Simulations of DNA-Origami Self-Assembly Reveal Design-Dependent Nucleation Barriers.
View / Open Files
Publication Date
2022-09-14Journal Title
Nano Lett
ISSN
1530-6984
Publisher
American Chemical Society (ACS)
Type
Article
This Version
AM
Metadata
Show full item recordCitation
Cumberworth, A., Frenkel, D., & Reinhardt, A. (2022). Simulations of DNA-Origami Self-Assembly Reveal Design-Dependent Nucleation Barriers.. Nano Lett https://doi.org/10.1021/acs.nanolett.2c01372
Abstract
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding of the scaffold strand, is unclear. Here, using Monte Carlo simulations of a lattice model of DNA origami, we find that some, but not all, designs can have a nucleation barrier and that this barrier disappears at lower temperatures, rationalizing the success of isothermal assembly. We show that the height of the nucleation barrier depends primarily on the coaxial stacking of staples that are adjacent on the same helix, a parameter that can be modified with staple design. Creating a nucleation barrier to DNA-origami assembly could be useful in optimizing assembly times and yields, while eliminating the barrier may allow for fast molecular sensors that can assemble/disassemble without hysteresis in response to changes in the environment.
Keywords
cond-mat.soft, cond-mat.soft, q-bio.BM
Relationships
Is supplemented by: https://doi.org/10.5281/zenodo.6414264
Sponsorship
This research was not externally funded.
Embargo Lift Date
2023-04-05
Identifiers
External DOI: https://doi.org/10.1021/acs.nanolett.2c01372
This record's URL: https://www.repository.cam.ac.uk/handle/1810/340035
Statistics
Total file downloads (since January 2020). For more information on metrics see the
IRUS guide.