Ibuki Kawamata's research while affiliated with Ochanomizu University and other places

Publications (46)

Preprint
Full-text available
We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Towards this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyh...
Chapter
This chapter reviews advancements in computer‐aided design software for nucleic acid nanostructures with some typical examples. It mainly focuses on DNA nanostructures, especially the DNA origami method, but also on some RNA nanostructures. A number of programs specialized for designing DNA and RNA nanostructures have been developed. The chapter al...
Article
Full-text available
The DNA origami technique is used to construct custom-shaped nanostructures that can be used as components of two-dimensional crystalline structures with user-defined structural patterns. Here, we designed a Mg²⁺-responsive hexagonal 3D DNA origami block with self-shape-complementary ruggedness on the sides. Hexagonal DNA origami blocks were electr...
Article
Nanomechanical devices are driven by chemical and/or physical signals, which exert their functions by transitioning between different molecular states. Many DNA-based nanomechanical devices proposed so far are typically driven by applying single-stranded DNAs representing instructions. To use these devices, it is necessary to manually deliver the s...
Article
Reaction-diffusion systems are one of the models of the formation process with various patterns found in nature. Inspired by natural pattern formation, several methods for designing artificial chemical reaction-diffusion systems have been proposed. DNA is a suitable building block to build such artificial systems owing to its programmability. Previ...
Article
We introduce an automated procedure of coarse-grained molecular dynamic simulation for DNA nanostructure that has great potential for realizing molecular robotics. As DNA origami is now a standardized technology to fabricate DNA nanostructures with high precision, various computer-aided design software has been developed. For example, a design tool...
Article
Intaking molecular information from the external environment is essential for the proper functioning of artificial cells/molecular robots. Herein, we report the design and function of a membrane nanopore using a DNA origami square tube with a cross-section of 100 nm². When the nanopore is added to a giant vesicle that mimics a cell membrane, the pe...
Article
Full-text available
Cell motions such as migration and change in cellular morphology are essential activities for multicellular organism in response to environmental stimuli. These activities are a result of coordinated clustering/declustering of integrin molecules at the cell membrane. Here, we prepared DNA origami nanosprings to modulate cell motions by targeting th...
Article
In this paper, we describe our activities on student competitions conducted by connecting multiple universities online. By combining online lectures, tutorials, and various types of groupwork, undergraduate student participants from 11 universities worked together to propose their original ideas in a short period of time. The results were evaluated...
Article
Full-text available
The invention of DNA origami has expanded the geometric complexity and functionality of DNA nanostructures. Using DNA origami technology, we develop a flexible multi-joint ring motif as a novel self-assembling module. The motif can connect with each other through self-complementary sequences on its segments. The flexible joints can be fixed in a st...
Preprint
Here, we report on the design and function of a membrane nanopore through a DNA origami square tube with a cross-section of 100 nm2 . When the nanopore is added onto the giant vesicle membrane, the permeation of hydrophilic fluorescent molecules was observed. It can be sealed by the existence of the four specific single strand DNAs. A controllable...
Article
Full-text available
Asynchronous Boolean totalistic cellular automata have recently attracted attention as promising models for implementation by 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 n...
Article
Making use of the programmability and structural flexibility of the DNA molecule, we designed a DNA origami nanoarm capable of undergoing large deformation. Our DNA origami nanoarm comprised serially repeated tension‐adjustable modules, the cumulative actuation of which resulted in a large deformation of the arm structure, which transformed from a...
Article
Ein DNA-Origami-Nanoarm wurde konstruiert, der große, reversible Konformationsänderungen resultierend aus der kumulativen Wirkung serieller, zugspannungsjustierbarer Module eingehen kann. Dieser Mechanismus könnte die Produktion von DNA-Nanofunktionseinheiten ermöglichen, die auf externe Stimuli hin ihre Form verändern. Abstract Making use of the...
Article
We demonstrate a method of pattern formation based on an artificial reaction diffusion system in hydrogel medium. By designing both the reaction term and the diffusion term of the system, we have succeeded in generating a sustainable DNA pattern in the gel. A DNA logic gate anchored in the gel detected the diffused molecules from distant source poi...
Article
Full-text available
An artificial DNA circuit in giant unilamellar vesicles allows isothermal amplification of DNA by over 5000-fold within several hours.
Article
In this paper, we consider the implementation of a cellular automaton by DNA computing. The proposed system is a reaction–diffusion system built on a structured hydrogel matrix that mimics cellular compartments of biological tissues. Since the cellular automaton is materialized by a hydrogel matrix, the system is called gellular automaton which is...
Article
We propose a method to control the diffusion speed of DNA molecules with a target sequence in a polymer solution. The interaction between solute DNA and diffusion-suppressing DNA that has been anchored to a polymer matrix is modulated by the concentration of the third DNA molecule called the competitor by a mechanism called toehold exchange. Experi...
Article
The most common way to fabricate DNA nanostructures is to mix individually synthesized DNA oligomers in one pot. However, if DNA nanostructures could be produced using enzymatic reactions, they could be applied in various environments, including in vivo. Here, we report an enzymatic method that we developed to construct a DNA nanostructure from a s...
Article
How to construct a reliable deoxyribonucleic acid (DNA) circuit is one of the most important issues in the field of molecular programming and computing. Such a circuit frequently suffers from various kinds of unintended binding reactions on account of a lower specificity of the molecular interaction emerging from base complementarity between DNA st...
Article
A new kind of the Vernier mechanism that is able to control the size of linear assembly of DNA origami nanostructures is proposed. The mechanism is realized by mechanical design of DNA origami, which consists of a hollow cylinder and a rotatable shaft in it connected through the same scaffold. This nanostructure stacks with each other by the shape...
Conference Paper
This paper deals with the programmability of a swarm of bio-micro-robots in order to display self-assembling behaviors into specific shapes. We consider robots that are DNA-functionalized micro-beads capable of sensing and expressing signals as well as self-assembling. We describe an in vitro experimentation with a million of micro-beads conditiona...
Article
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 sys...
Article
We constructed a rotary DNA origami device and tested its stepping operation on a mica substrate by sequential strand displacement with four different sets of signal DNA strands. This work paves the way for building a variety of dynamic rotary DNA nanodevices which respond to multiple signals.
Conference Paper
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...
Article
We show electric control of unzipping and shearing dehybridization of DNA duplex anchored to hydrogel. Tensile force is applied by electrophoresing (25 V cm⁻¹) gold nanoparticle pulling DNA duplex. DNA duplex is gradually released from hydrogel. Unzipping release rate is faster than shearing; for example, 3-fold for 15 base pairs duplex, which help...
Article
We investigated spatio-temporal pattern formation in a reaction-diffusion system assuming a periodic cellular space. The reaction space is an array of cells, where diffusion is assumed to be fast inside the cells and relatively slow in the walls separating them. The simulation results showed that the spatio-temporal development of the concentration...
Article
Full-text available
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...
Conference Paper
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-dimens...
Conference Paper
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 demon...
Conference Paper
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-t...
Article
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 through hybridization of self-complementary sticky ends. Embedding a photo-cross-linking artificial base i...
Article
In this study, a Langmuir–Blodgett (LB) system has been utilized for regulation of polymerization of a DNA origami structure at the air−water interface as a two-dimensionally confined medium, which enables dynamic condensation of DNA origami units through variation of the film area at the macroscopic level (ca. 10−100 cm2). DNA origami sheets were...
Chapter
Gene regulatory network (GRN) focuses on the topology of how genes coded in DNA interact each other. This chapter first introduces the original approaches to model, simulate, and automatically design nucleic acid reaction systems with desired functions. It then reviews the potential applications of nucleic acid reaction systems and outlines the pro...
Article
Full-text available
Controlled transfer of DNA nanowheels from a hydrophilic to a hydrophobic surface was achieved by complexation of the nanowheels with a cationic lipid (2C12N(+)). 2D surface-assisted extraction, '2D-extraction', enabled structure-persistent transfer of DNA wheels, which could not be achieved by simple drop-casting.
Conference Paper
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 in...
Article
An simulation analysis on the control of bionanonetworks of DNA nanomachines using solitons induced by the terahertz radiation is presented. It is expected that the soliton breather wave in DNA can promote the branch migration to lead the effective change of the network formation toward the successful missions. Our results show new possibilities of...
Conference Paper
We present an analysis on bond-dissociation dynamics of DNA-based molecular machines under terahertz radiation. Our goal is to control micro/nanoworld utilizing artificial molecular machines. In this work we aim to provide fundamental findings to construct platform technologies to control artificial molecular systems using terahertz waves.
Chapter
We will begin with a simplified view of systems biology and synthetic biology. Systems biology extracts information from life, while synthetic biology converts information to reality. This cycle allows the co-evolution of life and information, and accelerates the evolution of both. Additionally, the field of molecular robotics has recently emerged....
Conference Paper
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 chemic...
Conference Paper
The logical computation using a self-assembly process of DNA nanostructures can provide unbreakable cryptosystems or intelligent molecular robots. Focusing on the trade-off problem between the error-free robustness for stability and the error-tolerable fragility for error correction through reconnections, we present in silico analyses and propose a...
Article
Full-text available
We propose a graph model of DNA molecules and an abstraction of that model for efficient simulation of molecular systems powered by DNA hybridization. In this paper, we first explain our DNA molecule model composed of graph data structures and highlight the problem of the large number of DNA structures that results. We then define an abstraction of...
Article
Somewhere between the studies of information technology and organic chemistry, researchers are trying to make tiny robots out of DNA molecules.
Conference Paper
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...

Citations

... Conventionally, lattices on SLB and mica substrates have been assembled using 2D DNA origami structures, but recently it was demonstrated that also three-dimensional (3D) DNA origami structures can be utilized for lattice assembly on SLBs. 59 In this work, hexagonal DNA origami blocks with shape-complementary interfaces were assembled into predefined 2D lattices on a DOPC bilayer. To assemble highly ordered monolayers, the DNA origami hexagons were adsorbed onto the SLB at a relatively low Mg 2+ concentration (15 mM), after which the Mg 2+ concentration was increased to 50 mM in order to reduce the electrostatic repulsion at the interfaces and thus allowing the DNA origami units to stack together. ...
... Notably, reaction-diffusion systems were also realized in enzyme-free systems exclusively based on DNA strand displacement reactions. [18][19][20][21] Major challenges for cell-free systems operated in closed reactors, however, are the absence of a fully functional metabolism 22,23 and the inability to fully self-regenerate, 24,25 which limits their lifetime to several hours. 26 Dynamic circuits that require continuous production and degradation of their constituents are therefore difficult to realize. ...
... The downside of that approach is that the simulation of systems is stochastic and would thus neither generate an actual CRN nor prove the absence of interesting structures in a given system. Simulations are extremely costly and can take up to 5 days for 300 ns of simulated time on a dedicated computing server for large structures [58], preventing the application of that simulator at an earlier stage of the exploration. Alternatively, a different enumerator might be plugged in the framework instead of Peppercorn, or as an additional refinement stage for the CRN exploration. ...
... Self-assembled DNA-based synthetic nanopores, particularly those built from scaffolded DNA origami, benefit from the extensive design space of DNA as building materials. DNA nanopores with inner diameters of more than 3 nm have been shown to mediate the passage of large biomolecules, such as double-stranded DNA and proteins, across lipid bilayer membranes (18)(19)(20)(21)(22). Moreover, highly predictable DNA interactions are the basis for the creation of programmable DNA nanopores that initiate transport only in the presence of specific chemical or spatial cues (20,23). ...
... 15 Our previous finding has indicated that integrin heterodimers require about 25 pN for their clustering and declustering activities which require a nanospring having a stiffer spring constant for the study. 16 In addition, the dynamic response of the nanospring is difficult to be measured by these force-extension curves reported by Shih and co-workers. ...
... Finally, this editorial presents a bottom-up approach using DNAs for the fabrication of designed nanostructures. Liu et al. [9] reported a flexible DNA-ring motif with multiple joints. The shape of the DNA rings can be controlled by modulating the joints owing to the single-stranded nature of the DNAs. ...
... Biological development-the generation of a complex, differentiated organism starting from a single cell-is a notable example of selforganization in biology that has inspired chemists, materials scientists, molecular programmers, and synthetic biologists alike to envision autonomously developing, self-differentiating, and self-sustaining biomimetic systems (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12). Newly available techniques such as three-dimensional (3D) printing of soft materials have opened up the possibility to automate and standardize the assembly of materials, where properties are defined across scales by combining top-down specification via additive manufacturing with bottom-up pattern formation via molecular self-organization. ...
... The term gellular automata was coined in [5], where the diffusion of DNA molecules is controlled by opening and closing holes between cells. Gellular automata were later formalized as cellular automata with the features of asynchrony, Boolean totality and noncamouflage in [6,7], where two types of DNA molecules were assumed, one for states of cells and the other for signals transmitting states. ...
... For instance, oligonucleotide C 6 TC 6 folds into an intermolecular tetraplex structure, while C 6 T 3 C 6 , C 7 TC 7 , and C 7 T 3 C 7 -fold into intramolecular conformations 27 . Thus, sequences consisting of 3−5 consecutive Gs or Cs are commonly used in DNA nanotechnology [37][38][39][40] . Triplexes can form only with at least five TAT base triplets in their stems at room temperature, with longer stems giving generally higher stability 41 . ...
... Therefore, the shorter the length, the more bent the structures, leading to a smaller radius of curvature. The predicted radii were parallel within experiments, 32 and for the structure with 2-gaps, the observed out-of-plane bending suggests the possibility of increasing the radius in the imaging procedure ( Figure S20). ...