MECHANICAL ENGINEERING, SEOUL NATIONAL UNIVERSITY

Structural DNA/RNA Nanotechnology

Multiscale Modeling and Analysis

Performing a full atomic-scale simulation for structural DNA/RNA assemblies is inhibited by the high computational cost. On the other hand, simplified structural modeling often suffers from determining proper model parameters. We have been developing multiscale modeling and analysis methods by systematically identifying sequence-dependent properties of structural DNA/RNA motifs using molecular dynamics simulation and incorporating them into finite-element-based structural models. In this way, we can predict the three-dimensional shape and physical properties of DNA/RNA nanostructures quickly, expediting the design-analysis-manufacturing process significantly.









* Jae Gyung Lee, Kyung Soo Kim, Jae Young Lee, and Do-Nyun Kim. "Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint." ACS Nano (2022).
* Jae Young Lee, Myoungseok Kim, Chanseok Lee, and Do-Nyun Kim. "Characterizing and harnessing the mechanical properties of short single-stranded DNA in structured assemblies." ACS Nano (2021).
* Jae Young Lee, Jae Gyung Lee, Giseok Yun, Chanseok Lee, Young-Joo Kim, Kyung Soo Kim, Tae Hwi Kim, and Do-Nyun Kim. "Rapid computational analysis of DNA origami assemblies at near-atomic resolution." ACS Nano (2021).
* Jae Young Lee, Young-Joo Kim, Chanseok Lee, Jae Gyung Lee, Hiromasa Yagyu, Osamu Tabata, and Do-Nyun Kim. "Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design." Nucleic Acids Research (2019).
* Kim, Young-Joo, and Do-Nyun Kim. "Structural basis for elastic mechanical properties of the DNA double helix." PloS One (2016).
* Kim, Young-Joo, and Do-Nyun Kim. "Sensitivity analysis for the mechanical properties of DNA bundles." Journal of Nanomaterials (2016).
* Keyao Pan, Do-Nyun Kim, Fei Zhang, Matthew R. Adendorff, Hao Yan, Mark Bathe, "Lattice-free prediction of three-dimensional structure of programmed DNA assemblies." Nature Communications (2014).
* Do-Nyun Kim, Fabian Kilchherr, Hendrik Dietz, Mark Bathe, "Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures." Nucleic Acids Research (2011).

* Carlos Ernesto Castro, Fabian Kilchherr, Do-Nyun Kim, Enrique Lin Shiao, Tobias Wauer, Philipp Wortmann, Mark Bathe, Hendrik Dietz, "A primer to scaffolded DNA origami." Nature Methods (2011).