Force-induced structural transitions in DNA nanostructures

Mechanical properties of biomolecules provide valuable insights into their structural characteristics and translation to applications. Deformation modes and rigidity can be used to characterize soft objects such as DNA, exosomes, and liposomes. With the advent of DNA nanotechnology, DNA has been increasingly used as a key component of soft programmable materials. Among the many advantages of the technology, the ability to define and control the mechanical properties of these materials is enabling. However, the deformation of DNA nanostructures subject to forces remains underexplored.

Coarse-grained (CGMD) DNA simulations are a valuable tool to probe the mechanical response of these materials. In this study, we investigate the deformation of the building blocks of DNA nanostructures, linear dsDNA chains and circular rings, in elongational flow. We observe structural transitions in the DNA conformation which are otherwise beyond the resolution of experimental techniques. These transitions, related to overstretching and hyperstretching, are accompanied by increases in the DNA base-pair distances due to coordinated unwinding and force-induced melting.

Using CGMD simulations, we elucidate the role of the local tension force, DNA sequence and energy barrier in eliciting different structural transitions of DNA in flow. Our work provides valuable insights into the nonlinear elastic response regimes and structural conformations of DNA nanostructures that have not been previously probed.