Self-Assembly of Tiles: Theoretical Models, the Power of Signals, and Local Computing

DNA-based self-assembly is an autonomous process whereby a disordered system of DNA sequences forms an organized structure or pattern as a consequence of Watson-Crick complementarity of DNA sequences, without external direction. Here, we propose self-assembly (SA) hypergraph automata as an automata-theoretic model for patterned self-assembly. We investigate the computational power of SA-hypergraph automata and show that for every recognizable picture language, there exists an SA-hypergraph automaton that accepts this language. Conversely, we prove that for any restricted SA-hypergraph automaton, there exists a Wang Tile System, a model for recognizable picture languages, that accepts the same language. Moreover, we investigate the computational power of some variants of the Signal-passing Tile Assembly Model (STAM), as well as propose the concept of {\it Smart Tiles}, i.e., tiles with glues that can be activated or deactivated by signals, and which possess a limited amount of local computing capability. We demonstrate the potential of smart tiles to perform some robotic tasks such as replicating complex shapes

Design, Synthesis and Analysis of Self-Assembling Triangulated Wireframe DNA Structures

The field of DNA nanotechnology offers a wide range of design strategies with which nanometer-sized structures with a desired shape, size and aspect ratio can be built. The most established techniques in the field rely on close-packed 'solid' DNA nanostructures produced with either the DNA origami or the single-stranded tile techniques. These structures depend on high-salt buffer solutions and require more material than comparable size hollow wireframe structures. This dissertation explores the construction of hollow wireframe DNA nanostructures composed of equilateral triangles. To achieve maximal material efficiency the design is restricted to use a single DNA double helix per triangle edge. As a proof of principle, the DNA origami technique is extended to produce a series of truss structures including the flat, tetrahedral, octahedral, or irregular dodecahedral truss designs. In contrast to close packed DNA origami designs these structures fold at low-salt buffer conditions. These structures have defined cavities that may in the future be used to precisely position functional elements such as metallic nanoparticles or enzymes. The design process of these structures is simplified by a custom design software. Next, the triangulated construction motif is extended to the single-stranded DNA tile technique. A collection of finite structures, as well as one-dimensional crystalline assemblies is explored. The ideal assembly conditions are determined experimentally and using molecular dynamics simulations. A custom design software is presented to simplify the design and handling of these structures. At last, the cost-effective prototyping of triangulated wireframe DNA origami structures is explored. This is achieved through the introduction of single-stranded “gap” regions along the triangle edges. These gap regions are then filled using a DNA polymerase rather than by synthetic oligonucleotides. This technique also allows the mechanical transformation of these structures, which is exemplified by the transition of a bent into a straight structure upon completion of the gap filling.:Abstract v Publications vii Acknowledgements ix Contents xi Chapter 1 A short introduction into DNA nanotechnology 1 1.1 Nanotechnology 1 1.1.1 Top down 1 1.1.2 Bottom up 3 1.2 Deoxyribonucleic acid (DNA) 4 1.3 DNA Nanotechnology 6 1.3.1 Tile based assembly 9 1.3.2 DNA origami and single-stranded tiles 10 1.3.3 Some applications of DNA nanotechnology 12 1.3.4 Wireframe structures 15 1.3.5 Computational tools and DNA nanotechnology. 17 Chapter 2 Motivation and objectives 19 Chapter 3 Design and Synthesis of Triangulated DNA Origami Trusses 20 3.1 Introduction 20 3.2 Results and Discussion 21 3.2.1 Design 21 3.2.2 Nomenclature and parameters of the tube structures 23 3.2.3 Gel electrophoreses analysis 25 3.2.4 Imaging of the purified structures 26 3.2.5 Optimizing the folding conditions 28 3.2.6 Comparison to vHelix 29 3.3 Conclusions 29 3.4 Methods 30 3.4.1 Standard DNA origami assembly reaction. 30 3.4.2 Gel purification. 30 3.4.3 AFM sample preparation. 31 3.4.4 TEM sample preparation. 31 3.4.5 Instructions for mixing the staple sets. 31 Chapter 4 Triangulated wireframe structures assembled using single-stranded DNA tiles 33 4.1 Introduction 33 4.2 Results and Discussion 35 4.2.1 Designing the structures 35 4.2.2 Synthesis of test structures 37 4.2.3 Molecular dynamics simulations of 6-arm junctions 38 4.2.4 Assembly of the finite structures 40 4.2.5 Influence of salt concentration and folding times 42 4.2.6 Molecular dynamics simulations of the rhombus structure 43 4.2.7 1D SST crystals 44 4.2.8 Controlling the crystal growth 46 4.3 Conclusions 48 4.4 Methods 49 4.4.1 SST Folding 49 4.4.2 Agarose Gel Electrophoresis 49 4.4.3 tSEM Characterization 49 4.4.4 AFM Imaging 49 4.4.5 AGE-Based Folding-Yield Estimation 49 4.4.6 Molecular Dynamics Simulations 50 Chapter 5 Structural transformation of wireframe DNA origami via DNA polymerase assisted gap-filling 52 5.1 Introduction 52 5.2 Results and Discussion 54 5.2.1 Design of the Structures 54 5.2.2 Folding of Gap-Structures 56 5.2.3 Inactivation of Polymerase. 57 5.2.4 Secondary Structures. 58 5.2.5 Folding Kinetics of Gap Origami. 60 5.3 Conclusions 61 5.4 Methods 62 5.4.1 DNA origami folding 62 5.4.2 Gap filling of the wireframe DNA origami structures 63 5.4.3 Agarose gel electrophoresis 63 5.4.4 PAGE gel analysis 63 5.4.5 tSEM characterization 64 5.4.6 AFM imaging 64 5.4.7 AGE based folding-yield estimation 64 5.4.8 Gibbs free energy simulation using mfold 65 5.4.9 List of sequence for folding the DNA origami triangulated structures 65 Chapter 6 Summary and outlook 67 Appendix 69 A.1 Additional figures from chapter 369 A.2 Additional figures from chapter 4 77 A.3 Additional figures from chapter 5 111 Bibliography 127 Erklärung 13

DNA PROGRAMMABLE SOFT MATTER DEVICES

The ability to program soft materials to undergo observable shape transformations in response to environmental stimuli is critical to the development soft programmable matter. In recent years, chemomechanical shape-changing hydrogels have garnered interest because they do not require wires or batteries and can operate untethered at smaller size scales. Devices comprised of these materials can respond to only a limited set of spatially non-specific stimuli such as temperature or pH - and are therefore restricted to a small set of final states. On the other hand, due to the large sequence space and programmable interactions of DNA molecules, devices comprised of DNA-conjugated hydrogel domains can potentially access a much larger set of final configurations through sequence-specific, addressable actuation of individual domains. To investigate the shape-changing properties of single domain DNA-conjugated hydrogels, we first determine the swelling extent of DNA-crosslinked acrylamide networks in response to sequence-specific DNA stimuli. By coupling the DNA crosslinks to a DNA hybridization chain reaction that enables further incorporation of DNA to the crosslink sites, we demonstrate that specific DNA molecules can induce up to 100-fold volumetric hydrogel expansion. This large degree of swelling is then used to actuate approximately centimeter-sized gels containing multiple DNA-sensitive gel domains that each change shape in response to different DNA sequences. From swelling experiments and finite-element simulations we develop a simple design rule for the DNA-controlled shape change of a hydrogel bilayer. The next generation of soft programmable matter and robotics will require materials that not only respond to distinct chemical species, but mechanical forces as well. Prior work in developing mechanochemically responsive polymers makes use of mechanophores - molecules that change configuration and initiate chemical reactions in response to mechanical forces - to instill bulk materials with force sensing properties. In this work, we use established thermodynamic models to design two DNA mechanophore complexes capable of responding to two distinct ranges of applied force. We micromold PEGDA copolymer hydrogels containing DNA mechanophore complexes and examine the force-sensing properties of the bulk material through the use of a multifunctional force microscope and a DNA-based fluorescence reporting scheme. Because DNA molecules can be coupled to molecular sensors, amplifiers, and logic circuits, the incorporation of DNA complexes into hydrogel networks - whether as mechanophores or chemical crosslinkers -introduces the possibility of building soft matter devices that respond to numerous, distinct inputs and autonomously implement chemical control programs. These soft matter constructs have the potential to exhibit the multistage, goal-directed behaviors that are currently impossible to achieve in other soft robotic devices