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Int. J. Mol. Sci. 2018, 19(7), 1895; https://doi.org/10.3390/ijms19071895

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

1
School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea
2
Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
3
Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
*
Authors to whom correspondence should be addressed.
Received: 9 May 2018 / Revised: 22 June 2018 / Accepted: 25 June 2018 / Published: 27 June 2018
(This article belongs to the Special Issue Nucleic Acid Nanotechnology)
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Abstract

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. View Full-Text
Keywords: finite-size; DNA structure; self-assembly; elastic network model; normal mode analysis finite-size; DNA structure; self-assembly; elastic network model; normal mode analysis
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Jo, S.; Kim, S.; Lee, B.H.; Tandon, A.; Kim, B.; Park, S.H.; Kim, M.K. Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures. Int. J. Mol. Sci. 2018, 19, 1895.

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