Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra
Yu He1, Tao Ye1, Min Su2, Chuan Zhang1, Alexander E. Ribbe1, Wen Jiang2 & Chengde Mao1
DNA is renowned for its double helix structure and the base pairing that enables the recognition and highly selective binding of complementary DNA strands. These features,and the ability to create DNA strands with any desired sequence of bases, have led to the use of DNA rationally to design various nanostructures and even execute molecular computations1–4. Of the wide range of self-assembled DNA nanostructures reported, most are one- or two-dimensional5–9. Examples of three-dimensional DNA structures include cubes10, truncated octahedra11, octohedra12 andtetrahedra13,14, which are all comprised of many different DNA strands with unique sequences. When aiming for large structures, the need to synthesize large numbers (hundreds) of unique DNA strands poses a challenging design problem9,15. Here, we demonstrate a simple solution to this problem: the design of basic DNA building units in such a way that many copies of identical units assemble into largerthree-dimensional structures. We test this hierarchical self-assembly concept with DNA molecules that form three-point-star motifs, or tiles. By controlling the flexibility and concentration of the tiles, the one-pot assembly yields tetrahedra, dodecahedra or buckyballs that are tens of nanometres in size and comprised of four, twenty or sixty individual tiles, respectively. We expect that our assemblystrategy can be adapted to allow the fabrication of a range of relatively complex three-dimensional structures. Our approach to forming DNA polyhedra is a one-pot selfassembly process illustrated in Fig. 1: individual single strands of DNA first assemble into sticky-ended, three-point-star motifs (tiles), which then further assemble into polyhedra through sticky-end association between the tiles.The three-point-star motif contains a threefold rotational symmetry and consists of seven strands: a long repetitive central strand (blue-red; strand L or L9), three identical medium strands (green; strand M), and three identical short peripheral strands (black; strand S). At the centre of the motif are three single-stranded loops (coloured red). The flexibility of the motif can be easily adjustedby varying the loop length, with increased loop length increasing tile flexibility. The termini of each branch of the tile carry two complementary, four-base-long, single-stranded overhangs, or sticky ends. Association between the sticky-ends allows the tiles to further assemble into larger structures such as the polyhedra described here. The three-point-star motif has been used for the assemblyof flat two-dimensional (2D) crystals16,17, where neighbouring units face in opposite directions of the crystal plane to cancel the intrinsic curvature of the DNA tiles. Because polyhedra are closed threedimensional (3D) objects containing a finite number of component tiles, we reasoned that three factors would promote polyhedron formation. (1) If all component DNA tiles face in the samedirection, their curvatures would add up and promote the formation of closed structures. For example, some closed DNA tubular structures have
been observed when all DNA tiles face the same side of the crystal plane7. This requirement can be easily satisfied by choosing the length of each pseudo-continuous DNA duplex in the final structures to be four turns (42 bases). (2) Self-assembly is aninter-unit process. This means that higher (micromolar) DNA concentrations favour large assemblies such as flat 2D crystals, whereas lower DNA concentrations favour small assemblies such as polyhedra. This concentration-dependent kinetic effect should also provide some control over polyhedral size. (3) 2D crystal formation was found to require loops that are two to three bases long17. Elongating the...