Molecular Robots Research Articles

Synthetic Ion Channels and DNA Logic Gates as Components of Molecular Robots.

A molecular robot is a next-generation biochemical machine that imitates the actions of microorganisms. It is made of biomaterials such as DNA, proteins, and lipids. Three prerequisites have been proposed for the construction of such a robot: sensors, intelligence, and actuators. This Minireview focuses on recent research on synthetic ion channels and DNA computing technologies, which are viewed as potential candidate components of molecular robots. Synthetic ion channels, which are embedded in artificial cell membranes (lipid bilayers), sense ambient ions or chemicals and import them. These artificial sensors are useful components for molecular robots with bodies consisting of a lipid bilayer because they enable the interface between the inside and outside of the molecular robot to function as gates. After the signal molecules arrive inside the molecular robot, they can operate DNA logic gates, which perform computations. These functions will be integrated into the intelligence and sensor sections of molecular robots. Soon, these molecular machines will be able to be assembled to operate as a mass microrobot and play an active role in environmental monitoring and in vivo diagnosis or therapy.

Programmable Regulation of DNA Conjugation to Gold Nanoparticles via Strand Displacement.

Methods for conjugating DNA to gold nanoparticles (AuNPs) have recently attracted considerable attention. The ability to control such conjugation in a programmable way is of great interest. Here, we have developed a logic-based method for manipulating the conjugation of thiolated DNA species to AuNPs via cascading DNA strand displacement. Using this method, several logic-based operation systems are established and up to three kinds of DNA signals are introduced at the same time. In addition, a more sensitive catalytic logic-based operation is also achieved based on an entropy-driven process. In the experiment, all of the DNA/AuNPs conjugation results are verified by agrose gel. This strategy promises great potential for automatically conjugating DNA stands onto label-free gold nanoparticles and can be extended to constructing DNA/nanoparticle devices for applications in diagnostics, biosensing, and molecular robotics.

Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate

Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA–protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA–protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA–protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour.

A cargo-sorting DNA robot.

Two critical challenges in the design and synthesis of molecular robots are modularity and algorithm simplicity. We demonstrate three modular building blocks for a DNA robot that performs cargo sorting at the molecular level. A simple algorithm encoding recognition between cargos and their destinations allows for a simple robot design: a single-stranded DNA with one leg and two foot domains for walking, and one arm and one hand domain for picking up and dropping off cargos. The robot explores a two-dimensional testing ground on the surface of DNA origami, picks up multiple cargos of two types that are initially at unordered locations, and delivers them to specified destinations until all molecules are sorted into two distinct piles. The robot is designed to perform a random walk without any energy supply. Exploiting this feature, a single robot can repeatedly sort multiple cargos. Localization on DNA origami allows for distinct cargo-sorting tasks to take place simultaneously in one test tube or for multiple robots to collectively perform the same task.

Stereodivergent synthesis with a programmable molecular machine.

It has been convincingly argued that molecular machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångström precision are unlikely to be realized. However, biological molecular machines routinely position rather less reactive substrates in order to direct chemical reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered molecules are passed from active site to active site in multi-enzyme complexes. Artificial molecular machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host molecule has been described that is able to mechanically twist a bound molecular guest, and molecular fragments have been selectively transported in either direction between sites on a molecular platform through a ratchet mechanism. Here we detail an artificial molecular machine that moves a substrate between different activating sites to achieve different product outcomes from chemical synthesis. This molecular robot can be programmed to stereoselectively produce, in a sequential one-pot operation, an excess of any one of four possible diastereoisomers from the addition of a thiol and an alkene to an α,β-unsaturated aldehyde in a tandem reaction process. The stereodivergent synthesis includes diastereoisomers that cannot be selectively synthesized through conventional iminium-enamine organocatalysis. We anticipate that future generations of programmable molecular machines may have significant roles in chemical synthesis and molecular manufacturing.

Nanotechnology: A molecular assembler.

The idea of nanometre-scale machines that can assemble molecules has long been thought of as the stuff of science fiction. Such a machine has now been built — and might herald a new model for organic synthesis. See Letter p.374 It has been debated whether synthetic molecular machines could ever rival the complexity, precision and function of evolved biological machinery, with questions arising over whether atom-by-atom construction of molecules is possible, practicable or scalable. Key to the function of a hypothetical 'molecular assembler' is the ability of the machinery to position reactants. David Leigh and colleagues now use a molecular machine that can 'pick up' a substrate and position it at one of the two directing sites on the machine that control the stereochemistry of addition to the substrate. For two sequential chemical reactions, and depending on how the machine is programmed to move the substrate in between reactions, the molecular robot could make any one of four possible diastereoisomers, including one that cannot be made through conventional organocatalytic reactions.

Analysis of self-oscillating behaviors aimed at the development of a molecular robot with organic acids as fuel

We studied the transmittance self-oscillation of a polymer chain driven by an organic acid as the fuel. The self-oscillating polymer chain consists of 4-acryloylmorpholine (ACMO) and the Ru catalyst (Ru(bpy)3) of the Belousov–Zhabotinsky (BZ) reaction. The transmittance self-oscillating behavior was affected significantly by the temperature. As the amplitude of the transmittance self-oscillation, which is reflected by the aggregation state, decreased with time, the oscillation period also decreased. This trend indicates that the polymer aggregation affects the rate of the BZ reaction significantly. The activation energy of the self-oscillating value was almost the same in the normal BZ reaction, which does not include Ru(bpy)3 complexes in the polymer chains. In addition, we demonstrated the effect of one BZ substrate (sodium bromate or malonic acid) on the transmittance self-oscillation period.

Molecular Robots Obeying Asimov's Three Laws of Robotics.

Asimov's three laws of robotics, which were shaped in the literary work of Isaac Asimov (1920-1992) and others, define a crucial code of behavior that fictional autonomous robots must obey as a condition for their integration into human society. While, general implementation of these laws in robots is widely considered impractical, limited-scope versions have been demonstrated and have proven useful in spurring scientific debate on aspects of safety and autonomy in robots and intelligent systems. In this work, we use Asimov's laws to examine these notions in molecular robots fabricated from DNA origami. We successfully programmed these robots to obey, by means of interactions between individual robots in a large population, an appropriately scoped variant of Asimov's laws, and even emulate the key scenario from Asimov's story "Runaround," in which a fictional robot gets into trouble despite adhering to the laws. Our findings show that abstract, complex notions can be encoded and implemented at the molecular scale, when we understand robots on this scale on the basis of their interactions.

A Stability Analysis Method for Biochemical Reaction System with Inhibitory Feedback Loop

SUMMARYIn this study, we propose an application methodology of the Nyquist criterion for biochemical reaction systems with the biological negative feedback loops. The molecular robot or a real biochemical reaction system such as an intracellular signal transduction system utilizes negative feedback regulation to enhance the stability and robustness. However, since such a system tends to be a high dimensional, nonlinear, and complex system with multiple feedback loops, it is troublesome to quantitatively evaluate the stability margin of the whole system in terms of a particular feedback loop. We show that by modifying the system gain the Nyquist criterion can be appreciable for this problem, and as a result the stability margin can be calculated.

Dynamic DNA Origami Device for Measuring Compressive Depletion Forces

The ability to self-assemble nanodevices with programmed structural dynamics that can sense and respond to the local environment could enable transformative applications in fields including molecular robotics, nanomanufacturing, and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. Here, we mimic this approach by engineering inherent nanoscale structural dynamics (nanodynamics) into a DNA device that exhibits a distribution of conformations including two stable states separated by a transition state where the energy barrier height is on the scale of the thermal energy, kBT = 4.1 pN·nm, enabling spontaneous transitions between states. We further establish design principles to regulate the equilibrium and kinetic behavior by substituting a few DNA strand components. We use single-molecule Förster resonance energy transfer measurements to show these nanodynamic properties are sensitive to sub-piconewton depletion forces in the presence of molecular crowding agents, and the device can measure depletion forces with a resolution of ∼100 fN. We anticipate that this approach of engineering nanodynamic DNA devices will enable molecular-scale systems that sense and respond to their local environment with extremely high sensitivity.

Micrometer-sized molecular robot changes its shape in response to 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.

Toward the construction of molecular robots working in vivo: DNA computing using DNA molecule as information media

Toward the construction of molecular robots working in vivo: DNA computing using DNA molecule as information media

Fundamental Study of Soft Actuator Using Anisotropic Gel Hybridized with Nanosheet Liquid Crystal: Analysis of Heat Characteristics and Length Control

The fundamental heat characteristics of a gel actuator that uses nanosheet liquid crystals are studied. Owing to the structural anisotropy of nanosheets, the gel actuator exhibits anisotropic thermo-induced deformation, which makes it possible for the gel actuator to be applied to new materials for molecular robotics. As a fundamental study for the development, a relationship between the contraction length of the gel actuator and water temperature is investigated, and the mapping between them is obtained. Furthermore, using the mapping, fundamental controller methods are proposed to control the contraction length of the gel actuator. Controller performances are assessed through experimental results.

Perspective: Recent Developments in Hybrid Hydrogels Containing Inorganic Nanomaterials

Poly(N-isopropylacrylamide) (PNIPAm) has been well known as a thermosensitive polymer and has been extensively studied for many applications such as drug delivery systems (DDS) as well as biomedical and tissue engineering. Recently, the hybridization of hydrogels with well-defined nanostructured inorganic materials is emerging as a promising and efficient technique to improve their properties. Newly developed hydrogels with superior properties and smart functions can achieve a great performance in the field of drug delivery systems, sensors, coatings, artificial organs, and chemical actuators for microfluidics and molecular robots. Here we briefly review recent advances in this emerging field.

Molecular Governor: DNA Feedback Regulator for Molecular Robotics

In this study, we consider a regulation problem for molecular robotics realized by DNA reactions. The control objective is to regulate the concentration of a target DNA strand to a desired level us...

Logic Gate Operation by DNA Translocation through Biological Nanopores.

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs “1” and “0” as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment.

BIOMOD：分子ロボティクスの次世代育成大会

BIOMOD：分子ロボティクスの次世代育成大会

Molecular computers for molecular robots as hybrid systems

Various artificial molecular devices, including some made of DNA or RNA, have been developed to date. The next step in this area of research is to develop an integrated system from such molecular devices. A molecular robot consists of sensors, computers, and actuators, all made of molecular devices, and reacts autonomously to its environment by observing the environment, making decisions with its computers, and performing actions upon the environment. Molecular computers should thus be the intelligent controllers of such molecular robots. Such controllers can naturally be regarded as hybrid systems because the environment, the robot, and the controller are all state transition systems having discrete and continuous states and transitions. For modeling and designing hybrid systems, formal frameworks, such as hybrid automata, are commonly used. In this perspective paper, we examine how molecular controllers can be modeled as hybrid automata and how they can be realized in a molecular robot. We first summarize the requirements for such molecular controllers and examine existing frameworks of DNA computing with respect to these requirements. We then show the possibility of combining existing frameworks of DNA computing to implement a sample hybrid controller for a molecular robot.

Controlling the reversible assembly/disassembly of multicomponent using molecular recognition in molecular robots

Here, we report the multicomponent assembly and disassembly processes involving DNA strand displacement to construct molecular robots. The framework for development of molecular robots designates the components as parts of the robot. Molecular recognition is used to control the reversible processes of assembly and disassembly of multiple components. The molecular recognition system identifies not only a single-strand DNA but also a microribonucleic acid as molecular stimuli to control the processes. The processes were demonstrated by gel electrophoresis, fluorescence assays, and atomic force microscopy.

Molecular Robotics and Controlling

Molecular Robotics and Controlling