Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures

International Journal of Molecular Sciences

SungHa Park¹  Byunghoon Kim¹  Seungjae Kim¹  ByungHo Lee²  Soojin Jo²  MoonKi Kim²  Anshula Tandon³ 

[1] Department of Physics, Sungkyunkwan University, Suwon 16419, Korea;School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea;Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea;

关键词: finite-size;    DNA structure;    self-assembly;    elastic network model;    normal mode analysis;   

DOI  :  10.3390/ijms19071895

来源: DOAJ

【 摘 要 】

In order to incorporate functionalization into synthesized DNA nanostructures, enhance their production yield, and utilize them in various applications, it is necessary to study their physical stabilities and dynamic characteristics. Although simulation-based analysis used for DNA nanostructures provides important clues to explain their self-assembly mechanism, structural function, and intrinsic dynamic characteristics, few studies have focused on the simulation of DNA supramolecular structures due to the structural complexity and high computational cost. Here, we demonstrated the feasibility of using normal mode analysis for relatively complex DNA structures with larger molecular weights, i.e., finite-size DNA 2D rings and 3D buckyball structures. The normal mode analysis was carried out using the mass-weighted chemical elastic network model (MWCENM) and the symmetry-constrained elastic network model (SCENM), both of which are precise and efficient modeling methodologies. MWCENM considers both the weight of the nucleotides and the chemical bonds between atoms, and SCENM can obtain mode shapes of a whole structure by using only a repeated unit and its connectivity with neighboring units. Our results show the intrinsic vibrational features of DNA ring structures, which experience inner/outer circle and bridge motions, as well as DNA buckyball structures having overall breathing and local breathing motions. These could be used as the fundamental basis for designing and constructing more complicated DNA nanostructures.

【 授权许可】

Unknown