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Physical properties of DNA droplets formed by liquid–liquid phase separation of DNA nanostructures were investigated at a phase transition temperature. The surface tension was strongly influenced by the design of sticky ends.

We demonstrate remote-controlled microflow using photoresponsive DNA fluid. The DNA fluid was fabricated through the self-assembly of branched DNA motifs, nanostructures of base-paired single-stranded DNAs (ssDNAs): Three ssDNAs hybridized in the stem region to form a branched motif possessing sticky ends (SEs); via the hybridization of SEs, the branched DNA motifs self-assembled into DNA fluid, which was micrometer-scale condensates. The motifs were equipped with a photoresponsive capability by introducing azobenzene (Azo), well-studied photoisomerizable compound44, in the SEs. The photoswitchable Azo isomerization enabled the reversible association/dissociation between branched DNA motifs, leading to photoreversible fluidity regulation via gel–liquid–dispersed state transition. To design an energy-transducing system, we exploited the following sequence-specific programmability of DNA. By cross-linking the photoresponsive DNA motif with a branched DNA motif possessing nonphotoresponsive orthogonal SEs, we achieved photocontrollable “transporter” DNA and “cargo” DNA fluids; the photoresponsive DNA fluid hydrodynamically performed mechanical actions upon the nonphotoresponsive DNA fluid by transducing light energy. Notably, we discovered multiple modes in the generated fluid’s mechanical action as a function of the applied temperature and the Azo insertion site in the SE. Each flow mode was characterized as a single-peak-shaped profile in the temperature-dependent flow mobilities. The highest and lowest mobilities were obtainable in moderate and lower and higher temperature ranges, respectively. This anomalous profile was analogous to the reentrant phase behavior of DNA microstructures41,50,51, which behave as solid-like only in a moderate temperature range and as liquid-like in the lower and higher temperature ranges. Following thermodynamic arguments on the observed reentrancy, we describe the observed flow-mobility behavior as a manifestation of a transient non-equilibrium state in the SEs binding stability. We also explain the mode-changeability of the mechanical actions with experimental support by explaining the role of the Azo insertion site in the SE in determining the degree of the nonequilibrium in the binding stability.

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.

This paper describes repeatable detection of Ag

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.

Polydimethylacrylamide (PDMA) microgels and niobate nanosheet/PDMA composite microgels were fabricated by using a microfluidic device. Morphologies and sizes of the composite microgels were tuned by adjusting synthetic conditions such as viscosity of oil phases, hydrophilicity and concentration of surfactants, and flow rates of oil phase and water phase. Furthermore, it was found that the dispersion of nanosheets was better when the composite microgels were synthesized by photopolymerization compared to redox polymerization.

Modulating the electronic structure of semiconducting materials is critical to developing high-performance electronic and optical devices. Transition metal dichalcogenides (TMDCs) are atomically thin semiconducting materials. However, before they can be used successfully in electronic and optical devices, modulation of their carrier concentration at the nanometer scale must be achieved. Molecular doping has been successful in modulating the carrier concentration; however, the scientific approach for selective and local carrier doping at the nanometer scale is still missing. Here, we demonstrate a proof-of-concept of modulating the carrier concentration of TMDCs laterally on a scale of around 100 nm using spontaneous pattern formation of an ultrathin film consisting of molecular electron dopants. When the water made contact with the molecular film (∼10 nm), a spontaneous pattern formation was observed on both the monolayer and bulk TMDCs. We revealed that the pattern-formation dynamics and nanoscopic flow rate of the molecules were highly dependent on the thickness of the TMDCs, since the band gap varies based on the number of layers. Analyses of topographic images of the molecular patterns and photoluminescence spectra of the TMDCs indicated that the spontaneously patterned molecular films induced a local carrier doping. Our results demonstrate a spontaneous formation of a mosaic electronic structure. This work is useful for making tiny-scale electronic junctions on TMDCs and semiconducting materials to make numerous p/n junctions simultaneously for optoelectronic devices.

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 droplets via electrostatic interactions. The phase separation of DNA nanostructures led to the formation of hydrogels of 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 regulated 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. 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 mechano-chemical actuating functions, allowing the construction of functional molecular systems.

Biochemical systems in living cells have their optimum concentration ratio among each constituent element to maintain their functionality. However, in the case of the biochemical system with complex interactions and feedbacks among elements, their activity as a system greatly changes by the concentration shift of the entire system irrespective of the concentration ratio among elements. In this study, by using a transcription-translation (TX-TL) system as the subject, we illustrate the principle of the nonlinear relationship between the system concentration and the activity of the system. Our experiment and simulation showed that shifts of the system concentration of TX-TL by dilution and concentration works as a switch of activity and demonstrated its ability to emerge a biochemical system to confer the permeability of small molecules to liposomes. These results contribute to the creation of artificial cells using the switch and provide an insight into the birth of the origin of life.

Molecular machines and molecular robots are a highly interdisciplinary research field including material science, chemistry, biotechnology, biophysics, soft matter physics, micro-electromechanical systems (MEMS), and computer science [...]

Eukaryotic transcription is epigenetically regulated by chromatin structure and post-translational modifications (PTMs). For example, lysine acetylation in histone H4 is correlated with activation of RNA polymerase I-, II-, and III-driven transcription from chromatin templates, which requires prior chromatin remodeling. However, quantitative understanding of the contribution of particular PTM states to the sequential steps of eukaryotic transcription has been hampered partially because reconstitution of a chromatin template with designed PTMs is difficult. In this study, we reconstituted a di-nucleosome with site-specifically acetylated or unmodified histone H4, which contained two copies of theXenopussomatic 5S rRNA gene with addition of a unique sequence detectable by hybridization-assisted fluorescence correlation spectroscopy. Using aXenopusoocyte nuclear extract, we analyzed the time course of accumulation of nascent 5S rRNA-derived transcripts generated on chromatin templatesin vitro.Our mathematically described kinetic model and fitting analysis revealed that tetra-acetylation of histone H4 at K5/K8/K12/K16 increases the rate of transcriptionally competent chromatin formation ~3-fold in comparison with the absence of acetylation. We provide a kinetic model for quantitative evaluation of the contribution of epigenetic modifications to chromatin transcription.

This study examined the effects of surfactants on the motion and positioning of microparticles in an inhomogeneous electric field. The microparticles were suspended in oil with a surfactant and the electric field was generated using sawtooth-patterned electrodes. The microparticles were trapped, oscillated, or attached to the electrodes. The proportion of microparticles in each state was defined by the concentration of surfactant and the voltage applied to the electrodes. Based on the trajectory of the microparticles in the electric field, a newly developed physical model in which the surfactant was adsorbed on the microparticles allowed the microparticles to be charged by contact with the electrodes, with either positive or negative charges, while the non-adsorbed surfactant micellizing in the oil contributed to charge relaxation. A simulation based on this model showed that the charging and charge relaxation, as modulated by the surfactant concentration, can explain the trajectories and proportion of the trapped, oscillating, and attached microparticles. These results will be useful for the development of novel self-assembly and transport technologies and colloids sensitive to electricity., Comment: Supplementary videos available at https://takinouelab.github.io/MasukawaTakinoue2019/

Fusion, fission, and formation of complex shapes of droplets made of DNA were controlled by a sequence design approach., 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.

Cell-sized liposomes and droplets coated with lipid layers have been used as platforms for understanding live cells, constructing artificial cells, and implementing functional biomedical tools such as biosensing platforms and drug delivery systems. However, these systems are very fragile, which results from the absence of cytoskeletons in these systems. Here, we construct an artificial cytoskeleton using DNA nanostructures. The designed DNA oligomers form a Y-shaped nanostructure and connect to each other with their complementary sticky ends to form networks. To undercoat lipid membranes with this DNA network, we used cationic lipids that attract negatively charged DNA. By encapsulating the DNA into the droplets, we successfully created a DNA shell underneath the membrane. The DNA shells increased interfacial tension, elastic modulus, and shear modulus of the droplet surface, consequently stabilizing the lipid droplets. Such drastic changes in stability were detected only when the DNA shell was in the gel phase. Furthermore, we demonstrate that liposomes with the DNA gel shell are substantially tolerant against outer osmotic shock. These results clearly show the DNA gel shell is a stabilizer of the lipid membrane akin to the cytoskeleton in live cells.

This paper reports a twisting microfluidic method utilising a centrifuge-based fluid extruding system in a planetary centrifuge which simultaneously generates an orbital rotation and an axial spin. In this method, fluid extrusion from a micro-scale capillary to an 'open-space' solution or air enables release of the fluid from the capillary-based microchannel, which physically means that there is a release of fluids from a confined low-Reynolds-number environment to an open non-low-Reynolds-number environment. As a result, the extruded fluids are separated from the axial spin of the capillary, and the difference in the angular rates of the axial spin between the capillary and the extruded fluids produces the 'twisting' of the fluid. In this study, we achieve control of the twist of highly viscous fluids, and we construct a simple physical model for the fluid twist. In addition, we demonstrate the formation of twisted hydrogel microstructures (stripe-patterned microbeads and multi-helical microfibres) with control over the stripe pattern and the helical pitch length. We believe that this method will enable the generation of more sophisticated microstructures which cannot easily be formed by usual channel-based microfluidic devices. This method can also provide advanced control of microfluids, as in the case of rapid mixing of highly viscous fluids. This method can contribute to a wide range of applications in materials science, biophysics, biomedical science, and microengineering in the future.

Bio-inspired functional microcapsules have attracted increasing attention in many fields from physical/chemical science to artificial-cell engineering. Although particle-stabilised microcapsules are advantageous for their stability and functionalisation potential, versatile methods for their functionalisation are desired to expand their possibilities. This study reports a water-in-oil microdroplet stabilised with amphiphilic DNA origami nanoplates. By utilising DNA nanotechnology, DNA nanoplates were designed as a nanopore device for ion transportation and to stabilise the oil-water interface. Microscopic examination revealed the microcapsule formed by the accumulation of amphiphilic DNA nanoplates at the oil-water interface. Ion current measurements revealed the nanoplate pores functioned as channel to transport ions. These findings provide a general strategy for the programmable design of microcapsules to engineer artificial cells and molecular robots.

This paper describes a DNA aptamer-linked structural-color hydrogel sensor that can quantitatively and repeatably detect biochemical substances through visual information without any specific equipment. The initial color of structural-color hydrogel could be adjusted by controlling the concentration of the colloidal silica particle. We co-polymerized a DNA aptamer that specifically binds to silver ions into acrylamide hydrogel and evaluated its quantitative shrinking response to silver acetate solution. In addition, we succeeded in initializing our DNA aptamer hydrogel sensor by heating, indicating that our chemical sensor could repeatably measure the target chemical substance for the long term. We believe that our structural-color biochemical sensor could be applied to various routine monitoring such as healthcare diagnosis and water safety.

International audience; We precisely measure the effect of moderate magnetic field intensity on the surface tension of liquids, by placing pendant drops inside uniform fields where bulk forces due to gradients are eliminated. The surface tension of water is unaffected while that of paramagnetic salt solutions slightly decreases with increasing field strength.

In this paper, we describe a collective transport of microparticles emerged in a bottom-up manner. Our transport was spontaneously realized by collision and electrostatic interaction among transported microparticles. Unlike previous technique based on a top-down manner, the microparticles collectively transported even in a condition that there were no biased external force fields. We believe that this work will contribute to the development of the transporting technique with smartness and flexibility in a device of lab-on-a-chip and micro total analysis systems (microTAS).