One of the main objectives of the field of DNA Nanotechnology is to design and form 3D DNA crystalline lattices to serve as hosts for various macromolecules. Watson-Crick base pairing implies that with careful sequence design considerations, synthetic DNA structures can be programmed to self-assemble in a designed fashion. The basis of this work is the tensegrity triangle, a robust DNA structure with pseudo-three-fold rotational symmetry, consisting of three double helices whose helical axes are linearly independent. These double helices are connected pairwise by Holliday-like junctions, and each helical terminus is capped with short single-stranded oligonucleotide segments, termed “sticky-ends,” that allow the structure to propagate in 3D. Here, we expand the library of accessible motifs though symmetric (all triangle edges modified equally) and asymmetric extensions of inter-triangle regions, linkages of adjacent triangles with double helical segments, and the covalent fusion of one pair of these designs. These modifications center around exploring the tunability of cross-sectional areas and cavity sizes within the crystalline lattice – parameters significant to the harboring of macromolecules. We provide a design for 3 turn and 4 turn tensegrity triangles with 7 base pairs per inter-junction region through extension of inter-triangle regions (3T7 and 4T7, respectively), as well as analogous 3 turn and 4 turn triangles through sticky-end insertion of 10 and 21 base pair duplexes, respectively, between adjacent 2T7 triangles (2T7+10 and 2T7+21). We also investigate asymmetric modifications: a 223-turn triangle, in which one edge consists of 3 turns, a 224-turn triangle, in which one edge consists of 4 turns, and a 234-turn triangle, in which one turn consists of 2 turns, another 3 turns, and the last 4 turns. We report the successful formation of rhombohedral crystals that diffract to 7.5 Å for the 3T7, 7.9 Å for the 2T7+10, 11.1 Å for the 4T7, 11.9 Å for the 2T7+21, 5.6 Å for the 223, 5.7 Å for the 224, and 8.7 Å for the 234, as well as the crystal structures for all eight designs. We are optimistic that this work will allow for the creation of larger and more complex 3D DNA crystal lattices to serve as the scaffolding for diverse guest molecules.

Modulation of DNA crystalline triangle lattices by the extension and addition of double helical segments

ACS Fall 2021

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