Date of Award

2022

Degree Name

Chemistry

College

College of Science

Type of Degree

M.S.

Document Type

Thesis

First Advisor

Dr. Michael Norton, Committee Chairperson

Second Advisor

Dr. Scott Day

Third Advisor

Dr. Rosalynn Quinones-Fernandez

Abstract

DNA origami, invented by Paul Rothemund in 2006, provides many possible routes for the synthesis of complex macromolecular assemblies. This project involves the creation of 1-D and 2-D arrays of cross origami to support the development of DNA detection devices by providing precise platforms for these devices. The M13 plasmid is the most commonly used scaffold in DNA nanotechnology, limiting the size and complexity of an individual DNA origami construct. However, by creating larger assemblies, the dimensions can be multiplied. For example, by alternating two different types of cross origami, optical reporters can be separated by 200 nm, which is beyond the Abbe optical limit for optical microscopy. Due to apparent low yields of longer alternating structures and high amounts of shorter by-products, the research was directed into creating and purifying dimers to be utilized as “building blocks” for arrays. With dimers being utilized as the new “building blocks”, several different designs were created to expand the support systems for optical imaging. Two approaches were primarily utilized. The first approach is the assembly of 1-D arrays of origami dimers. The idea of generating and purifying dimers as the new “building block” was to simplify the process by maintaining a 1:1 stoichiometry of the two-component origami structure; however, a low yield of the new “building block” at the purification/isolation stage redirected the research to the second approach. The second approach consisted of a multi-step assembly approach which eliminated the dimer isolation stage and allowed the production of much more favorable yields. A primary 1-D array of controlled length was generated by using a fixed stoichiometry of chain termination constructs to monomer components. A second 1-D row array was then assembled on this primary array. This in turn led to the creation of an array of dimers. The final step in creating the 2-D array was to cross-link the DNA origami in the second row. After extensive research, it was observed that there was a limitation with on-surface immobilized dimer cross linking using mica as the substrate. Since glass is the desired final substrate for sample deposition, finding a technique to give a better population of arrays per unit area was necessary. Thus, in solution reaction on glass was employed to allow for inter-strand cross linking to create dimer arrays for the assembly of sensing device platforms.

Subject(s)

DNA nanotechnology.

DNA – Research.

DNA – Structure.

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