ISBN-13: 9781119682547 / Angielski / Twarda / 2022 / 464 str.
ISBN-13: 9781119682547 / Angielski / Twarda / 2022 / 464 str.
List of Contributors xiiiPreface xvii1 DNA Origami Technology: Achievements in the Initial 10 Years 1Masayuki Endo1.1 Introduction 11.1.1 DNA Nanotechnology Before the Emergence of DNA Origami 31.2 Two- Dimensional DNA Origami 31.3 Programmed Arrangement of Multiple DNA Origami Components 61.4 Three- Dimensional DNA Origami Structures 91.5 Modification and Functionalization of 2D DNA Origami Structures 111.5.1 Selective Placement of Functional Nanomaterials 111.5.2 Selective Placement of Functional Molecules and Proteins via Ligands 131.5.3 Distance- Controlled Enzyme Reactions and Photoreactions 131.6 Single- Molecule Detection and Sensing using DNA Origami Structures 141.6.1 Single- Molecule RNA Detection 141.6.2 Single- Molecule Detection of Chemical Reactions 141.6.3 Single- Molecule Detection using Mechanical DNA Origami 141.6.4 Single- Molecule Sensing using Mechanical DNA Origami 141.7 Application to Single Biomolecule AFM Imaging 161.7.1 High- Speed AFM- Based Observation of Biomolecules 161.7.2 Visualization of DNA Structural Changes in the DNA Nanospace 181.7.3 Visualization of the Reaction Events of Enzymes and Proteins in the DNA Nanospace 181.8 Single- Molecule Fluorescence Studies 191.8.1 Nanoscopic Ruler for Single- Molecule Imaging 191.8.2 Kinetics of Binding and Unbinding Events and DNA- PAINT 211.8.3 DNA Barcode Imaged by DNA- PAINT 211.9 DNA Molecular Machines 221.9.1 DNA Assembly Line Constructed on the DNA Origami 221.9.2 DNA Spider System Constructed on the DNA Origami 221.9.3 DNA Motor System Constructed on the DNA Origami 241.10 Selective Incorporation of Nanomaterials and the Applications 241.10.1 DNA Origami Plasmonic Structure with Chirality 241.10.2 Surface- Enhanced Fluorescence by Gold Nanoparticles and DNA Origami Structure 261.10.3 Placement of DNA Origami onto a Fabricated Solid Surface 261.11 Dynamic DNA Origami Structures Responsive to External Stimuli 271.11.1 DNA Origami Structures Responsive to External Stimuli 271.11.2 Stimuli- Responsive DNA Origami Plasmonic Structures 271.11.3 Photo- Controlled DNA Origami Plasmonic Structures 271.12 Conjugation of DNA Origami to Lipid 291.12.1 DNA Origami Channel with Gating 291.12.2 DNA Origami Templated Synthesis of Liposomes 291.13 DNA Origami for Biological Applications 291.13.1 Introduction of DNA Origami into Cells and Functional Expression 291.13.2 Drug Release Using the Properties Characteristic for DNA Origami 311.13.3 DNA Origami Structures Coated with Lipids and Polymers 321.13.4 Nanorobot with Dynamic Mechanism 321.13.5 Nanorobot Targeting Tumor In Vivo 321.14 Conclusions 33References 342 Wireframe DNA Origami and Its Application as Tools for Molecular Force Generation 41Marco Lolaico and Björn Högberg2.1 Introduction 412.2 Pre- Origami Wireframe DNA Nanostructures 422.3 Hierarchical DNA Origami Wireframe 432.4 Entire DNA Origami Design 452.5 DNA Origami Wireframe as Tools for Molecular Force Application 502.5.1 Introduction 502.5.2 Results and Discussion 512.6 Conclusions 542.6.1 Materials and Methods 54References 553 Capturing Structural Switching and Self- Assembly Events Using High- Speed Atomic Force Microscopy 59Yuki Suzuki3.1 Introduction 593.2 DNA Origami Nanomachines 603.3 Ion- Responsive Mechanical DNA Origami Devices 603.4 Photoresponsive Devices 623.5 Two- Dimensional Self- Assembly Processes 643.6 Sequential Self- Assembly 663.7 Photostimulated Assembly and Disassembly 673.8 Conclusions and Perspectives 69References 694 Advancement of Computer- Aided Design Software and Simulation Tools for Nucleic Acid Nanostructures and DNA Origami 75Ibuki Kawamata4.1 Introduction 754.2 General- Purpose Software 764.3 Software for Designing Small DNA Nanostructures 784.4 Software for Designing DNA Origami 814.5 Software for Designing RNA Nanostructures 844.6 Software for Designing Base Sequence 844.7 Software for Simulating Nucleic Acid Nanostructures 854.8 Summary and Future Perspective 86References 875 Dynamic and Mechanical Applications of DNA Nanostructures in Biophysics 101Melika Shahhosseini, Anjelica Kucinic, Peter Beshay, Wolfgang Pfeifer, and Carlos Castro5.1 Introduction 1015.1.1 What Makes DNA a Good Material for Dynamic Applications 1015.1.2 Rupture Forces 1035.2 Applications 1055.2.1 Force Spectroscopy 1055.2.1.1 Utilizing the Stiffness of DNA for Force Spectroscopy 1055.2.1.2 Applications that Utilize Rupture Forces 1075.2.2 DNA Devices that Probe and Control DNA-DNA Interactions 1085.2.2.1 Detection 1085.2.2.2 Modulation 1115.2.3 DNA Devices that Respond to Biomolecules 1115.2.4 DNA Devices to Study Biological Molecular Motors 1165.2.5 DNA Walkers 1165.2.6 DNA Computing 1195.3 Tools for Quantifying DNA Devices and their Functions 1205.4 Modeling and Analysis 1235.5 Conclusion 124References 1246 Plasmonic Nanostructures Assembled by DNA Origami 135Sergio Kogikoski, Jr, Anushree Dutta, and Ilko Bald6.1 Introduction 1356.2 Optical Properties of the DNA Origami- Based Plasmonic Nanostructures 1356.3 Nanoparticle Functionalization with DNA 1386.4 DNA Origami- Based Plasmonic Assemblies 1406.5 Surface- Enhanced Raman Scattering (SERS) and Other Plasmonic Effects 1436.6 Conclusion 152Acknowledgments 152References 1527 Assembly of Nanoparticle Superlattices Using DNA Origami as a Template 155Sofia Julin, Petteri Piskunen, Mauri A. Kostiainen, and Veikko Linko7.1 Introduction 1557.2 Gold Nanoparticles 1567.2.1 Oligonucleotide- Modified AuNPs 1567.2.2 Cationic AuNPs 1587.3 Formation of DNA Origami- Assisted Superlattices 1587.3.1 Superlattices Formed by Oligonucleotide- Functionalized AuNPs 1597.3.2 Superlattice Formed by Cationic AuNPs 1607.4 Characterization of Assemblies 1607.4.1 Electron Microscopy 1617.4.2 Small- Angle X- ray Scattering 1617.5 Conclusions and Future Perspectives 162Acknowledgments 164References 1648 Mechanics of DNA Origami Nanoassemblies 167Deepak Karna, Jiahao Ji, and Hanbin Mao8.1 Introduction 1678.2 Analytical Tools to Investigate Mechanical Properties of Nanoassemblies 1688.2.1 Optical Tweezers 1688.2.2 Magnetic Tweezers 1698.2.3 Atomic Force Microscopy (AFM) 1698.3 Mechanical Strength of DNA Origami Structures 1718.4 Applications of Origami Nanostructures by Exploiting their Mechanical Strength 1738.5 Mechanochemical Properties of DNA Origami 1758.6 Conclusions 177References 1779 3D DNA Origami as Single- Molecule Biophysical Tools for Dissecting Molecular Motor Functions 181Mitsuhiro Iwaki9.1 Introduction 1819.2 DNA Origami Nanospring 1819.2.1 Design of DNA Origami Nanospring 1819.2.2 Nanospring Mechanical Properties 1829.2.3 Application to a Myosin VI Processive Motor 1839.3 DNA Origami Thick Filament Mimicking Muscle Structure 1879.3.1 Mystery of Muscle Contraction 1879.3.2 Design of a DNA Origami- Based Thick Filament 1889.3.3 High- speed AFM Observation of Force Generation by Myosin 1899.3.4 High- Speed Darkfield Imaging of Force Generation by Myosin 1899.4 Perspective 193References 19310 Switchable DNA Origami Nanostructures and Their Applications 197Jianbang Wang, Michael P. O'Hagan, Verena Wulf, and Itamar Willner10.1 Introduction 19710.2 Switchable Machines Constructed from DNA Origami Scaffolds 19810.2.1 Chemical Triggers for Origami Scaffolds 19810.2.1.1 Triggering Origami Devices with Strand Displacement Reactions 19810.2.1.2 Triggering Origami with Ion Concentration 20010.2.1.3 Triggering Origami with Molecular Species 20210.2.2 Physical Triggers for Origami Scaffolds 20410.2.2.1 Triggering Origami with Temperature 20410.2.2.2 Triggering Origami with Electric Fields 20610.2.2.3 Triggering Origami with Magnetic Fields 20610.2.2.4 Triggering Origami with Light 20810.3 DNA Origami Scaffolds for Defined Mechanical Operations 21010.3.1 Origami Scaffolds that Dictate the Motility of Elements 21210.3.2 Engineering Mechanical Functions of Origami Tiles 21810.4 Switchable Interconnected 2D Origami Assemblies 21810.5 Dynamic Triggered Switching of Origami for Controlled Release 22310.6 Switchable Plasmonic Phenomena with DNA Origami Scaffolds 22710.7 Origami- Guided Organization of Nanoparticles and Proteins 23410.8 Conclusions and Perspectives 238References 23911 The Effect of DNA Boundaries on Enzymatic Reactions 241Richard Kosinski and Barbara Saccà11.1 Introduction 24111.2 DNA- Scaffolded Single Enzymes 24211.3 DNA- Scaffolded Enzyme Cascades 24711.4 On the Proximity Model and Other Hypotheses 25011.5 Conclusions 254Acknowledgments 256References 25612 The Methods to Assemble Functional Proteins on DNA Scaffold and their Applications 261Eiji Nakata, Shiwei Zhang, Huyen Dinh, Peng Lin, and Takashi Morii12.1 Introduction 26112.2 Overview of the Methods for Arranging Proteins on DNA Scaffolds 26212.2.1 Reversible Conjugation between Protein and DNA 26312.2.1.1 Biotin- Avidin 26412.2.1.2 Antibody- Antigen 26412.2.1.3 Ni- NTA- Hexahistidine 26612.2.1.4 Aptamers 26612.2.1.5 Apo- Protein Reconstitution by the Prosthetic Group 26612.2.2 Irreversible Conjugation between Protein and DNA 26612.2.2.1 Chemical Crosslinking of Protein and DNA via Cross- Linker 26712.2.2.2 Crosslinking of Genetically Fused Protein with Chemically Modified DNA 26712.2.2.3 Covalent Conjugation of Genetically Modified Proteins to Unmodified DNA 26912.2.2.4 Applications of the Enzyme Assembled DNA Scaffolds 26912.3 DNA- Binding Adaptor for Assembling Proteins on DNA Scaffold and its Application 27012.3.1 DNA- Binding Adaptor for Reversible Assembly of Proteins via Noncovalent Interactions 27012.3.2 Modular Adaptors for Covalent Conjugation of Genetically Modified Proteins to Chemically Modified DNA 27212.3.3 Application of DNA- Binding Adaptors for Assembling Proteins on DNA Scaffolds 27512.3.3.1 Assembling Protein of Interest on DNA Scaffold in Cell 27512.3.3.2 Enzymatic Reaction System on a DNA Scaffold 27512.4 Summary 278References 27813 DNA Origami for Synthetic Biology: An Integrated Gene Logic- Chip 281Hisashi Tadakuma13.1 Introduction 28113.2 Biomolecule Integration on DNA Nanostructure 28113.2.1 Nature Uses "Reaction Field" to Overcome the Cross- Talk Problem 28113.2.2 Synthetic Biology Approach 28213.2.3 DNA-Protein Complex 28213.2.4 Enzymatic Reaction on DNA Origami for Low- Molecular- Weight Substrate 28413.3 Gene Expression Control Using DNA Nanostructure 28513.3.1 Enzymatic Reaction on DNA Origami for High- Molecular- Weight Substrate 28513.3.2 Resolving Synthetic Biology Limitation by DNA Origami- Based Nano- Chip 28613.3.3 Unique Characters of the Nano- Chip 28813.3.4 Limitation of the Nano- Chip 29213.4 Summary and Perspective 292Acknowledgments 293References 29314 DNA Origami for Molecular Robotics 297Akinori Kuzuya14.1 DNA Origami as a Stage for DNA Walkers and Robotic Arms 29714.2 Nanomechanical DNA Origami 29814.3 DNA Origami Used in Combination with Molecular Motors 30014.4 Future Perspective 301References 30315 DNA origami Nanotechnology for the Visualization, Analysis, and Control of Molecular Events with Nanoscale Precision 305Xiwen Xing and Masayuki Endo15.1 Introduction 30515.2 Designing of DNA Origami Frames for the Direct Observation of DNA Conformational Changes 30815.3 Direct Observation of DNA Structural Changes in the DNA Origami Frame 30815.3.1 G- Quadruplex Formation and Disruption 30815.3.2 G- Quadruplex Formation by the Assembly of Four DNA Strands 30915.3.3 Light- Induced Hybridization and Dehybridization of the Photoswitchable DNA Strands 30915.3.4 Direct Observation of B-Z Transition in the Equilibrium State 31215.3.5 Topological Control of G- Quadruplex and I- Motif Formation in the dsDNA 31415.4 Direct Observation and Regulation of Enzyme Reactions in the DNA Origami Frame 31515.4.1 Direct Observation and Regulation of Cre- Mediated DNA Recombination in the DNA Origami Frame 31515.4.2 Holiday- Junction Resolution Mediated by DNA Resolvase 31715.4.3 DNA Oxidation in the DNA Demethylation Process Mediated by TET Enzyme 31715.4.4 Searching and Recognition of Target Sites by using Photoresponsive Transcription Factor GAL 4 31915.5 Direct Observation of a Mobile DNA Nanomachine using DNA Origami 32115.5.1 A DNA Linear Motor System Created on a DNA Origami System 32115.5.2 Single- Molecule Operation of DNA Motor by using Programmed Instructions 32115.5.3 Photo- Controlled DNA Motor System Constructed on DNA Origami 32415.5.4 Photo- Controlled DNA Rotator System Constructed on DNA Origami 32415.6 Limitations of AFM Imaging and Comparison with other Imaging Techniques 32615.7 Conclusions and Perspectives 326References 32716 Stability and Stabilization of DNA Nanostructures in Biomedical Applications 333Soumya Chandrasekhar, Praneetha Sundar Prakash, and Thorsten- Lars Schmidt16.1 Threats for DNA Nanostructures 33316.1.1 Errors from Nanostructure Synthesis 33416.1.1.1 Missing Strands 33416.1.1.2 Oligonucleotide Synthesis Errors 33516.1.2 Denaturation of DNA Duplexes 33616.1.2.1 Melting 33616.1.2.2 The Role of Cations 33616.1.2.3 Influence of pH on Duplex Stability 33716.1.3 Backbone Cleavage 33716.1.3.1 Acid- Induced Depurination 33716.1.3.2 Base- Induced Cleavage of RNA 33816.1.3.3 Enzymatic Digest 33816.1.4 Chemical Damage at the Nucleobases 33916.1.4.1 Ultraviolet Radiation 33916.1.4.2 Radiative and Oxidative DNA Damage 34016.1.4.3 Deamination 34016.1.5 DNA Structures for Biological Applications 34116.1.5.1 Bioimaging 34116.1.5.2 Biosensing 34116.1.5.3 Computing 34116.1.5.4 Single- Molecule Biophysics and Mechanobiology 34316.1.5.5 Drug Delivery and Gene Therapy 34316.1.6 In vitro and In vivo Degradation and Clearance of DNA Structures 34316.1.6.1 Common in vitro and in vivo Stability Assays 34416.1.6.2 Degradation of DN in in vitro and in vivo 34416.1.6.3 Low Mg2+ Conditions 34616.1.6.4 Presence of Nucleases 34616.1.6.5 Cellular Uptake and Clearance of DNs 34716.1.6.6 Immune Response 34816.2 Strategies to Protect DNA Origami Structures 34916.2.1 Stabilization by Design 34916.2.2 Stabilization by Covalent Strategies 35116.2.2.1 Enzymatic Ligation 35116.2.2.2 Chemical Crosslinking 35216.2.2.3 Photo Crosslinking 35416.2.2.4 Base Analogues and Backbone Modification 35616.2.3 Stabilization by Non- Covalent Strategies and Additives 35616.2.3.1 Inorganic Materials 35616.2.3.2 Proteins 35816.2.3.3 Polymer, Peptides, and Polycation Coatings 358References 36217 DNA Nanostructures for Cancer Diagnosis and Therapy 379Zhe Li and Yonggang Ke17.1 Introduction 37917.2 DNA Nanostructure- Based Diagnostics 38017.2.1 Nucleic Acid Detection 38017.2.2 Protein and Exosome Detection 38217.2.3 Tumor Cell Detection 38417.2.4 Imaging 38517.3 DNA Nanostructure- Based Drug Delivery 38617.3.1 Small Molecules 38617.3.1.1 Doxorubicin 38617.3.1.2 Platinum- Based Drugs 38717.3.2 Biologics 38917.3.2.1 CpG 38917.3.2.2 RNA 39017.3.2.3 Protein 39217.3.3 Inorganic Nanoparticles 39317.4 Challenges and Prospects 39417.4.1 Stability 39417.4.1.1 Nucleases 39517.4.1.2 Mg2+ 39517.4.1.3 Shape and Superstructure of DNA Nanostructures 39617.4.2 Drug Loading Efficiency 39617.4.3 Drug releasing efficiency 39717.4.4 Cell Internalization 398References 400Index 411
Masayuki Endo, PhD, is a project professor at Kansai University and a guest professor at Kyoto University, Japan. He received his PhD from the Department of Chemistry and Biotechnology, The University of Tokyo in 1997. Prof. Endo's research work involves DNA nanotechnology and single-molecule analysis.
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