Artificially Controllable Nanodevices Constructed by DNA Origami Technology (eBook)

Supervisor's Foreword 7
Acknowledgments 8
Contents 9
1 Introduction: Overview of DNA Origami as Biomaterials and Application 12
1.1 Introduction 12
1.2 2D DNA Origami Nanostructures 13
1.3 Programmed Arrangements of Large Sized DNA Nanostructures 14
1.4 3D DNA Origami Nanostructures 17
1.5 Functionalization of 2D Origami Nanostructures 19
1.5.1 Selective Placements of Functional Groups 19
1.5.2 Single-Molecule Chemical Reaction 19
1.5.3 Selective Modifications with Nanomaterial 20
1.6 Applications to Single Molecule Analysis 21
1.6.1 Control of DNA Methylation and DNA Repair in the DNA Nanospace 21
1.6.2 Visualization of DNA Structural Changes 22
1.6.3 Single Molecule Fluorescent Imaging 23
1.7 Applications to DNA Molecular Machines 25
1.8 Applications to Biological System 27
1.9 Conclusion and Prospects 28
References 29
2 Direct Observation of Single Hybridization and Dissociation of Photoresponsive Oligonucleotides in the Designed DNA Nanostructure 31
2.1 Introduction 31
2.2 Experimental Section 33
2.2.1 Synthesis of Oligonuleotides Containing Photoresponsive Domains 33
2.2.2 Preparation of the DNA Frame (Fig. 2.1b) 33
2.2.3 Introduction of Two dsDNAs Containing Photoresponsive Domains into the DNA Frame 33
2.2.4 Photoirradiation to the dsDNA-Attached DNA Frame 34
2.2.5 High-Speed AFM Imaging of the dsDNAs in the DNA Frame 34
2.3 Results and Discussion 34
2.3.1 Direct Imaging of the Single Photoresponsive Duplex by AFM 34
2.3.2 Photoirradiation of Oligonucleotides Containing Photoresponsive Domains 36
2.3.3 Photoirradiation of Photoresponsive Nanoframe in Solution 36
2.3.4 Direct Observation of Dissociation of Photoresponsive Domains in Nanoframe Under UV Irradiation 39
2.3.5 Direct Observation of Association of Photoresponsive Domains in Nanoframe Under Visible Light Irradiation 40
2.3.6 Reversible Photoswitching of Photoresponsive Domains Repeatly in a Single DNA Nanoframe 41
2.4 Conclusion 43
References 43
3 Direct Observation of Logic-Gated Dual-Switching Behaviors Inducing the State Transition in a DNA Nanostructure 44
3.1 Introduction 44
3.2 Experimental Section 46
3.2.1 Design of DNA Nanoframe Containing Six Connecting Positions 46
3.2.2 Assembly of Dual-Switching DNA Nanoframe Containing Photoresponsive Oligonucleotides and G-Tracts 46
3.2.3 Photoirradiation to the Dual-Switching DNA Nanoframe 47
3.3 Results and Discussion 48
3.3.1 Evaluation of the State Transition in Solution by Switching Photoirradiation and Potassium Ion 48
3.3.2 Direct Visualization of the State Transition from AS-1 to AS-2 Using High-Speed AFM 50
3.3.3 Direct Visualization of the Reverse State Transition from AS-2 to AS-1 Using High-Speed AFM 51
3.4 Conclusion 53
References 54
4 Multi-directional Assembly/Disassembly of Photocontrolled DNA Nanostructures in Programmed Patterns 55
4.1 Introduction 55
4.2 Experimental Sections 57
4.2.1 Modification of Staple Strands Along Hexagonal Edges with Photoresponsive Oligonucleotides 57
4.2.2 Assembly of Single Hexagonal Unit 57
4.2.3 Agarose Gel Electrophoresis Analysis 58
4.2.4 Fluorescent Analysis of Disassemble/Assemble of Hexagonal Dimers 58
4.3 Results and Discussions 58
4.3.1 Preparation and Characterization of Hexagonal Dimer 59
4.3.2 Hexagonal Trimmers in Linear and Curved Arrangement Without Facing Orientation Control 60
4.3.3 Hexagonal Oligomers Without Facing Orientation Control 62
4.3.4 Hexagonal Oligomers in Linear and Curved Arrangements with Facing Orientation Control 65
4.3.5 Large Hexagonal Oligomers with Restricted Facing Orientation Control 67
4.3.6 Evaluation of Reversible Assemble and Disassembly of Hexagonal Dimers by Gel Electrophoresis 68
4.3.7 Dynamic Analysis of Assemble and Disassembly of Photocontrolled Hexagonal Dimers 71
4.4 Conclusion 72
References 72
5 Arrangement of Gold Nanoparticles onto a Slit-Type DNA Nanostructure in Various Patterns 74
5.1 Introduction 74
5.2 Experimental Section 74
5.2.1 Preparation of Lipoic Acid Attached Oligonucleotides 74
5.2.2 DNA Slit Preparation 75
5.2.3 AuNPs Attachment onto the DNA Slit for Imaging 75
5.3 Results and Discussion 75
5.3.1 Design and Preparation of DNA Slit 75
5.3.2 Placement of AuNPs onto DNA Slit in Solution 76
5.3.3 Placement of AuNPs onto DNA Slit on Mica Surface 78
5.4 Conclusion 79
References 79
Curriculum Vitae 81
Education 81
Major Honors and Awards 82
Research Interests 82