Publication Date

12-2017

Date of Final Oral Examination (Defense)

2-28-2017

Type of Culminating Activity

Thesis

Degree Title

Master of Science in Materials Science and Engineering

Department

Materials Science and Engineering

Supervisory Committee Chair

Elton Graugnard, Ph.D.

Supervisory Committee Member

William L. Hughes, Ph.D.

Supervisory Committee Member

Wan Kuang, Ph.D.

Supervisory Committee Member

Bernard Yurke, Ph.D.

Abstract

As the cost to continue scaling photolithography to pattern smaller semiconducting devices increases exponentially, new materials and fabrication approaches are being sought to extend and enhance current capabilities. DNA nanostructures have been identified as a promising material for patterning nanoscale devices, and several studies have demonstrated the ability to program DNA nanostructures to self-assemble into large scale arrays. These DNA arrays can be designed to create the patterns necessary for fabricating semiconductor device features. However, these structures are far from ideal and contain a number of defects that limit the adoption of this approach for manufacturing. In order to create large defect-free DNA arrays, further study is needed into the fundamental mechanisms governing array formation. Toward this goal, the thermodynamics and kinetics of DNA array formation were investigated using a DNA origami cross-tile that assembles into arrays through DNA hybridization. The assembly of dimers, quadramers, and unbound arrays in solution from monomers with complementary dye and quencher labeled hybridization interfaces was monitored by observing the change in fluorescence of the solution as a function of temperature and over time under varying buffer conditions and temperatures. The melting temperature of each structure was measured and generally increased with an increasing number of active sticky-ends per monomer. Values for standard thermodynamic parameters were determined for each array design. The reaction kinetics data were fit with a second order reaction model, and the effective reaction rate increased with increasing buffer magnesium concentrations and increasing temperatures. Finally, it was determined that large, unbounded 2D DNA origami cross-tile arrays sediment out of solution in only a few hours. The findings of this study provide insight into the mechanisms of DNA array formation and establish practical ranges for key processing parameters.

DOI

https://doi.org/10.18122/B24Q50

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