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

Rationally designing DNA crystal lattices to scaffold molecular species and solve their structure with X-ray crystallography is the foundational goal of structural DNA nanotechnology. DNA is an ideal molecule for the construction of 3D crystals with tunable properties due 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. In this work, 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 were able to determine a high resolution (2.7 A) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 A) using a modified sticky-end sequence. The structure is distinct due to a unique immobile Holliday junction sequence, which in turn allowed us to produce crystals that provided a structure with unprecedented atomic detail. Furthermore, we expanded the crystal cavities by 50% by adding an additional helical turn between junctions, and we solved the structure of the resulting lattices to 4.5 A resolution by molecular replacement. These crystals will potentially enable the discrete placement of guest molecules-such as small molecule catalysts, nanoparticles, or peptides/proteins-amenable to the cavity size within the scaffold with atomic precision.