Biomedical Engineering Reference
In-Depth Information
Therefore, they advantaged the system by making DNA 2D arrays carrying bar-
coded fluorescent dyes and target sensing units to achieve multiplexed detection
(Fig.
2.6
b) [
82
]. The array assembly utilized AB tile system composed of cross-
shaped tiles with two sets of sticky ends hybridized with each other. The bar-coded
scheme laid on the modification of A tiles with different organic dyes. Two
subgroups of A tiles were prepared: A1 with red dye and A2 with group dye. The
detection function was based on strand-displacement mechanism by dangling blue-
dye-labeled detection probes out of B tiles. By tuning of molar ratios of A1/A2 tile in
the array assembly with different B tiles, a series of bar-coded arrays were achieved,
for example, 3R0G, 2R1G, 1R2G, and 0R3G with specific B tile to detect its own
target. Different bar-coded arrays were mixed together for multiplex sensing. Upon
target binding, the blue-dye-labeled strand on corresponding B tile would leave the
tile array, so that the color of the arrays changed from the blue-masked colors to the
original A tile-encoded colors. The results can be directly observed by fluorescence
microscope when depositing the arrays on the surface of a glass slide. The DNA tile
design not only is the foundation of bar code analysis but also allows the accurate
control of spatial distance between probes for fast and efficient binding as well as
spacing control between tiles to prevent signal reduction by fluorescence energy
transfer processes. Later on, they further combined this system with aforementioned
hybridization chain reaction for signal amplification to achieve improved sensitivity
as well as multiplexed biosensing [
83
].
Moreover, due to the precise addressability at nanometer resolution, DNA
nanostructure is superior for studying single-molecule interaction in chemistry and
biology. Komiyama's group [
84
] developed a versatile sensing system based on
DNA origami for a variety of analytes. As shown in Fig.
2.7
a, the target-ligand
interaction can selectively trigger the shape transitions of DNA origami, such as the
closing or opening of pliers, which can be directly visualized using AFM imaging
individually. Figure
2.7
b, c are the typical AFM images before (b) and after (c)
the addition of target ATP. In Fig.
2.7
b, most pliers were in the close state, while,
in the presence of targets, the pliers opened to show a cross form (Fig.
2.7
c). The
statistical data revealed the number of close state pliers was reduced from 72 to
40% upon ATP addition and the negative control of GTP did not affect the plier
conformation (Fig.
2.7
d). The observation of results using AFM is a completely
single-molecule method, which can reflect the information that has been covered
by the average behavior of a vast number of molecules in normal spectroscopic
methods.
2.3.4
DNA Assembly with FNAs for Drug Delivery
DNA nanoassemblies are ideal carrier for drug delivery because of their well-
defined nanostructure, biocompatibility, and biodegradability. Integration of
aptamers in DNA nanoassemblies will enable their targeted delivery capability
because of their specific recognition capability. Designing aptamers into DNA
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