A R T I C L E S
Miyoshi et al.
Chart 1
previous studies indicate that the one-dimensional G-wire can
be used as a structurally well-defined nanoscaffold.
There is growing interest in guanine-rich sequences as
functional elements in molecular electronics because guanine
has the lowest oxidation potential of the deoxynucleotide bases.8
Theoretical studies have further suggested that the G-wire
structure possesses enough conductivity for use in nanoscale
biomolecular electronics.9 Thus, the G-wire structure possesses
structural and electronic advantages as a nanomaterial; however,
a means of controlling or switching G-wire formation has not
yet been developed because the G-wire is an aggregated
structure. Therefore, further studies are needed to develop a
G-wire switch that can be controlled by chemical inputs.
Here, we designed and synthesized a DNA that can undergo
a reversible structural transition between a compact antiparallel
G-quadruplex and a long G-wire, depending on external signals.
To enable a reversible structural transition, we replaced the
thymines in the d(G4T4G4) chain with a metal ion-responsive
unit, 2,2′-bipyridine, which is composed of two aromatic rings
that rotate arbitrarily upon coordination with metal ions.10
Structural analysis utilizing circular dichroism (CD) and native
polyacrylamide gel electrophoresis (PAGE) showed that the
DNA that included the 2,2′-bipyridine units underwent a
structural transition from an antiparallel G-quadruplex to a high-
order parallel-stranded G-quadruplex upon addition of divalent
metal ions such as Ni2+, Co2+, and Zn2+. In addition, Na2EDTA
induced a reversible structural transition from the high-order
structure to the antiparallel G-quadruplex. Moreover, direct
observation of the reversible structural transition using AFM
showed that the high-order parallel-stranded structure is a G-wire
that contains numerous DNA oligonucleotides, which demon-
strates that the G-wire can be switched by divalent metal ions
and Na2EDTA. Alternating addition of Ni2+ and Na2EDTA
showed that the G-wire could be switched up to 8 times, with
a cycling efficiency of 0.95 (i.e., only 5% loss per cycle). These
results demonstrated that the G-wire switch developed here can
be readily controlled by chemical signals. Notably, in the
presence of divalent metal ions, the G-wire switch forms an
array of divalent metal ions because divalent metal ion-2,2′-
bipyridine complexes are adjacent to each G-quadruplex unit
and are separated by approximately 1.5 nm. This allows the
conductivity of the G-wire to be increased and introduces
addressability into the G-wire.
systems because it strongly chelates metals, is stable to redox
changes, and is easily added as a functional group.12 Peptides
containing 2,2′-bipyridine functionality spontaneously fold into
coiled-coil R-helix or â-sheet structures in the presence of metal
ions.13 Moreover, a nucleoside mimic in which the heterocyclic
base is replaced by 2,2′-bipyridine undergoes metal-mediated
base pair formation.14 Thus, 2,2′-bipyridine could be useful for
controlling DNA structures. We replaced the main-chain thym-
ines in d(G4T4G4) with 2,2′-bipyridine, connected to the main
chain via ether linkages (bipy), generating d(G4-bipy-G4) (G1;
Chart 1a). We synthesized G1 using a bipy phosphoramidite
(see the Supporting Information and ref 10) and d(G4T4G4) (G2)
as a control. Previous studies have shown that, in the presence
of Na+, G2 forms a hairpin dimer antiparallel G-quadruplex
with thymines residues in the loop (Chart 1b).15
Figure 1a shows CD spectra for 5 µM G1 in the absence of
divalent metal ions or the presence of 2.5 µM Mg2+, Ca2+, Zn2+
,
Co2+, or Ni2+ in a buffer containing 100 mM NaCl and 50 mM
MES (pH 6.0) at 4 °C. The CD spectra for G1 without divalent
metal ions and in the presence of Ca2+ or Mg2+ show negative
and positive peaks near 260 and 295 nm, respectively, indicating
an antiparallel G-quadruplex.16 Surprisingly, the CD spectra for
G1 in the presence of Zn2+, Co2+, or Ni2+ had positive and
negative peaks near 260 and 240 nm, respectively, indicating
that it forms a parallel-oriented G-quadruplex.17 These results
show that these divalent metal ions induce a structural transition
from an antiparallel to a parallel G-quadruplex. The CD spectra
for G1 in the presence of Zn2+, Co2+, or Ni2+ had a small
positive peak at 295 nm, indicating that the structural transition
from the antiparallel G-quadruplex to the G-wire does not
proceed perfectly, because the structural transition of G1 induced
by the divalent metal ions may be in equilibrium.18 On the other
hand, the CD spectra for G2 indicated an antiparallel G-
quadruplex structure in the presence or absence of divalent metal
Results and Discussion
Design of Oligonucleotides that Can Switch from a
G-Quadruplex to a G-Wire. DNA containing a main-chain
modification with a linker that tightly binds metal ions has been
shown to form a supramolecular structure.11 In particular, 2,2′-
bipyridine, which contains two pyridine rings that rotate
arbitrarily upon coordination with metal ions, has been inserted
into DNA to generate supramolecular structures and functional
(11) (a) Stewart, K. M.; McLaughlin, L. W. J. Am. Chem. Soc. 2004, 126, 2050-
2057. (b) Mitra, D.; Di Cesare, N.; Sleiman, H. F. Angew. Chem., Int. Ed.
2004, 43, 5804-5808. (c) Stewart, K. M.; Rojo, L.; McLaughlin, L. M.
Angew. Chem., Int. Ed. 2004, 43, 5808-5811. (d) Choi, J. S.; Kang, C.
W.; Jung, K.; Yang, J. W.; Kim, Y. G.; Han, H. J. Am. Chem. Soc. 2004,
126, 8606-8607.
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(18) We investigated the structure of G1 in the presence of higher concentrations
of Ni2+. However, much higher concentrations of Ni2+, for example, 1
mM, led to the aggregation and precipitation of G1.
(7) (a) Miyoshi, D.; Nakao, A.; Sugimoto, N. Nucleic Acids Res. 2003, 31,
1156-1163. (b) Miyoshi, D.; Karimata, H.; Sugimoto, N. Angew. Chem.,
Int. Ed. 2005, 44, 3740-3744.
(8) (a) Bixon, M.; Giese, B.; Wessely, S.; Langenbacher, T.; Michel-Beyerle,
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5920 J. AM. CHEM. SOC. VOL. 129, NO. 18, 2007