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Funding Information: The research of A.E., A.M., and P.O. was supported by Academy of Finland grant 311639. A.K. and A.K.N. have been supported by Academy of Finland grant 308992. The research of I.K. was supported by Japan Society for the Promotion of Science (JSPS) Early-Career Scientists 18K18144, Fund for the Promotion of Joint International Research (B) 19KK0261, and Young Researcher Dispatch Program (School of Engineering, Tohoku University). The research of A.M. was additionally supported by NSF-DMS (grant numbers 1800443/1764366) and Nokia Foundation (2017). The research of Y.S. has been supported by JSPS Grant-in-Aid for Scientific Research (KAKENHI; grant numbers 18K19831 and 19H04201). The research of L.O. and F.C.S. was supported by European Research Council grant agreement no. 694410, project AEDNA. Publisher Copyright: © 2022 The Authors. Published by American Chemical Society. 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. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism. The design software is openly available and also provides an export of the targeted 3D structure into the oxDNA molecular dynamics simulator for easy simulation and visualization.

Intaking molecular information from the external environment is essential for the normal 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 permeation of large external hydrophilic fluorescent molecules is observed. Furthermore, the addition of up to four ssDNA strands enables size-based selective transport of molecules. A controllable artificial nanopore should facilitate the communication between the vesicle components and their environment.

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. Previously, we reported a line pattern formed due to the reaction and diffusion of synthetic DNA; however, the width of the line was too wide to be used for further applications such as parallel and multi-stage pattern formations. Here, we propose a novel method to programme a reaction-diffusion system in a hydrogel medium to realise a sharp line capable of forming superimposed and cascaded patterns. The mechanism of this system utilises a two-segment polymerisation of DNA caused by hybridisation. To superimpose the system, we designed orthogonal DNA sequences that formed two lines in different locations on the hydrogel. Additionally, we designed a reaction to release DNA and form a cascade pattern, in which the third line appears between the two lines. To explain the mechanism of our system, we modelled the system as partial differential equations, whose simulation results agreed well with the experimental data. Our method to fabricate cascaded patterns may inspire combinations of DNA-based technologies and expand the applications of artificial reaction-diffusion systems.

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.

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 the clustering of integrin molecules. Each nanospring was modified with arginyl-glycyl-aspartic acid (RGD) domains with a spacing such that when the nanospring is coiled, the RGD ligands trigger the clustering of integrin molecules, which changes cell motions. The coiling or uncoiling of the nanospring is controlled, respectively, by the formation or dissolution of an i-motif structure between neighboring piers in the DNA origami nanodevice. At slightly acidic pH (

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 straightened position as desired, thereby allowing the motif to take various shapes. We can adjust the number of flexible joints and the number of connectable segments, thereby enabling programmable self-assembly of the motif. We successfully produced the motif and evaluated several self-assembly patterns. The proposed multi-joint ring motif can provide a novel method for creating functional molecular devices.

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 artificial nanopore should help to communicate the vesicle components with their environment

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 &ldquo, quick&rdquo, one-minute annealing conditions. In addition, the smaller droplets (average diameter: 1.2 &micro, m) 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.

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 strands, which results in low reliability of the molecular circuit. In this study, we propose a method to quantitatively evaluate the robustness of a DNA circuit created by DNA strand displacement reactions. The highlight of our method is representing the circuit system contaminated by unintended reactions by a standard form of a disturbed nonlinear system and evaluating the robustness with the L2 gain by solving the Hamilton–Jacobi inequality.

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.

International audience; 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 conditionally aggregating into clusters. Using a realistic simulation, we then address the question of how to automatically design the reaction networks that define the micro-robots' behavior, to self-assemble into a specific shape at a specific location. We use bioNEAT, an instantiation of the famous NEAT algorithm capable of handling chemical reaction networks, and CMA-ES to optimize the behavior of each micro-bead. As in swarm robotics, each micro-bead shares the same behavioral rules and the general outcome depends on interactions between neighbors and with the environment. Results obtained on four different target functions show that solutions optimized with evolutionary algorithms display efficient self-assembling behaviors, improving over pure hand-designed networks provided by an expert after a week-long trials and errors search. In addition, we show that evolved solutions are able to self-repair after damage, which is a critical property for smart materials.

Part 2: Regular Papers; International audience; 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.

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. This field is attempting to implement artificial life using biological molecules. We foresee that molecular robots will interface information and life, and the distinction among information, life and artificial life will eventually become a blur. Once molecular robots gain the ability to evolve, then co-evolution of the three will lead to a new stage of intelligence.