Biomedical Engineering Reference
In-Depth Information
molecule was attached to the connecting helix. The two unconnected domains of the
DX molecule lay on the same side of the central axis in buffer conditions favoring
B-DNA, while in Z-DNA promoting conditions, these domains switched to opposite
sides of the helix. Each tile (the free end) of the DX molecules carried a fluorophore,
the relative proximity of which is measured to detect the relative repositioning
of the domains by means of fluorescence resonance energy transfer (FRET). The
B-Z transition was triggered by changing the concentration of [Co(NH 3 ) 6 ] 3C from
0 to 0.25 mM. When the B-Z transition occurred, FRET measurements showed an
increase in the separation between the fluorophores consistent with the expected
relative rotation of the tiles by 3.5 turns.
Another example of cation-driven DNA nanomachine is achieved by using
magnesium-induced DNA supercoiling [ 27 ]. In this design, two neighboring DNA
duplexes could condense into a supercoiled structure in the presence of Mg 2C ions,
and the resulting change of the network connectivity could be monitored by atomic
force microscopy (AFM). A more recent example of divalent ion-triggered switch
design involving the Holliday junction motif modulates the Holliday junction to
create a nanoscale “metronome” [ 28 ](Fig. 11.3 a). The nanometronome is an inte-
grated structure of molecular beacon and Holliday junction. Induced by the ambient
thermal energy, the Holliday junction structure transacted between phase IsoI and
phase IsoII, which was considered as the ticking motion of the nanometronome. The
rate of ticking was controlled by Mg 2C or additional controlling elements, as well as
single-stranded deactivator and activator. The single-molecular FRET measurement
was conducted based on the molecular beacon structure to monitor the metronome
dynamics under different concentrations of Mg 2C or single strands.
Based on the G-quadruplex structures, a nanopinching device that can be
reversibly regulated in aqueous solution by the presence or absence of certain
specific cations is constructed by Fahlman et al. [ 29 ](Fig. 11.3 b). Duplex possessing
G-G mismatches is designed to form intramolecular guanine quartets in the presence
of G-quadruplex-promoting cations such as Sr 2C , resulting in a pinched duplex.
The process can be reversed by the removal of the cation from solution by using
a chelator such as EDTA. Another ion-triggered G-quadruplex nanomachine was
developed by employing modified DNA strands that contained an ion-sensitive
coordinative unit, 2,2 0 -bipyridine [ 30 ](Fig. 11.3 c). The modified strand adopted
antiparallel G-quadruplex conformation in the absence of divalent metal ions, while
it underwent a structural transition to high-order parallel-stranded G-quadruplex that
formed G-wire morphology upon addition of divalent metal ions, such as Ni 2C .The
reverse structural transition can be efficiently induced by adding EDTA to the system
to complex the metal ions.
11.3.1.2
Proton-Fueled DNA Nanomachines
The Balasubramanian research group validated a switch that adopts i-motif struc-
ture at pH 5 and duplex at near-neutral pH [ 31 ]. Interconversion of the i-motif
structure and extended duplex is mediated by alternating addition of H C and OH .
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