Highly Symmetric, Self‐Assembling 3D DNA Crystals with Cubic and Trigonal Lattices

Abstract

The rational design of nanoscopic DNA tiles has yielded highly ordered crystalline matter in 2D and 3D. The most well‐studied 3D tile is the DNA tensegrity triangle, which is known to self‐assemble into macroscopic crystals. However, contemporary rational design parameters for 3D DNA crystals nearly universally invoke integer numbers of DNA helical turns and Watson–Crick (WC) base pairs. In this study, 24‐bp edges are substituted into a previously 21‐bp (two helical turns of DNA) tensegrity triangle motif to explore whether such unconventional motif can self‐assemble into 3D crystals. The use of noncanonical base pairs in the sticky ends results in a cubic arrangement of tensegrity triangles with exceedingly high symmetry, assembling a lattice from winding helical axes and diamond‐like tessellation patterns. Reverting this motif to sticky ends with Watson–Crick pairs results in a trigonal hexagonal arrangement, replicating this diamond arrangement in a hexagonal context. These results showcase that the authors can generate unexpected, highly complex, pathways for materials design by testing modifications to 3D tiles without prior knowledge of the ensuing symmetry. This study expands the rational design toolbox for DNA nanotechnology; and it further illustrates the existence of yet‐unexplored arrangements of crystalline soft matter.

Divergence and Convergence: Complexity Emerges in Crystal Engineering from an 8-mer DNA

“…(i) The component (one 8-mer DNA strand) is arguably the smallest, unique DNA component for assembly of any DNA nanostructure, thus pushing the boundary of the minimalist approach for DNA nanotechnology. − (ii) The 8-mer DNAs simultaneously form two different structural motifs, and both motifs together assemble into the final crystals. In prior studies, one set of strands always forms only one particular motif under one specific assembly condition; − ,− instead, the DNA strands form two different types of motifs in this study, thus leading to higher structural complexity. Such an integration of divergent and convergent assembly is a fundamentally new concept for increasing structural complexity and reducing the number of unique, component DNA strands.…”

“…Such an integration of divergent and convergent assembly is a fundamentally new concept for increasing structural complexity and reducing the number of unique, component DNA strands. (iii) The DNA arrangement in the crystals has the most complicated arrangement in all engineered DNA crystals so far. − ,− (iv) The molecular organization is a surprising discovery (though straightforward in retrospective view) that the DNA prefers a compact packing arrangement over a porous packing arrangement. Our findings may provide a strategy for guiding the self-assembly of DNA strands into one particular structure when there are multiple potential structures.…”

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

“…Yan et al used the layered-crossover motif to construct 3D-framework DNA origami structures, using a set of diamond-shaped layered crossover DNA tiles with accurately adjustable angles to assemble into 3D crystals up to several hundred microns in size [ 71 ]. Mao et al found that 3D DNA patterns with 24 bp repeating edges and non-integer transitions can produce controlled macroscopic self-assembly in 3D ( Figure 1 d,e) [ 58 , 59 ]. The pattern transcends the integer transitions paradigm, and the “rule of thirds” approach opens the door for exploring the topological self-assembly in designed nanomaterials.…”

Multifunctional Exo III-assisted scalability strategy for constructing DNA molecular logic circuits

“…1,2 Based on the principle of complementary base pairing, DNA molecules are being used in frontier areas such as neural networks, 3,4 information encryption 5,6 disease detection 7,8 and DNA storage. [9][10][11] With great potential for information transfer and processing, DNA molecules enable molecular logic circuits, [12][13][14] tiles, [15][16][17] walker machines, [18][19][20] and protein interaction. 21 Molecular logic circuits are circuits that perform basic logic operations, and they are often used to implement functions such as parity checking, 22,23 logic computations, 24,25 drug delivery 26,27 and biosensing.…”