Three-dimensional molecular and nanoparticle crystallization by DNA nanotechnology
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Climbing the dimension ladder The basic notion of DNA nanotechnology requires two concepts—branched DNA and “sticky ends.” The ways in which the sequence of DNA strands could be designed, such that multiple strands could self-assemble into branched molecules rather than linear molecules, have been detailed.1 Branched molecules are designed to contain three to 12 arms,1 though the most commonly used branched molecules correspond to the four-arm Holliday junction recombination intermediate (Figure 1a). Sticky ends are short, single-stranded overhangs that extend from the end of a double helical DNA molecule; they result from one strand being longer at that site than the other. They can pair with each other just like other DNA strands, but, as seen in Figure 1a, they control intermolecular interactions. As a consequence, it is possible to imagine assembling branched molecules into larger assemblies. All the strands discussed for the self-assemblies here are synthetic, so it is easy to program the sticky ends, and the interactions they promote, as desired. The branched molecule in Figure 1a has sticky ends on all its extremities, and four of these are shown on the right side, having been assembled into a quadrilateral with many more sticky ends on the outside, suggesting the
possibility of forming a lattice. The four-arm junction is not as rigid as might be desired, so over the history of DNA nanotechnology, other motifs have been sought and found. The first notable object to be constructed by DNA nanotechnology methods was a DNA molecule with the connectivity of a stick-cube or a stick-rhombohedron, see Figure 1b.2 This is a “zero-dimensional object,” because it is entirely closed and cannot be extended to form a one-dimensional (1D), twodimensional (2D), or three-dimensional (3D) species. Each vertex corresponds to a three-arm branched junction, and each edge consists of two turns of double helical DNA. The angles between edges are variable, therefore there is no control on the absolute shape. In a sense, this is a topological construction, because the shape is not guaranteed, but the linking and branching are predetermined from the design. Each of the six faces corresponds to a cyclic single strand of DNA (single strand of DNA joined to itself from the beginning to the end, to form a cycle), and each strand is linked twice (because the edges are two turns long) to each of the four faces that flank it. For example, the front face corresponds to the red strand, and it is linked twice to the green strand, the cyan strand, the magenta strand, and the dark blue strands that flank it.
Nadrian C. Seeman, New York University, USA; [email protected] Oleg Gang, Department of Chemical Engineering, and Department of Applied Physics and Applied Mathematics, Columbia University, USA; [email protected] doi:10.1557/mrs.2017.280
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