Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 226

to form interparticle duplexes in high-pH solution, resulting in Au NP aggregates
[ 35 ]. The change in the optical properties of the clustered Au NPs induced by DNA
conformation transitions was exploited as an efficient colorimetric pH meter with
an impressive accuracy of 0.04 pH units [ 36 ]. More recent designs of i-motif-based
nanomachines employed pH change-triggered conformation change of i-motif to
induce second-order lever strand motions [ 37 , 38 ](Fig. 11.4 b, c).
DNA nanomachines based on pH-induced transition between duplex to triplex
forms have also been constructed. A ternary complex with a GC-rich duplex and a
single-stranded C-rich domain was designed by Mao et al. [ 39 ]. The protonation of
the C-rich domain under pH 5.0 caused the formation of the C C G-C triplex, which
brought the two fluorophores close to each other. At pH 8.0, the C C G-C triplex
collapsed and the open state of the ternary complex re-formed. The DNA machine
showed high reversibility between the closed state and the open state when the
solution pH oscillated between 5.0 and 8.0. Samori's research group used a similar
strategy. The open state of the nanomachine was a duplex with overhanged CT-rich
single strand at pH 5.0, while the overhanged single strand folded back to form
C-T triplex at pH 9.0, the close state [ 40 ]. The duplex-triplex transition was also
employed to reversibly control the separation and aggregation of the Au NPs [ 41 ].

11.3.2 DNA Nanomachines Activated by Fuel Strands

11.3.2.1 Tweezers

DNA tweezers are the first example of DNA nanomachine that was not only made
from but also driven by fuel DNA molecules, which pave the way to construct
complex DNA nanomachines by DNA hybridization. The tweezers, first constructed
by Yurk et al. in 2000 [ 42 ], contained three strands A, B, and C (Fig. 11.5 a) to form
a structure with 18 base pair double-stranded stiff arms connected by a four-base
single-stranded hinge. The closing and opening of the assembled tweezers are driven
by closing strand F, or “fuel” strand, and opening strand F or “antifuel” strand, and a
double-strand waste F F was produced within a cycle. The 56-base closing strand F
contained two domains, in which the 48-base domain is complement to the overhang
part of the two arms and the remaining 8-base domain is used as a “toehold” for
the opening strand F to initialize the opening process. The cycles around closed to
open states of the tweezers were monitored by FRET between a fluorophores and
a quencher labeled on the arms or by measuring the different conformational states
through gel electrophoresis.
Many DNA tweezers have since been developed based on various fuel mecha-
nisms, functions, the number of coactivated tweezers, and the functional structures.
Mao's research group constructed DNA tweezers integrating the DNA enzyme
cleavage reaction to cycle between the open and closed states [ 43 , 44 ]. Figure 11.5 b
shows the fuel mechanism of this design. The closed state was composed of
two strands that formed two rigid arms connected by a single strand containing