Metal–Salen-Base-Pair Complexes Inside DNA
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41.7, 65.0, 67.5, 77.4, 80.7, 82.8, 97.4, 118.4, 125.2, 127.0, 128.6, 129.1,
129.2, 129.7, 129.8, 132.8, 143.6, 144.0, 152.8, 166.1, 166.5 ppm; IR (KBr):
n˜ =2947 (m), 2867 (m), 1720 (s), 1613 (m), 1500 (m), 1466 (w), 1377 (w),
1275 (s), 1178 (m), 1150 (w), 1098 (s), 1001 (m), 906 (m), 884 cmꢀ1 (w);
ESI-HRMS: m/z calcd for C40H53O8Si [M+H]+: 689.3510; found:
689.3498.
added, and the mixture stirred for 3 h at room temperature. Then, con-
centrated HCl (200 mL) and one drop of water were added and the mix-
ture stirred for another 2 h. A further 10 mL of water was added and the
mixture was extracted three times with Et2O (20 mL). The combined or-
ganic extracts were dried with Na2SO4, the solvents removed in vacuo,
and the raw product purified by using flash column chromatography
(silica gel; CHCl3/CH3OH=9:1). The resulting brown solid was purified
by recrystallization from EtOAc to yield colorless needles (15 mg,
0.06 mmol, 32%). 1H NMR (400 MHz, CD3OD): d=1.90 (ddd, J=13.1,
10.4, 5.9 Hz, 1H), 2.26 (ddd, J=13.1, 10.4, 5.9 Hz, 1H), 3.68 (pseudo-
sept, J=5.1, 11.6 Hz, 2H), 3.98 (dt, J=5.1, 2.4 Hz, 1H), 4.32 (dt, J=5.9,
1.9 Hz, 1H), 5.13 (dd, J=10.4, 5.6 Hz, 1H), 7.03 (s, 1H), 7.06 (dd, J=8.0,
1.4 Hz, 1H), 7.66 (d, J=8.0 Hz, 1H), 9.98 ppm (s, 1H); 13C NMR
(100 MHz, CD3OD): d=44.81, 64.01, 74.28, 80.85, 89.50, 115.13, 118.50,
121.87, 134.11, 153.82, 162.79, 196.86 ppm; IR (diamond-ATR): n˜ =3262
(m), 2897 (m), 1650 (s), 1628 (s), 1434 (m), 1348 (m), 1309 (s), 1177 (m),
1153 (s), 1087 (s), 1051 (s), 988 (s), 956 (m), 874 (m), 810 (s), 680 cmꢀ1
(m); ESI-HRMS: m/z calcd for C12H13O5 [MꢀH]ꢀ: 237.0757; found:
237.0771.
Deprotected nucleoside 6a: The b-anomer of 6 (303 mg, 0.44 mmol) was
dissolved in dry methanol (7 mL) and K2CO3 (134 mg, 0.97 mmol) was
added. The suspension was stirred for 2 h at room temperature until all
the solids had dissolved. The yellow solution was diluted with chloroform
(50 mL) and water (50 mL). The aqueous phase was separated and ex-
tracted three times with chloroform (50 mL). The combined organic ex-
tracts were washed with saturated, aqueous NaCl and dried with Na2SO4.
After removal of the solvents in vacuo, the raw material was purified by
using flash column chromatography (silica gel; CHCl3/CH3OH=10:1) to
yield
a
colorless oil (86 mg, 0.19 mmol, 43%). 1H NMR (400 MHz,
CDCl3): d=1.11 (d, J=7.3 Hz, 18H), 1.29 (sept, J=7.3 Hz, 3H), 1.41 (d,
J=13.5 Hz, 1H), 1.95–2.04 (m, 1H), 2.13 (dd, J=10.2, 5.6 Hz, 1H), 2.17–
2.28 (m, 1H), 2.80 (s, 2 OH), 3.63–3.73 (m, 2H), 3.88–3.97 (m, 3H), 4.20–
4.24 (m, 2H), 4.27–4.30 (m, 1H), 5.07 (dd, J=10.2, 5.6 Hz, 1H), 5.86 (s,
1H), 6.75 (d, J=8.4 Hz, 1H), 7.16 (dd, J=8.4, 2.4 Hz, 1H), 7.54 ppm (d,
J=2.4 Hz, 1H); 13C NMR (100 MHz, CDCl3): d=13.0, 18.0, 25.8, 43.6,
63.3, 67.6, 73.6, 79.9, 87.20, 97.4, 118.2, 125.2, 127.7, 128.5, 133.4,
152.8 ppm; IR (KBr): n˜ =2946 (m), 2868 (m), 1654 (m), 1618 (m), 1500
(m), 1466 (w), 1389 (w), 1279 (m), 1150 (w), 1127 (w), 1095 (m), 1051
(w), 1000 cmꢀ1 (w); ESI-HRMS: m/z calcd for C24H40ClO6Si [M+Cl]ꢀ:
487.2283; found: 487.2257.
Salen ligand 2b: The fully deprotected ligand 2 (45 mg, 0.19 mmol) was
dissolved in dry methanol (10 mL) and ethylenediamine (0.5 equiv,
6.32 mL, 0.095 mmol) was added. The color of the solution changed to
yellow and a microcrystalline yellow material precipitated over several
days. The reaction was also carried out in CD3OD in an NMR tube and
quantitative conversion was observed by NMR spectroscopy. 1H NMR
(400 MHz, CD3OD): d=1.90 (ddd, J=13.2, 10.4, 5.9 Hz, 1H), 2.21 (dtd,
J=12.5, 5.2, 1.7 Hz, 1H), 3.53–3.76 (m, 3H), 3.95 (s, 2H), 4.30 (m, 1H),
5.07 (dd, J=10.4, 5.6 Hz, 1H), 6.83–6.93 (m, 2H), 7.30 (dd, J=19.2,
8.0 Hz, 1H), 8.43 ppm (s, 1H); 13C NMR (100 MHz, CD3OD): d=44.85,
59.59, 63.83, 73.95, 80.63, 88.71, 114.38, 115.96, 117.88, 131.75, 147.55,
162.14, 166.12 ppm; IR (diamond-ATR): n˜ =3253 (w), 2890 (w), 2853
(w), 2428 (s), 1984 (w), 1627 (s), 1429 (m), 1372 (m), 1265 (m), 1186 (w),
1138 (m), 1089 (m), 1055 (s), 1021 (s), 976 (s), 938 (m), 898 (m), 866 (m),
816 (s), 808 (s), 755 cmꢀ1 (m); ESI-HRMS: m/z calcd for C26H33O8N2
[M+H]+: 501.2231; found: 501.2229.
DMT-protected nucleoside 6b: Compound 6a (86 mg, 0.19 mmol) was
coevaporated twice with 2 mL of dry pyridine. It was then dissolved in
1 mL of pyridine and stirred over 4 molecular sieves for 2 h. 4,4’-Di-
A
tion was stirred for 2 h at room temperature. Subsequently, dry methanol
(2 mL) was added, the mixture stirred for 1 h, filtered, and the solvents
removed in vacuo. Flash chromatography (silica gel; hexane/EtOAc
(9:1)+0.1% pyridine) yielded a colorless oil (79 mg, 0.11 mmol, 55%).
1H NMR (400 MHz, CDCl3): d=1.11 (d, J=7.6 Hz, 18H), 1.29–1.33 (m,
4H), 2.02–2.11 (m, 2H), 2.17 (dd, J=13.1, 5.6 Hz, 1H), 3.25–3.34 (m,
2H), 3.78 (s, 6H), 3.87–3.93 (m, 2H), 4.01 (m, 1H), 4.09–4.18 (m, 2H),
4.38 (m, 1H), 5.10 (dd, J=10.1, 5.6 Hz, 1H), 5.85 (s, 1H), 6.73 (d, J=
8.4 Hz, 1H), 6.82 (d, J=9.0 Hz, 4H), 7.17–7.30 (m, 4H), 7.36 (d, J=
9.0 Hz, 4H), 7.48 (d, J=8.3 Hz, 2H), 7.60 ppm (d, J=2.1 Hz, 1H);
13C NMR (150 MHz, CDCl3): d=13.0, 18.0, 25.8, 43.9, 55.2, 64.6, 67.4,
74.8, 79.8, 86.1, 97.4, 113.1, 118.1, 125.3, 126.7, 127.3, 127.8, 128.3, 128.6,
130.1, 134.0, 136.2, 144.9, 152.5, 158.4 ppm; IR (KBr): n˜ =1719 (m), 1654
(m), 1618 (m), 1560 (w), 1542 (w), 1508 (m), 1458 (w), 1272 (m),
1097 cmꢀ1 (m); ESI-HRMS: m/z calcd for C45H59O8Si [M+H]+: 755.3979;
found: 755.3961.
Cu–salen complex 8: A solution of ligand 2b (50 mg, 0.10 mmol) in dry
methanol (5 mL) was combined with a methanolic solution of [Cu(acac)2]
G
(26 mg, 0.10 mmol) and heated under reflux for 10 min. The color
changed from yellow to green to purple. Slow cooling of a saturated
methanolic solution yielded small, dichroic green-purple crystals which
were used for crystallographic examination. IR (diamond-ATR): n˜ =3305
(m), 2919 (w), 2888 (w), 1634 (s), 1614 (s), 1526 (s), 1482 (m), 1427 (s),
1387 (m), 1322 (s), 1302 (m), 1312 (m), 1187 (m), 1064 (s), 1038 (s), 998
(s), 966 (s), 959 (s), 873 (s), 795 cmꢀ1 (s); ESI-HRMS: m/z calcd for
C26H31CuN2O8 [M+H]+: 562.1371; found: 562.1369. For crystallographic
data, see ref. [11].
Phosphoramidite 7: Compound 6b (66 mg, 87 mmol) was coevaporated
twice with 2 mL of dry THF and finally dissolved in 2 mL of degassed
DNA synthesis, cleavage, and purification: DNA synthesis was per-
formed using Ultramild Bases and reagents (Glen Research) and follow-
ing standard phosphoramidite protocols. The coupling times and amounts
of ligands could be reduced to match the parameters for coupling the
natural bases. The trityl values showed good incorporation of the modi-
fied nucleoside. After additional treatment with 2% dichloroacetic acid
plus 1% H2O in dichloromethane to remove the acetal protecting
groups, the controlled-pore-size glass (CPG) solid support was treated
with concentrated, aqueous NH3/EtOH (3:1) for 12 h at room tempera-
ture to cleave the strands. The solvents were removed in a SpeedVac con-
centrator and the pellet redissolved in doubly distilled water. Analysis
and purification was performed on Merck LaChrome HPLC systems
using 5m Silica-C18 RP columns and 0.1m NHEt3OAc in H2O/CH3CN
(typically 0–40% CH3CN in 40 min) as eluent. Prior to HPLC purifica-
tion, 20% HOAc was added and the mixture incubated for 20 min. The
purified fractions were concentrated, desalted on Waters Sepac-C18 car-
tridges, and concentrated again. The concentration was estimated by UV
spectroscopy following standard procedures, taking into account the
molar extinction coefficient for the ligand 2 (e=10290 Lmolꢀ1 cmꢀ1).
THF. NEt(iPr)2 (31 mL, 170 mmol) and (iPr2N)(NCCH2CH2O)PCl (28 mL,
A
130 mmol) were then added and the reaction mixture was stirred for 2 h.
The solvents were removed in vacuo and the residue was dissolved in de-
gassed EtOAc (1 mL) and purified by using column chromatography
under a protecting gas atmosphere (deactivated silica gel; hexane/EtOAc
(2:1)+0.1% pyridine; all solvents degassed). The solvent was removed
under high vacuum to yield a mixture of diastereomers as a colorless oil
(76 mg, 80 mmol, 92%), which was immediately used in DNA synthesis.
1H NMR (200 MHz, CDCl3): d=1.05–1.20 (m, 30H), 1.25–1.33 (m, 4H),
1.96–2.12 (m, 2H), 2.23–2.29 (m, 1H), 2.44 (t, J=6.5 Hz, 2H), 2.61 (t, J=
6.5 Hz, 2H), 3.21–3.32 (m, 2H), 3.46–3.74 (m, 2H), 3.77 (s, 3H), 3.78 (s,
3H), 3.90–3.97 (m, 2H), 4.11–4.24 (m, 3H), 4.43–4.45 (m, 1H), 5.10 (dd,
J=10.6, 5.0 Hz, 1H), 5.86 (s, 1H), 6.73–6.84 (m, 5H), 7.23–7.31 (m, 4H),
7.35–7.41 (m, 4H), 7.48–7.52 (m, 2H), 7.64 ppm (d, J=2.3 Hz, 1H);
31P NMR (80 MHz, CDCl3): d=149.0, 148.6 ppm; ESI-HRMS: m/z calcd
for C54H76N2O9PSi [M+H]+: 955.5058; found: 955.5083.
Deprotected ligand nucleoside 2: b-1’-(4-[1,3]Dioxan-2-yl-3-(triisopropyl-
silyloxy)phenyl)-2’-desoxyribose (85 mg, 0.17 mmol) was dissolved in dry
THF (2 mL), tetrabutylammonium fluoride (1.7 equiv, 1.1m in THF) was
Chem. Eur. J. 2006, 12, 8708 – 8718
ꢁ 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
8717