From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal

Abstract

We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4 A resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

Figure 1. Schematic Design, Sequence, and Crystal Pictures

(a) Schematic of the Tensegrity Triangle. The three unique strands are shown in magenta (strands restricted to a single junction), green (strands that extend over each edge of the tensegrity triangle) and dark blue (one unique nicked strand at the center passing through all three junctions). Arrowheads indicate the 3′ ends of strands. Nucleotides with A-form-like characteristics are written in bright blue. Cohesive ends are shown in red letters. (b) An Optical Image of Crystals of the Tensegrity Triangle. The rhombohedral shape of the crystals and the scale are visible.

Figure 2. Views of the Tensegrity Triangle

(a) Stereoscopic View of the Triangle Down its 3-Fold Axis. It is in the same orientation as the schematic in Figure 1a. The helix on the top edge starts above the mean plane of the molecule at the left and proceeds to the rear as it moves to the right. (b) Stereoscopic View of Two Triangles in Electron Density. This image is perpendicular to an edge of the rhombohedron, showing the connection of two triangles by sticky ends. Sticky ends are magenta for emphasis. Some density features belong to neighboring molecules not depicted.

Figure 3. Lattice Formed by Tensegrity Triangles

(a) Surroundings of a Triangle. This stereoscopic image distinguishes three independent directions by base pair color. The central triangle is flanked by six other triangles. (b) Rhombohedral Cavity Formed by Tensegrity Triangles. This stereoscopic image shows seven of the eight triangles that comprise the rhombohedron’s corners. The cavity outline is drawn white. The rear red triangle connects through one edge each to the three yellow triangles in a plane closer to the viewer. The yellow triangles are connected through two edges each to two different green triangles that are even nearer the viewer.