DNA Origami Nanostructures - DNA Nanotechnology: From Structure to Function - page 209

they prepared a 26-kilobase single- strand DNA fragment, which was obtained from
long-range PCR amplification and subsequent enzymatic digestion, for folding large
DNA origami (Fig. 10.4 a). The results showed that this strand could fold into a
supersized DNA with a theoretical size of 238 108 nm 2 . Accordingly, 800 short
staple strands were used to aid the folding. Yan's group reported a more complex
design by using a double-stranded scaffold to fabricate integrated DNA origami
structures that incorporate both of the constituent ssDNA molecules (Fig. 10.4 b)
[ 44 ]. Unlike Shih's dsDNA strategy mentioned above, this design requires a certain
level of cooperation between the two ssDNA components to form the integrated
structure. This is particularly challenging because there is an increased possibility
that the complementary ssDNA molecules will recombine to form the initial dsDNA
due to their spatial proximity. To address this issue, they extensively studied the
experimental conditions and found an optimized nonlinear annealing program for
making a big DNA origami triangle which has an edge length of 215 nm and
utilized one-fourth of the ds

DNA scaffold. Compared with the M13-based triangle
presented in Rothemund's Nature paper in 2006 [ 8 ], this big triangle is 3.4 and
2.8 times larger in molecular weight and area, respectively. However, they failed in
using the entire double-stranded

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DNA genome to construct an even larger DNA
origami structure with an amazing size of 500 500 nm 2 in theory, implying that
there is still a significant bottleneck in using very long dsDNA templates to scale up
DNA origami assembly.
Different from the long scaffold strategy, a more efficient and practical strategy
is the higher-order assembly of individual DNA origami units into large arrays. This
idea was first proposed by Rothemund in his pioneer work in which he designed
extended staples on DNA triangle edges to induce the assembly of six triangles into
a big hexagon [ 8 ]. Such principle was then followed by other researchers. Andersen
and Kjems constructed a DNA origami dolphin dimer [ 13 ]. Shih and Chou prepared
a DNA origami nanotube which was assembled from two short nanotubes, and
this dimer nanotube could facilitate the induced alignment of membrane proteins
for NMR structure determination [ 45 ]. Simmel's group manufactured micrometer-
long DNA nanoribbons by multimerization of rectangular DNA origami units, and
they performed single-molecule kinetics and super-resolution microscopy studies
on these nanoribbons [ 46 ]. They later compared the different bridging methods for
DNA nanoribbon polymerization and investigated the length distribution and twist
in long nanoribbons [ 47 ]. Lieberman's group also compared assembly strategies for
orienting and aligning DNA origami into long nanoribbons [ 48 ]. Since individual
DNA origami rectangle has a certain amount of curvature which may cause twist
in assembled long nanoribbons, Yan's group developed a “zigzag DNA origami”
strategy to overcome this problem (Fig. 10.4 c) [ 49 ]. By alternating the number of
base pairs between consecutive crossovers of neighboring helices between 14 and
28 bp, two adjacent crossovers within the same helix are spaced exactly four turns
apart. Thus, the twist density of this design is 10.5 bp per turn, the same as in B-form
DNA, so the global twisting of the structure should be minimized.

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