Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly

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Title: Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly
Authors: Fonseca, P
Romano, F
Schreck, JS
Ouldridge, TE
Doye, JPK
Louis, AA
Item Type: Journal Article
Abstract: Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so) and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
Issue Date: 5-Apr-2018
Date of Acceptance: 28-Feb-2018
URI: http://hdl.handle.net/10044/1/58303
DOI: https://dx.doi.org/10.1063/1.5019344
ISSN: 0021-9606
Publisher: AIP Publishing
Journal / Book Title: Journal of Chemical Physics
Volume: 148
Issue: 13
Copyright Statement: © 2018 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in The Journal of Chemical Physics 148, 134910 (2018); https://doi.org/10.1063/1.5019344
Sponsor/Funder: The Royal Society
Funder's Grant Number: UF150067
Keywords: cond-mat.soft
cond-mat.soft
cond-mat.soft
cond-mat.soft
02 Physical Sciences
03 Chemical Sciences
09 Engineering
Chemical Physics
Article Number: 134910
Appears in Collections:Faculty of Engineering
Bioengineering



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