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1 Chapter 1Figure 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 2Figure 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...

3 Chapter 3Figure 3.1 DNA origami nanoscissors exhibiting open/closed switching in resp...Figure 3.2 G‐quadruplex induced large deformation of the DNA origami bending...Figure 3.3 Photoregulated DNA rotary device. (a) A bar‐shaped rotor composed...Figure 3.4 Dynamic events involved in a lipid bilayer‐assisted self‐assembly...Figure 3.5 Placing square‐shaped DNA origami into lipid bilayer‐supported 2D...Figure 3.6 Photoresponsive reversible assembly of a hexagonal DNA origami di...

4 Chapter 4Figure 4.1 Schematic design process of nucleic acid structures with a simple...Figure 4.2 Software for visualizing macromolecules. (a) Typical screenshot o...Figure 4.3 The result of molecular dynamic simulation of DNA tile. Six repre...Figure 4.4 Snapshot of NAMOT software. A DNA cube structure is visualized us...Figure 4.5 Software for abstract design of DNA nanostructure. Snapshots of (...Figure 4.6 Snapshots of SARSE software designing a dolphin‐shaped DNA origam...Figure 4.7 Snapshots of caDNAno software. (a) The new version of caDNAno tha...Figure 4.8 Software dedicated to the design of wireframe DNA origami structu...Figure 4.9 Snapshots of the simulation results of a DNA origami smiley face ...

5 Chapter 5Figure 5.1 DNA properties and capabilities.Figure 5.2 DNA rupture modes: (a) shearing mode, where forces are applied at...Figure 5.3 DNA in force spectroscopy. (a) DNA‐origami molecular force clamp...Figure 5.4 DNA devices that control biomolecular interactions. (a) DNA nanov...Figure 5.5 DNA frames, Tweezers, and calipers to probe biomolecular interact...Figure 5.6 DNA machines to probe biomolecular interactions. (a) Wireframe DN...Figure 5.7 DNA devices to study biological motors. (a) Disengagement of one ...Figure 5.8 DNA walkers. (I) A plasmonic nanorod that walks on a DNA origami ...Figure 5.9 DNA computing. (a) Molecular logic gates on DNA origami for micro...

6 Chapter 6Figure 6.1 (a) Excitation of the LSPR in a spherical AuNP. The incident lase...Figure 6.2 Summary of the advantages and disadvantages of the three nanopart...Figure 6.3 (a). Schematic representation of the self‐assembly process of pla...Figure 6.4 (a) Design of the DNA origami chiral plasmonic sensor and the ope...Figure 6.5 Formation of AuNP dimers using a triangular DNA origami scaffold....Figure 6.6 (a) AFM images of AuDG hybrid (A, B, C) structures (first row; ph...Figure 6.7 (a) Silver nanolenses assembled from 10, 20, and 60 nm silver NPs...Figure 6.8 (a) Schematic representation of the DNA origami nanofork design s...Figure 6.9 Cartoon depicting DNA origami pillar (grey) employed to build an ...

7 Chapter 7Figure 7.1 Functionalized gold nanoparticles (AuNPs) used for DNA origami‐te...Figure 7.2 DNA‐functionalized AuNPs can be hybridized to polyhedral DNA orig...Figure 7.3 Highly ordered AuNP superlattices are formed by dialyzing the mix...Figure 7.4 Electron microscopy characterization of nanoparticle superlattice...Figure 7.5 Small‐angle X‐ray scattering (SAXS) characterization of the forme...

8 Chapter 8Figure 8.1 Schematic diagram of a dual‐beam OT.Figure 8.2 Schematic diagram of magnetic tweezers.Figure 8.3 In addition to imaging of surface topology of nanoassemblies, AFM...Figure 8.4 Mechanical properties of various DNA origami structures. (a). A t...Figure 8.5 Applications using mechanical properties of origami structures. (...Figure 8.6 Folding and unfolding of DNA origami structures from a mechanoche...

9 Chapter 9Figure 9.1 (a, b) Three‐dimensional structure of a two‐helix bundle (2‐HB) (...Figure 9.2 (a) Experimental setup for OT assay. (b) Averaged force‐extension...Figure 9.3 (a) Myosin VI tethered to a 2‐HB nanospring moves unidirectionall...Figure 9.4 Dual‐color imaging of single‐molecule tug‐of‐war. Black triangles...Figure 9.5 (a) Simultaneous observation of both heads under load. (b, c) Dis...Figure 9.6 (a) Schematic of a native thick filament. (b) Schematic of a DNA ...Figure 9.7 (a) Successive AFM images showing actin sliding along thick filam...Figure 9.8 (a) Experimental design for high‐speed darkfield imaging. (b) Sch...Figure 9.9 (a) Tracking the myosin head with microsecond time resolution. (b...Figure 9.10 (a) A representative trajectory of transient weak binding states...

10 Chapter 10Figure 10.1 Concept of hybridization and toehold‐mediated strand displacemen...Figure 10.2 DNA origami nanodevice and the regulation of eGFP complementatio...Figure 10.3 DNA origami rotor and the regulation of an enzymatic cascade. (a...Figure 10.4 Opening and closing of a DNA origami box through DNA strand disp...Figure 10.5 DNA origami flag driven by Mg²⁺ ions. (a) The composition of the...Figure 10.6 DNA origami nanodevice driven by Mg²⁺ ions with shape‐complement...Figure 10.7 Streptavidin/biotin‐mediated switching of a DNA origami plier. (...Figure 10.8 Transition of DNA origami through modulation of hydrophobic inte...Figure 10.9 Thermoresponsive DNA origami scissors. (a) The closed (left) and...Figure 10.10 Thermoresponsive DNA origami flexor. (a) Schematics of the DNA ...Figure 10.11 DNA origami nanolever switched by electric field. (a) Schematic...Figure 10.12 DNA robotic arm and its rotary movement by electric fields. (a)...Figure 10.13 Magnetic driven DNA origami machine. (a) Schematics of the DNA ...Figure 10.14 DNA origami nanoscissor regulated by light. (a) The open and cl...Figure 10.15 Light‐responsive DNA origami rotary machine. (a) The OFF switch...Figure 10.16 DNA walker on origami with prescriptive landscape. (a) Schemati...Figure 10.17 DNA motor traveling along branched tracks. (a) The DNA tracks o...Figure 10.18 DNA navigator traveling through a DNA origami maze. (a) Schemat...Figure 10.19 Programmable nanoscale assembly line on DNA origami. (a) Schema...Figure 10.20 DNA origami tile containing a mechanical window to control an e...Figure 10.21 Triggered irreversible dissociation of a 2D origami nanoassembl...Figure 10.22 Reversible dissociation of a 2D origami nanoassembly by pH swit...Figure 10.23 Reversible assembly of 2D networks of origami hexagons triggere...Figure 10.24 Triggered exchange of constituents in 2D origami assemblies. (a...Figure 10.25 DNA nanocapsule and the pH‐controlled cargo display. (a) Schema...Figure 10.26 Thrombin‐functionalized DNA origami nanorobot for inhibiting tu...Figure 10.27 DNA origami nanorobot and the targeted transport of molecules. ...Figure 10.28 Control of chirality of plasmonic assembly with origami based o...Figure 10.29 A chiral plasmonic structure controlled by an origami‐supported...Figure 10.30 A switchable helical plasmonic/origami hybrid system. (a) Forma...Figure 10.31 A plasmonic nanoclock controlled by DNA origami. (a) Schematic ...Figure 10.32 Plasmonic waveguides supported by DNA origami. (a) Design of a ...Figure 10.33 Organization of nanoparticles by DNA origami leading to transla...Figure 10.34 A multilayered nanoparticle/origami hybrid system. (a) A three‐...Figure 10.35 Responsive control of an enzyme cascade by positioning of compo...

11 Chapter 11Figure 11.1 Effect of DNA conjugations on enzyme performance. (a) Two differ...Figure 11.2 DNA‐scaffolded enzymes in different geometric configurations. (a...Figure 11.3 Channeling of an intermediate within a multienzyme cascade react...Scheme 11.1 Enzymatic turnover of substrate (S) to product (P) through an in...Figure 11.4 Current hypotheses on the activity enhancement of DNA nanostruct...

12 Chapter 12Figure 12.1 (a) A general scheme for construction of a DNA origami scaffold ...Figure 12.2 Representative noncovalent (reversible) protein‐DNA conjugation ...Figure 12.3 Representative covalent (irreversible) protein‐DNA conjugation m...Figure 12.4 Application of protein‐assembled DNA scaffold. (a) Assembly of a...Figure 12.5 The assembling of the proteins of interest on DNA origami scaffo...Figure 12.6 Assembling POIs on the DNA origami scaffold by sequence‐specific...Figure 12.7 (a) An illustration of a modular adaptor. (b) Types of DNA‐bindi...Figure 12.8 Application of zinc finger protein adaptors to arrange functiona...Figure 12.9 Assembling various types of adaptor‐fused enzymes on DNA scaffol...

13 Chapter 13Figure 13.1 DNA‐kinesin provides unique experimental methods that are diffic...Figure 13.2 Properties and rational design of the gene nano‐chip activity. (...Figure 13.3 Features of Sensor‐Integrated Nano‐Chip. (a), Modulation of the ...Figure 13.4 Integration and reprogramming of the logic gate on the nanochip....Figure 13.5 Photoresponsive genetic circuits. Schematic drawing of the genet...

14 Chapter 14Figure 14.1 (a) Design of DNA origami pinching devices: DNA origami pliers (...Figure 14.2 Schematic illustration of “artificial molecular smooth muscle mo...Figure 14.3 Schematic illustration of “amoeba‐type molecular robot.”

15 Chapter 15Figure 15.1 Single‐molecule observation of DNA conformational changes and en...Figure 15.2 DNA frame structure used as an observation platform for the conf...Figure 15.3 Direct observation of G‐quadruplex (GQ) formation by monitoring ...Figure 15.4 The direct observation of the B–Z transition in the DNA frame. (...Figure 15.5 Direct observation of G‐quadruplex (GQ) and i‐motif (iM) formati...Figure 15.6 Regulation and single‐molecule observation of Cre‐mediated DNA r...Figure 15.7 Effect of DNA structures on the TET‐mediated 5mC oxidation. (a) ...Figure 15.8 Direct observation of GAL4‐VVD on the dsDNA bridge in the DNA fr...Figure 15.9 Direct observation of DNA motor movement on the DNA origami surf...Figure 15.10 Molecular transportation performed using a branched DNA motor t...Figure 15.11 Photo‐controlled DNA nanomachine constructed on the DNA origami...

16 Chapter 16Figure 16.1 The four‐step solid phase DNA synthesis cycle starting with acid...Figure 16.2 Acid catalyzed depurination of DNA.Figure 16.3 Mechanism of cleavage of RNA under alkaline pH [51, 53].Figure 16.4 General mechanism of bimolecular nucleophilic substitution react...Figure 16.5 Photoinduced pyrimidine base alterations occurring in DNA as a c...Figure 16.6 Deamination of exocyclic amines on nucleobases.Figure 16.7 Some applications of functionalized DNs. (a) Multiarmed DNA nano...Figure 16.8 (i) Common techniques to assess the stability of DNA structures:...Figure 16.9 Stabilization of DNs by design. (i) Design of DNA trusses using ...Figure 16.10 Enzymatic ligation to enhance stability of DNA nanostructures: ...Figure 16.11 Chemical crosslinking of DNs (a) DNA strands modified with azid...Figure 16.12 Photo‐crosslinking of DNs. (a) Formation of thermally stable DN...Figure 16.13 Noncovalent coating strategies to protect DNs. (a) Coating of D...Figure 16.14 Protecting DNs with protein‐based coatings. (a) Coating of huma...Figure 16.15 Noncovalent polymer and peptide coatings to protect DNs. (a) Re...

17 Chapter 17Figure 17.1 (a) DNA tetrahedron‐based structured probe.Figure 17.2 DNA tetrahedron based surface control and the HRP–antibody–gold ...Figure 17.3 Schematic illustration of the NTH‐assisted electrochemical aptas...Figure 17.4 DNA gelation‐based cloaking and decloaking of CTCs.Figure 17.5 Illustration of rSANTs (a) and rSANTs Mediated cHCR for Telomera...Figure 17.6 DNA nanostructures used as DOX delivery platforms. (a) DOX inter...Figure 17.7 Delivery of CpG with different DNA nanostructures. (a) With DNA ...Figure 17.8 DNA nanostructures for RNA delivery and regulation. (a) DNA tetr...Figure 17.9 DNA nanostructure‐based protein delivery system. (a) Polymer DNA...Figure 17.10 DNA origami‐gold nanorod (DO‐GNR) theranostic system. The intra...