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DOI: 10.1055/s-0031-1290599
Covalent Modification of 2′-Deoxyuridine with Two Different Molecular Switches
Publikationsverlauf
Publikationsdatum:
28. Februar 2012 (online)
![](https://www.thieme-connect.de/media/synlett/201205/lookinside/thumbnails/10.1055-s-0031-1290599-1.jpg)
Abstract
Two different molecular switches, a spiropyran and a diarylethene, were attached synthetically to the 5-position of 2′-deoxyuridine. The diarylethene-modified nucleoside can be incorporated synthetically into DNA while preserving its characteristic photochromism.
Key words
oligonucleotide - palladium - DNA - photochromism - phosphoramidite
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References and Notes
Compound 5: Compound 4 ¹9 (490 mg, 3.35 mmol) was dissolved in anhyd EtOH (50 mL), freshly distilled 3 ¹9 (0.59 mL, 3.33 mmol) was added in one portion, and the reaction mixture was sonicated at 35 kHz under Ar. After 53 min the solvent was removed under reduced pressure. The crude product was purified by gradient flash chromatography on silica gel (hexane-THF, 70:1 → 50:1) yielding 5 (762 mg, 76%) as a pale blue foam; R f 0.36 (hexane-THF, 50:1). ¹H NMR (600 MHz, CDCl3): δ = 7.15-7.27 (m, 2 H, ArH), 7.20 (dt, 1 H, J = 1.2, 7.7 Hz, ArH), 7.09 (d, 1 H, J = 7.2 Hz, ArH), 6.87 (t, 1 H, J = 7.4 Hz, ArH), 6.83 (d, 1 H, J = 10.3 Hz, ArH), 6.67 (d, 1 H, J = 8.3 Hz, ArH), 6.55 (d, 1 H, J = 7.7 Hz, ArH), 5.74 (d, 1 H, J = 10.2 Hz, ArH), 2.98 (s, 1 H, CºCH), 2.74 (s, 3 H, NMe), 1.31 (s, 3 H, Me), 1.18 (s, 3 H, Me). ¹³C NMR (150 MHz, CDCl3): δ = 155.0, 148.1, 136.6, 133.7, 130.5, 128.8, 127.6, 121.5, 120.3, 119.3, 118.8, 115.2, 113.5, 106.9, 104.8, 83.6, 75.5, 51.9, 28.9, 25.9, 20.1. MS (CI, NH3): m/z (%) = 302.1 (100) [MH+]. HRMS (EI-MS): m/z [M+] calcd for C21H19NO: 301.1467; found: 301.1465.
21Compound 8: Compound 6 ¹9 (335 mg, 1.11 mmol) was dissolved in freshly distilled EtOH (10 mL) and anhyd Et3N (200 µL, 1.43 mmol). Compound 7 ¹9 (220 mg, 1.09 mmol) was added and the reaction mixture was sonicated at 35 kHz under Ar. After 2 h the solvent was removed under reduced pressure, the residue was dissolved in CH2Cl2 and dried over anhyd Na2SO4. The solvent was evaporated under reduced pressure, and the residue was dried in vacuo and purified by gradient flash chromatography on silica gel (hexane-EtOAc, 30:1 → 15:1) to yield 8 (300 mg, 77%) as a pale pink solid; R f 0.49 (hexane-EtOAc, 19:1). ¹H NMR (300 MHz, CDCl3): δ = 7.15-7.27 (m, 3 H, ArH), 7.09 (d, 1 H, J = 7.2 Hz, ArH), 6.87 (t, 1 H, J = 7.4 Hz, ArH), 6.80 (d, 1 H, J = 10.3 Hz, ArH), 6.61 (d, 1 H, J = 9.2 Hz, ArH), 6.55 (d, 1 H, J = 7.7 Hz, ArH), 5.74 (d, 1 H, J = 10.2 Hz, ArH), 2.74 (s, 3 H, NMe), 1.32 (s, 3 H, 3-Me), 1.18 (s, 3 H, 3-Me). ¹³C NMR (75 MHz, CDCl3): δ = 153.6 (Cquat), 148.0 (Cquat), 136.5 (Cquat), 132.2 (+, CH), 129.1 (+, CH), 128.4 (+, CH), 127.7 (+, CH), 121.5 (+, CH), 120.7 (+, CH), 120.6 (Cquat), 119.3 (+, CH), 116.9 (+, CH), 111.8 (Cquat), 106.9 (+, CH), 104.5 (Cquat), 51.9 (Cquat), 28.9 (+, Me), 25.9 (+, Me), 20.1 (+, Me). MS (EI, 70 eV): m/z (%) = 357.0(100) [M+˙], 339.9 (47) [M+ - Me.]. HRMS (EI-MS): m/z [M+] calcd for C19H18BrNO: 355.0572; found: 355.0570.
23Compound 1:
Compound 5 (53 mg, 0.176 mmol), 9 (50 mg, 0.141 mmol), CuI (6 mg, 0.0315
mmol) and Pd(dppf)Cl2 (20 mg, 0.0245 mmol) were dissolved
in anhyd DMF (2.0 mL) and anhyd Et3N (100 µL,
0.717 mmol). The mixture was degassed and stirred at r.t. for 26
h. Then all was poured into an EtOAc-H2O mixture
(20 mL, 1:1). After separation, the aqueous phase was extracted
with CH2Cl2, and the combined organic layers
were dried over anhyd Na2SO4 and the solvent was
evaporated under reduced pressure. The residue was dried in vacuo
and purified by gradient flash chromatography on silica gel (CH2Cl2-MeOH,
10:1 → 5.1) to yield 1 (50 mg,
67%) as glistening green crystals; R
f
0.29 (CH2Cl2-MeOH,
10:1). ¹H NMR (600 MHz, MeOD): δ = 8.36
(s, 1 H, H-6), 7.27 (d, 1 H, J = 2.0
Hz), 7.23 (dd, 1 H,
J = 8.4
Hz), 7.10 (dt, 1 H, J = 7.6
Hz), 7.03 (d, 1 H, J = 7.2 Hz),
6.92 (d, 1 H, J = 10.3 Hz),
6.78 (t, 1 H, J = 7.1 Hz), 6.61 (d,
1 H, J = 8.4 Hz), 6.52 (d, 1
H, J = 7.8 Hz), 6.26 (t, 1 H,
J = 6.6 Hz, H-1′),
5.80 (d, 1 H, J = 10.3 Hz),
4.40-4.43 (m, 1 H, H-3′), 3.94 (q, 1 H, J = 3.3 Hz, H-4′),
3.83 (dd, 1 H, J = 3.0, 12.0
Hz, H-5′), 3.75 (dd, 1 H, J = 3.4,
12.0 Hz, H-5′), 2.70 (s, 3 H, NMe), 2.29-2.34
(m, 1 H, H-2′), 2.22-2.28 (m, 1 H, H-2′),
1.26 (s, 3 H, MeC), 1.14 (s, 3 H, Me). ¹³C
NMR (150 MHz, MeOD): δ = 164.4, 156.2, 151.2,
149.5, 144.5 (C6), 137.8, 134.2, 131.1, 130.0, 128.6, 122.4, 121.4,
120.5, 120.4, 116.0, 107.9, 106.3, 100.9, 93.9, 89.1 (C-4′),
87.0 (C-1′), 80.1, 72.0 (C-3′), 62.6 (C-5′),
52.9, 41.8 (C-2′), 29.2 (NMe), 26.3 (Me), 20.4 (Me), 9.3.
MS (ESI): m/z (%) = 528.2
(100) [MH+].
Compound 12: Compound 11 (2.50 g, 11.7 mmol) was dissolved under argon atmosphere in anhyd THF (30 mL) and cooled to -78 ˚C. A 2 M lithium diisopropylamide solution in THF-heptane-ethylbenzene (8.79 mL, 17.6 mmol) was added dropwise and the mixture was stirred for 1 h at 0 ˚C. After cooling down to -78 ˚C, MeI (1.10 mL, 17.6 mmol) was added dropwise. The mixture was stirred for 2 additional hours. Then H2O (30 mL) was added, the phases were separated and the aqueous phase was extracted with EtOAc. The combined organic layers were dried over anhyd Na2SO4 and the solvent was evaporated under reduced pressure. The residue was dried in vacuo and purified by flash chromatography on silica gel(hexanes) to yield 12 (2.66 g, 99%) as a white solid; R f 0.57 (hexanes). ¹H NMR (300 MHz, CDCl3): δ = 7.78 (d, 1 H, J = 1.9 Hz, ArH), 7.59 (d, 1 H, J = 8.5 Hz, ArH), 7.34 (dd, 1 H, J = 8.5, 1.9 Hz, ArH), 6.90 (s, 1 H, ArH), 2.59 (d, 3 H, J = 1.2 Hz, Me). ¹³C NMR (75 MHz, CDCl3): δ = 143.1 (Cquat), 142.2 (Cquat), 138.4 (Cquat), 126.5 (Carom), 125.3 (Carom), 123.4 (Carom), 121.0 (Carom), 118.2 (Carom), 16.3 (Me). MS (EI, 70 eV): m/z (%) = 228.0(100) [M+], 147.1 (24) [M - Me].
26Compound 13: Compound 12 (969 mg, 4.3 mmol) and glutaryl chloride (0.27 mL, 2.1 mmol) were dissolved under argon atmosphere in anhyd CH2Cl2 (20 mL) and the solution was cooled to 0 ˚C. Then AlCl3 (626 mg 4.7 mmol) was added and the reaction mixture was stirred for 3 h at r.t. After completion of the reaction, a mixture of ice and 1 M aq HCl was added. The solution was let to be warmed to r.t., the phases were separated and the aqueous phase was extracted with EtOAc. The combined organic layers were dried over anhyd Na2SO4 and the solvent was evaporated under reduced pressure. The residue was dried in vacuo and purified by flash chromatography on silica gel (hexanes-EtOAc, 10:1) to yield 13 (896 mg, 74%) as a white solid; R f 0.31 (hexanes-EtOAc, 10:1). ¹H NMR (400 MHz, CDCl3): δ = 8.36 (d, 2 H, J = 1.8 Hz, ArH), 7.57 (d, 2 H, J = 8.5 Hz, ArH), 7.42 (dd, 2 H, J = 8.5, 1.8 Hz, ArH), 3.06 (t, 4 H, J = 6.9 Hz, CH2), 2.77 (s, 6 H, Me), 2.27 (quin, 2 H, J = 7.0 Hz, CH2). ¹³C NMR (75 MHz, CDCl3): δ = 168.6 (CO), 146.1 (Cquat), 142.9 (Cquat), 140.5 (Cquat), 136.5 (Cquat), 127.2 (Carom), 125.0 (Carom), 123.4 (Carom), 118.8 (Carom), 28.6 (CH2), 19.6 (CH2), 15.3 (Me). MS (EI, 70 eV): m/z (%) = 549.9 (14) [M+].
27Compound 14: To a suspension of zinc dust (301 mg, 4.6 mmol, stabilized, grading <63 µm) in anhyd THF (50 mL) TiCl4 (0.26 mL, 2.3 mmol) was added under argon atmosphere dropwise at 0 ˚C. The suspension was heated to 40 ˚C and stirred for 1 h. Compound 13 (631 mg, 1.1 mmol) was added and the mixture was stirred for 18 h. After cooling to r.t. the reaction mixture was poured through a silica gel pallet and rinsed with hexanes. The solvent was removed under reduced pressure and the residue was dried in vacuo and purified by flash chromatography on silica gel(hexanes) to yield 14 (328 mg, 55%) as a white solid; R f 0.25 (hexanes). ¹H NMR (300 MHz, CDCl3): δ = 7.64 (s, 2 H, ArH), 7.46 (d, 2 H, J = 8.4 Hz, ArH), 7.24 (s, 2 H, ArH), 2.88-3.02 (m, 4 H, CH2), 2.28 (quin, 2 H, J = 7.22 Hz, CH2), 2.12 (s, 6 H, Me). ¹³C NMR (75 MHz, CDCl3): δ = 140.9 (Cquat), 137.0 (Cquat), 136.8 (Cquat), 129.72 (Carom), 126.5 (Carom), 125.1 (Carom), 123.3 (Carom), 118.1 (Carom), 37.8 (CH2), 24.1 (CH2), 15.2 (Me). MS (EI, 70 eV): m/z (%) = 517.9 (100) [M+].
28Compound 15: Compound 14 (131 mg, 0.25 mmol), trimethylsilylacetylene (72 µL, 0.51 mmol), anhyd Et3N (41 µL, 0.51 mmol), Pd(PPh3)4 (30 mg, 0.03 mmol) and CuI (5 mg, 0.03 mmol) were dissolved in anhyd THF (3 mL) under argon. The mixture was degassed and refluxed for 19 h. After cooling to r.t. the solvent was removed under reduced pressure, the residue was dried in vacuo and purified by flash chromatography on silica gel(hexanes) to yield 15 (58 mg, 43%) as a white solid; R f 0.26 (hexanes). ¹H NMR (300 MHz, CDCl3): δ = 7.67 (s, 2 H, ArH), 7.54 (d, 1 H, J = 8.2 Hz, ArH), 7.47 (d, 1 H, J = 8.0 Hz, ArH), 7.29 (s, 2 H, ArH), 2.83-3.12 (m, 4 H, CH2), 2.28 (quin, 2 H, J = 7.8 Hz, CH2), 2.04 (s, 6 H, Me), 0.29 (s, 9 H, SiMe3). ¹³C NMR (75 MHz, CDCl3): δ = 139.1 (Cquat), 138.6 (Cquat), 137.3 (Cquat), 136.7 (Cquat), 127.1 (Carom), 126.4 (Carom), 125.9 (Carom), 125.1 (Carom), 123.3 (Carom), 121.9 (Carom), 118.0 (Carom), 105.9 (CºC), 37.9 (CH2), 29.9 (CºC), 24.2 (CH2), 15.3 (Me), 0.3 (SiMe3). MS (EI, 70 eV): m/z (%) = 536.0(100) [M+].
29Compound 16: Compound 15 (35 mg, 0.07 mmol) was dissolved in anhyd MeOH (3 mL) and K2CO3 (27 mg, 0.19 mmol) was added. The reaction mixture was stirred for 18 h at 40 ˚C. After cooling to r.t. MeOH was removed under reduced pressure. The residue was dried in vacuo and purified by flash chromatography on silica gel (hexanes) to yield 16 (30 mg, 99%) as a white solid; R f 0.65 (hexanes-EtOAc, 20:1) ¹H NMR (300 MHz, CDCl3): δ = 7.71 (s, 2 H, ArH), 7.57 (d, 2 H, J = 8.0 Hz, ArH), 7.46 (d, 1 H, J = 7.5 Hz, ArH), 7.28 (s, 1 H, ArH), 3.07 (s, 1 H, CºCH), 2.84-3.01 (m, 4 H, CH2), 2.28 (quin, 2 H, J = 8.0 Hz, CH2), 2.02 (s, 6 H, Me). ¹³C NMR (75 MHz, CDCl3): δ = 146.8 (Cquat), 139.2 (Cquat), 137.2 (Cquat), 136.9 (Cquat), 126.9 (Carom), 126.4 (Carom), 125.1 (Carom), 123.3 (Carom), 122.0 (Carom), 118.1 (Carom), 117.6 (Carom), 76.5 (CºC), 37.8 (CH2), 29.9 (CºC), 24.1 (CH2), 15.2 (Me). MS (EI, 70 eV): m/z (%) = 461.9 (100) [M+].
30Compound 2: Compound 16 (126 mg, 0.27 mmol), 9 (97 mg, 0.27 mmol), anhyd Et3N (45 µL, 0.54 mmol), Pd(PPh3)4 (63 mg, 0.05 mmol) und CuI (11 mg, 0.05 mmol) were dissolved in anhyd DMF (10 mL). The mixture was degassed and stirred for 18 h at 60 ˚C. After cooling to r.t. the solvent was removed under reduced pressure, the residue was dried in vacuo and purified by flash chromatography on silica gel (CH2Cl2-MeOH, 25:1) to yield 2 (121 mg, 65%) as a light yellow foam; R f 0.40 (CH2Cl2-MeOH, 10:1). ¹H NMR (300 MHz, MeOD): δ = 8.37 (s, 1 H, NH), 7.72 (s, 2 H, ArH), 7.58-7.68 (m, 1 H, C=CH), 7.55 (d, 1 H, J = 8.2 Hz, ArH), 7.46 (d, 1 H, J = 6.8 Hz, ArH), 6.95-7.29 (m, 2 H, ArH), 6.26 (t, 1 H, J = 6.2 Hz, 1′-H), 4.28-4.50 (m, 1 H, 3′-H), 3.88-4.03 (m, 1 H, 4′-H), 3.78-3.87 (m, 1 H, 5′-H), 3.66-3.78 (m, 1 H, 5′-H), 2.19-2.61 (m, 4 H, CH2), 2.00-2.48 (m, 9 H, 2′-H, CH2, Me), 1.95 (s, 1 H, 2′-H). ¹³C NMR (75 MHz, MeOD): δ = 151.2 (CO), 144.7 (C=C), 140.4 (CO), 139.8 (Cquat), 138.6 (Cquat), 138.5 (Cquat), 138.1 (Cquat), 131.3 (Cquat), 127.3 (Carom), 126.0 (Carom), 124.3 (Carom), 122.9 (Carom), 118.9 (Carom), 94.5 (CºC), 89.2 (4′-C), 87.1 (1′-C), 72.1 (3′-C), 62.6 (5′-C), 41.8 (2′-C), 38.6 (CH2), 25.0 (CH2), 15.1 (Me). MS (FAB): m/z (%) = 689.1 (6) [M+]. HRMS (ESI): m/z [M + H+] calcd for C34H30BrN2O5S2: 691.0759; found: 691.0766.
31Compound 17: Compound 2 (50 mg, 0.07 mmol), dimethoxytrityl chloride (37 mg, 0.11 mmol) and anhyd Et3N (10 µL, 0.12 mmol) were dissolved in anhyd pyridine (2 mL) under argon atmosphere. The solution was stirred for 18 h at 40 ˚C. The solvent was removed, the residue was dried in vacuo and purified by flash chromatography on silica gel (CH2Cl2-MeOH, 100:3 + 0.1% Et3N) to yield 17 (62 mg, 90%) as a light yellow foam; R f 0.61 (CH2Cl2-MeOH, 10:1). ¹H NMR (300 MHz, DMSO): δ = 8.05 (s, 1 H, NH), 7.70 (d, 2 H, J = 8.2 Hz, ArHbt), 7.63 (s, 1 H, C=CH), 7.43 (d, 2 H, J =7.4 Hz, ArHbt), 7.18-7.37 (m, 8 H, ArHDMT), 7.14 (d, 2 H, J = 7.3 Hz, ArHbt), 6.75-6.96 (m, 5 H, ArHDMT), 6.16 (t, 1 H, J = 6.7 Hz, 1′-H), 4.26-4.34 (m, 1 H, 3′-H), 3.93-398 (m, 1 H, 4′-H), 3.66-3.80 (m, 2 H, 5′-H), 3.61 (d, 6 H, J = 2.5 Hz, CH3,DMT), 2.79-2.93 (m, 4 H, CH2), 2.06-2.37 (m, 9 H, 2′-H, CH2, Me), 1.95-2.03 (m, 1 H, 2′-H). ¹³C NMR (75 MHz, acetone): δ = 163.9 (Cquat), 161.9 (Cquat), 159.6 (Cquat), 157.7 (Cquat), 150.4 (CO), 146.0 (Cquat), 143.1 (C=C), 140.3 (CO), 139.0 (Cquat), 138.1 (Cquat), 137.9 (Cquat), 136.6 (Cquat), 131.0 (Carom), 128.9 (Carom), 127.6 (Carom), 127.1 (Carom), 126.0 (Carom), 122.7 (Carom), 114.1 (CºC), 87.7 (4′-C), 86.6 (1′-C), 64.8 (5′-C), 58.4 (3′-C), 55.4 (2′-C), 46.4 (5′-C), 41.9 (s), 38.3 (CH2), 24.4 (CH2), 15.4 (Me), 8.9 (Me). MS (ESI): m/z (%) = 1015.2 (4)[(M + Na)+].
32Compound 18: Compound 17 (62 mg, 0.06 mmol), diisopropylethylamine (36 µL, 0.16 mmol) and 2-cyano-ethyldiisopropylphosphoramidite (27 µL, 0.16 mmol) were dissolved in anhyd CH2Cl2 (3 mL). The solution was stirred at r.t. for 40 min. The product was purified by flash chromatography on silica gel (CH2Cl2-MeOH, 100:4 + 0.1% Et3N) and additionally lyophilized out of benzene to yield 18 (74 mg, 99%) as a light yellow foam; R f 0.85, 0.91 (CH2Cl2-MeOH, 25:1). ³¹P NMR (101 MHz, DMSO): δ = 150.6 [P(III), 37%], 16.3 [P(V), 63%]. MS (MALDI): m/z (%) = 1191.3 (28) [M+].
33DNA 1: MS (MALDI): m/z (%) = 5950.0(100) [(M + DMT)+], 5647.9 (38) [M+], 2974.6 (17) [(M + DMT)²+/2], 2823.6 (7) [M²+/2].