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Numerical Evidence for Nucleated Self-Assembly of DNA Brick Structures

Aleks Reinhardt and Daan Frenkel
Phys. Rev. Lett. 112, 238103 – Published 11 June 2014
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Abstract

The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, predesigned DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever achieved the same degree of complexity. That failure seemed easy to rationalize: the larger the number of distinct building blocks, the higher the expected error rate for self-assembly. The experiments of Ke et al. have disproved this argument. Here, we report Monte Carlo simulations of the self-assembly of a DNA brick cube, comprising approximately 1000 types of DNA strand, using a simple model. We model the DNA strands as lattice tetrahedra with attractive patches, the interaction strengths of which are computed using a standard thermodynamic model. We find that, within a narrow temperature window, the target structure assembles with high probability. Our simulations suggest that misassembly is disfavored because of a slow nucleation step. As our model incorporates no aspect of DNA other than its binding properties, these simulations suggest that, with proper design of the building blocks, other systems, such as colloids, may also assemble into truly complex structures.

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  • Received 25 February 2014

DOI:https://doi.org/10.1103/PhysRevLett.112.238103

© 2014 American Physical Society

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A Recipe for Error-Free Self-Assembly

Published 11 June 2014

Computer simulations suggest that mixtures of hundreds of distinct nanoparticles or colloids can self-assemble into well-defined structures.

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Authors & Affiliations

Aleks Reinhardt and Daan Frenkel*

  • Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom

  • *Corresponding author. df246@cam.ac.uk

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Issue

Vol. 112, Iss. 23 — 13 June 2014

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