Publication Date


Date of Final Oral Examination (Defense)


Type of Culminating Activity


Degree Title

Doctor of Philosophy in Materials Science and Engineering


Materials Science and Engineering

Major Advisor

William L. Hughes, Ph. D.


Bernard Yurke, Ph.D.


Jeunghoon Lee, Ph.D.


Peter B. Allen, Ph.D.


Because of the elegance of Watson-Crick base pairing and the programmability of toehold-mediated strand displacement, DNA is a model material for designing, building, and testing molecular assemblies. DNA assemblies are categorized as structural when they are at thermodynamic equilibrium and dynamic when they are not. Through programmed perturbations, metastable assemblies perform physical, chemical, and computational work. When integrated into a diagnostic package, disease-specific nucleic acid sequences can be identified, amplified, and analyzed via standard DNA nanotechnology rules. In order for these rules to make an impact, two critical challenges in the field have been undertaken in this dissertation. First, the selectivity to distinguish an on-target sequence from off-target sequences, with a resolution of a single-nucleotide mutation, has been explored by site-specifically integrating locked nucleic acids into DNA sequences. Locked nucleic acids are RNA analogues that have higher thermal and hence mechanical stability than RNA and DNA. Second, the initiation of metastable chemical reaction networks, in the absence of on-target sequences, has been explored to suppress network leakage; which is the single greatest problem in dynamic DNA nanotechnology. To address this challenge, original catalytic substrates were designed, built, and tested to increase the energy barrier of the leakage reactions without sacrificing the performance of the favorable catalytic reactions. The experimental results showed that site-specific integration of LNA into DNA sequences improved the sequence selectivity by over 2 orders of magnitude. They also showed that network leakage could be suppressed by 2 orders of magnitude by decoupling the leakage pathway from the catalytic pathway in the original catalytic substrates. When combined, these results constitute a substantial contribution to the field of dynamic DNA nanotechnology and represent important steps towards the creation of low-cost, early-stage diagnostic tools for difficult to detect diseases such as lung, breast, and pancreatic cancers.