DNA Origami Nanostructures - DNA Nanotechnology: From Structure to Function - page 204

switchable lid [ 15 ]. Endo and Sugiyama reported hollow DNA prism structures
constructed by folding planar DNA origami with multiple rectangular arms [ 16 ].
Yan's group created a 3D DNA origami tetrahedron with estimated total external
volume and internal cavity of about 1.8 10 23 and 1.5 10 23 m 3 , respectively

(Fig. 10.2 d) [ 17 ].
The above DNA origami 3D nanostructures were all constructed by folding
planar sheets. This design principle is simple and straightforward but since planar
DNA origami has intrinsic flexibility, it would be difficult to build rigid and various
3D nano-objects. The next breakthrough in this field was reported by Shih's group
[ 18 ]. They used a different strategy to achieve the building of custom 3D shapes
(Fig. 10.2 e). The key in their design principle is that the 3D shapes are composed
of honeycomb lattice. This design could be conceptualized as stacking corrugated
sheets of antiparallel helices. The resulting structures resemble bundles of double
helices constrained to a honeycomb lattice. The shape and size could be adjusted
by changing the number, arrangement, and lengths of the helices in the lattice.
They also developed a new program called caDNAno to assist the design [ 19 ]. In
addition, hierarchical assembly of structures can be achieved by programming staple
strands to link separate scaffold strands. Based on this design, they also engineered
complex 3D shapes with controlled twist and curvature at the nanoscale, by targeted
insertions and deletions of base pairs [ 20 ]. Later on, Shih's group collaborated with
Yan's group to achieve a more compact design which used square lattice instead
of honeycomb lattice (Fig. 10.2 f) [ 21 ]. A square lattice provides a more natural
framework for designing rectangular structures with the ability to create surfaces
that are more flat than that using the honeycomb lattice. In brief, Shih's strategy
shows the amazing versatility of DNA in building 3D nano-objects. However, there
remains a challenge that they need about 1 week for the annealing process and the
yield is considerably low.
Following the effort to increase the complexity of DNA origami shapes, Yan's
group reported the first topological DNA origami architecture - a Mobius strip
[ 22 ]. It is a topological ribbonlike structure that has only one side. Due to
intrinsic curvature of the helices, the authors observed a preference for right-handed
structures. A seam could also be incorporated in the strip. Depending on the position
of the seam, the strip could be split into different topological objects such as
supercoiled ring and catenane structures by using strand displacement to open the
seam.
Recently, in an escape from the rigid lattice model used for conventional DNA
origami nanostructures, Yan's group reported a new strategy for the building
of 3D DNA origami with complex curvatures [ 23 ]. Firstly, a designed curved
shape composed of concentric rings is filled by following the contours of the
outline and conceptually “winding” double-helical DNA into rings. Secondly,
crossovers between helices and nick points are placed carefully in order to provide a
combination of structural flexibility and stability. Concentric rings of DNA are used
to generate in-plane curvature, constrained to 2D by rationally designed geometries
and crossover networks. Out-of-plane curvature is introduced by adjusting the
particular position and pattern of crossovers between adjacent DNA double helices.