Ph. D. Defense

Programming & Building Molecular Devices using Nucleic Acid Hairpins

Speaker:Sudhanshu Garg
sgarg at cs.duke.edu
Date: Monday, March 28, 2016
Time: 1:00pm - 4:00pm
Location: D106 LSRC, Duke

Abstract

Nucleic Acid hairpins have been a subject of study for the last four decades. They stabilize single stranded RNA, serve as nucleation sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand, DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.

DNA hairpins as fuel for molecular devices, including locomotion, were proposed in 2003. They were interesting because they bring to the table an on-demand energy supply mechanism. The energy is hidden, until required. The energy is harnessed by opening the stem region, and exposing the loop. The hidden energy coupled with programmability provides another functionality, of selectively choosing what reactions to hide and what reactions to allow to proceed, that helps develop a topological sequence of events. In this thesis, we program four different molecular devices using DNA hairpins, and experimentally validate them in the laboratory. The first device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly. The second device: A novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. The third device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct regardless of differences in the arrival time of different inputs; b) renewable circuits which can be used multiple times without major degradation of the gate motifs (so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs). The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite amount of gain. Hairpins have been utilized as a source of fuel for many different DNA devices. Nucleic acid circuits with the ability to perform complex logic operations have the ability to achieve point of care diagnostics. We discuss the designs of our devices, the results we have obtained, and the challenges we have overcome to make these truly functional.

Advisor(s): John Reif
Committee: Thom LaBean, Chris Dwyer, Gleb Finkelstein