Understanding the structural mechanics of ligated DNA crystals via molecular dynamics simulation

Abstract

DNA self-assembly is a highly programmable method to construct arbitrary architectures based on sequence complementarity. Among various constructs, DNA crystals are macroscopic crystalline materials formed by assembling motifs via sticky end association. Due to their high structural integrity and size ranging from tens to hundreds of micrometers, DNA crystals offer unique opportunities to study the structural properties and deformation behaviors of DNA assemblies. For example, enzymatic ligation of sticky ends can selectively seal nicks resulting in more robust structures with enhanced mechanical properties. However, the research efforts have been mostly on experiments involving different motif designs, structural optimization, or new synthesis methods, while their mechanics are not yet fully understood. The complex properties of DNA crystals are difficult to study via experiments alone, and numerical simulation can complement and aid the experiments. The coarse-grained molecular dynamics (MD) simulation is a powerful tool that can probe the mechanics of DNA assemblies. Here, we investigate DNA crystals made of four different motif lengths with various ligation patterns (full ligation, major directions, connectors, and in-plane) using oxDNA, an open-source, coarse-grained MD platform. We found that several distinct deformation stages emerge in response to mechanical loading and that the number and the location of ligated nucleotides can significantly modulate structural behaviors. These findings should be useful for predicting crystal properties and thus improving the design.

Graphical abstract: Understanding the structural mechanics of ligated DNA crystals via molecular dynamics simulation

Supplementary files

Article information

Article type
Communication
Submitted
23 Jul 2025
Accepted
09 Sep 2025
First published
10 Sep 2025
This article is Open Access
Creative Commons BY-NC license

Nanoscale Horiz., 2025, Advance Article

Understanding the structural mechanics of ligated DNA crystals via molecular dynamics simulation

Y. H. Kim, A. S. Madhvacharyula, R. Li, A. A. Swett, S. Seo, E. J. Batchelder-Schwab, N. Siraj, C. Mao and J. H. Choi, Nanoscale Horiz., 2025, Advance Article , DOI: 10.1039/D5NH00524H

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. You can use material from this article in other publications, without requesting further permission from the RSC, provided that the correct acknowledgement is given and it is not used for commercial purposes.

To request permission to reproduce material from this article in a commercial publication, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party commercial publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements