Date of Award

2001

Degree Name

Chemistry

College

College of Science

Type of Degree

M.S.

Document Type

Thesis

First Advisor

Michael Norton

Second Advisor

Robert Morgan

Third Advisor

William Price

Fourth Advisor

Leonard J. Deutsch

Abstract

In this study, the temperature dependence of self-assembling DNA structures was investigated. Specially designed two-dimensional DNA nanoarrays offer not only structural stability not normally associated with DNA, but also provide several possible sites of interaction, referred to as free ends, which can be easily exploited through conventional Watson-Crick base pairing. The ability to synthesize two-dimensional DNA nanoarrays was corroborated by confirming the presence of the nanoarrays by AFM imaging in air. The physical characteristics of two-dimensional DNA nanoarrays were also studied. DNA nanoarray synthesis occurs via a self-assembly process based on Watson-Crick base pairing. This self-assembly occurs through an annealing process, during which stringently coded single-stranded oligonucleotides form duplexes with their conjugates to give rise to a Building Block, the basic unit of these nanoarrays. The blocks in turn are assembled through the base pairing of the free ends to create a full two-dimensional nanoarray. The annealing process was studied to determine the extent of influence neighboring oligonucleotides had on the self-assembly process, a phenomenon referred to as cooperativity. The annealing process was investigated employing available temperature-dependent spectroscopic methods, ultraviolet-visible and fluorescence spectrophotometry. The UV method, which depends on the hypochromic affect, involves monitoring the change in absorbance at 260nm as a function of temperature. The fluorometric method employs an intercalating fluorescent dye whose intensity is multiplies nearly 1000 fold in the presence of double-stranded DNA. This intensity can be measured at a wavelength characteristic to the dye versus temperature to monitor the progress of annealing. An example of a melting curve is shown below, where the experimental data is shown as and a non-linear fit is displayed as X. The melting behavior closely follows a model based on a two-component annealing process, which displays limited cooperativity. Future work for this study will include the design and implementation of sequences that will employ higher degrees of cooperativity. Higher cooperativity can ensure increased control over the annealing, and therefore, the self-assembly process.

Subject(s)

DNA – Synthesis.

Nanotechnology.

Biochemistry.

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