Augmented DNA Nanoarchitectures: A Structural Library of 3D Self‐Assembling Tensegrity Triangle Variants

Abstract

The DNA tensegrity triangle is known to reliably self‐assemble into a 3D rhombohedral crystalline lattice via sticky‐end cohesion. Here, the library of accessible motifs is expanded through covalent extensions of intertriangle regions and sticky‐end‐coordinated linkages of adjacent triangles with double helical segments using both geometrically symmetric and asymmetric configurations. The molecular structures of 18 self‐assembled architectures at resolutions of 3.32–9.32 Å are reported; the observed cell dimensions, cavity sizes, and cross‐sectional areas agree with theoretical expectations. These data demonstrate that fine control over triclinic and rhombohedral crystal parameters and the customizability of more complex 3D DNA lattices are attainable via rational design. It is anticipated that augmented DNA architectures may be fine‐tuned for the self‐assembly of designer nanocages, guest–host complexes, and proscriptive 3D nanomaterials, as originally envisioned. Finally, designer asymmetric crystalline building blocks can be seen as a first step toward controlling and encoding information in three dimensions.

Engineering DNA Crystals toward Studying DNA–Guest Molecule Interactions

“…As the motifs here could accommodate different DNA sequences and most drugs recognize only up to six base pairs, − ,, this system could allow study of a wide range of DNA–drug interactions. (3) In the crystals, the interhelical angles of the DNA junctions are ∼0° as in most of the DNA nanostructures − ,− (in contrast to 40–60° in previously reported crystal structures of DNA 4-arm junctions ,− ,− , ). The obtained, detailed, structure of the DNA junctions in this configuration would be highly valuable for designing fine DNA nanostructures at the Å level.…”

“…(3) In the crystals, the interhelical angles of the DNA junctions are ∼0°as in most of the DNA nanostructures 21−24,26−30 (in contrast to 40−60°in previously reported crystal structures of DNA 4-arm junctions 25,[31][32][33][34][35][36][37][39][40][41]44 ). The obtained, detailed, structure of the DNA junctions in this configuration would be highly valuable for designing fine DNA nanostructures at the Å level.…”

“…The key of this approach is engineering high-resolution DNA crystals. DNA as a programmable biomolecule provides a general and powerful tool for crystal engineering and nanoconstructions. − Though a series of engineered 3D DNA crystals have been reported, ,− they exhibit only modest quality of 3D order with modest X-ray diffraction resolutions. Such modest resolutions limit the applications of DNA crystals such as organizing guest molecules into hybrid crystals for structural determination by X-ray diffraction. , An urgent and critical problem is how we can engineer highly ordered DNA crystals.…”

An RNA Paranemic Crossover Triangle as A 3D Module for Cotranscriptional Nanoassembly

“…Due to the interconnectedness of the cube-shaped assembly, lower energy KLs in this context could lead to more cooperative and homogeneous assemblies. By optimizing the geometry of the PXT units and further understanding the energetics of intermolecular KL formation, it may be possible to make polycubes and periodic nanocages, [27] and potentially, the growth of RNA-based crystals.…”

“…[26] Importantly, the DNA TT was used as a rigid motif with sticky-end connections for self-asssembly of 3D lattices. [2,27] However, the TT concept has not been used in RNA nanostructures yet.…”