[SY-H7] Symposium H-7

[SY-H7] Computational modeling approach for the rational design of DNA nanostructures

Invited

^○Do-Nyun Kim, Jae Young Lee, Jae Gyung Lee, Young-Joo Kim, Kyung Soo Kim, Chanseok Lee (Department of Mechanical and Aerospace Engineering, Seoul National University, Korea)

Structural DNA nanotechnology has recently been advanced significantly enabling the construction of nanometer-scale structures with controllable three-dimensional shapes and properties. While overall mechanical properties of single and double DNA helices have been relatively well characterized both experimentally and computationally, those of various DNA motifs essential to build a DNA bundle structure are still hardly known due to experimental limits despite their importance for the rational design of DNA nanostructures. In this presentation, we introduce our computational modeling approach to establishing an efficient design process in order to achieve fine control over the geometrical shape and mechanical properties of self-assembling DNA nanostructures. Molecular dynamics simulations are highly utilized to extract the unknown mechanical properties of local DNA motifs that are fed into a more coarse-grained DNA model built on the finite element method. Then, this finite-element-based model of DNA nanostructure is used to predict its three-dimensional shape and mechanical properties, which provides designers structural feedback as quick as possible offering a chance to revise the design before actual synthesis. We expect our multiscale analysis framework facilitates the rational design of DNA nanostructures with a target shape and mechanical (or other derived) properties with precision.

This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korea government (Ministry of Science and ICT) (NRF-2016R1C1B2011098, NRF-2017M3D1A1039422, and NRF-2014M3A6B3063711).