1. Department of Cancer Biology, Dana-Farber Cancer Institute
2. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
3. Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA.

Correspondence to: William M. Shih^1,2,3 Correspondence and requests for materials should be addressed to W.M.S. (Email: william_shih@dfci.harvard.edu).

Molecular self-assembly offers a 'bottom-up' route to fabrication with subnanometre precision of complex structures from simple components¹. DNA has proved to be a versatile building block^{2, 3, 4, 5} for programmable construction of such objects, including two-dimensional crystals⁶, nanotubes^{7, 8, 9, 10, 11}, and three-dimensional wireframe nanopolyhedra^{12, 13, 14, 15, 16, 17}. Templated self-assembly of DNA¹⁸ into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase 'scaffold strand' that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide 'staple strands'^{19, 20}. Here we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six shapes—monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross—with precisely controlled dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and heterotrimeric wireframe icosahedra. Proper assembly requires week-long folding times and calibrated monovalent and divalent cation concentrations. We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometre scale.

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