Biomedical Engineering Reference
In-Depth Information
The assembly proteins by DNA nanostructure have been further extended to
two-dimensional (2D) nanoarrays [
69
]. The DNA nanoscaffold is designed to
contain multiple aptamers with precise distance. There are four kinds of double-
crossover (DX) tiles utilized in the formation of 2D array shown by a different
color in Fig.
2.2
c. Tile B (red) contains PDGF aptamer, while tile C (dark green)
is decorated by thrombin aptamer. The ABCD tile system forms 2D periodic array
by sticky end complementation with desired aptamer distance. Upon the protein
binding, the height of aptamer binding position increases from
0.7 to
2.0 nm
as measured by AFM, and the distance was observed to be 32 nm between two
different lines of PDGF proteins and 64 nm between two adjacent thrombin proteins.
The experiments demonstrated that the assembly of proteins by multiple aptamers
on 2D DNA architecture can be achieved. The aptamers remain their activity after
assembled on the rigid tile plane.
Further, protein assembly on more complex DNA nanostructure with aptamers
has also been proven. DNA origami was designed as rectangular-shaped DNA
nanoarrays with aptamer sequences at specific positions, such as an S-shaped
pattern. In Fig.
2.2
d, the AFM evidence showed that DNA origami with thrombin
aptamers can arrange thrombin proteins into the S-shaped pattern. The rigid
surface avoided the undesired sandwich of proteins which was also observed in
the previous work [
68
]. Moreover, not only the aptamer can be patterned on DNA
nanostructures but also DNAzymes have been organized into specific patterns using
self-assembly of DNA DX tiles to realize both structural and catalytic facets of DNA
nanotechnology [
70
].
Besides mounting items on assembled DNA template, aptamer-ligand inter-
action can also act as “glues” to synthesize linear or branched nanostructures.
Willner's group took the advantage that thrombin has two specific aptamers binding
to different sites of the protein to fabricate protein-DNA hybrid nanostructures
[
71
]. As shown in Fig.
2.2
e, the linear assembling unit contains
“
-aptamer at
3
0
end and
-aptamer at 5
0
end. Upon binding with thrombin, a supramolecular
nanowire formed by the assembly of aptamer units to thrombin units with a 1:2
ratio. To design branched aptamer-protein assembly, a triangle assembling unit was
created with three edges formed by self-hybridized duplex DNA and
'
-aptamer
at each vertex. The combination of linear and triangle assembling units induced
the formation of Y-shaped nanowires. The nanostructures could be observed with
atomic force microscopy and even with fluorescent microscopy after modification
of fluorophore.
'
2.3.2
DNA Assembly with FNAs for Interaction Study
The assembly of multiple molecules while controlling the spacing between them is
an important goal for nanotechnology. It provides an excellent platform for studying
as well as manipulating the distance-dependent molecular interactions, enzymatic
cascade reactions, and even cell-cell interaction. Several examples using DNA
assembly with FNAs for such interaction study are listed here.
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