Functional DNA-Integrated Nanomaterials for Biosensing - DNA Nanotechnology: From Structure to Function - page 271

from DNAzyme and produced a red color. In the absence of Pb 2C , the AuNPs
and DNAzyme could be reassembled upon the system cooling down to room
temperature. However, in the presence of Pb 2C , the DNAzyme-mediated reassembly
of the AuNPs was inhibited due to the cleavage of the substrate, resulting in a
permanent red color. A detection limit of 100 nM was achieved for the sensor, and
it allowed on-site and real-time detection of Pb 2C in paint.
For the above sensor design, however, an annealing step was required to
overcome the high steric hindrance of the head-to-tail aggregate formation. In order
to facilitate the nanoparticle assembly and the sensor operation, the design was
improved by using a tail-to-tail arrangement in the AuNP assemblies (Fig. 13.1 f)
[ 33 ]. Although aggregation at room temperature was observed, the assembly speed
was still slow. The Lu group found that the usage of AuNPs with a larger size
(42 nm) could overcome this limitation, which allowed fast detection of Pb 2C
at ambient temperature with a clear color change in 5 min. These Pb 2C sensing
systems are “light-down” sensors because the color remained red and AuNPs
remained unassembled in the presence of the target. They further demonstrated the
transformation of these “light-down” colorimetric sensors into “light-up” sensors
based on control of the disassembly of AuNP aggregates (Fig. 13.1 g,h) [ 34 , 35 ].
Due to large steric hindrance of the head-to-tail alignment toward the DNAzyme
active site, only the tail-to-tail construct worked. Based on usage of small pieces of
DNA to invade the cleaved substrate of the DNAzyme and thus to accelerate the rate
of disassembly of AuNPs, this optimal design allowed fast “light-up” detection of
Pb 2C . In addition to the DNAzymes with cleavage activities, a ligation DNAzyme-
based colorimetric method has been reported for the detection of copper ions based
on similar design [ 36 ]. Ligation DNAzyme could provide the advantage of an
extremely low background and therefore a high sensitivity.
The colorimetric sensors described above require the functionalization of
DNAzyme onto the surface of AuNPs through alkane thiol at the ends of functional
DNA. The label-free colorimetric sensors could simplify the design based on
different adsorption properties of single-stranded (ssDNA) and double-stranded
DNA (dsDNA) on citrate-coated AuNPs. Since ssDNA is flexible and can be readily
adsorbed on AuNP surface, salt-induced AuNP aggregation can be inhibited due
to the enhanced electrostatic repulsion between ssDNA-adsorbed AuNPs. On the
other hand, dsDNA has negligible binding with negatively charged citrate-modified
AuNPs because it is stiff and has its negatively charged phosphate backbone exposed
[ 37 ]. On the basis of this phenomenon, label-free-based sensors to detect specific
DNA [ 38 ]orRNA[ 39 ] sequences using unmodified AuNPs were reported. Label-
free metal ion-specific colorimetric sensors were further developed using AuNPs
and DNAzyme. As shown in Fig. 13.2 ,UO 2 2C -cleavable substrate-DNAzyme
complex was first reacted with UO 2 2C . The presence of UO 2 2C led to cleavage of
substrate by the DNAzyme, which released short ssDNA fragments that could be
adsorbed on AuNPs and protect them from salt-induced aggregation [ 40 ]. In the
absence of UO 2 2C , however, the complex would not interact with AuNPs, resulting
in AuNP aggregation with color change from red to blue. Compared with labeled