Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 238

Fig. 11.12 ( a ) Analysis of M13 phage ssDNA by the hairpin and the DNA machine (Reproduced
from Ref. [ 73 ] by permission of John Wiley & Sons Ltd). ( b ) Protein tagging and pH mapping
using the I-switch inside cells (Reprinted by permission from Macmillan Publishers Ltd: Ref. [ 37 ],
copyright 2009)
Recently, the target recognition ability and dynamic property of DNA nanoma-
chines have been extensively utilized to construct sensors for detecting a series of
chemical or biological analysts. Among those applications, the concept of signal
amplification through DNA catalytic reactions takes full advantage of dynamic
properties of DNA machines. Willner's research group proposed this concept that
was realized starting with the detection of M13 phase DNA, shown in Fig. 11.12 a
[ 73 ]. The machine contains two structure elements. One is a hairpin structure acting
as a recognition unit with its loop sequence complementary to a fraction of M13
DNA. The other is a responsive machine track consisting of three main parts: a
primer-binding region (I) that is complementary to one stem of the hairpin unit, a
nicking enzyme recognition site (II), and a reporter sequence (III) that includes the
region complementary to the HRP-mimicking DNAzyme. Upon recognition of the
input M13 DNA by the hairpin structure, one stem of the opening hairpin is able to
hybridize to the primer-binding region, initiating the replication of the machine track
in the presence of a DNA polymerase. The resulting nick site is cut by the nicking
enzyme, which generates a new primer available for replication of the track. The
synthesized DNAzyme sequence is then displaced by the new round of replication