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 shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. 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-assembly. Although ribbons and tubes with controlled circumferences 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.

Figure 1. Self-assembly of molecular shapes using single-stranded tiles

a, The canonical SST motif, adapted from ref. . b, Design of an SST rectangle structure. Left and middle: two different views of the same secondary structure diagram. Each standard (full) tile has 42 bases (labelled U), and each top and bottom boundary (half) tile has 21 bases (labelled L). Right: a simplified ‘brick-wall’ diagram. Standard tiles are depicted as thick rectangles, boundary tiles are depicted as thin rectangles and the unstructured single-stranded portions of the boundary tiles are depicted as rounded corners. Each strand has a unique sequence. Colours distinguish domains in the left panel and distinguish strands in the middle and right panels. c, Selecting an appropriate subset of SST species from the common pool in b makes it possible to design a desired target shape, for example a triangle (left) ora rectangular ring (right).d, Design of a tube with prescribed width and length. e, Arbitrary shapes can be designed by selecting an appropriate set of monomers from a pre-synthesized pool that corresponds to a molecular canvas (top right). To make a shape, the SST strands corresponding to its constituent pixels (dark blue) will be included in the strand mixture and the remainder (light blue) will be excluded.

Figure 2. Self-assembly of SST rectangles and tubes

a–c, 24H × 28T SST rectangle. a, Schematic of rectangle formation. For a more detailed depiction, see Supplementary Fig. 2. Supplementary Information, section 6, contains strand diagrams for this and all other SST rectangles and tubes, and sections 7 and 8 contain sequences for all the structures constructed in this paper. b, 2% native agarose gel electrophoresis. U, unpurified; P, purified (by gel extraction from lane U). c, AFM image. Inset shows a magnified view of the outlined structure. See Supplementary Fig. 2 for a larger AFM image. d–f, 24H × 28T SST tube. d, Schematic of tube design. e, 2% native agarose gel electrophoresis. f, TEM image. Inset shows a magnified view of the outlined structure. See Supplementary Information, section 2.5, for a larger image. g–i, Rectangles and tubes across scales. g, AFM images of SST rectangles. The designed dimensions are 4H×4T (R1), 6H×7T (R2), 10H×10T (R3), 12H×14T (R4), 18H×20T (R5), 24H×28T (R6) and 36H×41T (R7). h, Logarithmic molecular weight. The pink asterisk indicates the weight of a typical M13 DNA origami as a reference point. nt, nucleotide. i, TEM images of SST tubes. The designed dimensions are 8H × 28T (T1), 8H × 55T (T2), 8H × 84T (T3), 24H × 28T (T4) and 12H × 117T (T5). All scale bars, 100 nm. See Supplementary Information, section 3.1, for the schematics of the rectangles and tubes and for a depiction of the molecular weights of all 118 distinct structures we constructed. See Supplementary Information, section 3.2, for the number of distinct constituent SST species (ranging from 12 to 1,068), the number of nucleotides (420 to 44,856), the measured widths (11 to 91 nm) and lengths (16 to 621 nm), the measured gel yield (0.4% to 32%), and the measured AFM yield (25% to 61%) of the 12 rectangles and tubes shown here. See Supplementary Information, sections 3.3 (rectangles) and 3.4 (tubes), for gel results, larger AFM and TEM images, and gel- and imaging-based yield analyses. The formation of full-length 8H × 84T tubes and full-length 12H × 177T tubes was also confirmed by streptavidin labelling of the tube ends (Supplementary Information, section 3.4.4).

Figure 3. Simple shapes designed using a molecular canvas

Top, schematics; bottom, 500nm × 500nm AFM images. The structures were constructed using the edge protector strategy, with respective gel yields of 16%, 19%, 22% and 16% (left to right; Supplementary Information, section 4.5), and AFM yields of 37%, 37%, 51% and 36% (left to right; Supplementary Information, section 4.7).

Figure 4. Complex shapes designed using a molecular canvas

AFM images of 100 distinct shapes, including the 26 capital letters of the Latin alphabet, 10 Arabic numerals, 23 punctuation marks and other standard keyboard symbols, 10 emoticons, 9 astrological symbols, 6 Chinese characters and various miscellaneous symbols. Each image is 150 nm × 150 nm in size.