From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal

Abstract

We live in a macroscopic three-dimensional world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires that we bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter.1 The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: [1] A motif whose 3D structure is robust, [2] dominant affinity interactions between parts of the motif when it self-associates, and [3] a predictable structures for these affinity interactions. Fulfilling all these criteria to produce a 3D periodic system is not easy, but it should readily be achieved by well-structured branched DNA motifs tailed by sticky ends.2 Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so;3 the helically repeating nature of DNA facilitates the construction of a periodic array. It is key that the directions of propagation associated with the sticky ends not share the same plane, but extend to form a 3D arrangement of matter. Here, we report the crystal structure at 4 Å resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle.4 The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

DNA self-assembly scaled up

“…Various DNA self-assembly methods (see ref. 8, for example) have been developed for constructing synthetic architectures that exhibit great geometrical complexity and nanoscale accuracy.…”

Nucleic Acid Nanotechnology

“…The initial target of the field was the formation of robust 3D crystals to solve the "crystallization problem" of macromolecular v crystallography (Seeman 1982). However, while awaiting the realization of this aim (Zheng et al 2009), numerous other milestones have been achieved, and other new directions have been enunciated. These have included the construction of DNA objects Seeman 1991), 2D lattices (Winfree et al 1998), nanomechanical devices (Mao et al 1999), robots (Sherman and Seeman 2004), and assembly lines (Gu et al 2010).…”

Supramolecular Wireframe DNA Polyhedra: Assembly and Applications

“…Mao et al have largely simplified the tile design for the assembly of 2D DNA lattices [27][28][29][30] as well as a 3D crystal [12] based on a sequence symmetry criterion that considers the intrinsic, geometrical symmetry of a DNA tile. For example, only three synthetic DNA single strands with different sequences are needed to form an n-point-star tile, including 3-, [27] 4-, [28] 5-, [29] and 6-point-star tiles, [30] though an n-point-star tile contains 2n＋1 strands.…”

“…After a fruitful development of almost three decades, DNA nanotechnology has been dramatically expanded to enable many unprecedented possibilities in fundamental scientific research and technical developments. [2][3][4][5][6][7][8][9][10][11] Besides the macroscopic DNA crystal which was reported in 2009 based on a DNA tensegrity triangle motif, [12] a variety of 1D, 2D and 3D DNA nanostructures have been built with precise, structural controls through multi-arm tile (n-point-star) assembly, [13,14] scaffolded DNA origami, [15] and single-stranded tile (SST) assembly. [16] Among various self-assembled DNA nano-objects (DNA supramolecular complexes) available so far, an enclosed structure in the form of a wireframe polyhedron is interesting due to various possible applications.…”