DNA Origami Nanostructures - DNA Nanotechnology: From Structure to Function - page 202

widely used throughout the shape for rigidity, and the distance between successive
crossovers is carefully designed to lessen twist. The scaffold sequence does not need
a specific design, because the success of DNA origami is ensured by strand dis-
placement reaction [ 10 ], in which a longer region of complementarity between the
staple and the scaffold stabilizes the staple-scaffold interaction over the scaffold's
secondary structure. Rothemund chose the genomic DNA from the virus M13mp18
with more than 7,000 bases as the scaffold. More than 200 staple strands were used
to help folding, and different shapes were able to be assembled from different sets
of staple strands, such as square, triangle, star, and disk (Fig. 10.1 b). The resulting
DNA structures all conform well to the design and have a diameter of roughly
100 nm and a spatial resolution of 6 nm. Moreover, since each staple can serve as a
pixel of a canvas, Rothemund programmed the structures to bear complex patterns
through modifying specific staples with dumbbell hairpins. He also achieved large
combinational shapes by designing extended staples that connected shapes along
their edges.
DNA origami is considered as a breakthrough in structural DNA nanotechnology,
which has produced two main achievements. The first is the amazing nano-
architecture it has made possible. Besides the arbitrary geometry, the patterns
on the 100-nm-sized DNA shapes have a tenfold higher complexity than that of
any tile-based patterns. Fifty billion copies of the pattern are created at once via
DNA origami, whereas only one copy can be made at a time by AFM or STM
manipulation. Individual unpatterned origami is about 4.7 MDa, comparable to
that of nature's most complex self-assembled machines, eukaryotic ribosome with
4.2 MDa [ 11 ]. The second achievement is experiment simplification. Conventional
DNA assembly usually needs all the involved strands to be highly purified and
precisely equimolar and has an annealing procedure extending to several days.
In contrast, unpurified staples have been used successfully at stoichiometries that
varied over an order of magnitude in DNA origami, and a thermal ramp of less than
2 h is generally enough.

10.3 Structural Evolutions: From 2D to 3D, from Flat

to Curved

Since the technique of DNA origami has so many advantages, several studies have
undertaken the construction of a number of intricate and creative architectures.
In the cases of 2D nanopatterns, Qian et al. created an asymmetric shape via
DNA origami, the analogic China map (Fig. 10.2 a) [ 12 ]. CDNA team in Aarhus
constructed the shape of a common dolphin (Fig. 10.2 b), with a flexible tail by
controlling the amount of seam crossover strands within the region [ 13 ]. The DNA
origami technique has also been extended to create 3D nanostructures. Andersen
et al. designed an addressable DNA cubic box with a controllable lid (Fig. 10.2 c)
[ 14 ]. In that design, an entire M13 strand was divided into six sections, and each
section was used to build one sheet (face). Two neighboring faces in the box were