Direct Simulation of the Self-Assembly of a Small DNA Origami.
File(s)main_evenmorefinal.pdf (6.77 MB)
Accepted version
Author(s)
Type
Journal Article
Abstract
By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies.
Date Issued
2016-01-14
Date Acceptance
2016-01-14
Citation
ACS Nano, 2016, 10 (2), pp.1724-1737
ISSN
1936-086X
Publisher
American Chemical Society
Start Page
1724
End Page
1737
Journal / Book Title
ACS Nano
Volume
10
Issue
2
Copyright Statement
This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Nano, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://dx.doi.org/10.1021/acsnano.5b05865
Subjects
DNA nanotechnology
DNA origami
coarse-grained modeling
self-assembly
simulation
Nanoscience & Nanotechnology
MD Multidisciplinary
Publication Status
Published