An Organic Semiconductor Organized into 3D DNA Arrays by “Bottom‐up” Rational Design

Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles

Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson-Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.

Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds

A quasi-one-dimensional organic semiconductor, hepta(p-phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self-assembled from an HPV-DNA pseudo-rhombohedron edge by rational design and characterized by X-ray diffraction. Templated by the DNA motif, HPV molecules exist as single-molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV-DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.

A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail

DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.

Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering

DNA tile-based assembly provides a promising bottom-up avenue to create designer two-dimensional (2D) and three-dimensional (3D) crystalline structures that may host guest molecules or nanoparticles to achieve novel functionalities. Herein, we introduce a new kind of DNA tiles (named layered-crossover tiles) that each consists of two or four pairs of layered crossovers to bridge DNA helices in two neighboring layers with precisely predetermined relative orientations. By providing proper matching rules for the sticky ends at the terminals, these layered-crossover tiles are able to assemble into 2D periodic lattices with precisely controlled angles ranging from 20° to 80°. The layered-crossover tile can be slightly modified and used to successfully assemble 3D lattice with dimensions of several hundred micrometers with tunable angles as well. These layered-crossover tiles significantly expand the toolbox of DNA nanotechnology to construct materials through bottom-up approaches.