DNA Origami: Structures, Technology, and Applications

Description

DNA ORIGAMI Discover the impact and multidisciplinary applications of this subfield of DNA nanotechnology DNA origami refers to the technique of assembling single-stranded DNA template molecules into target two- and three-dimensional shapes at the nanoscale. This is accomplished by annealing templates with hundreds of DNA strands and then binding them through the specific base-pairing of complementary bases. The inherent properties of these DNA molecules―molecular recognition, self-assembly, programmability, and structural predictability―has given rise to intriguing applications from drug delivery systems to uses in circuitry in plasmonic devices. The first book to examine this important subfield, DNA Origami brings together leading experts from all fields to explain the current state and future directions of this cutting-edge avenue of study. The book begins by providing a detailed examination of structural design and assembly systems and their applications. As DNA origami technology is growing in popularity in the disciplines of chemistry, materials science, physics, biophysics, biology, and medicine, interdisciplinary studies are classified and discussed in detail. In particular, the book focuses on DNA origami used for creating new functional materials (combining chemistry and materials science; DNA origami for single-molecule analysis and measurements (as applied in physics and biophysics); and DNA origami for biological detection, diagnosis and therapeutics (medical and biological applications). DNA Origami readers will also find: A complete guide for newcomers that brings together fundamental and developmental aspects of DNA origami technologyContributions by a leading team of experts that bring expert views from different angles of the structural developments and applications of DNA origamiAn emerging and impactful research topic that will be of interest in numerous multidisciplinary areasA helpful list of references provided at the end of each chapter to give avenues for further study Given the wide scope found in this groundbreaking work, DNA Origami is a perfect resource for nanotechnologists, biologists, biophysicists, chemists, materials scientists, medical scientists, and pharmaceutical researchers. 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