Publication Date


Date of Final Oral Examination (Defense)


Type of Culminating Activity


Degree Title

Master of Science in Materials Science and Engineering


Materials Science and Engineering

Major Advisor

Elton Graugnard, Ph.D.


William L. Hughes, Ph.D.


Wan Kuang, Ph.D.


Bernard Yurke, Ph.D.


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.