Jump to main content
Jump to site search

Issue 8, 2017
Previous Article Next Article

Investigating the role of boundary bricks in DNA brick self-assembly

Author affiliations

Abstract

In the standard DNA brick set-up, distinct 32-nucleotide strands of single-stranded DNA are each designed to bind specifically to four other such molecules. Experimentally, it has been demonstrated that the overall yield is increased if certain bricks which occur on the outer faces of target structures are merged with adjacent bricks. However, it is not well understood by what mechanism such ‘boundary bricks’ increase the yield, as they likely influence both the nucleation process and the final stability of the target structure. Here, we use Monte Carlo simulations with a patchy particle model of DNA bricks to investigate the role of boundary bricks in the self-assembly of complex multicomponent target structures. We demonstrate that boundary bricks lower the free-energy barrier to nucleation and that boundary bricks on edges stabilize the final structure. However, boundary bricks are also more prone to aggregation, as they can stabilize partially assembled intermediates. We explore some design strategies that permit us to benefit from the stabilizing role of boundary bricks whilst minimizing their ability to hinder assembly; in particular, we show that maximizing the total number of boundary bricks is not an optimal strategy.

Graphical abstract: Investigating the role of boundary bricks in DNA brick self-assembly

Back to tab navigation

Publication details

The article was received on 05 Dec 2016, accepted on 31 Jan 2017 and first published on 31 Jan 2017


Article type: Paper
DOI: 10.1039/C6SM02719A
Citation: Soft Matter, 2017,13, 1670-1680
  • Open access: Creative Commons BY license
  •   Request permissions

    Investigating the role of boundary bricks in DNA brick self-assembly

    H. K. Wayment-Steele, D. Frenkel and A. Reinhardt, Soft Matter, 2017, 13, 1670
    DOI: 10.1039/C6SM02719A

    This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Material from this article can be used in other publications provided that the correct acknowledgement is given with the reproduced material.

    Reproduced material should be attributed as follows:

    • For reproduction of material from NJC:
      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the Centre National de la Recherche Scientifique (CNRS) and the RSC.
    • For reproduction of material from PCCP:
      [Original citation] - Published by the PCCP Owner Societies.
    • For reproduction of material from PPS:
      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the European Society for Photobiology, the European Photochemistry Association, and RSC.
    • For reproduction of material from all other RSC journals:
      [Original citation] - Published by The Royal Society of Chemistry.

    Information about reproducing material from RSC articles with different licences is available on our Permission Requests page.

Search articles by author

Spotlight

Advertisements