Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 222

Fig. 11.2 Design of the B-Z nanomechanical device. The device consists of two DX molecules
connected by a helix ( yellow section ) that can undergo the B-Z transition. During the transition,
the bottom domain of the right DX molecule switches from the bottom to the top through a
rotary motion (Reprinted by permission from Macmillan Publishers Ltd: Ref. [ 26 ], copyright 1999)
(Color figure online)

11.3.1 Buffer-Dependent DNA Nanomachines

11.3.1.1 Cation-Triggered Devices

The first example of DNA-based nanomechanical device is motivated by ethidium
ions that are used as intercalators to induce branch point migration in a four-
way junction structure [ 25 ]. In this study, it is proposed that transition from the
B to the Z structure drives the motion of the junction. B-DNA and Z-DNA are
the only conformations of DNA that have been directly observed in functional
organisms. Their major difference in the structure is the helical winding direction,
in addition to parameters such as diameter, number of bases per turn, and turn
of helix. The more commonly found B-form DNA adopts a right-handed helical
structure, while Z-form DNA adopts the left-handed structure. The B-Z transition
can be realized by alternating purine and pyrimidine sequences in the presence of
certain cations such as hexamminecobalt (III) ([Co(NH 3 ) 6 ] 3C ). So it is useful to
exploit the B-Z transition to produce torque or a rotary motion. Nadrian C. Seeman
and coworkers demonstrated the first rotary nanomechanical device that was based
on B-Z transition triggered by the addition of [Co(NH 3 ) 6 ] 3C . This supramolecular
mechanical device consisted of two rigid DNA “double-crossover” (DX) molecules
connected by 4.5 double-helical turns (Fig. 11.2 )[ 26 ]. One domain of each DX