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Complex shapes self-assembled from single-stranded DNA tiles

Abstract

Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape9,14,15,16,18,19,20,21,25. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA2,3,4,5,8,10,11,12,13,17,23 or RNA7,22 tiles into periodic3,4,7,22 and algorithmic5 two-dimensional lattices, extended ribbons10,12 and tubes4,12,13, three-dimensional crystals17, polyhedra11 and simple finite two-dimensional shapes7,8. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a ‘single-stranded tile’ (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly12. Although ribbons and tubes with controlled circumferences12 have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands—folded into a 3 nm-by-7 nm tile and attached to four neighbouring tiles—acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.

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Figure 1: Self-assembly of molecular shapes using single-stranded tiles.
Figure 2: Self-assembly of SST rectangles and tubes.
Figure 3: Simple shapes designed using a molecular canvas.
Figure 4: Complex shapes designed using a molecular canvas.

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Acknowledgements

We thank S. Chandarasekaran, X. Lim, W. Sun and R. Conturie for technical assistance; A. Marblestone, R. Barish, W. Shih, Y. Ke, E. Winfree, S. Woo, P. Rothemund and D. Woods for discussions; and J. Aliperti for help with preparation of the draft. This work was funded by Office of Naval Research Young Investigator Program Award N000141110914, Office of Naval Research Grant N000141010827, NSF CAREER Award CCF1054898, NIH Director’s New Innovator Award 1DP2OD007292 and a Wyss Institute for Biologically Inspired Engineering Faculty Startup Fund (to P.Y.).

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Authors and Affiliations

Authors

Contributions

B.W. designed the system, conducted the experiments, analysed the data and wrote the paper. M.D. conducted the experiments, analysed the data and wrote the paper. P.Y. conceived and guided the study, analysed the data and wrote the paper.

Corresponding author

Correspondence to Peng Yin.

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The authors declare competing financial interests in the form of a pending provisional patent.

Supplementary information

Supplementary Information

This folder contains 3 files. The file “Supplementary-Information-s1-s5” (Primary information) is the primary supplementary information file, and contains details of system design, experimental results, data analysis, and discussions. The file “sup-1.info.s6” (Diagrams) shows schematics of rectangles across scales, tubes across scale and four sets of edge protectors are shown on pages 2, 3 and 4 respectively. In order to see the segment names properly, one should print the file with a minimal size of 11×17 inches, 34×11 inches and 11×17 inches respectively for pages 2, 3 and 4. The file “Sup.info.s7” (Sequences and lists) contains firstly Sequence information of the structures in the paper and secondly lists of the names of the constituent strands for different shapes constructed from the molecular canvas. (ZIP 14311 kb)

Supplementary Table S8

The file contains sequence information of the structures in the paper. The sequence information is identical as the first part of Supplementary Information S7, but is presented in Excel format, and is easier to retrieve for a reader who wants to repeat the experiments described in the paper. (XLS 539 kb)

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Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–626 (2012). https://doi.org/10.1038/nature11075

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