Chemical and Biological Engineering ETDs
Publication Date
Winter 12-15-2024
Abstract
DNA nanotechnology takes advantage of the self-assembling properties of DNA to form 1D, 2D, and 3D nanostructures by utilizing the immobile four-way junction (4WJ). By attaching an additional two DNA duplex arms onto the 4WJ, the six- way junction (6WJ) is created. In this study we simulate fourteen unique 6WJ isomers across seven structural motifs using all-atom molecular dynamics (MD), then quantifying the structural and energetic properties of each motif. The structural properties measured include the angles between individual duplexes and the average base-pair step parameters in each motif. Interestingly, we found two motifs analogous to the 4WJ X conformation, the twisted motifs, which contain a 60◦ offset between each duplex. Energetic calculations preformed using the MM-PBSA method showed the free energy of the twisted motifs were the most energetically favorable out of the isomers simulated. Furthermore, we have also proposed several larger nanostructures that can be constructed using the 6WJ.
Keywords
DNA Nanotechnology, Molecular Dynamics, DNA Origami
Document Type
Thesis
Language
English
Degree Name
Chemical Engineering
Level of Degree
Masters
Department Name
Chemical and Biological Engineering
First Committee Member (Chair)
William P. Bricker
Second Committee Member
Eva Chi
Third Committee Member
Matthew Lakin
Recommended Citation
Baten, Alexander J.. "A Computational Study of the Structure and Energetics of Stacked DNA Crossover Junctions." (2024). https://digitalrepository.unm.edu/cbe_etds/124
