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.
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7 April 2018
Research Article|
April 05 2018
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
Pedro Fonseca;
Pedro Fonseca
a)
1
Rudolf Peierls Centre for Theoretical Physics, University of Oxford
, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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Flavio Romano;
Flavio Romano
2
Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari
, Via Torino 155, 30172 Venezia Mestre, Italy
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John S. Schreck
;
John S. Schreck
3
Department of Chemical Engineering, Columbia University
, 500 W 120th St., New York, New York 10027, USA
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Thomas E. Ouldridge
;
Thomas E. Ouldridge
4
Department of Bioengineering, Imperial College London
, London SW7 2AZ, United Kingdom
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Jonathan P. K. Doye
;
Jonathan P. K. Doye
5
Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford
, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Ard A. Louis
Ard A. Louis
1
Rudolf Peierls Centre for Theoretical Physics, University of Oxford
, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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a)
Electronic mail: pedro.fonseca@physics.ox.ac.uk
J. Chem. Phys. 148, 134910 (2018)
Article history
Received:
December 13 2017
Accepted:
February 28 2018
Citation
Pedro Fonseca, Flavio Romano, John S. Schreck, Thomas E. Ouldridge, Jonathan P. K. Doye, Ard A. Louis; Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly. J. Chem. Phys. 7 April 2018; 148 (13): 134910. https://doi.org/10.1063/1.5019344
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