Knowledge Bank

The macro-scale behavior of engineering and biological materials is governed by the composition of the constituent molecules. Therefore, understanding connections between behaviors at different scales is of vital importance for understanding complex materials such as polymer solutions, human tissue, or cellular cytoplasm. DNA origami, a technique which uses complementary base pairing of deoxyribonucleic acid (DNA) molecules to build nanostructures with unprecedented spatial precision, involves the combination of dozens of polymer molecules. In this work, the connection between DNA origami, rheology, and material structure will be explored. Specifically, this thesis will work towards two goals: Connecting the physical properties of DNA with the DNA origami folding process, and using a DNA origami nanosensor to measure properties of the microenvironment. A two state DNA origami sensor, called the Nanodyn, was designed which can change shape based on the presence of molecular crowding agents in solution. The dynamics of the Nanodyn were measured in solutions with varying weight percentages of polyethylene glycol (PEG) and it was shown that molecular crowding in solution can be measured using a fluorescent assay. Full characterization of the Nanodyn will allow for the in situ measurement of of biological materials. It also demonstrates the ability for DNA origami to study rheological behavior. We also aimed to establish methods to study the viscoelastic properties of DNA origami solutions. DNA origami structures are formed from hundreds of polymeric molecules, giving rise to potentially complex rheological behaviors that could vary through the course of self-assembly. As a foundation for studying complex DNA origami solutions, two techniques, bulk rheology and microrheology, were applied to study simpler solutions containing DNA. Bulk rheology showed that DNA has viscoelastic properties at concentrations relevant to DNA origami. However, the required sample size makes it incompatible with current scales of DNA origami production. Microrheology allowed for the measurement of solution viscosity and the microliter volume requirements make it highly amenable for DNA origami, but methods need to be improved before they can be applied to quantitatively study to DNA origami solution properties or self-assembly.