Date of Award

Spring 1-1-2018

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

First Advisor

Noel A. Clark

Second Advisor

Joseph E. MacLennan

Third Advisor

Matthew A. Glaser

Fourth Advisor

Meredith D. Betterton

Fifth Advisor

David M. Walba

Abstract

When dissolved in water, base paired DNA oligomers form double helices with sufficient structural rigidity that, if they are at high enough concentration, can undergo a phase transition into chiral nematic or hexagonal columnar liquid crystalline (LC) order. Within these LC phases, constrained orientation allows these rods to stack more efficiently by hydrophobic forces than they would otherwise, building them into long double helical aggregates that can be chemically glued together (ligated) to further increase their lengths. Even in absence of chemical ligation, this stacking effect is strong enough that short DNA oligomers, which are otherwise too short to form phases, can stack reversibly with one another into aggregates with sufficient length to force the creation of LC phases. If these stacked aggregates are then ligated within an LC phase, the lengthened rods become able to form LC phases at lower concentrations than they could have previously, given their improved aspect ratio, making it easier for them to form liquid crystals later. This effect forms a feedback loop where self-assembly of short oligomers into aggregates and chemical ligation of these aggregates within LC phases to form longer DNA double helices enhances later rounds of assembly and ligation, leading to the hypothesis that LC phases could have helped to provide a feedstock of long, complementary oligonucleotide strands as a basis for biology and helped to bootstrap the origin of Life. This thesis presents research exploring the limits of this effect, detailing examination and discovery of LC phases with shorter and more basic DNA oligomers and ending with the discovery of LC phases by base paired DNA monomers, which has never been previously seen.

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