A Computational Study of the Structure and Energetics of Stacked DNA Crossover Junctions

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.