H. Asanuma et al.
because stacked dyes of 10 ꢂ size that are in close proximity
(3.5 ꢂ) cannot be approximated as a “point”.[1] A further
improved model (such as the extended dipole approxima-
tion[1] and/or molecular transition density[22]) will be needed
to explain the bathochromic shift of heterodimerization. At
present, we think that this discord may be due to the orbital
overlap between two dyes firmly stacked close to each other
in a duplex. Currently, quantum calculation (ab initio calcu-
lation) of the heterodimer is being applied to explain the
bathochromic shift.
tal results with theoretical predictions based on ab initio cal-
culations.
Our results partly explain the spectroscopic behavior of
intercalation. In general, dyes show batho- and hypochro-
micity when they are intercalated between the base pairs of
a duplex. According to Sarkar et al., this bathochromic shift
is due to the change in local polarity around the chromo-
phore.[19] However, we demonstrate here that exciton cou-
pling of a natural nucleobase (lmax ꢀ260 nm) with an inter-
calated dye (lmax should be longer than 260 nm) also partly
contributes to the weak but distinct bathochromic shift and
hypochromicity. Furthermore, the design of a fluorophore
and a quencher pair, tethered to d-threoninols, with a small-
er Dlmax should result in a highly sensitive molecular beacon
based on a firmly stacked fluorophore–quencher hetero-
Heteroclustering of the dyes: As shown in Figure 9, an in-
crease in the dye number resulted in intensification of the
in-phase transition together with a hypsochromic shift,
whereas the corresponding out-of-phase transition did not.
This spectroscopic behavior is very similar to that of homo
H-aggregates in which identical dyes are axially stacked. Al-
though the hypsochromic shift was smaller than that seen
for homo H-aggregates, these results clearly demonstrate
that strong coherent coupling occurred even among the het-
eroclusters. Even H3a/M3b, which had a Dlmax of 82 nm, ex-
hibited almost a single band due to the strong coherent cou-
pling within the heterocluster. We can predict from this
result that one- or two-dimensional clusters, composed of
two different dyes with different absorption maxima, should
exhibit essentially a single band when the dyes are assem-
bled in an orderly fashion, and should show strong coheren-
cy (exciton coupling).[4]
AHCTUNGTREGdNNUN imer with greater coherency. The molecular design of a
new heterodimer of a fluorophore–quencher pair as a com-
ponent of a molecular beacon is currently underway.
Experimental Section
Materials: All the conventional phosphoramidite monomers, CPG col-
umns, reagents for DNA synthesis, and Poly-Pak II cartridges were pur-
chased from Glen Research. Other reagents for the synthesis of the phos-
phoramidite monomer were purchased from Tokyo Kasei Co. and Sigma-
Aldrich.
Synthesis of DNA modified with H, M, N, R, or Z: All the modified
DNAs were synthesized by using an automated DNA synthesizer (ABI-
3400 DNA synthesizer, Applied Biosystems) with conventional and dye-
carrying phosphoramidite monomers. Azobenzene, Methyl Red, and
Naphthyl Red phosphoramidite monomers were synthesized according to
a previous report.[9b,23] The compounds 4’-methylthioazobenzene and 4’-
dimethylamino-2-nitroazobenzene, synthesized according to the litera-
ture,[24, 25] were converted to phosphoramidite monomers as described in
Scheme 1 of the Supporting Information. The coupling efficiency of the
monomers with modified residues was as high as that of the conventional
monomers, as judged from the intensity of the color of the released trityl
cation. After the recommended workup, the oligomers were purified by
reverse-phase HPLC and characterized by MALDI-TOFMS (Autoflex II,
Bruker Daltonics).
Conclusions
The NMR study revealed that different dyes incorporated at
the center of an ODN through tethering to d-threoninols
were stacked antiparallel to each other, and were located
adjacent to the 5’-side of a natural nucleobase.
Heterodimerization induced hyperchromism of the band
of the shorter wavelength (in-phase transition), but hypo-
chromism of the band of the longer wavelength, and these
absorbance changes were enhanced when the Dlmax of the
two dyes was decreased. Furthermore, both bands exhibited
a distinct bathochromic shift. These spectroscopic behaviors
were consistent with the shifts predicted from the molecular
exciton theory, except for the bathochromic shift of the in-
phase transition. This discordance might be due to limita-
tions of the point dipole approximation of the conventional
molecular exciton theory.
An increase in dye number dramatically intensified the
in-phase transition, which resulted in the spectrum of the
heterocluster being almost a single absorption band even
though the two dyes had different absorption maxima.
Thus, we have presented, for the first time, a qualitative
comparison of the actual spectroscopic behavior of hetero-
dimers with the spectroscopic behavior predicted for such
heterodimers by the molecular exciton theory, by systemati-
cally changing the Dlmax of the two dyes. We are now con-
ducting a quantitative comparison of the present experimen-
The MALDI-TOFMS data, observed (found) versus calculated (calcd.),
for the monomers were: Z1a: calcd for [Z1a+H]+: 4020; found: 4020;
Z2a: calcd for [Z2a+H]+: 4395; found: 4395; Z3a: calcd for [Z3a+H]+:
4770; found: 4770; H1a: calcd for [H1a+H]+: 4066; found: 4067; H2a:
calcd for [H2a+H]+: 4487; found: 4488; H3a: calcd for [H3a+H]+:
4908; found: 4909; R1a: calcd for [R1a+H]+: 4108; found: 4108; R2a:
calcd for [R2a+H]+: 4571; found: 4572; R3a: calcd for [R3a+H]+:
5034; found: 5035; N1a: calcd for [N1a+H]+: 4113; found: 4113; N2a:
calcd for [N2a+H]+: 4581; found: 4581; N3a: calcd for [N3a+H]+:
5049; found: 5050; M1b: calcd for [M1b+H]+: 4063; found: 4065; M2b:
calcd for [M2b+H]+: 4481; found: 4481; M3b: calcd for [M3b+H]+:
4899; found: 4899; NMR-Ma: calcd for [MMR-Ma+H]+: 2211; found:
2211; NMR-Zb: calcd for [MMR-Zb+H]+: 2167; found: 2168.
Spectroscopic measurements: The UV/Vis and CD spectra were mea-
sured on a JASCO model V-550 spectrophotometer and a JASCO model
J-820 spectropolarimeter, respectively, with a 10 mm quartz cell. Both
models were equipped with programmable temperature controllers. The
conditions of the sample solutions were as follows (unless otherwise
noted): [NaCl]=100 mm, pH 7.0 (10 mm phosphate buffer), [DNA]=
5 mm. For measurements at pH 5.0, 10 mm MES buffer was used. All sam-
ples of DNA–dye conjugates were heated at 808C for 5 min in the dark,
to thermally isomerize the cis form, which might be photoisomerized by
the ambient light, to trans form before spectroscopic measurement.[26]
10100
ꢀ 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Chem. Eur. J. 2009, 15, 10092 – 10102