Fig. 1. Schematic of the composition of the Holliday junction which is required for the self-assembly of 3D DNA lattices.

a Three oligonucleotides mediate the crystallization of two self-assembling motifs (4 × 5 and 4 × 6) along with a “scrambled” sequence variant. A representative example of a 3D crystal is shown. b The structure of the Holliday junction is the key building block for assembly, and contains four arms using two oligonucleotides (S1; red) and (S3; tan) serving as crossover strands, with S2 (green) serving as a third “linear” complementary strand on each side. The complementary region of S1 contained either five or six bases (N bp) on each arm before each crossover at which point an identical sequence repeats in each consecutive arm for a total of four times (4×N) before beginning the series again (4 × 5 or 4 × 6). S1 subsequently serves as the scaffolding strand for the entire lattice. c The central building “block” that facilitates the 3D assembly. S1 tethers four 21-bp duplexes with the Holliday junction (boxed; translucent) at the core of the structure. The linear 21 base ssDNA oligonucleotide (S2) comprises one half of each duplex with the second crossover strand (S3) flanking each end (boxed). Each duplex is tailed by 2 bp complementary “sticky ends” (asterisks) which cohere to form continuous 3D arrays. d Representative bases where sequence asymmetry was imposed to prevent “sliding” of the strands to create 36 immobilized junctions. e Three unique symmetries (P3₂21, P3₂, and R3) are dictated by the 4×N scaffolding strand working in concert with the sequence at each immobile junction. f The 36 immobile junction sequences represented in an open Holliday junction format with each strand colored in accordance with (b). Nucleotides on each corresponding strand are indicated with the sequence positions on each component oligonucleotide corresponding to the colored scheme in (d).