Date of Award

Spring 1-1-2015

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Chemical & Biochemical Engineering

First Advisor

Daniel K. Schwartz

Second Advisor

Jennifer N. Cha

Third Advisor

Joel L. Kaar

Fourth Advisor

Matthew Glaser

Fifth Advisor

Arthi Jayaraman

Abstract

Biosensors, and other diagnostic techniques, are dependent on the specific interactions of nucleotides on a functionalized surface. Here, we study oligonucleotide dynamics and hybridization at solid-liquid interfaces. In particular we are interested in understanding how oligonucleotides, behave in various solid-liquid interfacial environments. First, we prepared substrates with varying hydrophobicity to explore the effects of molecular size and surface hydrophobicity on oligonucleotide interfacial dynamics. Next we studied the mechanisms of surface-mediated oligonucleotide hybridization. This study cultivated an interest in the search strategies of interfacial reactions. The majority of this field is dominated by theoretical and ecological studies. We felt that with our technique we could further the understanding of these fields. This led us to our final study exploring the effects of hydrophobicity on the interfacial search strategies of oligonucleotides.

The findings presented here provided further understanding of oligonucleotide interfacial behavior that may be used to enhance biosensor and other nucleotide based technologies. For example, studies at the solid-liquid interface revealed that surface residence time decreased with increasing ssDNA length on hydrophobic surfaces, particularly for longer oligonucleotide chains. Similarly, the interfacial mobility of polynucleotides slowed with increasing chain length on hydrophilic, but became faster, on hydrophobic surfaces. These combined observations suggest that long oligonucleotides adopt conformations minimizing hydrophobic interactions. Furthermore, when pathways of DNA hybridization were explored, the vast majority of molecules from solution adsorbed non-specifically (without directly hybridizing) to the surface, where a brief 2-dimensional search was performed with a 7% chance of hybridization. We observed that hybridization was reversible, and had two distinct modes of melting (i.e. de-hybridization) corresponding to long-lived (~15s) and short-lived (~1.4s) hybridized time intervals. Finally, we designed experiments to probe the search behavior of oligonucleotides as a function of surface hydrophobicity. This study demonstrates that oligonucleotides adopt alternating Lévy-flight and Brownian search behavior regardless of surface hydrophobicity. This search strategy was enhanced in the hydrophobic environment, however, duplex DNA had shorter hybridized time intervals. These studies advance the understanding of oligonucleotide interfacial dynamics and provide examples of surface modifications that can influence hybridization stability and molecular search efficiency. Thus we have used a comprehensive study of oligonucleotides to gain a better understanding of oligonucleotide dynamics and hybridization at solid-liquid interfaces.

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