transportation by a swarm of molecular machines. Sci Robot 2022; 7:eabm0677. [PMID: 35442703 DOI: 10.1126/scirobotics.abm0677] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cooperation is a strategy that has been adopted by groups of organisms to execute complex tasks more efficiently than single entities. Cooperation increases the robustness and flexibility of the working groups and permits sharing of the workload among individuals. However, the utilization of this strategy in artificial systems at the molecular level, which could enable substantial advances in microrobotics and nanotechnology, remains highly challenging. Here, we demonstrate molecular transportation through the cooperative action of a large number of artificial molecular machines, photoresponsive DNA-conjugated microtubules driven by kinesin motor proteins. Mechanical communication via conjugated photoresponsive DNA enables these microtubules to organize into groups upon photoirradiation. The groups of transporters load and transport cargo, and cargo unloading is achieved by dissociating the groups into single microtubules. The group formation permits the loading and transport of cargoes with larger sizes and in larger numbers over long distances compared with single transporters. We also demonstrate that cargo can be collected at user-determined locations defined by ultraviolet light exposure. This work demonstrates cooperative task performance by molecular machines, which will help to construct molecular robots with advanced functionalities in the future.
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Affiliation(s)
- M Akter
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - J J Keya
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - K Kayano
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - A M R Kabir
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - D Inoue
- Faculty of Design, Kyushu University, Fukuoka 815-8540, Japan
| | - H Hess
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - K Sada
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - A Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University, Osaka 564-8680, Japan
| | - H Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - A Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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4
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Keya JJ, Akter M, Kabir AMR, Ishii S, Kakugo A. Fabrication of Artificial Muscle from Microtubules, Kinesins, and DNA Origami Nanostructures. Methods Mol Biol 2022; 2430:231-240. [PMID: 35476336 DOI: 10.1007/978-1-0716-1983-4_15] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fabrication of molecular devices using biomolecules through biomimetic approaches has witnessed a surge in interest in recent years. DNA a versatile programmable material offers an opportunity to realize complicated operations through the designing of various nanostructures such as DNA origami. Here we describe the methods to use DNA origami for the self-assembly of the biomolecular motor system, microtubule (MT)-kinesin. A rodlike DNA origami motif facilitates the self-assembly of MTs into asters. A smooth muscle like molecular contraction system could be realized following the method where DNA mediated self-assembly of MTs permits dynamic contraction in the presence of kinesins through an energy dissipative process.
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Affiliation(s)
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Satsuki Ishii
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
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5
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Keya JJ, Kabir AMR, Akter M, Kakugo A. Dynamic Pattern Formation of Active Matters Triggered by Mechanical Stimuli. Methods Mol Biol 2022; 2430:193-203. [PMID: 35476333 DOI: 10.1007/978-1-0716-1983-4_12] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In vitro gliding assay of the filamentous protein microtubule (MT) on a kinesin motor protein coated surface has appeared as a classic platform for studying active matters. At high densities, the gliding MTs spontaneously align and self-organize into fascinating large-scale patterns. Application of mechanical stimuli e.g., stretching stimuli to the MTs gliding on a kinesin-coated surface can modulate their self-organization and patterns according to the boundary conditions. Depending on the mode of stretching, MT at high densities change their moving direction and exhibit various kinds of patterns such as stream, zigzag and vortex pattern. In this chapter, we discuss detail procedures on how to apply mechanical stimuli to the moving MTs on a kinesin coated substrate.
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Affiliation(s)
| | | | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
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6
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Hayashi K, Keya JJ. Japan–US symposium on motor proteins and associated single-molecule biophysics. Biophys Physicobiol 2022; 19:e190030. [PMID: 36349328 PMCID: PMC9592572 DOI: 10.2142/biophysico.bppb-v19.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Jakia Jannat Keya
- Institute for Molecular Science, National Institutes of Natural Sciences
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Keya JJ, Akter M, Kabir AMR, Rashid MR, Kakugo A. Construction of Molecular Robots from Microtubules for Programmable Swarming. Methods Mol Biol 2022; 2430:219-230. [PMID: 35476335 DOI: 10.1007/978-1-0716-1983-4_14] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Swarm robotics has been attracting much attention in recent years in the field of robotics. This chapter describes a methodology for the construction of molecular swarm robots through precise control of active self-assembly of microtubules (MTs). Detailed protocols are presented for the construction of molecular robots through conjugation of DNA to MTs and demonstration of swarming of the MTs. The swarming is mediated by DNA-based interaction and photoirradiation which act as processors and sensors respectively for the robots. Furthermore, the required protocols to utilize the swarming of MTs for molecular computation is also described.
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Affiliation(s)
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Mst Rubaya Rashid
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
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Akter M, Keya JJ, Kabir AMR, Asanuma H, Murayama K, Sada K, Kakugo A. Photo-regulated trajectories of gliding microtubules conjugated with DNA. Chem Commun (Camb) 2020; 56:7953-7956. [PMID: 32537622 DOI: 10.1039/d0cc03124k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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 regulate the persistency in motion of kinesin-driven microtubules (MTs) simply using a photoresponsive DNA (pDNA) and ultraviolet (UV)-visible light. The path persistence length of MTs, which is a measure of the persistency in their motion, increases and decreases upon illuminating the MTs with UV and visible light respectively. Moreover, pDNA is found to work as a shield for MTs against damage under UV irradiation.
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Affiliation(s)
- Mousumi Akter
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
| | | | | | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Osaka, 564-8680, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Osaka, 564-8680, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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9
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Keya JJ, Kudoh H, Kabir AMR, Inoue D, Miyamoto N, Tani T, Kakugo A, Shikinaka K. Radial alignment of microtubules through tubulin polymerization in an evaporating droplet. PLoS One 2020; 15:e0231352. [PMID: 32275729 PMCID: PMC7147791 DOI: 10.1371/journal.pone.0231352] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/21/2020] [Indexed: 01/08/2023] Open
Abstract
We report the formation of spherulites from droplets of highly concentrated tubulin solution via nucleation and subsequent polymerization to microtubules (MTs) under water evaporation by heating. Radial alignment of MTs in the spherulites was confirmed by the optical properties of the spherulites observed using polarized optical microscopy and fluorescence microscopy. Temperature and concentration of tubulins were found as important parameters to control the spherulite pattern formation of MTs where evaporation plays a significant role. The alignment of MTs was regulated reversibly by temperature induced polymerization and depolymerization of tubulins. The formation of the MTs patterns was also confirmed at the molecular level from the small angle X-ray measurements. This work provides a simple method for obtaining radially aligned arrays of MTs.
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Affiliation(s)
| | - Hiroki Kudoh
- Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | | | - Daisuke Inoue
- Department of Human Science Faculty of Design, Kyushu University, Fukuoka, Japan
| | - Nobuyoshi Miyamoto
- Department of Life, Environment and Materials Science, Fukuoka Institute of Technology, Fukuoka, Japan
| | - Tomomi Tani
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail: (AK); (KS)
| | - Kazuhiro Shikinaka
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology, Sendai, Miyagi, Japan
- * E-mail: (AK); (KS)
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Abstract
Biomolecular motor systems are the smallest natural machines with an ability to convert chemical energy into mechanical work with remarkably high efficiency. Such attractive features enabled biomolecular motors to become classic tools in soft matter research over the past decade. For designing suitably engineered biomimetic systems, the biomolecular motors can potentially be used as molecular engines that can transform energy and ensure great advantages for the construction of bio-nanodevices and molecular robots. From the optimization of their prolonged lifetime to coordinate them into highly complex and ordered structures, enormous efforts have been devoted to make them useful in the synthetic environment. Synchronous operation of the biomolecular engines is one of the key criteria to coordinate them into certain different patterns, which depends on the local interaction of biomolecular motors. Utilizing chemical and physical stimuli, synchronization of biomolecular motor systems has become possible, which allows them to coordinate into different higher ordered patterns with different modes of functionality. Recently, programmed synchronous operation of the biomolecular engines has also been demonstrated, using a smart biomaterial to build up swarms reminiscent of nature. Here, we review the recent progress in the synchronized operation of biomolecular motors in engineered systems to explicitly program their interaction and further their applications. Such developments in the coordination of biomolecular motors have opened a broad way to explore the construction of future autonomous molecular machines and robots based on synchronization of biomolecular engines.
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Affiliation(s)
- Jakia Jannat Keya
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
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11
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Abstract
Recently we demonstrated swarming of a self-propelled biomolecular motor system microtubule (MT)-kinesin where interactions among thousands of motile MTs were regulated in a highly programmable fashion by using DNA as a processor. However, precise control of this potential system is yet to be achieved to optimize the swarm behavior. In this work, we systematically controlled swarming of MTs on kinesin adhered surface by different physicochemical parameters of MT-kinesin and DNA. Tuning the length of DNA sequences swarming was precisely controlled with thermodynamic and kinetic feasibility. In addition, swarming was regulated using different concentration of DNA crosslinkers. Reversibility of swarming was further controlled by changing the concentration of strand displacement DNA signal allowing dissociation of swarm. The control over the swarm was accompanied by variable stiffness of MTs successfully, providing translational and circular motion. Moreover, the morphology of swarm was also found to be changed not only depending on the stiffness but also body length of MTs. Such detail study of precise control of swarming would provide new insights in developing a promising molecular swarm robotic system with desired functions.
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Affiliation(s)
- Jakia Jannat Keya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | | | - Daisuke Inoue
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave., New York, NY, 10027, USA
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University, Osaka, 564-8680, Japan.
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave., New York, NY, 10027, USA.
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12
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Keya JJ, Suzuki R, Kabir AMR, Inoue D, Asanuma H, Sada K, Hess H, Kuzuya A, Kakugo A. DNA-assisted swarm control in a biomolecular motor system. Nat Commun 2018; 9:453. [PMID: 29386522 PMCID: PMC5792447 DOI: 10.1038/s41467-017-02778-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/22/2017] [Indexed: 01/10/2023] Open
Abstract
In nature, swarming behavior has evolved repeatedly among motile organisms because it confers a variety of beneficial emergent properties. These include improved information gathering, protection from predators, and resource utilization. Some organisms, e.g., locusts, switch between solitary and swarm behavior in response to external stimuli. Aspects of swarming behavior have been demonstrated for motile supramolecular systems composed of biomolecular motors and cytoskeletal filaments, where cross-linkers induce large scale organization. The capabilities of such supramolecular systems may be further extended if the swarming behavior can be programmed and controlled. Here, we demonstrate that the swarming of DNA-functionalized microtubules (MTs) propelled by surface-adhered kinesin motors can be programmed and reversibly regulated by DNA signals. Emergent swarm behavior, such as translational and circular motion, can be selected by tuning the MT stiffness. Photoresponsive DNA containing azobenzene groups enables switching between solitary and swarm behavior in response to stimulation with visible or ultraviolet light.
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Affiliation(s)
- Jakia Jannat Keya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | - Ryuhei Suzuki
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | | | - Daisuke Inoue
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Osaka, 564-8680, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Avenue, New York, NY, 10027, USA
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University, Osaka, 564-8680, Japan.
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Avenue, New York, NY, 10027, USA.
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Keya JJ, Islam MM, Rahman MM, Mollah MYA, Susan MABH. Effect of a water structure modifier on the aqueous electrochemistry of supramolecular systems: Redox-active versus conventional surfactants. J Electroanal Chem (Lausanne) 2014. [DOI: 10.1016/j.jelechem.2013.11.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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