Browsing by Subject "DNA self"

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.

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

techniques which use DNA as a nano-construction material and

explores the computational capabilities of DNA self-assembly.

For this dissertation, I set out to build a biomolecular computing device with several

useful properties, including compactness, robustness, high degrees of complexity, flexibility, scalability and easily characterized yields

and convergence rates. However, a unified device that satisfies all these properties is still many years away. Instead, this thesis presents designs, simulations,

and experimental results for several distinct DNA nano-systems, as

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

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.

We suggest two modifications of an existing DNA computing device,

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.

Nanoscale devices offer the technological advances to enable a new era in computing. Device sizes at the molecular-scale have the potential to expand the domain of conventional computer systems to reach into environments and application domains that are otherwise impractical, such as single-cell sensing or micro-environmental monitoring.

New potential application domains, like biological scale computing, require processing elements that can function inside nanoscale volumes (e.g. single biological cells) and are thus subject to extreme size and resource constraints. In this thesis we address these critical new domain challenges through a synergistic approach that matches manufacturing techniques, circuit technology, and architectural design with application requirements. We explore and vertically integrate these three fronts: a) assembly methods that can cost-effectively provide nanometer feature sizes, b) device technologies for molecular-scale computing and sensing, and c) architectural design techniques for nanoscale processors, with the goal of mapping a potential path toward achieving molecular-scale computing.

We make four primary contributions in this thesis. First, we develop and experimentally demonstrate a scalable, cost-effective DNA self-assembly-based fabrication technique for molecular circuits. Second, we propose and evaluate Resonance Energy Transfer (RET) logic, a novel nanoscale technology for computing based on single-molecule optical devices. Third, we design and experimentally demonstrate selective sensing of several biomolecules using RET-logic elements. Fourth, we explore the architectural implications of integrating computation and molecular sensors to form nanoscale sensor processors (nSP), nanoscale-sized systems that can sense, process, store and communicate molecular information. Through the use of self-assembly manufacturing, RET molecular logic, and novel architectural techniques, the smallest nSP design is about the size of the largest known virus.