Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Creating combinatorial patterns with DNA origami arrays

DNA origami (Rothemund 2006) and smaller DNA tiles (Winfree et. al. 1998) have been used as effective scaffolds to create complex patterns for organizing molecules with nanometer precision but of a limited size. Arrays of DNA origami (Liu et. al. 2011) and DNA tiles have been shown to be capable of creating patterns in a larger scale, either periodically or following a specific set of rules defined by a cellular automaton (Rothemund et. al. 2004). Here we aim to create a variety of large-scale complex patterns by using a combinatorial approach with a mathematically simple and elegant rule called Truchet tiling. We developed a symmetric square DNA origami tile that can rotate and attach to one another on all four sides, with which we constructed two-dimensional finite and unbounded arrays. Labeling the origami tile with Truchet patterns using double-stranded extensions, we successfully observed a combinatorial number of complex maze-like patterns on the origami arrays created in one test tube. With a combination of just pi-pi stacking bonds and very short sticky ends, we identified edge designs of the origami tile that simultaneously allow cooperativity and sufficient specificity in tile-tile interactions and yielded robust crystallization with a simple incubation protocol. Origami arrays on the scale of ten by ten microns were reliably generated. The DNA origami arrays with combinatorial patterns can be used to test molecular robots against diverse operating environment with increasing complexity, thus help us to better understand the engineering principles for building robust molecular devices. As combinatorial approaches have been used to substantially accelerate drug discovery (combinatorial organic synthesis), identification of functional nucleic acids (SELEX), and optimization of new materials (combinatorial material screening), our approach could also potentially be used to efficiently screen functional molecular devices and advance nanoscale fabrication that involves the organization of components in molecular electronic, photonic and plasmonic devices.


This research was supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund (1010684), a Faculty Early Career Development Award from NSF (1351081), and the Molecular Programming Project under NSF expedition in computing (1317694).

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    E. Winfree, F. Liu, L. A. Wenzler & N. C. Seeman (1998). Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539-544.

    W. Liu, H. Zhong, R. Wang & N. C. Seeman (2011). Crystalline two-dimensional DNA - origami arrays. Angewandte Chemie 123, 278-281.

    P. W. Rothemund, N. Papadakis & E. Winfree (2004). Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology 2, e424.

Grigory Tikhomirov
Philip Petersen
Lulu Qian*

California Institute of Technology
Pasadena, CA 91125, USA

*Phone: (626)395-1228