Programming Molecular Devices using Nucleic Acid Hairpins

<p>Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is </p><p>hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation</p><p>sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand, </p><p>DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.</p><p>The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They</p><p>were interesting because they bring to the table an on-demand energy/information supply mechanism. </p><p>The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.</p><p>The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.</p><p>The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.</p><p>The hidden energy and information coupled with </p><p>programmability provides another functionality, of selectively choosing what reactions to hide and </p><p>what reactions to allow to proceed, that helps develop a topological sequence of events. </p><p>Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different </p><p>molecular devices using DNA hairpins, and experimentally validate them in the</p><p>laboratory. 1) The first device: A </p><p>novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second</p><p>device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct </p><p>regardless of differences in the arrival time of different inputs.</p><p>b) renewable circuits which can be used multiple times without major degradation of the gate motifs </p><p>(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).</p><p>3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances </p><p>its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly. </p><p>4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification</p><p>of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite</p><p>amount of gain.</p><p>Nucleic acid circuits with the ability </p><p>to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.</p><p>We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome</p><p>to make these truly functional.</p>

Dissertation