DNA Origami

1 Cover

2 Title Page

3 Copyright Page

4 List of Contributors

5 Preface

6 1 DNA Origami Technology: 1.1 Introduction 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 1.6 Single‐Molecule Detection and Sensing using DNA Origami Structures 1.7 Application to Single Biomolecule AFM Imaging 1.8 Single‐Molecule Fluorescence Studies 1.9 DNA Molecular Machines 1.10 Selective Incorporation of Nanomaterials and the Applications 1.11 Dynamic DNA Origami Structures Responsive to External Stimuli 1.12 Conjugation of DNA Origami to Lipid 1.13 DNA Origami for Biological Applications 1.14 Conclusions References

7 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 2.6 Conclusions References

8 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

9 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

10 5 Dynamic and Mechanical Applications of DNA Nanostructures in Biophysics 5.1 Introduction 5.2 Applications 5.3 Tools for Quantifying DNA Devices and their Functions 5.4 Modeling and Analysis 5.5 Conclusion References

11 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

12 7 Assembly of Nanoparticle Superlattices Using DNA Origamias a Template 7.1 Introduction 7.2 Gold Nanoparticles 7.3 Formation of DNA Origami‐Assisted Superlattices 7.4 Characterization of Assemblies 7.5 Conclusions and Future Perspectives Acknowledgments References

13 8 Mechanics of DNA Origami Nanoassemblies 8.1 Introduction 8.2 Analytical Tools to Investigate Mechanical Properties of Nanoassemblies 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

14 9 3D DNA Origami as Single‐Molecule Biophysical Tools for Dissecting Molecular Motor Functions 9.1 Introduction 9.2 DNA Origami Nanospring 9.3 DNA Origami Thick Filament Mimicking Muscle Structure 9.4 Perspective References

15 10 Switchable DNA Origami Nanostructures and Their Applications 10.1 Introduction 10.2 Switchable Machines Constructed from DNA Origami Scaffolds 10.3 DNA Origami Scaffolds for Defined Mechanical Operations 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

16 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

17 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 12.3 DNA‐Binding Adaptor for Assembling Proteins on DNA Scaffold and its Application 12.4 Summary References

18 13 DNA Origami for Synthetic Biology: An Integrated Gene Logic‐Chip 13.1 Introduction 13.2 Biomolecule Integration on DNA Nanostructure 13.3 Gene Expression Control Using DNA Nanostructure 13.4 Summary and Perspective Acknowledgments References

19 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

20 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 15.4 Direct Observation and Regulation of Enzyme Reactions in the DNA Origami Frame 15.5 Direct Observation of a Mobile DNA Nanomachine using DNA Origami 15.6 Limitations of AFM Imaging and Comparison with other Imaging Techniques 15.7 Conclusions and Perspectives References

21 16 Stability and Stabilization of DNA Nanostructures in Biomedical Applications 16.1 Threats for DNA Nanostructures 16.2 Strategies to Protect DNA Origami Structures References

22 17 DNA Nanostructures for Cancer Diagnosis and Therapy 17.1 Introduction 17.2 DNA Nanostructure‐Based Diagnostics 17.3 DNA Nanostructure‐Based Drug Delivery 17.4 Challenges and Prospects References

23 Index

24 End User License Agreement

1 Chapter 8Table 8.1 Brief comparison of OT, MT, and AFM.

2 Chapter 12Table 12.1 Protein and DNA conjugation methods via noncovalent interaction....Table 12.2 Classification of protein‐DNA conjugation methods (covalent conj...

3 Chapter 16Table 16.1 Overview over the most common damages to nucleic acids and nucle...

1 Chapter 1 Figure 1.1 History of DNA nanotechnology and DNA origami technology. Progres... Figure 1.2 DNA nanotechnology before the emergence of DNA origami. (a) DNA d... Figure 1.3 DNA origami. (a) Method to prepare a DNA origami structure from t... Figure 1.4 Programmed self‐assembly of DNA origami. (a) Structure of DNA ori... Figure 1.5 Design and construction of three‐dimensional DNA origami structur... Figure 1.6 Selective incorporation of nanoparticles, proteins, enzymes, and ... Figure 1.7 Detection of target RNA by hybridization with probe DNA strands i... Figure 1.8 (a) Schematic illustration of pinching of a target molecule.(... Figure 1.9 Direct observation of DNA structural change and enzyme reactions ... Figure 1.10 DNA‐PAINT super‐resolution imaging. (a) DNA origami tile with tw... Figure 1.11 Assembly line with a DNA walker capturing gold particles and DNA... Figure 1.12 Helical AuNP plasmonic structures constructed on a DNA origami. ... Figure 1.13 A dynamic DNA origami structure that changes the structure in re... Figure 1.14 (a) DNA origami channel structure. Tubular pores (dark gray), ma... Figure 1.15 Delivery of DNA origami structures to cells and functional contr... Figure 1.16 A DNA nanorobot that recognizes cells. Schematic drawings of the...

2 Chapter 2 Figure 2.1 Pre‐origami wireframe DNA structures. (a) Nadrian Seeman’s DNA cu... Figure 2.2 Hierarchical DNA origami wireframe. (a) Schematics for the strate... Figure 2.3 Entire DNA origami design. (a) DNA origami tetrahedron based on c... Figure 2.4 Entire DNA origami design. (a) (I) BSCOR and vHelix design pipeli... Figure 2.5 DNA origami barrel‐like structure. (a) Perspective view. (b) Fron... Figure 2.6 Quantification of the movement of the internal block during the s...