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

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.

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Cited by in corpus (6)

• Coarse-grained modelling of the structural properties of DNA origami
• A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
• Designing the self-assembly of arbitrary shapes using minimal complexity building blocks
• Direct observation and rational design of nucleation behavior in addressable self-assembly
• Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers
• Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling