Undergraduate Honors Theses

Thesis Defended

Fall 2017

Document Type

Thesis

Type of Thesis

Departmental Honors

Department

Physics

First Advisor

Noel Clark

Abstract

The organic molecule Sunset Yellow, a chromonic dye, and reverse Dickerson dodecamer DNA, a self-complementary, 12 base pair strand of nucleic acids, both self-assemble into rod shaped aggregates that exhibit liquid crystal phases in solution. The sunset yellow molecules and the nano-DNA duplexes have similar structure with hydrophobic cores and peripheral hydrophilic ions. The focus of this research is on mixtures of these two aggregates in miscible liquid crystal states and the phase separation that occurs at higher concentrations in the columnar phase. The structure and phase space of this mixture was determined using polarized optical microscopy and x-ray diffraction. In the columnar phase, these mixtures provide experimental data on the two-dimensional arrangement of binary, hard disks. Moreover, studying these mixtures will further the understanding of polymer, liquid crystal mixtures. Our results demonstrate selectivity in DNA aggregation, supporting the hypothesis that liquid crystal ordering auto-catalyzed the polymerization of nucleic acids before the biological mechanisms responsible for assembly existed.