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

Published version
Peer-reviewed

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Authors

Wayment-Steele, H 
Reinhardt, A 

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.

Description

Keywords

DNA, Single-Stranded, Models, Molecular, Molecular Conformation, Monte Carlo Method

Journal Title

Soft Matter

Conference Name

Journal ISSN

1744-683X
1744-6848

Volume Title

13

Publisher

Royal Society of Chemistry
Sponsorship
Engineering and Physical Sciences Research Council (EP/I001352/1)
Engineering and Physical Sciences Research Council (EP/I000844/1)
This work was supported by the Engineering and Physical Sciences Research Council [Programme Grant EP/I001352/1]. HKWS acknowledges support from the Winston Churchill Foundation of the United States. Research carried out in part at the Center for Functional Nanomaterials, Brookhaven National Laboratory, which is supported by the US Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-SC0012704.
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