Mechanical deformation behaviors and structural properties of ligated DNA crystals

• Published in: Biophysical journal Vol. 121; no. 21
• Main Authors: Li, Ruixin, Zheng, Mengxi, Madhvacharyula, Anirudh S., Du, Yancheng, Mao, Chengde, Choi, Jong Hyun
• Format: Journal Article
• Language: English
• Published: United States Elsevier 30.09.2022
• Subjects: BASIC BIOLOGICAL SCIENCES; DNA crystal; DNA self-assembly; mechanical property; molecular dynamics simulation; nanoindentation
• ISSN: 0006-3495; 1542-0086

DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here we have investigated the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We performed coarse-grained molecular dynamics simulations and confirmed the results with nanoindentation experiments using atomic force microscopy. Here, we observed various deformation modes including un-tension, linear elasticity, duplex dissociation, and single-stranded component stretch. We found that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.