covalently-linked models. Therefore, it is further demonstrated
that CPD photolyase binding the substrate and the active-
site solvation in photoreactivation are important reasons why
CPD photolyases can repair the substrates with high quantum
efficiencies.
was recorded by a Shimadzu UV-2401PC spectrometer. The rates
of the dimer/oxetane unit split were measured by the monitoring
the increase in absorbance at 270 nm due to the regeneration
of the 5,6-double bond of the thymines and benzophenone. The
intensity of the light beam (I0 einsteins/min) was measured by
ferrioxalate actinometry.13 Thus, the rate of photons absorbed
was obtained from the absorbance (A) at 295 or 310 nm in terms
of Beer’s law, Ia = I0(1 − 10− A). The observed quantum yields
of dimer/oxetane splitting of TD-CD/Ox-CD were calculated
according to U = (rate of dimer/oxetane split)/(rate of photon
absorbed). In order to avoid competition of absorbing between the
model compound and the photosplitting products, the splitting
reaction was controlled within 10% yield in the measurements.
Despite the forward electron transfer (charge separation) in
the tryptophan-containing model systems with similar quantum
efficiencies (ca. 0.8)3c,4 to CPD photolyase,2c the splitting quantum
yields of the dimer or the oxetane are very low, ca. 0.1 for dimer–
tryptophan models3c and ca. 0.3 for oxetane–tryptophan models4
due to unproductive back electron transfer (charge recombina-
tion). In the case of flavin-containing systems, the deactivation of
the excited flavin by non-radiative processes, which compete with
forward electron transfer, is another important reason causing
low splitting quantum yields.4 Therefore, inefficient suppression
of non-radiative processes and/or charge recombination may be
responsible for the low repair efficiency of (6–4) photolyase. The
mechanistic detail warrants co-crystal structures of photolyase–
DNA complexes and ultrafast spectroscopic studies on (6–4)
photolyase.
Mono-6-deoxy-6-amino-b-cyclodextrin. 1H NMR (300 MHz,
D2O, [D6]acetone): d = 3.46–3.69 (m, 14H), 3.87–4.02 (m, 28H),
5.09 (d, 7H). 13C NMR (75 MHz, D2O, [D6]acetone): d = 61.47,
73.05, 73.33, 74.52, 82.42, 82.59, 84.34, 103.08, 103.28.
6-Deoxy-6-cis-syn thymine dimer-b-cyclodextrin (TD-CD).
A
dimethylformide (DMF, 20 mL) solution of the cis-syn thymine
dimer diacid (220 mg, 0.55 mmol) and 6-amino-b-cyclodextrin
(0.57 g, 0.5 mmol) was stirred at 0–5 ◦C for 30 min. Dicyclohexyl-
carbodiimide (DCC) (160 mg, 0.75 mmol) and hydroxybenzotria-
zole (HOBt) (110 mg, 0.75 mmol) were added to the above mixture,
Experimental
General
◦
and the solution was stirred at 0–5 C for 2 h and then at room
b-Cyclodextrin was recrystallized three times and dried in vacuo at
100 ◦C for 12 h before use. Indole was purified by recrystallization
from EtOH–water (1 : 10) before use. N,N-Dimethylaniline
(DMA) was purified by distillation in vacuo. Deionized water was
used throughout the experiments. The samples are fully aqueous
temperature for 2 d. After the insoluble material was removed
by filtration, the filtrate was poured into acetone (200 mL) to
precipitate the product. After being washed with acetone twice, the
crude product was absorbed on a column of macroporous resin
and eluted with an aqueous solution of ethanol (0 to 20%, v/v).
The eluted solution was concentrated to obtain the desired product
solutions unless otherwise indicated. H and 13C NMR spectra
1
were recorded on a Bruker AV (300 MHz for 1H, 75 MHz for 13C)
spectrometer. The chemical shifts were referenced to acetone (d
2.05, 29.8) in [D6]acetone and DMSO (d 2.50, 39.5) in [D6]DMSO
as a white powder (140 mg, 19%). Mp > 250 ◦C; mmax(KBr)/cm−1
=
3419 s, 1702 s, 1646 s, 1155 m, 1081 m, 1034 s; 1H NMR (300 MHz,
D2O, [D6]acetone): d = 1.30 (s, 6 H, CH3), 2.47 (m, 4H, CH2), 3.02
(m, 2H, CH2), 3.11–3.79 (m, majority, proton of CD unit + CH2),
4.02 (s, 2 H, CH), 4.90 (broad s, 7 H, H-1); 13C NMR (75 MHz,
D2O, [D6]acetone): d = 17.05 (2C, CH3), 33.00, 39.58, 39.73, 42.96,
47.34 (C), 47.42 (C), 59.20 (CH), 59.31 (CH), 59.64, 59.87, 69.68,
71.36, 71.48, 71.61, 72.32, 72.63, 80.46, 80.67, 82.39, 82.76, 101.41,
152.35, 152.39, 172.08, 172.73, 172.83; TOFMS (MALDI) calc.
for [M + Na]+ C58H89N5O41: 1535.3, found 1534.5.
1
for H and 13C NMR, respectively. Mass spectra were measured
on a Bruker BIFLEXTM III mass spectrometer. Elemental analysis
was performed at the Analytic Center of University of Science and
Technology of China. FTIR spectra were recorded on a BRUKER
VECTOR22 infrared spectrometer. UV-Vis spectra were measured
on a Shimadzu UV-2401PC spectrometer. Fluorescence emission
spectra were measured on a Shimadzu RF-5301PC fluorescence
spectrometer.
6-Deoxy-6-oxetane-b-cyclodextrin (Ox-CD). Using the oxe-
tane acid instead of the cis-syn thymine dimer diacid (183 mg,
0.5 mmol), the same procedure was performed, and the desired
product Ox-CD was obtained as a white powder (115 mg, 16%).
Rf = 0.18 (EtOAc–MeOH–AcOH 3 : 4 : 1); mp > 250 ◦C;
Measurement of quantum yield of splitting
The photosensitized splitting of the dimer/oxetane unit of TD-
CD/Ox-CD by DMA or indole was first performed through
1
determining the H NMR spectra of solutions irradiated with
1
a 300 W high pressure Hg lamp (k > 290 nm) for 20 min. The
solutions were prepared through dissolving TD-CD/Ox-CD and
DMA/indole in D2O in a Pyrex NMR tube, irradiating under
ultrasonic waves for 15 min, then allowing to stand overnight.
The sample solutions (3 mL) of indole and DMA added to TD-
CD or Ox-CD aqueous solutions were placed in quartz cuvettes
(10 × 10 mm) with a Teflon stopper, and after standing for sev-
eral hours at room temperature after ultrasonification for 15 min
were then irradiated with 295 nm (for indole) or 310 nm (for DMA)
light from a Shimadzu RF-5301PC spectrofluorophotomer. After
certain time intervals, the absorbance of the irradiated solutions
mmax(KBr)/cm−1 = 3424 s, 1705 s, 1155 m, 1081 m, 1032 s; H
NMR (300 MHz, [D6]DMSO): d = 1.58 (s, 3 H, CH3), 3.22–3.76
(m, majority, proton of CD unit), 4.45 (m, 2 H), 4.84 (broad s,
7H, H-1), 5.73 (m, proton of CD unit), 7.27–7.44 (m, 10 H,
Ar–H), 8.06 (s, 1 H, CONH), 10.39 (s, 1 H, NH); 13C NMR
(75 MHz, [D6]DMSO): d = 23.28 (CH3), 47.68 (CH2), 59.82,
59.93, 60.01, 65.11 (CN), 69.54, 72.08, 72.38, 72.99, 76.12 (CCH3),
81.33, 81.54, 81.74, 83.37, 90.83 (OCC), 101.97, 102.07, 102.36,
124.89 (2C), 124.97, 125.51, 127.77, 128.25, 128.60 (2C), 139.61,
144.60, 151.26, 167.70, 169.86; Anal. calc. for C62H87N3O38·6H2O
(1590.46): C, 46.82; H, 6.27; N, 2.64. Found: C, 47.07; H, 6.41;
This journal is The Royal Society of Chemistry 2006
Org. Biomol. Chem., 2006, 4, 2575–2580 | 2579
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