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

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.

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• The Statistical Mechanics of Dynamic Pathways to Self-assembly
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• DNA brick self-assembly with an off-lattice potential
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Cited by in corpus (4)

• Recent advances in DNA origami-engineered nanomaterials and applications
• Direct observation and rational design of nucleation behavior in addressable self-assembly
• Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers
• Lattice models and Monte Carlo methods for simulating DNA origami self-assembly