Alkynyl C-Nucleosides
FULL PAPER
Spectroscopic measurements: Steady-state absorption and emission spec-
tra were recorded by using a JASCO V-560 UV/Vis spectrophotometer
and a JASCO FP-6500 spectrofluorometer, respectively. Fluorescence
lifetimes were measured by using a HORIBA NAES-550 nanosecond flu-
orometer equipped with a SSU-111A photomultiplier, SCU-121A optical
chamber, SGM-121A monochromator, and LPS-111 lamp power supply.
These measurements were carried out at 258C using a 1-cm pathlength
cell. Fluorescence quantum yields, Ff, of the monomers in H2O were de-
termined by using 9,10-diphenylanthracene[17] and perylene[18] as a stan-
dard with a known Ff in EtOH of 0.95 and 0.92, respectively. The fluo-
rescence quantum yields were calculated according to the following equa-
tion: Ff(spl) =Ff(std) [Astd/Aspl][Istd/Ispl][nstd/nspl]2. In this equation, Ff(spl)
and Ff(std) are the quantum yields of a sample and a standard, respective-
ly. Aspl, Ispl, and nspl are the optical density, the integrated emission inten-
sity at the excitation wavelength, and the value of the refractive index of
the sample, respectively. Astd, Istd, and nstd are those for the standard.
Fluorescence lifetimes were obtained by time correction, a single-photon
counting methodology, by means of a nanosecond fluorometer. Sample
solutions (5.010À6 m) were prepared in Milli-Q water under aerated con-
dition (not degassed). Excitation wavelengths were 275 nm (for 7(An)
and ab-An-An-ab), 350 nm (for 7(Py), ab-Py-Py-ab, ab-Py-Py-Py-ab, ab-
Py-Py-Py-Py-ab, ab-Py-Pe-ab, ab-Py-An-ab, ab-Pe-An-ab, and ab-Py-Pe-
Py-ab), and 430 nm (for 7(Pe) and ab-Pe-Pe-ab). Cut-off filters used
were UV35 (for 7(Py), ab-Py-Py-ab, ab-Py-Py-Py-ab, ab-Py-Py-Py-Py-
ab, 7(An), and ab-An-An-ab) and Y45 (for 7(Pe), ab-Pe-Pe-ab, ab-Py-
Pe-ab, ab-Py-An-ab, and ab-Pe-An-ab). All decay curves were calculated
by using single or double exponential on the basis of the equation I(t)=
excimer emissions for the shorter lifetime (minor compo-
nent) and the longer one (major component). Similar ten-
dency was observed in the perylene-linked monomer and
oligomer. However, in the case of ab-An-An-ab, the decay
corresponding to its excimer could hardly be detected be-
cause the excimer emission is very weak, as shown in Fig-
ure 3B. Upon applying the heterooligomers, we used a cut-
off filter (passing photons at >450 nm) to discard the pho-
tons emitted from the monomeric excited states in the oligo-
mers. Thus, both the components observed for the heteroo-
ligomers must be assigned to fluorescence lifetimes from the
heteroexcimers. This finding means that two or more confor-
mational isomers emitted individually in agreement with
their ground states deduced by the UV-visible spectra. Un-
fortunately, the emissive components in ab-Py-Pe-Py-ab
were too numerous to be analyzed.
Conclusion
Our artificial DNA skeleton based on alkynyl C-nucleosides
was found to be a superior scaffold for investigating homo-
and heteroexcimer formation in aqueous media. The fluo-
rescent oligomers made of the skeleton predominantly
showed excimer emissions not only from homoexcimers but
also from heteroexcimers. Because of the synthetic versatili-
ty of the alkynyl C-nucleosides, a large number of fluoro-
phores can be attached to the skeleton. Therefore, these flu-
orophore-linked oligomers may be used for labeling various
biomolecules, and such an approach is now underway.
ꢀAiexp
A
components, and Ai =fluorescence intensity of component i at t=0.
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Experimental Section
Synthesis of fluorescent oligomers: The fluorescent oligomers were syn-
thesized from 5 by using an Applied Biosystems 392 synthesizer using
standard b-cyanoethylphosphoramidite chemistry with the coupling reac-
tion time of 15 min. The solid support (Universal Support II), which
allows for 3’ placement of nonnatural nucleosides, was purchased from
Glen Research. After automated synthesis, the oligomers were deprotect-
ed and removed from the solid support with 2-m ammonia methanol solu-
tion at room temperature for 30 min. The oligomers were then purified
by reverse-phase HPLC by using a CHEMCOBOND 5-ODS-H column
(10150 mm with an eluent of 510À3 m ammonium formate and the fol-
lowing CH3CN percentages of linear gradient (0–40 min) at a flow rate of
2.0 mLminÀ1: ab-Py-Py-ab (20–45%), ab-Py-Py-Py-ab (30–60%), ab-Py-
Py-Py-Py-ab (30–60%), ab-Pe-Pe-ab (30–50%), ab-An-An-ab (20–50%),
ab-Py-Pe-ab (20–50%), ab-Py-Pe-Py-ab (30–60%), ab-Py-An-ab (20–
40%), ab-Pe-An-ab (20–50%).
MALDI-TOF measurements: MALDI-TOF mass spectra were recorded
by using a Bruker-Daltonics-Autoflex mass spectrometer with 3-hydroxy-
picolinic acid as
a matrix. ab-Py-Py-ab: m/z: calcd for C56H54O18P3
[MH+]: 1107.25; found: 1107.27, ab-Py-Py-Py-ab: m/z: calcd for
C79H71O23P4 [MH+]: 1511.33; found: 1511.10, ab-Py-Py-Py-Py-ab: m/z:
calcd for C102H88O28P5 [MH+]: 1915.41; found: 1915.09, ab-Pe-Pe-ab: m/z:
calcd for C64H58O18P3 [MH+]: 1207.28; found: 1206.87, ab-An-An-ab:
m/z: calcd for C52H54O18P3 [MH+]: 1059.25; found: 1059.31, ab-Py-Pe-ab:
m/z: calcd for C60H56O18P3 [MH+]: 1157.27; found: 1156.87, ab-Py-Pe-Py-
ab: m/z: calcd for C83H73O23P4 [MH+]: 1561.35; found: 1561.02, ab-Py-
An-ab: m/z: calcd for C54H54O18P3 [MH+]: 1083.25; found: 1082.99, ab-
Pe-An-ab: m/z: calcd for C58H56O18P3 [MH+]: 1133.27; found: 1132.92.
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Chem. Eur. J. 2007, 13, 8124 – 8130
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