The Thermo-Mechanical Dynamics of DNA Self-Assembled Nanostructures

Abstract

The manufacturing of molecular-scale computing systems requires a scalable, reliable, and economic approach to create highly interconnected, dense arrays of devices. As a candidate substrate for nanoscale logic circuits, DNA self-assembled nanostructures have the potential to fulfill these requirements. However, a number of open challenges remain, including the scalability of DNA self-assembly, long-range signal propagation, and precise patterning of functionalized components. These challenges motivate the development of theory and experimental techniques to illuminate the connections among the physical, optical, and thermodynamic properties of DNA self-assembled nanostructures. In this thesis, three tools are developed, validated, and applied to study the thermo-mechanical properties of DNA nanostructures: 1) a method to quantitatively measure the quality of DNA grid self-assembly, 2) a spectrofluorometer capable of capturing fluorescence and absorbance data under simultaneous multi-wavelength excitation, and 3) a Monte Carlo simulator that models the ensemble response of DNA nanostructures as simple harmonic oscillators. The broad contributions of this dissertation are as follows: 1) insight into the thermo-mechanical properties of DNA grid nanostructures, and 2) a categorization of self-assembly defects and their impact on proposed logic circuits. The results of the work presented in this dissertation show that: 1) the quality of self-assembly of DNA grid nanostructures can be quantitatively calculated to demonstrate the impact of changes in temperature or structure, 2) the optical absorbance of complex DNA nanostructures can be modeled to capture their thermo-mechanical properties (i.e., worst case within 10% of experimental melting temperatures and 70% of experimental thermodynamic parameters), 3) the structural resilience of DNA nanostructures can be quantifiably improved by chemical cross-linking with up to 60% retaining their original structure, and 4) DNA self-assembly introduces structural defects which create new fault models with respect to conventional technologies for logic circuits.