DNA Origami: Structures, Technology, and Applications

Cover
Title Page
Copyright Page
Contents
List of Contributors
Preface
Chapter 1 DNA Origami Technology: Achievements in the Initial 10 Years
1.1 Introduction
1.1.1 DNA Nanotechnology Before the Emergence of DNA Origami
1.2 Two-Dimensional DNA Origami
1.3 Programmed Arrangement of Multiple DNA Origami Components
1.4 Three-Dimensional DNA Origami Structures
1.5 Modification and Functionalization of 2D DNA Origami Structures
1.5.1 Selective Placement of Functional Nanomaterials
1.5.2 Selective Placement of Functional Molecules and Proteins via Ligands
1.5.3 Distance-Controlled Enzyme Reactions and Photoreactions
1.6 Single-Molecule Detection and Sensing using DNA Origami Structures
1.6.1 Single-Molecule RNA Detection
1.6.2 Single-Molecule Detection of Chemical Reactions
1.6.3 Single-Molecule Detection using Mechanical DNA Origami
1.6.4 Single-Molecule Sensing using Mechanical DNA Origami
1.7 Application to Single Biomolecule AFM Imaging
1.7.1 High-Speed AFM-Based Observation of Biomolecules
1.7.2 Visualization of DNA Structural Changes in the DNA Nanospace
1.7.3 Visualization of the Reaction Events of Enzymes and Proteins in the DNA Nanospace
1.8 Single-Molecule Fluorescence Studies
1.8.1 Nanoscopic Ruler for Single-Molecule Imaging
1.8.2 Kinetics of Binding and Unbinding Events and DNA-PAINT
1.8.3 DNA Barcode Imaged by DNA-PAINT
1.9 DNA Molecular Machines
1.9.1 DNA Assembly Line Constructed on the DNA Origami
1.9.2 DNA Spider System Constructed on the DNA Origami
1.9.3 DNA Motor System Constructed on the DNA Origami
1.10 Selective Incorporation of Nanomaterials and the Applications
1.10.1 DNA Origami Plasmonic Structure with Chirality
1.10.2 Surface-Enhanced Fluorescence by Gold Nanoparticles and DNA Origami Structure
1.10.3 Placement of DNA Origami onto a Fabricated Solid Surface
1.11 Dynamic DNA Origami Structures Responsive to External Stimuli
1.11.1 DNA Origami Structures Responsive to External Stimuli
1.11.2 Stimuli-Responsive DNA Origami Plasmonic Structures
1.11.3 Photo-Controlled DNA Origami Plasmonic Structures
1.12 Conjugation of DNA Origami to Lipid
1.12.1 DNA Origami Channel with Gating
1.12.2 DNA Origami Templated Synthesis of Liposomes
1.13 DNA Origami for Biological Applications
1.13.1 Introduction of DNA Origami into Cells and Functional Expression
1.13.2 Drug Release Using the Properties Characteristic for DNA Origami
1.13.3 DNA Origami Structures Coated with Lipids and Polymers
1.13.4 Nanorobot with Dynamic Mechanism
1.13.5 Nanorobot Targeting Tumor In Vivo
1.14 Conclusions
References
Chapter 2 Wireframe DNA Origami and Its Application as Tools for Molecular Force Generation
2.1 Introduction
2.2 Pre-Origami Wireframe DNA Nanostructures
2.3 Hierarchical DNA Origami Wireframe
2.4 Entire DNA Origami Design
2.5 DNA Origami Wireframe as Tools for Molecular Force Application
2.5.1 Introduction
2.5.2 Results and Discussion
2.6 Conclusions
2.6.1 Materials and Methods
References
Chapter 3 Capturing Structural Switching and Self-Assembly Events Using High-Speed Atomic Force Microscopy
3.1 Introduction
3.2 DNA Origami Nanomachines
3.3 Ion-Responsive Mechanical DNA Origami Devices
3.4 Photoresponsive Devices
3.5 Two-Dimensional Self-Assembly Processes
3.6 Sequential Self-Assembly
3.7 Photostimulated Assembly and Disassembly
3.8 Conclusions and Perspectives
References
Chapter 4 Advancement of Computer-Aided Design Software and Simulation Tools for Nucleic Acid Nanostructures and DNA Origami
4.1 Introduction
4.2 General-Purpose Software
4.3 Software for Designing Small DNA Nanostructures
4.4 Software for Designing DNA Origami
4.5 Software for Designing RNA Nanostructures
4.6 Software for Designing Base Sequence
4.7 Software for Simulating Nucleic Acid Nanostructures
4.8 Summary and Future Perspective
References
Chapter 5 Dynamic and Mechanical Applications of DNA Nanostructures in Biophysics
5.1 Introduction
5.1.1 What Makes DNA a Good Material for Dynamic Applications
5.1.2 Rupture Forces
5.2 Applications
5.2.1 Force Spectroscopy
5.2.2 DNA Devices that Probe and Control DNA–DNA Interactions
5.2.3 DNA Devices that Respond to Biomolecules
5.2.4 DNA Devices to Study Biological Molecular Motors
5.2.5 DNA Walkers
5.2.6 DNA Computing
5.3 Tools for Quantifying DNA Devices and their Functions
5.4 Modeling and Analysis
5.5 Conclusion
References
Chapter 6 Plasmonic Nanostructures Assembled by DNA Origami
6.1 Introduction
6.2 Optical Properties of the DNA Origami-Based Plasmonic Nanostructures
6.3 Nanoparticle Functionalization with DNA
6.4 DNA Origami-Based Plasmonic Assemblies
6.5 Surface-Enhanced Raman Scattering (SERS) and Other Plasmonic Effects
6.6 Conclusion
Acknowledgments
References
Chapter 7 Assembly of Nanoparticle Superlattices Using DNA Origamias a Template
7.1 Introduction
7.2 Gold Nanoparticles
7.2.1 Oligonucleotide-Modified AuNPs
7.2.2 Cationic AuNPs
7.3 Formation of DNA Origami-Assisted Superlattices
7.3.1 Superlattices Formed by Oligonucleotide-Functionalized AuNPs
7.3.2 Superlattice Formed by Cationic AuNPs
7.4 Characterization of Assemblies
7.4.1 Electron Microscopy
7.4.2 Small-Angle X-ray Scattering
7.5 Conclusions and Future Perspectives
Acknowledgments
References
Chapter 8 Mechanics of DNA Origami Nanoassemblies
8.1 Introduction
8.2 Analytical Tools to Investigate Mechanical Properties of Nanoassemblies
8.2.1 Optical Tweezers
8.2.2 Magnetic Tweezers
8.2.3 Atomic Force Microscopy (AFM)
8.3 Mechanical Strength of DNA Origami Structures
8.4 Applications of Origami Nanostructures by Exploiting their Mechanical Strength
8.5 Mechanochemical Properties of DNA Origami
8.6 Conclusions
References
Chapter 9 3D DNA Origami as Single-Molecule Biophysical Tools for Dissecting Molecular Motor Functions
9.1 Introduction
9.2 DNA Origami Nanospring
9.2.1 Design of DNA Origami Nanospring
9.2.2 Nanospring Mechanical Properties
9.2.3 Application to a Myosin VI Processive Motor
9.3 DNA Origami Thick Filament Mimicking Muscle Structure
9.3.1 Mystery of Muscle Contraction
9.3.2 Design of a DNA Origami-Based Thick Filament
9.3.3 High-speed AFM Observation of Force Generation by Myosin
9.3.4 High-Speed Darkfield Imaging of Force Generation by Myosin
9.4 Perspective
References
Chapter 10 Switchable DNA Origami Nanostructures and Their Applications
10.1 Introduction
10.2 Switchable Machines Constructed from DNA Origami Scaffolds
10.2.1 Chemical Triggers for Origami Scaffolds
10.2.2 Physical Triggers for Origami Scaffolds
10.3 DNA Origami Scaffolds for Defined Mechanical Operations
10.3.1 Origami Scaffolds that Dictate the Motility of Elements
10.3.2 Engineering Mechanical Functions of Origami Tiles
10.4 Switchable Interconnected 2D Origami Assemblies
10.5 Dynamic Triggered Switching of Origami for Controlled Release
10.6 Switchable Plasmonic Phenomena with DNA Origami Scaffolds
10.7 Origami-Guided Organization of Nanoparticles and Proteins
10.8 Conclusions and Perspectives
References
Chapter 11 The Effect of DNA Boundaries on Enzymatic Reactions
11.1 Introduction
11.2 DNA-Scaffolded Single Enzymes
11.3 DNA-Scaffolded Enzyme Cascades
11.4 On the Proximity Model and Other Hypotheses
11.5 Conclusions
Acknowledgments
References
Chapter 12 The Methods to Assemble Functional Proteins on DNA Scaffold and their Applications
12.1 Introduction
12.2 Overview of the Methods for Arranging Proteins on DNA Scaffolds
12.2.1 Reversible Conjugation between Protein and DNA
12.2.2 Irreversible Conjugation between Protein and DNA
12.3 DNA-Binding Adaptor for Assembling Proteins on DNA Scaffold and its Application
12.3.1 DNA-Binding Adaptor for Reversible Assembly of Proteins via Noncovalent Interactions
12.3.2 Modular Adaptors for Covalent Conjugation of Genetically Modified Proteins to Chemically Modified DNA
12.3.3 Application of DNA-Binding Adaptors for Assembling Proteins on DNA Scaffolds
12.4 Summary
References
Chapter 13 DNA Origami for Synthetic Biology: An Integrated Gene Logic-Chip
13.1 Introduction
13.2 Biomolecule Integration on DNA Nanostructure
13.2.1 Nature Uses “Reaction Field” to Overcome the Cross-Talk Problem
13.2.2 Synthetic Biology Approach
13.2.3 DNA–Protein Complex
13.2.4 Enzymatic Reaction on DNA Origami for Low-Molecular-Weight Substrate
13.3 Gene Expression Control Using DNA Nanostructure
13.3.1 Enzymatic Reaction on DNA Origami for High-Molecular-Weight Substrate
13.3.2 Resolving Synthetic Biology Limitation by DNA Origami-Based Nano-Chip
13.3.3 Unique Characters of the Nano-Chip
13.3.4 Limitation of the Nano-Chip
13.4 Summary and Perspective
Acknowledgments
References
Chapter 14 DNA Origami for Molecular Robotics
14.1 DNA Origami as a Stage for DNA Walkers and Robotic Arms
14.2 Nanomechanical DNA Origami
14.3 DNA Origami Used in Combination with Molecular Motors
14.4 Future Perspective
References
Chapter 15 DNA origami Nanotechnology for the Visualization, Analysis, and Control of Molecular Events with Nanoscale Precision
15.1 Introduction
15.2 Designing of DNA Origami Frames for the Direct Observation of DNA Conformational Changes
15.3 Direct Observation of DNA Structural Changes in the DNA Origami Frame
15.3.1 G-Quadruplex Formation and Disruption
15.3.2 G-Quadruplex Formation by the Assembly of Four DNA Strands
15.3.3 Light-Induced Hybridization and Dehybridization of the Photoswitchable DNA Strands
15.3.4 Direct Observation of B–Z Transition in the Equilibrium State
15.3.5 Topological Control of G-Quadruplex and I-Motif Formation in the dsDNA
15.4 Direct Observation and Regulation of Enzyme Reactions in the DNA Origami Frame
15.4.1 Direct Observation and Regulation of Cre-Mediated DNA Recombination in the DNA Origami Frame
15.4.2 Holiday-Junction Resolution Mediated by DNA Resolvase
15.4.3 DNA Oxidation in the DNA Demethylation Process Mediated by TET Enzyme
15.4.4 Searching and Recognition of Target Sites by using Photoresponsive Transcription Factor GAL4
15.5 Direct Observation of a Mobile DNA Nanomachine using DNA Origami
15.5.1 A DNA Linear Motor System Created on a DNA Origami System
15.5.2 Single-Molecule Operation of DNA Motor by using Programmed Instructions
15.5.3 Photo-Controlled DNA Motor System Constructed on DNA Origami
15.5.4 Photo-Controlled DNA Rotator System Constructed on DNA Origami
15.6 Limitations of AFM Imaging and Comparison with other Imaging Techniques
15.7 Conclusions and Perspectives
References
Chapter 16 Stability and Stabilization of DNA Nanostructures in Biomedical Applications
16.1 Threats for DNA Nanostructures
16.1.1 Errors from Nanostructure Synthesis
16.1.2 Denaturation of DNA Duplexes
16.1.3 Backbone Cleavage
16.1.4 Chemical Damage at the Nucleobases
16.1.5 DNA Structures for Biological Applications
16.1.6 In vitro and in vivo Degradation and Clearance of DNA Structures
16.2 Strategies to Protect DNA Origami Structures
16.2.1 Stabilization by Design
16.2.2 Stabilization by Covalent Strategies
16.2.3 Stabilization by Non-Covalent Strategies and Additives
References
Chapter 17 DNA Nanostructures for Cancer Diagnosis and Therapy
17.1 Introduction
17.2 DNA Nanostructure-Based Diagnostics
17.2.1 Nucleic Acid Detection
17.2.2 Protein and Exosome Detection
17.2.3 Tumor Cell Detection
17.2.4 Imaging
17.3 DNA Nanostructure-Based Drug Delivery
17.3.1 Small Molecules
17.3.2 Biologics
17.3.3 Inorganic Nanoparticles
17.4 Challenges and Prospects
17.4.1 Stability
17.4.2 Drug Loading Efficiency
17.4.3 Drug releasing efficiency
17.4.4 Cell Internalization
References
Index
EULA