Investigation of the structural stability and electronic properties of DNA origami nanostructures by simulations of molecular dynamics and density functional theory

Deoxyribonucleic acid (DNA) is the fundamental molecule that is responsible from the genetic information in living organisms. It also has a great potential in nanotechnology applications due to its unique interactions of complementary base pairs and the ability to be produced easily in a desired sequence. Combination of a long, single DNA strand with shorter DNA strands can result in desired two- or three – dimensional nanostructures which is called "DNA Origami". DNA origami nanostructures have a high potential for various applied research such as drug delivery, biosensing, inorganic material synthesis, as well as molecular electronics applications, which have gained momentum in recent years due to their ease of production. DNA origami nanostructures designed for these applications should maintain their structural stability and should be able to be designed with desired properties for electronic applications. Although it is known that the stability of the DNA origami structures depends on geometry, helix number, and environmental conditions, the nature of these effects has so far been poorly understood. In addition, understanding the effects of structural changes on the electronic properties of DNA origami is crucial for the development of new electronic devices. In this thesis, three-dimensional structures of different DNA origami nanostructures were modeled by using molecular dynamics methods with AMBER and NAMD programs. The effects of three different parameters on the conformation of DNA origami nanostructures were investigated via modeling methods: 1) gold (111) surface, 2) frequency of junction points of DNA helixes, and 3) salt concentration difference. Smaller double-stranded DNA molecules representing DNA origami structures were created and the effects of structural deformations due to the gold (111) surface on electronic properties were inspected using the GAUSSIAN program. In addition, the structural stability of the DNA origami nanostructure within the 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer for bioelectronic applications was examined. Then, energy band diagrams and molecular orbital positions were studied with Extended Hückel and density functional theory calculations. The transmission of electrical conductivity between the helices in DNA origami structures was explored. It is expected that these studies will contribute to the development of new nanotechnological devices and applications in the future by paving the way for the understanding of the structural stability of DNA origami and the long-term use of DNA origami structures.