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Characterizing DNA star-tile-based nanostructures using a coarse-grained model

John S. Schreck, Flavio Romano, Ard A. Louis and Jonathan P.K. Doye

submitted

Abstract

We use simulations to investigate a key reaction in the self-assembly of many polyhedral structures from DNA star-tiles: the closure of open trimers into triangles. By using rare event methods, we find that the closure rate of trimers for tiles containing 7-nucleotide bulges is nearly ∼ 1000 times faster compared to those containing 3-nucleotide bulges, thus favoring the assembly of polyhedra with triangular faces. This variation is caused by the increased flexibility of tiles with larger bulge size, which leads to a significantly lower free-energy barrier to forming the initial base pair between the trimer ends. Our results help to rationalize and to guide DNA nanotechnology experiments that exploit the physical properties of the components as a means to control the assembly product.