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Udono H, Fan M, Saito Y, Ohno H, Nomura SIM, Shimizu Y, Saito H, Takinoue M. Programmable Computational RNA Droplets Assembled via Kissing-Loop Interaction. ACS NANO 2024. [PMID: 38831645 DOI: 10.1021/acsnano.3c12161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
DNA droplets, artificial liquid-like condensates of well-engineered DNA sequences, allow the critical aspects of phase-separated biological condensates to be harnessed programmably, such as molecular sensing and phase-state regulation. In contrast, their RNA-based counterparts remain less explored despite more diverse molecular structures and functions ranging from DNA-like to protein-like features. Here, we design and demonstrate computational RNA droplets capable of two-input AND logic operations. We use a multibranched RNA nanostructure as a building block comprising multiple single-stranded RNAs. Its branches engaged in RNA-specific kissing-loop (KL) interaction enables the self-assembly into a network-like microstructure. Upon two inputs of target miRNAs, the nanostructure is programmed to break up into lower-valency structures that are interconnected in a chain-like manner. We optimize KL sequences adapted from viral sequences by numerically and experimentally studying the base-wise adjustability of the interaction strength. Only upon receiving cognate microRNAs, RNA droplets selectively show a drastic phase-state change from liquid to dispersed states due to dismantling of the network-like microstructure. This demonstration strongly suggests that the multistranded motif design offers a flexible means to bottom-up programming of condensate phase behavior. Unlike submicroscopic RNA-based logic operators, the macroscopic phase change provides a naked-eye-distinguishable readout of molecular sensing. Our computational RNA droplets can be applied to in situ programmable assembly of computational biomolecular devices and artificial cells from transcriptionally derived RNA within biological/artificial cells.
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Affiliation(s)
- Hirotake Udono
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Minzhi Fan
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yoko Saito
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Hirohisa Ohno
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shin-Ichiro M Nomura
- Department of Robotics, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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2
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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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3
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Sato Y, Takinoue M. Pioneering artificial cell-like structures with DNA nanotechnology-based liquid-liquid phase separation. Biophys Physicobiol 2024; 21:e210010. [PMID: 38803334 PMCID: PMC11128300 DOI: 10.2142/biophysico.bppb-v21.0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/26/2024] [Indexed: 05/29/2024] Open
Abstract
Recent studies have revealed that liquid-liquid phase separation (LLPS) plays crucial roles in various cellular functions. Droplets formed via LLPS within cells, often referred to as membraneless organelles, serve to concentrate specific molecules, thus enhancing biochemical reactions. Artificial LLPS systems have been utilized to construct synthetic cell models, employing a range of synthetic molecules. LLPS systems based on DNA nanotechnology are particularly notable for their designable characteristics in droplet formation, dynamics, properties, and functionalities. This review surveys recent advancements in DNA-based LLPS systems, underscoring the programmability afforded by DNA's base-pair specific interactions. We discuss the fundamentals of DNA droplet formation, including temperature-dependence and physical properties, along with the precise control achievable through sequence design. Attention is given to the phase separation of DNA nanostructures on two-dimensional closed interfaces, which results in spatial pattern formation at the interface. Furthermore, we spotlight the potential of DNA droplet computing for cancer diagnostics through specific microRNA pattern recognition. We envision that DNA-based LLPS presents a versatile platform for the exploration of cellular mimicry and opens innovative ways for the development of functional synthetic cells.
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Affiliation(s)
- Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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4
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Utagawa Y, Ino K, Takinoue M, Shiku H. Fabrication and Cell Culture Applications of Core-Shell Hydrogel Fibers Composed of Chitosan/DNA Interfacial Polyelectrolyte Complexation and Calcium Alginate: Straight and Beaded Core Variations. Adv Healthc Mater 2023; 12:e2302011. [PMID: 37478383 DOI: 10.1002/adhm.202302011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 07/23/2023]
Abstract
Core-shell hydrogel fibers are widely used in cell culture applications. A simple and rapid method is presented for fabricating core-shell hydrogel fibers, consisting of straight or beaded core fibers, for cell culture applications. The core fibers are prepared using interfacial polyelectrolyte complexation (IPC) with chitosan and DNA. Briefly, two droplets of chitosan and DNA are brought in contact to form an IPC film, which is dragged to prepare an IPC fiber. The incubation time and DNA concentration are adjusted to prepare straight and beaded IPC fibers. The fibers with Ca2+ are immersed in an alginate solution to form calcium alginate shell hydrogels around the core IPC fibers. To the best of the knowledge, this is the first report of core-shell hydrogel fibers with IPC fiber cores. To demonstrate cell culture, straight hydrogel fibers are applied to fabricate hepatic models consisting of HepG2 and 3T3 fibroblasts, and vascular models consisting of human umbilical vein endothelial cells and 3T3 fibroblasts. To evaluate the effect of co-culture, albumin secretion, and angiogenesis are evaluated. Beaded hydrogel fibers are used to fabricate many size-controlled spheroids for fiber and cloning applications. This method can be widely applied in tissue engineering and cell analysis.
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Affiliation(s)
- Yoshinobu Utagawa
- Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Kosuke Ino
- Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, 226-8502, Japan
| | - Hitoshi Shiku
- Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
- Graduate School of Environmental Studies, Tohoku University, Sendai, 980-8579, Japan
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5
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Takinoue M. DNA droplets for intelligent and dynamical artificial cells: from the viewpoint of computation and non-equilibrium systems. Interface Focus 2023; 13:20230021. [PMID: 37577000 PMCID: PMC10415743 DOI: 10.1098/rsfs.2023.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
Living systems are molecular assemblies whose dynamics are maintained by non-equilibrium chemical reactions. To date, artificial cells have been studied from such physical and chemical viewpoints. This review briefly gives a perspective on using DNA droplets in constructing artificial cells. A DNA droplet is a coacervate composed of DNA nanostructures, a novel category of synthetic DNA self-assembled systems. The DNA droplets have programmability in physical properties based on DNA base sequence design. The aspect of DNA as an information molecule allows physical and chemical control of nanostructure formation, molecular assembly and molecular reactions through the design of DNA base pairing. As a result, the construction of artificial cells equipped with non-equilibrium behaviours such as dynamical motions, phase separations, molecular sensing and computation using chemical energy is becoming possible. This review mainly focuses on such dynamical DNA droplets for artificial cell research in terms of computation and non-equilibrium chemical reactions.
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Affiliation(s)
- Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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6
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Utagawa Y, Ino K, Hiramoto K, Shiku H. Simple, Rapid, and Large-Scale Fabrication of Multi-Branched Hydrogels Based on Viscous Fingering for Cell Culture Applications. Macromol Biosci 2023; 23:e2300069. [PMID: 37055930 DOI: 10.1002/mabi.202300069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/23/2023] [Indexed: 04/15/2023]
Abstract
Hydrogels are widely used in cell culture applications. For fabricating tissues and organs, it is essential to produce hydrogels with specific structures. For instance, multiple-branched hydrogels are desirable for the development of network architectures that resemble the biological vascular network. However, existing techniques are inefficient and time-consuming for this application. To address this issue, a simple, rapid, and large-scale fabrication method based on viscous fingering is proposed. This approach utilizes only two plates. To produce a thin solution, a high-viscosity solution is introduced into the space between the plates, and one of the plates is peeled off. During this procedure, the solution's high viscosity results in the formation of multi-branched structures. Using this strategy, 180 mm × 200 mm multi-branched Pluronic F-127 hydrogels are successfully fabricated within 1 min. These structures are used as sacrificial layers for the fabrication of polydimethylsiloxane channels for culturing human umbilical vein endothelial cells (HUVECs). Similarly, multi-branched Matrigel and calcium (Ca)-alginate hydrogel structures are fabricated, and HUVECs are successfully cultured inside the hydrogels. Also, the hydrogels are collected from the plate, while maintaining their structures. The proposed fabrication technique will contribute to the development of network architectures such as vascular structures in tissue engineering.
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Affiliation(s)
- Yoshinobu Utagawa
- Graduate School of Environmental Studies, Tohoku University, Sendai, 980-8579, Japan
- Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Kosuke Ino
- Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Kaoru Hiramoto
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Hitoshi Shiku
- Graduate School of Environmental Studies, Tohoku University, Sendai, 980-8579, Japan
- Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
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7
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Allen ME, Hindley JW, O’Toole N, Cooke HS, Contini C, Law RV, Ces O, Elani Y. Biomimetic behaviors in hydrogel artificial cells through embedded organelles. Proc Natl Acad Sci U S A 2023; 120:e2307772120. [PMID: 37603747 PMCID: PMC10466294 DOI: 10.1073/pnas.2307772120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/23/2023] Open
Abstract
Artificial cells are biomimetic structures formed from molecular building blocks that replicate biological processes, behaviors, and architectures. Of these building blocks, hydrogels have emerged as ideal, yet underutilized candidates to provide a gel-like chassis in which to incorporate both biological and nonbiological componentry which enables the replication of cellular functionality. Here, we demonstrate a microfluidic strategy to assemble biocompatible cell-sized hydrogel-based artificial cells with a variety of different embedded functional subcompartments, which act as engineered synthetic organelles. The organelles enable the recreation of increasingly biomimetic behaviors, including stimulus-induced motility, content release through activation of membrane-associated proteins, and enzymatic communication with surrounding bioinspired compartments. In this way, we showcase a foundational strategy for the bottom-up construction of hydrogel-based artificial cell microsystems which replicate fundamental cellular behaviors, paving the way for the construction of next-generation biotechnological devices.
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Affiliation(s)
- Matthew E. Allen
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - James W. Hindley
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Nina O’Toole
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Hannah S. Cooke
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Claudia Contini
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Robert V. Law
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Oscar Ces
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
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8
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Shil S, Tsuruta M, Kawauchi K, Miyoshi D. Biomolecular Liquid-Liquid Phase Separation for Biotechnology. BIOTECH 2023; 12:26. [PMID: 37092470 PMCID: PMC10123627 DOI: 10.3390/biotech12020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The liquid-liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The physical and chemical properties of LLPS exert a variety of functions in living cells: activating and deactivating biomolecules involving enzymes; controlling the localization, condensation, and concentration of biomolecules; the filtration and purification of biomolecules; and sensing environmental factors for fast, adaptive, and reversible responses. The versatility of LLPS plays an essential role in various biological processes, such as controlling the central dogma and the onset mechanism of pathological diseases. Moreover, biomolecular LLPS could be critical for developing new biotechnologies such as the condensation, purification, and activation of a series of biomolecules. In this review article, we introduce some fundamental aspects and recent progress of biomolecular LLPS in living cells and test tubes. Then, we discuss applications of biomolecular LLPS toward biotechnologies.
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Affiliation(s)
| | | | | | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
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9
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Sato Y, Takinoue M. Sequence-dependent fusion dynamics and physical properties of DNA droplets. NANOSCALE ADVANCES 2023; 5:1919-1925. [PMID: 36998664 PMCID: PMC10044877 DOI: 10.1039/d3na00073g] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/12/2023] [Indexed: 06/19/2023]
Abstract
Liquid-liquid phase separation (LLPS) of biopolymer molecules generates liquid-like droplets. Physical properties such as viscosity and surface tension play important roles in the functions of these droplets. DNA-nanostructure-based LLPS systems provide useful model tools to investigate the influence of molecular design on the physical properties of the droplets, which has so far remained unclear. Herein, we report changes in the physical properties of DNA droplets by sticky end (SE) design in DNA nanostructures. We used a Y-shaped DNA nanostructure (Y-motif) with three SEs as a model structure. Seven different SE designs were used. The experiments were performed at the phase transition temperature where the Y-motifs self-assembled into droplets. We found that the DNA droplets assembled from the Y-motifs with longer SEs exhibited a longer coalescence period. In addition, the Y-motifs with the same length but different sequence SEs showed slight variations in the coalescence period. Our results suggest that the SE length greatly affected the surface tension at the phase transition temperature. We believe that these findings will accelerate our understanding of the relationship between molecular design and the physical properties of droplets formed via LLPS.
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Affiliation(s)
- Yusuke Sato
- Department of Computer Science, Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokoham Kanagawa 226-8502 Japan
- Department of Intelligent and Control Systems, Kyushu Institute of Technology 680-4 Kawazu, IIzuka Fukuoka 820-8502 Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokoham Kanagawa 226-8502 Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8501 Japan
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10
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Liu W, Lupfer C, Samanta A, Sarkar A, Walther A. Switchable Hydrophobic Pockets in DNA Protocells Enhance Chemical Conversion. J Am Chem Soc 2023; 145:7090-7094. [PMID: 36971596 DOI: 10.1021/jacs.3c00997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Synthetic cell models help us understand living cells and the origin of life. Key aspects of living cells are crowded interiors where secondary structures, such as the cytoskeleton and membraneless organelles/condensates, can form. These can form dynamically and serve structural or functional purposes, such as protection from heat shock or as crucibles for various biochemical reactions. Inspired by these phenomena, we introduce a crowded all-DNA protocell and encapsulate a temperature-switchable DNA-b-polymer block copolymer, in which the synthetic polymer phase-segregates at elevated temperatures. We find that thermoreversible phase segregation of the synthetic polymer occurs via bicontinuous phase separation, resulting in artificial organelle structures that can reorient into larger domains depending on the viscoelastic properties of the protocell interior. Fluorescent sensors confirm the formation of hydrophobic compartments, which enhance the reactivity of bimolecular reactions. This study leverages the strengths of biological and synthetic polymers to construct advanced biohybrid artificial cells that provide insights into phase segregation under crowded conditions and the formation of organelles and microreactors in response to environmental stress.
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11
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Nakamura K, Kubota R, Aoyama T, Urayama K, Hamachi I. Four distinct network patterns of supramolecular/polymer composite hydrogels controlled by formation kinetics and interfiber interactions. Nat Commun 2023; 14:1696. [PMID: 36973291 PMCID: PMC10042874 DOI: 10.1038/s41467-023-37412-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Synthetic composite hydrogels comprising supramolecular fibers and covalent polymers have attracted considerable attention because their properties are similar to biological connective tissues. However, an in-depth analysis of the network structures has not been performed. In this study, we discovered the composite network can be categorized into four distinct patterns regarding morphology and colocalization of the components using in situ, real-time confocal imaging. Time-lapse imaging of the network formation process reveals that the patterns are governed by two factors, the order of the network formation and the interactions between the two different fibers. Additionally, the imaging studies revealed a unique composite hydrogel undergoing dynamic network remodeling on the scale of a hundred micrometers to more than one millimeter. Such dynamic properties allow for fracture-induced artificial patterning of a network three dimensionally. This study introduces a valuable guideline to the design of hierarchical composite soft materials.
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Affiliation(s)
- Keisuke Nakamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
| | - Takuma Aoyama
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Kyoto, Japan
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kenji Urayama
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan.
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12
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Zhang Q, Gao L, Li F, Bi Y. Sensing and manipulating single lipid vesicles using dynamic DNA nanotechnology. NANOSCALE 2023; 15:5158-5166. [PMID: 36825547 DOI: 10.1039/d2nr07192d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Natural and artificial lipid vesicles have been widely involved in nano-delivery, bio-analysis and diagnosis. For sensing and manipulating single lipid vesicles, dynamic DNA reactions were constructed inside or on the surface of lipid vesicles. In this review, we interpreted various ways of integrating lipid vesicles and dynamic DNA nanotechnology by summarizing the latest reports in bio-analysis and biomimetic cell research.
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Affiliation(s)
- Qi Zhang
- School of Pharmaceutical Sciences, Shandong First Medical University, Tai'An, Shandong, 271016, P. R. China.
- Key laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Sichuan, 610064, P. R. China.
| | - Lu Gao
- Key laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Sichuan, 610064, P. R. China.
| | - Feng Li
- Key laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Sichuan, 610064, P. R. China.
| | - Yanping Bi
- School of Pharmaceutical Sciences, Shandong First Medical University, Tai'An, Shandong, 271016, P. R. China.
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13
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Udono H, Gong J, Sato Y, Takinoue M. DNA Droplets: Intelligent, Dynamic Fluid. Adv Biol (Weinh) 2023; 7:e2200180. [PMID: 36470673 DOI: 10.1002/adbi.202200180] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.
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Affiliation(s)
- Hirotake Udono
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Jing Gong
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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Li DY, Zhou ZH, Yu YL, Deng NN. Microfluidic construction of cytoskeleton-like hydrogel matrix for stabilizing artificial cells. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Kim CG, Hwang DE, Kumar R, Chung M, Eom YG, Kim H, Koo DH, Choi JM. Recent trends in studies of biomolecular phase separation. BMB Rep 2022. [PMID: 35880435 PMCID: PMC9442351 DOI: 10.5483/bmbrep.2022.55.8.101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biomolecular phase separation has recently attracted broad in-terest, due to its role in the spatiotemporal compartmentalization of living cells. It governs the formation, regulation, and dissociation of biomolecular condensates, which play multiple roles in vivo, from activating specific biochemical reactions to organizing chromatin. Interestingly, biomolecular phase separation seems to be a mainly passive process, which can be ex-plained by relatively simple physical principles and reproduced in vitro with a minimal set of components. This Mini review focuses on our current understanding of the fundamental principles of biomolecular phase separation and the recent progress in the research on this topic.
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Affiliation(s)
- Chan-Geun Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Rajeev Kumar
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Min Chung
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Hyunji Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Hyun Koo
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
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16
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Kim CG, Hwang DE, Kumar R, Chung M, Eom YG, Kim H, Koo DH, Choi JM. Recent trends in studies of biomolecular phase separation. BMB Rep 2022; 55:363-369. [PMID: 35880435 PMCID: PMC9442351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 03/08/2024] Open
Abstract
Biomolecular phase separation has recently attracted broad interest, due to its role in the spatiotemporal compartmentalization of living cells. It governs the formation, regulation, and dissociation of biomolecular condensates, which play multiple roles in vivo, from activating specific biochemical reactions to organizing chromatin. Interestingly, biomolecular phase separation seems to be a mainly passive process, which can be explained by relatively simple physical principles and reproduced in vitro with a minimal set of components. This Mini review focuses on our current understanding of the fundamental principles of biomolecular phase separation and the recent progress in the research on this topic. [BMB Reports 2022; 55(8): 363-369].
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Affiliation(s)
- Chan-Geun Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Rajeev Kumar
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Min Chung
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Hyunji Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Hyun Koo
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
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Abstract
Recent years have seen substantial efforts aimed at constructing artificial cells from various molecular components with the aim of mimicking the processes, behaviours and architectures found in biological systems. Artificial cell development ultimately aims to produce model constructs that progress our understanding of biology, as well as forming the basis for functional bio-inspired devices that can be used in fields such as therapeutic delivery, biosensing, cell therapy and bioremediation. Typically, artificial cells rely on a bilayer membrane chassis and have fluid aqueous interiors to mimic biological cells. However, a desire to more accurately replicate the gel-like properties of intracellular and extracellular biological environments has driven increasing efforts to build cell mimics based on hydrogels. This has enabled researchers to exploit some of the unique functional properties of hydrogels that have seen them deployed in fields such as tissue engineering, biomaterials and drug delivery. In this Review, we explore how hydrogels can be leveraged in the context of artificial cell development. We also discuss how hydrogels can potentially be incorporated within the next generation of artificial cells to engineer improved biological mimics and functional microsystems.
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Jahnke K, Huth V, Mersdorf U, Liu N, Göpfrich K. Bottom-Up Assembly of Synthetic Cells with a DNA Cytoskeleton. ACS NANO 2022; 16:7233-7241. [PMID: 35377150 PMCID: PMC9134502 DOI: 10.1021/acsnano.1c10703] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cytoskeletal elements, like actin and myosin, have been reconstituted inside lipid vesicles toward the vision to reconstruct cells from the bottom up. Here, we realize the de novo assembly of entirely artificial DNA-based cytoskeletons with programmed multifunctionality inside synthetic cells. Giant unilamellar lipid vesicles (GUVs) serve as cell-like compartments, in which the DNA cytoskeletons are repeatedly and reversibly assembled and disassembled with light using the cis-trans isomerization of an azobenzene moiety positioned in the DNA tiles. Importantly, we induced ordered bundling of hundreds of DNA filaments into more rigid structures with molecular crowders. We quantify and tune the persistence length of the bundled filaments to achieve the formation of ring-like cortical structures inside GUVs, resembling actin rings that form during cell division. Additionally, we show that DNA filaments can be programmably linked to the compartment periphery using cholesterol-tagged DNA as a linker. The linker concentration determines the degree of the cortex-like network formation, and we demonstrate that the DNA cortex-like network can deform GUVs from within. All in all, this showcases the potential of DNA nanotechnology to mimic the diverse functions of a cytoskeleton in synthetic cells.
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Affiliation(s)
- Kevin Jahnke
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Vanessa Huth
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Ulrike Mersdorf
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Na Liu
- 2nd
Physics Institute, University of Stuttgart, Im Pfaffenwaldring 57, D-70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Kerstin Göpfrich
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
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