Modeling technologies and methods for DNA origami

Abstract

Without the help of several people during my research, this thesis would not have been possible. In no particular order I'd like to thank the following people. I'd like to thank: reduce the salt buffers results in dissociation of DNA origami structures (Scheible et al. (2014)). Origin: This problem motivated the invention of a protocol for patterning DNA origami without using electrostatic binding to avoid the salt buffer problem mentioned. Cause: Salt concentrations are necessary in solution in order for DNA to hybridize. Other studies on electrostatic arrays have done more intense inquiries of this aspect (Fuchs et al. (2010)). Salts that bind with DNA often contain Magnesium2+ and Sodium+. The binding affects the polarity of the DNA's backbone, making salt an important factor in experiments. This effect has also been studied in Walter et al. (2013). Detection: Evident from the design of the experiment. Solution/Mitigation: origami can be attached using gold (which causes thiol-gold linkages with the origami) on passivated glass substrates that are etched using e-beam lithography. Samples were then measured using DNA-paint (Jungmann et al. (2014)) and TIRFM.