Knitting complex weaves with DNA origami

Abstract

The past three decades have witnessed steady growth in our ability to harness DNA branched junctions as building blocks for programmable self-assembly of diverse supramolecular architectures. The DNA-origami method, which exploits the availability of long DNA sequences to template sophisticated nanostructures, has played a major role in extending this trend through the past few years. Today, two-dimensional and three-dimensional custom-shaped nanostructures comparable in mass to a small virus can be designed, assembled, and characterized with a prototyping cycle on the order of a couple of weeks.

Figure 1

Branched DNA molecules as basic building blocks for nanoconstruction. (A) A Holliday junction is formed by four DNA oligonucleotides each pairing with its neighboring two partners. (B) An antiparallel double-crossover molecule with single-stranded overhangs is formed by five DNA oligonucleotides. It can be conceptualized as two parallel DNA double helices brought together through strand exchange at junction points. (C) A two-dimensional array assembled from the molecule shown in (B) through base paring between the single-stranded overhangs. Note the green-tinted molecules are identical to the red-tinted ones but rotated 180 degrees in the plane of the page.

Figure 2

Design scheme and examples of planar, single-layer DNA origami. (A) Top: the finished design layout of a planar, single-layer origami. The dark blue strand represents the long DNA scaffold that winds through the entire structure, which is held together by many short DNA oligonucleotides (colored strands) known as staple strands. This diagram was rendered with caDNAno [21]. Bottom: abstract models of the same origami structure with each cylinder representing a DNA double helix. The left diagram is more realistic as it shows the bowing of DNA helices caused by the electrostatic repulsion. (B) Selected examples of planar, single-layer origami. Top row (from left to right): a star [6], a smiley face [6,10], and a dolphin; middle row (from left to right): a long strip with repeated small cavities [37] and a rectangle with a large cavity [38]; bottom row (from left to right): two different triangles and a rectangle [6].

Figure 3

Objects formed by folding single-layer origami. Front row (from left to right): a spiral [20] and a wireframe triangle [23]. Middle: a six-helical bundle tube. Back row (from left to right): a closed face tetrahedron [18]; a box with the top lid controllable for opening and closing (shown only the closed state) [16]; open end prisms with six, four and three faces [14]; a wire-framed beach ball [20]; a box with two sets of three faces closed by face-sharing staples (detail not shown here) [17]; a wire-framed icosahedron [15]. Note that the depiction of spacing between parallel cylinders used here is meant to reflect qualitatively the relative density of crossovers per helical interface. Each underlying grid square has dimensions 20 nm by 20 nm.

Figure 4

Design scheme and examples of multi-layer origami. (A) The finished design layout (rendered in caDNAno [21]) of a three-layer origami with a honeycomb-lattice cross section. In total, 18 double helices are held together through crossovers within scaffold DNA (black) and staple strands (orange, grey and blue). (B) Inset figures: upper left: an abstract model of the three-layer origami shown in (A) with each cylinder representing a double helix; lower left: a partially unfolded intermediate, useful for conceptual purposes, of the three-layer origami; upper right: a zoom-out view of a multilayer DNA origami consisting of 64 helices based on the square-lattice design [19]. Main figure: Multi-layer origami with a diverse of shapes. On the sides: 60-helix ribbons with global right-handed or left-handled twist [20]. In the middle, first row in the front: a series of multi-layer DNA origami with different aspect ratios based on the honeycomb lattice design [21]; second row, from left to right: multi-layer, honeycomb DNA origami that resemble the shape of a square nut, a slotted cross, a stacked cross, a genie bottle and a railed bridge [15]; third row: a series of multi-layer DNA origami, based on the square-lattice design, with different aspect ratios [19]; behind the third row: multi-layer, honeycomb DNA origami consisting of 18-helix ribbons bent at angles from 0 to 180° [20]. The bent segments are highlighted in red. Each underlying grid square has dimensions 20 nm by 20 nm.