DNA Origami

3 Chapter 3 Figure 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 4 Figure 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 Mg 2+ions. (a) The composition of the...Figure 10.6 DNA origami nanodevice driven by Mg 2+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...