Journal article
Coarse-grained modelling of the structural properties of DNA origami
- Abstract:
- We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Å, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
Actions
Access Document
- Files:
-
-
(Preview, Version of record, pdf, 17.2MB, Terms of use)
-
(Preview, Version of record, pdf, 1.3MB, Terms of use)
-
- Publisher copy:
- 10.1093/nar/gky1304
Authors
- Publisher:
- Oxford University Press
- Journal:
- Nucleic Acids Research More from this journal
- Volume:
- 47
- Issue:
- 3
- Pages:
- 1585–1597
- Publication date:
- 2019-01-03
- Acceptance date:
- 2018-12-20
- DOI:
- EISSN:
-
1362-4962
- ISSN:
-
0305-1048
- Keywords:
- Pubs id:
-
pubs:921469
- UUID:
-
uuid:a04b433b-87c2-407d-946d-9af84dd30f79
- Local pid:
-
pubs:921469
- Source identifiers:
-
921469
- Deposit date:
-
2019-01-08
Terms of use
- Copyright holder:
- Snodin et al
- Copyright date:
- 2019
- Notes:
-
Copyright © 2019 The Authors. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
- Licence:
- CC Attribution (CC BY)
If you are the owner of this record, you can report an update to it here: Report update to this record