Molecular Robotics: An Introduction

Organization of this Book
Foreword
Preface
Contents
1 Introduction: Welcome to Molecular Robotics!
	1.1 What is a Molecular Robot?
	1.2 How to Make a Molecular Robot?
	1.3 Development of an Amoeba-Type Molecular Robot
	1.4 Development of Sciences Leading to Molecular Robotics
	1.5 Situation Surrounding Molecular Robotics
	1.6 Evolutionary Scenario of Molecular Robots
	1.7 Future Applications of Molecular Robotics
2 Design Theory of Molecular Robots
	2.1 Secondary Structure Prediction and Sequence Design Technology
	2.2 Trends in DNA Logic Circuit Technology
	2.3 Design of Reactive DNA Circuits
	2.4 DNA Amplification Circuit
	2.5 Design of Dynamic Reaction Circuits Based on Control Theory
		2.5.1 DNA Circuit Based on DNA Strand Displacement Reaction
		2.5.2 Mathematical Modeling of DNA Circuits
		2.5.3 Three Major Problems in DNA Circuit Design
		2.5.4 Example: Role of Control Theory in the Design of a Concentration Regulator Circuit
		2.5.5 Concluding Remarks
	2.6 PEN DNA Toolbox
	2.7 Design of Chemical Reaction Networks with Unknown Reaction Dynamics
	2.8 Real-Time Visualization of Swarm Molecular Robot Dynamics
		2.8.1 Introduction
		2.8.2 Microtubule Particle Modeling
		2.8.3 Motion Pattern Formation
		2.8.4 Real-Time Visualization
		2.8.5 Real-Time High-Performance Computing
		2.8.6 Summary
	2.9 Molecular Robot System as a Distributed System
	2.10 Toward the Molecular Artificial Intelligence
	2.11 Molecular Robots as Emergent Systems
	References
3 Systemization Technology for Molecular Robots
	3.1 Artificial Cell Research and Molecular Robotics
		3.1.1 Introduction
		3.1.2 Artificial Cell Research
		3.1.3 Synthetic Cell Research
		3.1.4 Lipid Bilayer Vesicles: As Body of Artificial Cells and Molecular Robots
		3.1.5 Functional Artificial Cells
		3.1.6 Artificial Cells and DNA Nanotechnology
		3.1.7 Conclusion
	3.2 Amoeba-Type Molecular Robot Prototype
		3.2.1 Design of the Amoeba-Type Molecular Robot
		3.2.2 Robot Production
		3.2.3 Robot Performance: Active and Inactive State
		3.2.4 Switching the Robot State
		3.2.5 Outlook: From Prototype to Advanced Molecular Robots
	3.3 Gellular Automata and Molecular Computing Expanding to Space
		3.3.1 Cellular Automata
		3.3.2 Gellular Automata
		3.3.3 Computational Universality of Gellular Automata
		3.3.4 Gellular Automata and Distributed Algorithms
		3.3.5 From Gellular Automata to Self-Healing Materials
	3.4 Implementation of Gel Automata
		3.4.1 Introduction
		3.4.2 Implementation of a Hollow Gel Bead Model
	3.5 Molecules to Condition the Diffusion Coefficient
	3.6 1.1 “(Column) Moving Gel”
	3.7 Molecular Robotics Based on Droplet Microfluidics
	3.8 Nanopores for Single Molecule Measurement and Their Potential as Membrane Gates
		3.8.1 Introduction
		3.8.2 Principle of Nanopore Measurement
		3.8.3 Application of Nanopore Technology: DNA Sequencing
		3.8.4 Application of Nanopore Technology: The Wide Variety of Molecular Sensing
		3.8.5 Application of Nanopore Technology: Diagnostic Tool as a Liquid Biopsy
		3.8.6 Conclusion
	3.9 Synthetic Biology
		3.9.1 Artificial Photosynthetic Cells
		3.9.2 Cell Division Using Canonical or Non-Canonical Lipids
		3.9.3 CO2 Fixatioin by Artificial Cells
		3.9.4 Conclusion and Challenges
	References
4 Molecular Nanotechnology for Molecular Robots
	4.1 Basics of DNA Origami Design and Construction
		4.1.1 Two-Dimensional (2D) DNA Origami
		4.1.2 Three-Dimensional (3D) DNA Origami
		4.1.3 Selection of Scaffold Strands
		4.1.4 Addressability of Staple Strands
		4.1.5 Toward Larger DNA Origami Structures
		4.1.6 Summary and Future Prospects
	4.2 Lipid-Bilayer-Assisted Two-Dimensional Self-assembly of DNA Origami Nanostructures into Higher-Order Architecture
	4.3 Trends in DNA Tile and DNA Brick Technology
	4.4 Liposomes Mechanically Supported by the Cytoskeletal Structure of DNA
	4.5 Molecular Nanomachines Constructed Using DNA Origami
		4.5.1 Introduction
		4.5.2 Controllable DNA Nanomachines and Designable DNA Nanostructures
		4.5.3 Direct Observation of Mobile DNA Nanomachines on DNA Origami Surface
		4.5.4 Mechanical DNA Origami for Device Applications
		4.5.5 Mechanical DNA Origami for Biological Applications
		4.5.6 Summary and Perspectives
	4.6 DNA Origami for Biological Applications
		4.6.1 Introduction
		4.6.2 Intracellular Delivery and Control of Cellular Functions Using DNA Origami Structure
		4.6.3 DNA Nanorobot
		4.6.4 Conclusion
	4.7 Single-Molecule Imaging of Enzymatic Reactions on DNA Origami-Based Nanochip
	4.8 RNA Nanotechnology
		4.8.1 What Is RNA?
		4.8.2 RNA Nanotechnology Based on RNA-Specific Structural Motifs
		4.8.3 RNA Nanotechnology Based on the Same Methodology as DNA
		4.8.4 Other RNA Nanotechnology
		4.8.5 Application of RNA Nanostructures
		4.8.6 Future Challenges for RNA Nanostructures
	4.9 Trends in the Peptide/protein Design Technology
		4.9.1 Nano-architectures Based on Protein Self-assembly
		4.9.2 Nano-architectures Based on a Peptide Self-assembly
	4.10 Peptide Design and Molecular Robotics
	4.11 Molecular Machine and Nanocar
		4.11.1 Molecular Machine with Supramolecular Chemistry
		4.11.2 Molecular Machine at the Air–Water Interface
		4.11.3 Nanocar (Molecular Car) and Nanocar Race
		4.11.4 Short Perspectives
	References
5 Molecular Actuator for Molecular Robots
	5.1 Construction of Swarm-Type Molecular Robots Driven by Biomolecular Motors
		5.1.1 Introduction
		5.1.2 What is a Swarm?
		5.1.3 Fabrication of Molecular Robots
		5.1.4 Demonstration of Flocking by Molecular Robots
		5.1.5 Conclusion
	5.2 Peptide Actuator
	5.3 Photo-Regulation of Actin-Encapsulating Cell-Sized Giant Liposomes
	5.4 Rotary Molecular Motors
	5.5 BZ Gel Actuators
	5.6 Inorganic Crystal Actuator
	References
6 Molecular Material for Molecular Robots
	6.1 Large-Scale Synthesis of DNA and Its Application to Stimuli Responsive Gels
	6.2 DNA Hydrogel and Its Applications
		6.2.1 Design and Fabrication
		6.2.2 Applications
	6.3 DNA/RNA Photo-Cross-Linker
	6.4 DNA Computing Using Photoresponsive Artificial Nucleic Acid
	6.5 Orthogonality of Nucleic Acids
		6.5.1 Orthogonality of DNA
		6.5.2 Expansion of Orthogonality by Artificial Nucleic Acids
		6.5.3 Orthogonality Between DNA and D-aTNA
		6.5.4 SNA Interface Converts RNA Signal into D-aTNA Signal
	6.6 Regulation of DNA Reaction by Cationic Comb-Type Copolymer as an Artificial Nucleic Acid Chaperone
		6.6.1 Nucleic Acid Chaperone Activity of Cationic Comb-Type Copolymer
		6.6.2 Enhancement of DNA Enzyme Activity by Cationic Comb-Type Copolymers
		6.6.3 Boosting of DNA Logic Gate by Cationic Comb-Type Copolymers
	References
7 Medical Application of Molecular Robots
	7.1 Cell-Fate Control by RNA/RNP
		7.1.1 Synthetic RNA Switches for Gene Regulation
		7.1.2 Artificial Molecular Scaffolds for Spatio-temporal Regulation of Biomolecules
		7.1.3 CRISPR-Cas System and Genetic Manipulation
		7.1.4 RNA/RNP for iPS Cell Research and Application
		7.1.5 Perspective and Challenges
	7.2 Giant Vesicles Actively Involved in Biological Systems
		7.2.1 Artificial Cells and Their Practical Applications
		7.2.2 Giant Vesicles
		7.2.3 Self-contained Chemical Sensor
		7.2.4 Low-Bending-Modulus Compartment That Changes Its Morphology
		7.2.5 Self-propulsion
		7.2.6 Cascade Reaction Systems for Information Conversion
		7.2.7 Summary: Toward GUV-Based Molecular Robotics
	7.3 Towards Artificially Controllable Nucleic Acid Drugs
	7.4 Dream of Molecular Hayabusa
	7.5 Engineered Cell
		7.5.1 Engineered Cells
		7.5.2 Engineered Cell as a Chemical Plant
		7.5.3 Engineered Cell as a Functional Material with Sensing Ability
		7.5.4 Engineered Cell as a Biosensor
		7.5.5 Engineered Cells Behave as a Microcomputer
		7.5.6 Engineered Cell to Understand Life and Its Origin
		7.5.7 Summary and Futures in Engineered Cells
	References
8 Social Acceptance of Molecular Robots
	8.1 Ethics in Molecular Robotics: Issues and Needs
		8.1.1 Background
		8.1.2 Ethical, Legal, and Social Issues (ELSI) in Molecular Robotics
		8.1.3 Technology Assessment of Molecular Robotics
		8.1.4 Formulating Guidelines for Molecular Robotics
		8.1.5 Molecular Robotics ELSI Practices in BIOMOD Japan
		8.1.6 Summary
	8.2 Ethical, Legal, and Social Issues (ELSI) in Molecular Robotics: An Introduction for Further Discussion
		8.2.1 Lessons from Genetically Modified Organism (GMO) Controversies
		8.2.2 Synthetic Biology Case Studies
		8.2.3 Issues in Communication with Society: A Case Study of Regenerative Medicine
		8.2.4 Responsible Research and Innovation
	References