UCLA

Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) are molecules that store and transmit genetic information and are present nearly all living organisms. The field of nucleic acid nanotechnology uses these molecules out of its biological context and employs it to build structures and then to connect their operation. Although DNA nanotechnology was originally developed to elucidate protein crystallization, recent developments in the field are testing the limits of its application towards a multitude of fields ranging from nanofabrication to computation. One of the important frontiers that remain to be addressed is the production of ‘active’ material that can interact with its environment and adapt to it intelligently, rivalling organelles present inside cells. This dissertation reports on the construction of responsive nucleic acid structures that can demonstrate autonomous function and capability to respond to physical and chemical inputs.

As the first example, we show how the self-assembly process of monomers made out of DNA strands can be triggered into activation by specific chemical inputs, in our case RNA molecules to build tubular structures. These ‘nanotubes’ can be temporally controlled by simple molecular programs, mimicking the architecture used by biological cells to direct their internal scaffolds. Our molecular programs use enzymes to produce or degrade RNA molecules embedded in the DNA nanotubes. Our results indicate that RNA can be used as a fuel for assembly, and that genetic circuits and enzymes can be an integral part in the operation of active nanostructures. This activatable self-assembly technique could be used to create a programmable synthetic version of filaments whose operation may mimic the cytoskeleton.

The second theme of this dissertation is the autonomous control of assembly and disassembly of nucleic acid nanotubes inside cell-sized environments. We used different designs to observe and control nucleation, polymerization and depolymerization steps in the self-assembly dynamics of encapsulated structures. The kinetics of growth and degradation of these encapsulated tubular structures were quantified using epi-fluorescence microscopy. We were also able to demonstrate the production of nucleotide assemblies with external stimuli, such as heat and light. These demonstrations can pave the way for designing and observing the functionality of responsive materials across the nanometer to micron size scales.