Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 243

operation, the thrombin-binding DNA aptamers are mechanically switched between
a binding and nonbinding form. In another study, pH is used to switch the DNA
motif to release a telomere DNA binding protein by acidification that recognizes
specifically the duplex structure or a small molecule TMPyP4 by neutralization [ 85 ].
Another strategy is surface-supported self-assembly monolayer (SAM) of
thiol-terminated DNA molecular motifs on gold surface, reported by Liu et al.
(Fig. 11.14 b) [ 86 ]. Each device unit is composed for a motor part containing i-motif
sequence on the upper domain and a single-stranded spacer on the lower domain.
When pH is acidified or neutralized, the packing density of motor domain could
be switched between high (i-motif folds to close the container) and low (i-motif
extends to result in open state) states. In the closed state, small molecules are
encapsulated in the nanocontainer sealed by the densely packed i-motif quadruplex
domain, while in the open state, i-motif extends to random-coiled conformation,
allowing the small molecules to diffuse freely. Instead of on the surface, Liu et al.
encapsulated nanoscale objects, gold nanoparticles, into the acidified pH resulting
in DNA hydrogel [ 87 ]. Upon the increase of pH, the nanomotor consisting of i-motif
extends and the gel is melted, leading to the fast release of the nanoparticles.
Other than utilizing the buffer-dependent transition between single strand and
quadruplex, researchers have made full use of the programmability of structural
DNA nanotechnology to fabricate DNA objects containing a cavity and control
the trap and release of nanoobjects. Two attractive devices were constructed by the
groups of Turberfield and Kurt, respectively. The first is a reconfigurable tetrahedral
DNA cage (Fig. 11.14 c) [ 88 ]. By fueling the tetrahedral with the complementary
DNA segment, the cage is enabled to expand. Conversely, when the antifuel strands
are added, the “fuel” strands are pulled away from the edge of the cage, which is
contracted again. A tetrahedron with two different length edges is also made, and
they could independently change the volume of the cage. Recently, Turberfield et al.
have further demonstrated that the tetrahedral DNA cages could enter and survive
inside cultured mammalian cells effectively either with or without the aid of a
transfection reagent [ 89 ]. These results provide the great potential for the molecular
cage out of DNA to take a step forward to entrap and target delivery of biological
molecules.
In a different approach, Gothelf and coworkers built a three-dimensional DNA
box by using DNA origami technique, which could be dynamically manipulated
(Fig. 11.15 a) [ 14 ]. The lid of the box is functionalized with a dual “lock-key” system
composed of DNA duplexes with a sticky toehold for the displacement by the
externally added “key” strands. The opening process of the DNA lid was monitored
by a FRET process, since two fluorophores with overlapped fluorescence-absorption
spectra are inserted into adjacent positions of box. Based on the same principle of
DNA origami technique, Church's research group combined encapsulation and
logic release function of DNA containers, a big step forward to realize biological
applications [ 90 , 91 ]. They constructed an autonomous DNA nanorobot capable
of transporting molecular payloads to cells through an aptamers-lock mechanism
(Fig. 11.15 b). The nanorobot is a 3D DNA origami in the shape of a hexagonal
barrel with dimensions of 35 nm 35 nm 45 nm. The barrel consists of two