Biomedical Engineering Reference
In-Depth Information
and folds into its active G-quadruplex conformation, which intercalates hemin to
mimic peroxidase activity, generating colorimetric or chemiluminescence readout
signals. Multiple rounds of isothermal strand replication amplifies the readout signal
significantly and enables the detection of the target vital DNA with a sensitivity of
10 6 M. The research was then expanded by engineering the binding domain of the
track to recognize cocaine [ 74 ]orHg 2C [ 75 ], and signal detection was achieved by
lighting a molecular beacon or HRP-mimicking DNAzyme catalysis, respectively,
to obtain low detection limit. Using a similar concept but with an adaption of
the detection mechanism (binding of thrombin inhibited the turnover of the DNA
machine), the thrombin was also analyzed [ 76 ].
As mentioned above, machines based on i-motif have proved to be robust
sensors of pH values. Tracking changes of pH is very important and challenging
as it is associated to many physiological incidents inside living organisms such as
development of embryo, secretion, and cell-cell fusion. A key advance for DNA
scaffolds as intracellular devices was recent reported by the Krishnan research
group. They built an i-motif-based device on to a protein such as transferring
through a biotin-streptavidin interaction, which could sense changes in pH inside
cell organelles (Fig. 11.12 b) [ 37 ]. The nanomachine is made of two DNA duplexes
connected by a flexible hinge. At the ends of the duplexes, two cytosine-rich strand
extensions adopt random coil conformation at neutral pH condition and bind to each
other to form i-motif structure at acidic condition. Additionally, two fluorophore
molecules are attached to each end of the duplex such that their interaction is directly
proportional to the distance between them. Hence, the change in pH was directly
reflected in the efficiency of FRET which could be monitored outside the organism.
The nanodevice was injected into the nematode Caenorhabditis elegans ,whereit
entered the specialized cells called coelomocytes and was trapped in endosomes.
Endosomes are known to undergo a series of maturation stages, each of which is
associated with a change of pH. Therefore, it is able to track each stage of endosome
maturation by monitoring the FRET of the nanomachine.
DNA origami-derived mechanical device was developed recently by Kuzuya
et al. to sense the chemical and biological targets at molecular resolution [ 77 ]. The
device consists of two levers 170 nm long connected at a fulcrum, with a detection
mechanism relying on shape transition induced by target single molecules from
protein to metal ions. The shape transition of DNA pliers, imaged by the AFM and
fluorescence, is triggered by three mechanisms: pinching, zipping, and unzipping,
in the presence of the corresponding targets.
11.4.2
DNA-Templated Synthesis
The concept of DNA-templated synthesis (DTS) is based on the idea that two
chemical reactants linked on the ends of two single-stranded DNA can be held
in close proximity by DNA hybridization, which confines the reactive groups to
the same region in space, increasing their local concentration and accelerating the
reactivity [ 78 ]. Typically, a DNA “code” can be translated into novel compounds
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