Biomolecular Machines - Bionanoelectronics: Bioinquiring and Bioinspired Devices - page 175

Fig. 6.1 Photon-driven
nanomotor in the closed state
( a ) and the opened state ( b )

a b

Q F

described in Kang et al. ( 2009 ). The hairpin is formed from a 19-base loop and
a 6-base pair (bp) stem section. This nanomotor generates no waste and operates
under UV irradiation based on the isomerization between the trans and cis forms
of azobenzene, which have planar and nonplanar conformations. As shown in
Fig. 6.1 , in the closed state, the azobenzene moiety tethered on one end of the
hairpin backbone is in the trans form, and the DNA molecule is in the hairpin
structure, conformation that changes to cis under the action of UV light and
transition that destabilizes the stem duplex and disrupts the hairpin structure; the
DNA adopts in this case a linear form. The operation of the nanomotor can be
monitored by observing the fluorescence of a fluorophore F bound at the end of
the hairpin structure opposed to that where azobenzene moieties are tethered, which
can be quenched or not by a quencher Q attached to the other end depending on
the distance between F and Q. In the closed state, the fluorescence is quenched
since F and Q are in close proximity, while in the opened state, the fluorescence
increases. The nanomotor is fully reversible; the inverse transition, between cis and
trans azobenzene, implies a transition between opened and closed states, occurring
under illumination with visible light. The distance between the two ends of the
DNA molecule increases from 2.2 nm in the closed state to 10.2 nm in the opened
configuration, these values corresponding to estimated forces of 3.1 pN and 1.5 pN,
respectively. Regarding the work needed to extend the molecule as the output
mechanical energy, the conversion efficiency of the energy provided by UV photons
is of the order of 10 7 -10 6 . A similar photon-driven switching of RNA digestion
based on changes in topological confirmation of a photoresponsive DNAzyme,
containing azobenzene-modified sequences at its ends, has been detailed in Zhou
et al. ( 2010 ).
RNA control of DNA rotary machines that rely on conformation changes has
been reported in Zhong and Seeman ( 2006 ). Rotary devices such as PX-JX 2 can
convert DNA sequences in instructions for polymer assembly when controlled
by DNA strands in solution, RNA control allowing device response to signals
originating by transcriptional logic circuits.
Conformation change of a DNA molecule in response to pH modification has
been reported in Liu et al. ( 2006 ). In this case, the nanomachine is fueled by
protons and switches its conformation between a closed, quadruplex state, called
i-motif, stable for pH <6:5, and an open, rigid double-stranded structure, which
is stable for pH >6:5; no waste products exist that could limit the lifetime of
the machine. Figure 6.2 illustrates this conformation change. The quadruplex state
forms due to noncanonical base pairs between cytosine C and protonated cytosine,
CH C (denoted also as C C ), the i-motif DNA folding at the locations of the four CCC