担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

DOI： 10.2142/biophys.62.345

担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

記述言語：英語   掲載種別：研究論文（学術雑誌）

DNA is an excellent material for constructing self-assembled nano/microstructures. Owing to the widespread use of DNA as a building block in laboratories and industry, it is desirable to increase the efficiency of all steps involved in producing self-assembled DNA structures. One of the bottlenecks is the purification required to separate the excess components from the target structures. This paper describes a purification method based on the fractionation by water-in-water (W/W) droplets composed of phase-separated dextran-rich droplets in a polyethylene glycol (PEG)-rich continuous phase. The dextran-rich droplets facilitate the selective uptake of self-assembled DNA nano/microstructures and allow the separation of the target structure. This study investigates the ability to purify DNA origami, DNA hydrogels, and DNA microtubes. The W/W-droplet fractionation allows the purification of structures of a broad size spectrum without changes to the protocol. By quantifying the activity of deoxyribozyme-modified DNA origami after W/W-droplet purification, this study demonstrates that this method sufficiently preserves the accessibility to the surface of a functional DNA nanostructure. It is considered that the W/W-droplet fractionation could become one of the standard methods for the purification of self-assembled DNA nano/microstructures for biomedical and nanotechnology applications owing to its low cost and simplicity.

DOI： 10.1002/cbic.202200240

Scopus

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記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

記述言語：英語   掲載種別：研究論文（学術雑誌）

Phase-separated biomolecular droplets are formed in cells to regulate various biological processes. This phenomenon can be applied to constructing self-assembled dynamic molecular systems such as artificial cells and molecular robots. Recently, programmable phase-separated droplets called DNA droplets have been reported as a possible method to construct such dynamic molecular systems. This study reports a computational DNA droplet that can recognize a specific combination of tumor biomarker microRNAs (miRNAs) as molecular inputs and output a DNA logic computing result by physical DNA droplet phase separation. A mixed DNA droplet consisting of three DNA nanostructures with orthogonal sticky-end sequences and two linker DNAs to cross-bridge the orthogonal DNA nanostructures is proposed. By the hybridization of miRNAs with the linkers, the cross-bridging ability is lost, causing the phase-separation of the mixed DNA droplet into three DNA droplets, resulting in executing a miRNA pattern recognition described by a logical expression ((miRNA-1 ∧ miRNA-2) ∧ (miRNA-3 ∧ ¬miRNA-4)). This experimentally demonstrates that the computational DNA droplets recognize the above specific pattern of chemically synthesized miRNA sequences as a model experiment. In the future, this method will provide potential applications such as diagnosis and therapy with integration to biomolecular robots and artificial cells.

DOI： 10.1002/adfm.202202322

Scopus

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担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：記事・総説・解説・論説等（学術雑誌）

Deoxyribonucleic acid (DNA) nanotechnology, a frontier in biomedical engineering, is an emerging field that has enabled the engineering of molecular-scale DNA materials with applications in biomedicine such as bioimaging, biodetection, and drug delivery over the past decades. The programmability of DNA nanostructures allows the precise engineering of DNA nanocarriers with controllable shapes, sizes, surface chemistries, and functions to deliver therapeutic and functional payloads to target cells with higher efficiency and enhanced specificity. Programmability and control over design also allow the creation of dynamic devices, such as DNA nanorobots, that can react to external stimuli and execute programmed tasks. This review focuses on the current findings and progress in the field, mainly on the employment of DNA nanostructures such as DNA origami nanorobots, DNA nanotubes, DNA tetrahedra, DNA boxes, and DNA nanoflowers in the biomedical field for therapeutic purposes. We will also discuss the fate of DNA nanostructures in living cells, the major obstacles to overcome, that is, the stability of DNA nanostructures in biomedical applications, and the opportunities for DNA nanostructure-based drug delivery in the future.

DOI： 10.3390/mi13020315

Scopus

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

Phase separation is a key phenomenon in artificial cell construction. Recent studies have shown that the liquid-liquid phase separation of designed-DNA nanostructures induces the formation of liquid-like condensates that eventually become hydrogels by lowering the solution temperature. As a compartmental capsule is an essential artificial cell structure, many studies have focused on the lateral phase separation of artificial lipid vesicles. However, controlling phase separation using a molecular design approach remains challenging. Here, we present the lateral liquid-liquid phase separation of DNA nanostructures that leads to the formation of phase-separated capsule-like hydrogels. We designed three types of DNA nanostructures (two orthogonal and a linker nanostructure) that were adsorbed onto an interface of water-in-oil (W/O) droplets via electrostatic interactions. The phase separation of DNA nanostructures led to the formation of hydrogels with bicontinuous, patch, and mix patterns, due to the immiscibility of liquid-like DNA during the self-assembly process. The frequency of appearance of these patterns was altered by designing DNA sequences and altering the mixing ratio of the nanostructures. We constructed a phase diagram for the capsule-like DNA hydrogels by investigating pattern formation under various conditions. The phase-separated DNA hydrogels did not only form on the W/O droplet interface but also on the inner leaflet of lipid vesicles. Notably, the capsule-like hydrogels were extracted into an aqueous solution, maintaining the patterns formed by the lateral phase separation. In addition, the extracted hydrogels were successfully combined with enzymatic reactions, which induced their degradation. Our results provide a method for the design and control of phase-separated hydrogel capsules using sequence-designed DNAs. We envision that by incorporating various DNA nanodevices into DNA hydrogel capsules, the capsules will gain molecular sensing, chemical-information processing, and mechanochemical actuating functions, allowing the construction of functional molecular systems.

DOI： 10.1021/jacsau.1c00450

Scopus

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記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）

記述言語：日本語   掲載種別：研究論文（学術雑誌）

DOI： https://doi.org/10.4307/jsee.69.4_31

担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：記事・総説・解説・論説等（学術雑誌）

<p>Self-assembled supramolecular structures in living cells and their dynamics underlie various cellular events, such as endocytosis, cell migration, intracellular transport, cell metabolism, and gene expression. Spatiotemporally regulated association/dissociation and generation/degradation of assembly components is one of the remarkable features of biological systems. The significant advancement in DNA nanotechnology over the last few decades has enabled the construction of various-shaped nanostructures via programmed self-assembly of sequence-designed oligonucleotides. These nanostructures can further be assembled into micrometer-sized structures, including ordered lattices, tubular structures, macromolecular droplets, and hydrogels. In addition to being a structural material, DNA is adopted to construct artificial molecular circuits capable of activating/inactivating or producing/decomposing target DNA molecules based on strand displacement or enzymatic reactions. In this review, we provide an overview of recent studies on artificially designed DNA-based self-assembled systems that exhibit dynamic features, such as association/dis­sociation of components, phase separation, stimulus responsivity, and DNA circuit-regulated structural formation. These biomacromolecule-based, bottom-up approaches for the construction of artificial molecular systems will not only throw light on bio-inspired nano/micro engineering, but also enable us to gain insights into how autonomy and adaptability of living systems can be realized.</p>

DOI： 10.2142/biophysico.bppb-v18.013

Scopus

CiNii Article

CiNii Research

その他リンク： https://www.jstage.jst.go.jp/article/biophysico/18/0/18_bppb-v18.013/_pdf

担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

<p>1．はじめに</p><p>細胞は，機能を持った分子や超分子で構成された天然の分子システムである。そのようなシステムを人工的に作るアプローチの一つとして，細胞型分子ロボット^（1）の構築に注目が集まっている。細胞型分子ロボットは，機能性分子デバイスをシステムとして組み上げたものである。分子レ</p>

DOI： 10.1541/ieejjournal.140.582

CiNii Article

CiNii Research

その他リンク： https://www.jstage.jst.go.jp/article/ieejjournal/140/9/140_582/_pdf

担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

DNA has the potential to achieve a controllable macromolecular structure, such as hydrogels or droplets formed through liquid-liquid phase separation (LLPS), as the design of its base sequence can result in programmable interactions. Here, we constructed "DNA droplets"via LLPS of sequence-designed DNA nanostructures and controlled their dynamic functions by designing their sequences. Specifically, we were able to adjust the temperature required for the formation of DNA droplets by designing the sequences. In addition, the fusion, fission, and formation of Janus-shaped droplets were controlled by sequence design and enzymatic reactions. Furthermore, modifications of proteins with sequence-designed DNAs allowed for their capture into specific droplets. Overall, our results provide a platform for designing and controlling macromolecular droplets via the information encoded in component molecules and pave the way for various applications of sequence-designed DNA such as cell mimics, synthetic membraneless organelles, and artificial molecular systems.

DOI： 10.1126/sciadv.aba3471

Scopus

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：記事・総説・解説・論説等（その他）

DOI： 10.1007/s12551-020-00647-y

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記述言語：英語   掲載種別：研究論文（学術雑誌）

We report a photolithographic method for the shape control of DNA hydrogels based on photo-activated self-assembly of Y-shaped DNA nanostructures (Y-motifs). To date, various methods to control the shape of DNA hydrogels have been developed to enhance the functions of the DNA hydrogel system. However, photolithographic production of shape-controlled DNA hydrogels formed through the self-assembly of DNA nanostructures without the use of radical polymerizations has never been demonstrated, although such a method is expected to be applied for the shape-control of DNA hydrogels encapsulating sensitive biomolecules, such as proteins. In this study, we used a photo-activated linker to initiate the self-assembly of Y-motifs, where the cross-linker DNA was at first inactive but was activated after UV light irradiation, resulting in the formation of shape-controlled DNA hydrogels only at the UV-exposed area produced by photomasks. We believe that this method will be applied for the construction of biohybrid machines, such as molecular robots and artificial cells that contain intelligent biomolecular devices, such as molecular sensors and computers.

DOI： 10.1063/1.5132929

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記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）

Hydrogels lie at the heart of the organ-on-chip approach. Their physicochemistry and rheology largely determine the outcome of tissue engineering. DNA hydrogels are emerging as a promising medium due to their biocompatibility and physicochemical programmability. However their use as a scaffold for tissue engineering has been little studied. Here we study the buoyancy and sedimentation of microbeads suspended in DNA gels and culture medium. We identify the parameters (binding strengths and concentration of DNA strands) that should enable stable suspension and culture of cells.

Scopus

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記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）

DNA hydrogels have emerged in the recent decade as a powerful substrate to program soft matter at the nanoscale. In particular, DNA hydrogels exhibit liquid/liquid phase separation in vitro, a phenomenon that is appearing to be ubiquitous in cells. Yet, a quantitative understanding of their physics is missing. Here we use a droplet microfluidics platform to prepare tens of thousands of droplets with DNA motifs inside.

Scopus

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記述言語：英語   掲載種別：研究論文（学術雑誌）

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.

DOI： 10.3390/molecules25010008

Scopus

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担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）

DNA is a promising materials to design, construct, and control micrometer-sized structures. A few studies have focused on the phase transition of DNA microstructures. However, there is less knowledge of the effects of the base sequence of DNA on the phase behavior. Here, we reports DNA microdroplets that is a novel and unique DNA microstructure. We designed sequences of DNAs and successfully visuzalized the formation of DNA microdroplets via phase transition. We believe that our results provide new aspects of DNA as a soft/fluid material, which would contribute to various fields such as bioengineering, microfluidics, and artificial cell engineering.

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

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.

DOI： 10.1039/c9cc03277k

Scopus

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：記事・総説・解説・論説等（学術雑誌）

The creation of artificial cells is an immensely challenging task in science. Artificial cells contribute to revealing the mechanisms of biological systems and deepening our understanding of them. The progress of versatile biological research fields has clarified many biological phenomena, and various artificial cell models have been proposed in these fields. Microfluidics provides useful technologies for the study of artificial cells because it allows the fabrication of cell-like compartments, including water-in-oil emulsions and giant unilamellar vesicles. Furthermore, microfluidics also allows the mimicry of cellular functions with chip devices based on sophisticated chamber design. In this review, we describe contributions of microfluidics to the study of artificial cells. Although typical microfluidic methods are useful for the creation of artificial-cell compartments, recent methods provide further benefits, including low-cost fabrication and a reduction of the sample volume. Microfluidics also allows us to create multi-compartments, compartments with artificial organelles, and on-chip artificial cells. We discuss these topics and the future perspective of microfluidics for the study of artificial cells and molecular robotics.

DOI： 10.3390/MI10040216

Scopus

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担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

Self-assembly of designed nanostructures on a lipid membrane offers a powerful approach for enhancing the functionality of its surface. Here, the environment-dependent assembly of blunt-ended DNA origami structures on a phase-separated lipid-bilayer membrane consisting of liquid-disordered (Ld) and solid-ordered (So) phases is reported. Fluorescence microscopy and atomic force microscopy (AFM) imaging reveal that DNA origami structures preferentially bind to the So phase. At higher concentrations, blunt-ended origamis form 2D lattices on the Ld phase through surface-mediated self-assembly. In contrast, those adsorbed on the So phase are less mobile and pack into aggregates. However, this situation is changed by adding NaCl. High-speed AFM imaging reveals the mechanism underlying the NaCl-induced changes, wherein the lattices on the Ld phase desorb from the surface while the packed aggregates on the So phase reorganize into the lattices. These results indicate that the formation of 2D lattices depends on the phase of the lipids; however, it can be tuned by ionic conditions, enabling us to select the domain on which the lattice is formed. The present results may guide the creation of membrane-supported DNA nanostructures that self-assemble into functional states in a lipid phase or ion-responsive manner.

DOI： 10.1002/admi.201800437

Scopus

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担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

Plasma in a liquid has been anticipated as an effective tool for medical applications, however, few reports have described cellular responses to plasma generated in a liquid similar to biological fluids. Herein we report the effects of plasma generated in a culture medium on HeLa cells. The plasma in the culture medium produced not only heat, shock waves, and reactive chemical species but also a jet flow with sub millimeter-sized bubbles. Cells exposed to the plasma exhibited detachment, morphological changes, and changes in the actin cytoskeletal structure. The experimental results suggest that wall shear stress over 160 Pa was generated on the surface of the cells by the plasma. It is one of the main factors that cause those cellular responses. We believe that our findings would provide valuable insight into advancements in medical applications of plasma in a liquid.

DOI： 10.1088/1361-6463/aab058

Scopus

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）

The realization of a tiny-wet machine assembled from the molecular devices such as sensors, actuators, and even logic circuits is one of the major goals of the bioinspired micro-nano robotics. We constructed an ameba-like molecular robot capable of expressing continuous shape change in response to specific signal molecules [1]. The robot includes a main body, an actuator, and an actuator control device (molecular clutch). When the clutch was engaged, the robot showed continuous shape change. When the clutch was disconnected, the shape change behavior stopped. These results show that the components of the robot are consistently integrated into the functional system. We are expecting that this research can provide a platform for constructing increasingly complex and functional molecular systems with controllable motility.

DOI： 10.1109/MHS.2017.8305293

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担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

Rapid progress in nanoscale bioengineering has allowed for the design of biomolecular devices that act as sensors, actuators, and even logic circuits. Realization of micrometer-sized robots assembled from these components is one of the ultimate goals of bioinspired robotics. We constructed an amoeba-like molecular robot that can express continuous shape change in response to specific signal molecules. The robot is composed of a body, an actuator, and an actuator-controlling device (clutch). The body is a vesicle made from a lipid bilayer, and the actuator consists of proteins, kinesin, and microtubules. We made the clutch using designed DNA molecules. It transmits the force generated by the motor to the membrane, in response to a signal molecule composed of another sequence-designed DNA with chemical modifications. When the clutch was engaged, the robot exhibited continuous shape change. After the robot was illuminated with light to trigger the release of the signal molecule, the clutch was disengaged, and consequently, the shape-changing behavior was successfully terminated. In addition, the reverse process-that is, initiation of shape change by input of a signal-was also demonstrated. These results show that the components of the robot were consistently integrated into a functional system. We expect that this study can provide a platform to build increasingly complex and functional molecular systems with controllable motility.

DOI： 10.1126/scirobotics.aal3735

Scopus

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

We describe a positive pulse voltage method for generating plasma in culture medium with a composition similar to biological fluids. We also describe the plasma's characteristics, liquid quality, and the effect of organic compounds in the culture medium on the plasma characteristics through comparisons to a solution containing inorganic salts at the same concentrations as in the culture medium. Light emission with Na and OH spectra was observed within a vapor bubble produced by Joule heating at the tip of the electrode. A downward thermal flow and shock wave were caused by the behavior of the vapor bubble. The culture medium pH gradually increased from 7.9 to 8.3 over the discharge time of 300 s. H2O2 was generated 1.1 mg l-1 in the culture medium after discharge for 300 s, and this value was 0.5 mg l-1 lower than the inorganic salts solution which does not contain organic compounds. This study provides important data that will help facilitate more widespread application of plasma medicine.

DOI： 10.1088/0963-0252/25/6/065023

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担当区分：筆頭著者   記述言語：日本語   掲載種別：記事・総説・解説・論説等（学術雑誌）

開催期間： 2022年10月25日 - 2022年10月27日   記述言語：日本語  

開催期間： 2022年10月17日 - 2022年10月18日   記述言語：日本語  

開催期間： 2022年10月17日 - 2022年10月18日   記述言語：日本語  

開催期間： 2022年10月07日   記述言語：日本語  

開催期間： 2022年09月28日 - 2022年09月30日   記述言語：英語  

開催期間： 2022年09月25日 - 2022年09月27日   記述言語：日本語  

受賞国：日本国

受賞国：ドイツ連邦共和国

受賞国：日本国

受賞国：日本国