Self-assembly of irregular graphs whose edges are DNA helix axes

Phiset Sa-Ardyen, Natasha Jonoska, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

A variety of computational models have been introduced recently that are based on the properties of DNA. In particular, branched junction molecules and graphlike DNA structures have been proposed as computational devices, although such models have yet to be confirmed experimentally. DNA branched junction molecules have been used previously to form graph-like three-dimensional DNA structures, such as a cube and a truncated octahedron, but these DNA constructs represent regular graphs, where the connectivities of all of the vertexes are the same. Here, we demonstrate the construction of an irregular DNA graph structure by a single step of self-assembly. A graph made of five vertexes and eight edges was chosen for this experiment. DNA branched junction molecules represent the vertexes, and duplex molecules represent the edges; in contrast to previous work, specific edge molecules are included as components. We demonstrate that the product is a closed cyclic single-stranded molecule that corresponds to a double cover of the graph and that the DNA double helix axes represent the designed graph. The correct assembly of the target molecule has been demonstrated unambiguously by restriction analysis.

Original languageEnglish (US)
Pages (from-to)6648-6657
Number of pages10
JournalJournal of the American Chemical Society
Volume126
Issue number21
DOIs
StatePublished - Jun 2 2004

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Self assembly
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Self-assembly of irregular graphs whose edges are DNA helix axes. / Sa-Ardyen, Phiset; Jonoska, Natasha; Seeman, Nadrian.

In: Journal of the American Chemical Society, Vol. 126, No. 21, 02.06.2004, p. 6648-6657.

Research output: Contribution to journalArticle

Sa-Ardyen, Phiset ; Jonoska, Natasha ; Seeman, Nadrian. / Self-assembly of irregular graphs whose edges are DNA helix axes. In: Journal of the American Chemical Society. 2004 ; Vol. 126, No. 21. pp. 6648-6657.
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