abstract: DNA is a unique, highly programmable and addressable biomolecule. Due to its reliable and predictable base recognition behavior, uniform structural properties, and extraordinary stability, DNA molecules are desirable substrates for biological computation and nanotechnology. The field of DNA computation has gained considerable attention due to the possibility of exploiting the massive parallelism that is inherent in natural systems to solve computational problems. This dissertation focuses on building novel types of computational DNA systems based on both DNA reaction networks and DNA nanotechnology. A series of related research projects are presented here. First, a novel, three-input majority logic gate based on DNA strand displacement reactions was constructed. Here, the three inputs in the majority gate have equal priority, and the output will be true if any two of the inputs are true. We subsequently designed and realized a complex, 5-input majority logic gate. By controlling two of the five inputs, the complex gate is capable of realizing every combination of OR and AND gates of the other 3 inputs. Next, we constructed a half adder, which is a basic arithmetic unit, from DNA strand operated XOR and AND gates. The aim of these two projects was to develop novel types of DNA logic gates to enrich the DNA computation toolbox, and to examine plausible ways to implement large scale DNA logic circuits. The third project utilized a two dimensional DNA origami frame shaped structure with a hollow interior where DNA hybridization seeds were selectively positioned to control the assembly of small DNA tile building blocks. The small DNA tiles were directed to fill the hollow interior of the DNA origami frame, guided through sticky end interactions at prescribed positions. This research shed light on the fundamental behavior of DNA based self-assembling systems, and provided the information necessary to build programmed nanodisplays based on the self-assembly of DNA. / Dissertation/Thesis / Ph.D. Chemistry 2014

<p>Synthetic biology is an emerging technology field whose goal is to use biology as a substrate for engineering. Self-assembly is one of the many methods for fabricating such synthetic biosystems.</p><p>Self-assembly is a process where components spontaneously arrange themselves into organized aggregates by the selective affinity of substructures. DNA is an excellent candidate for making synthetic biological systems using self-assembly because of its modular structure and simple chemistry. This thesis describes several</p><p>techniques which use DNA as a nano-construction material and</p><p>explores the computational capabilities of DNA self-assembly.</p><p>For this dissertation, I set out to build a biomolecular computing device with several</p><p>useful properties, including compactness, robustness, high degrees of complexity, flexibility, scalability and easily characterized yields</p><p>and convergence rates. However, a unified device that satisfies all these properties is still many years away. Instead, this thesis presents designs, simulations,</p><p>and experimental results for several distinct DNA nano-systems, as</p><p>well as experimental protocols, each of which satisfies a subset of the above-mentioned properties. The hope is that the lessons learned from building all these biomolecular computational devices would bring us closer to our ultimate goal and would eventually pave the path for a computing device that satisfies all the properties. We experimentally demonstrate how we can reduce errors in tiling assembly using an optimized set of physical parameters. We propose a novel DNA tile design</p><p>which enforces directionality of growth, reducing assembly errors. We build simulation models to characterize damage in fragile nanostructures under the impact of various external forces. Furthermore, we investigate reversible computation as a means to provide self-repairability to such damaged structures.</p><p>We suggest two modifications of an existing DNA computing device,</p><p>called Whiplash PCR machine, which allow it to operate robustly outside of controlled laboratory conditions and allow it to implement a simple form of inter-device communication. We present analysis techniques which characterize the yields and time convergence of self-assembled DNA nanostructures. We also present an experimental demonstration of a novel DNA nanostructure which is capable of tiling the plane and could prove to be a way of building 3D DNA assemblies.</p> / Dissertation

DNA nanotechnology uses the Watson-Crick base-pairing of DNA to self-assemble structures at the nanoscale. DNA nanomachines are active structures that take energy from the system to drive a programmed motion. In this thesis, a new design for a reversible DNA motor and an automatically regenerating track is presented. Ensemble fluorescence measurements observe motors walking along the same 42nm track three times. A second new motor was designed to allow motors on intersecting tracks to block each other, which can be used to perform logical computation. Multiple design approaches are discussed. The chosen approach showed limited success during ensemble fluorescence measurements. The 'burnt bridges' motor originally introduced by Bath et al. 2005 was also sent down tracks placed along the inside of stacked origami tubes that are able to polymerise to micrometre lengths. Preliminary optical microscopy experiments show promise in using such a system for observing micrometre motor movement. Scaffold-based DNA origami is the technique of folding a long single-stranded DNA strand into a specific shape by adding small staple strands that hold it in place. Extended staple strands can be modified to functionalise the origami surface. In this thesis, the threading of staple extensions through a freely-floating origami tile was observed using single-molecule Förster resonance energy transfer (smFRET). Threading was reduced by bracing the bottom of the extension or by using a multilayered origami. smFRET was also used to investigate the process of staple repair, whereby a missing staple is added to a pre-formed origami missing the staple. This was found to be successful when the staple is single-stranded, and imperfect when partially double-stranded. Finally the idea for a new "DNA cage", a dynamic octahedron called the "Holliday Octahedron", is presented. The octahedron is made of eight strands, one running around each face. Mobile Holliday junctions at each face allow the stands to rotate causing a conformational change.