Ibuki Kawamata

Micrometer-sized molecular robot changes its shape in response to signal molecules

An amoeba-like molecular robot changes its shape in response to sequence-designed DNA signal molecules. 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.

Automatic Design of DNA Logic Gates Based on Kinetic Simulation

Recently, DNA logic gates and DNA machines have been developed using only a simple complementary base pairing of DNA, that is, hybridization and branch migration. Because such reaction systems have been designed by trial and error, it has been difficult to design a complex system and to correctly verify the reaction. The purpose of this research is to develop a method for automatically searching and designing DNA logic gates based on a kinetic simulation. Since the solution space that should be searched is quite large, a simulated-annealing method is used to search for a highly evaluated system from many candidates and find a semi-optimal one. A simulator based on a kinetic model is developed, which calculates the time change of concentrations of abstracted DNA molecules. An evaluation function, in which the evaluation value rises when the logic gate works correctly, is also designed. The effectiveness of the proposed method is evaluated experimentally with an AND gate, which is designed automatically.

DNA cytoskeleton for stabilizing artificial cells

Significance Although liposomes and lipid droplets have been used for numerous applications, the fragility of the lipid membrane causes an unintentional collapse, which is problematic for advanced applications. To solve this problem, we constructed an artificial cytoskeleton with DNA nanotechnology (a DNA cytoskeleton). The DNA cytoskeleton is a DNA network formed underneath the membrane of positively charged lipids through electrostatic interactions without the need for special handling. The DNA cytoskeleton significantly improves mechanical stability and, therefore, confers tolerance against osmotic shock to liposomes like the cytoskeleton in live cells. Because of its biocompatibility and the easiness of implementing design changes, the DNA cytoskeleton could become a tool for great stabilizer of liposomes and lipid droplets. 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.

On DNA-Based Gellular Automata

We propose the notion of gellular automata and their possible implementations using DNA-based gels. Gellular automata are a kind of cellular automaton in which cells in space are separated by gel materials. Each cell contains a solution with designed chemical reactions whose products dissolve or construct gel walls separating the cells. We first introduce the notion of gellular automata and their computational models. We then give examples of gellular automata and show that computational universality is achieved through the implementation of rotary elements by gellular automata. We finally examine general strategies for implementing gellular automata using DNA-based gels and report results of preliminary experiments.

Universal Totalistic Asynchonous Cellular Automaton and Its Possible Implementation byźDNA

This paper presents a Cellular Automaton CA model designed for possible implementation by the reaction and diffusion of DNA strands. The proposed CA works asynchronously, whereby each cell undergoes its transitions independently from other cells and at random times. The state of a cell changes in a cyclic manner, rather than according to an any-to-any mapping. The transition rules are designed as totalistic, i.e., the next state of a cell is determined only by the number of states in the neighborhood of the cell, not by their relative positions. Universal circuit elements are designed for the CA as well as wires and crossings to connect them, which implies that the CA is Turing-complete.

Discrete DNA Reaction-Diffusion Model forźImplementing Simple Cellular Automaton

We introduce a theoretical model of DNA chemical reaction-diffusion network capable of performing a simple cellular automaton. The model is based on well-characterized enzymatic bistable switch that was reported to work in vitro. Our main purpose is to propose an autonomous, feasible, and macro DNA system for experimental implementation. As a demonstration, we choose a maze-solving cellular automaton. The key idea to emulate the automaton by chemical reactions is assuming a space discretized by hydrogel capsules which can be regarded as cells. The capsule is used both to keep the state uniform and control the communication between neighboring capsules. Simulations under continuous and discrete space are successfully performed. The simulation results indicate that our model evolves as expected both in space and time from initial conditions. Further investigation also suggests that the ability of the model can be extended by changing parameters. Possible applications of this research include pattern formation and a simple computation. By overcoming some experimental difficulties, we expect that our framework can be a good candidate to program and implement a spatio-temporal chemical reaction system.

Reversible Gel–Sol Transition of a Photo-Responsive DNA Gel

Stimuli‐responsive DNA gels that can undergo a sol‐gel transition in response to photo‐irradiation provide a way to engineer functional gel material with fully designed DNA base sequences. We propose an X‐shaped DNA motif that turns into a gel by hybridization of self‐complementary sticky ends. By embedding a photo‐crosslinking artificial base in the sticky‐end sequence, repetitive gel–sol transitions are achieved through UV irradiation at different wavelengths. The concentration of the DNA motif necessary for gelation is as low as 40 μm after modification of the geometrical properties of the motif. The physical properties, such as swelling degree and diffusion coefficient, were assessed experimentally.

Abstraction of graph-based models of bio-molecular reaction systems for efficient simulation

We propose a technique to simulate molecular reaction systems efficiently by abstracting graph models. Graphs (or networks) and their transitions give rise to simple but powerful models for molecules and their chemical reactions. Depending on the purpose of a graph-based model, nodes and edges of a graph may correspond to molecular units and chemical bonds, respectively. This kind of model provides naive simulations of molecular reaction systems by applying chemical kinetics to graph transition. Such naive models, however, can immediately cause a combinatorial explosion of the number of molecular species because combination of chemical bonds is usually unbounded, which makes simulation intractable. To overcome this problem, we introduce an abstraction technique to divide a graph into local structures. New abstracted models for simulating DNA hybridization systems and RNA interference are explained as case studies to show the effectiveness of our abstraction technique. We then discuss the trade-off between the efficiency and exactness of our abstracted models from the aspect of the number of structures and simulation error. We classify molecular reaction systems into three groups according to the assumptions on reactions. The first one allows efficient and exact abstraction, the second one allows efficient but approximate abstraction, and the third one does not reduce the number of structures by abstraction. We conclude that abstraction is a useful tool to analyze complex molecular reaction systems and measure their complexity.

Turing-Completeness of Asynchronous Non-camouflage Cellular Automata

Asynchronous Boolean totalistic cellular automata have recently attracted attention as promising models for the implementation of reaction-diffusion systems. It is unknown, however, to what extent they are able to conduct computation. In this paper, we introduce the so-called non-camouflage property, which means that a cell’s update is insensitive to neighboring states that equal its own state. This property is stronger than the Boolean totalistic property, which signifies the existence of states in a cell’s neighborhood, but is not concerned with how many cells are in those states. We argue that the non-camouflage property is extremely useful for the implementation of reaction-diffusion systems, and we construct an asynchronous cellular automaton with this property that is Turing-complete. This indicates the feasibility of computation by reaction-diffusion systems.

Pattern Formation and Computation by Autonomous Chemical Reaction Diffusion Model Inspired by Cellular Automata

We introduce two autonomous chemical reaction-diffusion models that can emulate the behavior of specific cellular automata. One model conducts formation of a 3-color checker-board pattern using an abstract chemical reaction network. The other model is based on a DNA reaction-diffusion system that is capable of emulating a Turing-complete one-dimensional cellular automaton. These frameworks can be used to systematically program spatiotemporal pattern formation, and thus has a potential for an effective macro-scale control of molecular systems.