DNA Origami Nanostructures - DNA Nanotechnology: From Structure to Function - page 211

Furthermore, Endo and Sugiyama proposed a programmed-assembly system
using DNA jigsaw pieces, and on each jigsaw piece, it contains sequence-
programmed connection sites, a convex connector, and a corresponding concavity
[ 50 ]. They suggested that three interactions were responsible for the programmable
higher-order assembly: (1) Watson-Crick base pairing at the connector through
extended staples, (2) shape fitting of the adjacent jigsaw pieces, and (3) -stacking

interactions of the side edges. They achieved both 1D [ 50 ] and 2D (Fig. 10.4 d) [ 51 ]
self-assembly of multiple DNA origami jigsaw pieces.
The aforementioned linking strategy gained remarkable success in constructing
1D higher-order DNA origami shapes. But in the case of 2D assembly, the yield
was relatively low. In a report published by Seeman's group [ 52 ], they suggested
that the key of this problem is that all the helix axes in rectangular DNA origami lie
parallel to the direction in which the origami units actually cohere. Thus, a possible
alternative method for the creation of a 2D origami array would be to use an origami
tile whose helix axes propagate in two independent directions (Fig. 10.4 e). This
design principle led to the using of a “cross”-shaped DNA origami unit in which
there are two orthogonal domains to the origami tile, one in a plane above the other.
They also showed that this strategy could overcome the problem of twist by using
two independent cross-shaped units for polymerization. As the two layers of each
origami unit have opposite orientations relative to the tile plane, they alternated the
origami units with the same units rotated by 90 ı , so that the top layer of one tile
was bonded to the bottom layer of the next. Thus, the designed alternating structure
looked like a braided origami pattern. Using a similar but simpler strategy, Endo and
Sugiyama achieved the construction of two finite-sized 2D DNA origami patterns
with four-way DNA origami units [ 53 ]. Unlike Seeman's work, the four-way unit
used here has a planar structure.
Another different strategy for scaling up was invented by Yan's group. In that
design [ 54 ], they suggested that instead of ssDNA staples used in DNA origami, an
origami itself may also mimic the function of a staple if single-stranded overhangs
are extended at the four corners. By introducing bridge strands, each origami-
based “staple tiles” could hybridize with the scaffold and form large structures
that contain several small staple tiles. The size of an individual staple tile is
dependent on the length of its scaffold (scaffold for staple tile). The final size of
the assembled structure is dependent on the size of staple tiles and also the length of
its scaffold (scaffold for large structure). As a proof-of-concept demonstration, they
tested the construction of three fully packed 2D origami structures using altered
numbers of staple tiles. The total numbers of tiles used in the three constructs
were 5 5 D 25 (90 110 nm 2 ), 7 8 D 56 (140 200 nm 2 ), and 5 11 D 55
(100 280 nm 2 ). This strategy was further improved by using preformed scaffold
frames [ 55 ]. In this work, several original origami staple tiles (M13 scaffold) were
assembled along a preformed loose DNA framework (PhiX174 scaffold) rather
than the ssDNA scaffold. It was found that various superorigami structures (e.g.,
a superstructure, with an area of 220 375 nm 2 , assembled from mixed hexagonal
and diamond staple tiles) could be obtained by this method with relatively high
yields (Fig. 10.4 f).