Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 228

While the free energy released from RNA hydrolysis was used to activate the
DNA machines, Simmel et al. used the power of DNA transcription into RNA to
control the machine [ 45 ]. The DNA tweezers switched from the open to the closed
conformation were triggered by an mRNA fuel strand, which was biocatalytically
generated from a template DNA strand encoding the mRNA by an RNA polymerase.
This approach was further refined by placing the gene that encoded the RNA fuel
strand under the control of either a negative (LexA) or a positive regulator (LacI).
Both concepts relied on bacterial expression control systems, in which the presence
of an outside effector molecule either stopped (LexA) or started (LacI) transcription
of a gene. The template DNA was designed to contain the respective binding sites
for the regulator molecules of the fuel gene. In the presence of the positive and the
absence of its negative regulator, a much higher percentage of tweezers adopted the
closed structure. The reopening of a closed tweezers was reliant upon the manual
addition of a complementary opening oligonucleotide.
Other than utilizing fuel strands with biological activity, researchers have made
some attempts to combine light-triggered transition with fuel strands to control the
motion of tweezers [ 46 , 47 ]. DNA strands modified with azobenzene can be induced
by light to stabilize and destabilize DNA duplex. Azobenzene can be switched from
its trans to the cis configuration by illumination with light with a wavelength of
330-350 nm, while back to the trans form by illumination at 440-460 nm. Only
trans -azobenzene efficiently intercalates into the DNA double helix; by contrast,
cis -azobenzene destabilizes a DNA duplex and results in a considerably reduced
melting temperature. Asanuma and coworkers synthesized azobenzene-modified
fuel strands for DNA tweezers that were able to close the tweezers only in the trans
form [ 46 ]. Ogura et al. modified with azobenzene only half of the fuel strand of a
tweezers to greatly increase the kinetics compared to conventional tweezers [ 47 ].
The modified half of the fuel strand was bound to one of the arms of the tweezers,
while the other unmodified half can be photoswitched to successively open and close
the tweezers. It is the intramolecular interaction in this design that greatly enhanced
the close kinetics.
The complexity of the tweezers system was enhanced significantly through
cooperation of multimachinery units by Willner's group. An idea that the coupling
of two tweezers could reveal richer number of configurations is formulated based
on the fact that each tweezer can present two states, that is, open and closed
configurations, in which a manner of communication is established between the
two tweezers. Typically, the open and close states of tweezers produce high and low
fluorescence outputs, respectively, in FRET measurements. It is easier to use the
digital number “1” and “0” to represent the high and low fluorescence outputs, thus
the open and closed structure configurations. Coactivation of two tweezers can result
in a maximum of four configurations: (1,1), (0,0), (0,1), and (1,0), using the fuels as
inputs. Such operation of the system requires strict consideration of the energetics
inside each tweezers unit, according to which the nucleic sequences of the tweezers
arms are carefully designed. Based on the specific recognition of DNA aptamer
to adenosine monophosphate (AMP) molecule, Willner's group constructed a two-
tweezers system, in which one tweezer (tweezer A) can capture the target DNA