Functional Nucleic Acids for DNA Nanotechnology - DNA Nanotechnology: From Structure to Function - page 20

Fig. 2.9 ( a ) Scheme of the thrombin aptamer-based molecular machine with cyclic action
(Reproduced from Ref. [ 87 ] by permission of John Wiley & Sons Ltd.). ( b ) Scheme of a DNA
nanomotor with 10-23 DNA enzyme domain to autonomously cleave RNA substrate to act like a
tweezer and reversibly controlled by a break DNA (Reprinted with the permission from Ref. [ 88 ].
Copyright 2004 American Chemical Society)
As shown in Fig. 2.9 a, upon the addition of thrombin, the machine adopts a
G-quadruplex structure and binds with thrombin. In the presence of complementary
DNA (Q), a stable duplex Q-AP forms and thrombin has been released. Cycling of
the machine is realized by the addition of another removal strand (R) to form more
stable duplex Q-R and return the device to its original conformation to bind with
thrombin. The machine can be instructed repeatedly to bind and release a protein,
therefore precisely controlling the concentration of protein in solution.
An autonomous nanodevice with controllability is always more desired than the
device with human intervention for each motion. Mao's group reported a delicate
autonomous DNA nanomotor that can be reversibly controlled by a break [ 88 ].
In Fig. 2.9 b, the DNA motor has a tweezer-like shape, with two rigid arms made
of double-stranded DNA and an RNA-cleaving enzyme, named 10-23 DNAzyme,
which can cleave its RNA substrate. Once the RNA substrate binds with the motor
as the open state, the DNAzyme will cleave the substrate into two short fragments,
and the motor would return to its close state. As long as there are uncleaved
RNA substrates, the nanomotor will continuously repeat the open-close motion.
To stop the machine, a break molecule (B) is used, which is a DNA analogue of
RNA substrate strand. B has better binding with DNAzyme than RNA substrate
and cannot be cleaved by DNAzyme, thus halting the machine. The introduction
of removal strand (R) removes the break and resumes the motion of machine.
Therefore, this nanodevice can not only move autonomously but also be precisely
controlled by a brake.
Later on, Mao's group [ 89 ] fabricated a synthetic molecular device (walker)
analogous to kinesin. The walking system is composed of a DNAzyme as the
walker and a DNA-RNA chimera as the track. The track is assembled from a long