Compound 8a

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InChIKey RKYDYOXFFNFAPH-GBWPHOAASA-N

Synthetic procedure: See article for the definitive version of this procedure and for full experimental details.

A 6.1 mM RNA aptamer solution (sequences: 5'-GGA CUG GGC GAG AAG UUU AGU CC-3' (apt1) or 5'-CUG CAG UCC GAA AAG GGC CAG-3', (apt2)) (816 µL, 4.98 µmol) in 10 mM sodium phosphate buffer (pH 6.8) was heated to 85°C for 10 min and was afterwards kept at room temperature for 15 min. Then a 4.8 mM solution of the neomycin B 1 (684 µL, 3.28 µmol) in 10 mM sodium phosphate buffer (pH 7.4) was added and the mixture was allowed to stand for 30 min at room temperature. Afterwards 15 equiv. phenyl isocyanate 7a (7.3 mg, 49.2 µmol) dissolved in DMF (108 µL) were added and the reaction mixture was allowed to react for 24 hours at 40°C. After addition of a 7 wt. % ethylamine water solution (180 µL) and further incubation for 30 min at room temperature, a 2 M sodium hydroxide solution (240 µl) was added and the crude mixture was heated to 90°C for 30 min. After cooling to room temperature each fraction (50 µL) was purified by HPLC using a Waters Spherisorb ODS-2C₁₈ analytic column (water/acetone 1.0 : 0.81 containing 16.9 mM HFBA) at a flow rate of 1 ml/min at 40°C to yield 8a (R_t = 16.4 min). TLC (Chloroform/MeOH/17% NH₄OH 2:1:1 v/v/v) R_f = 0.45. ¹H-NMR (D₂O, 500 MHz) δ (p.p.m.) 7.23 (d, J = 9 Hz, 2H, Ar-H3, Ar-H5), 7.00 (d, J = 9 Hz, 2H, Ar-H2, Ar-H6), 6.05 (d, J = 3.5 Hz, 1H, 1-H^I), 5.42 (d, J = 1.5 Hz, 1H, 1-H^II), 5.11 (s, 1H, 1-H^III), 4.43 (t, J = 5.25 Hz, 1H, 3-H^II), 4.33 (m, 1H, 2-H^II), 4.26-4.19 (m, 2H, 5-H^III, 4-H^II), 4.12-4.07 (m, 2H, 4-H, 2-H^III), 4.04 (m, 1H, 3-H^III), 4.00 (t, J = 14.5 Hz, 1H, 5-H^I), 3.95 – 3.88 (m, 3H, 5-H^II, 5-H, 3-H^I), 3.83 (s, 3H, OCH₃), 3.76-3.67 (m, 3H, 5-H^II, 6-H, 4-H^III), 3.55 (dt, J = 3 Hz, J = 9.5 Hz, 1H, 3-H), 3.61-3.41 (m, 3H, 2-H^I, 4-H^I, 6a-H^I), 3.38-3.28 (m, 4H, 1-H, 6a-H^III, 6b-H^III, 6b-H^I), 2.50 (dt, J = 11.5 Hz; J = 3 Hz, 1H, 2-H_e), 1.90 (dd, J = 12.7 Hz, 1H, 2-H_a). APT (D₂O, 500 MHz) δ (p.p.m.) 158.47 (Carbonyl-C), 156.10 (Ar-C4), 130.32 (Ar-C1), 125.11 (2C, Ar-C2,C6), 114.93 (2C, Ar-C3,C5), 110.12 (C-1^II), 98.72 (C-1^III), 95.64 (C-1^I), 84.75 (C-5), 82.05 (C-4^II), 75.82 (C-3^II), 74.95 (C-4), 74.31 (C-2^II), 72.79 (C-6), 70.61 (C-4^I), 70.18 (C-5^III), 67.78 (C-3^III), 69.41 (C-3^I), 68.07 (C-4^III), 68.09 (C-5^I), 60.00 (C-5^II), 55.58 (CH₃), 53.36 (C-2^I), 51.13 (C-2^III), 49.75 (C-1), 48.42 (C-3), 40.61 (C-6^III), 39.95 (C-6^I), 27.93 (C-2). MS (EI+) (m/z): found 764.36742 [M+H]⁺, 786.34508 [M+Na]⁺; calculated 764.36724 [M+H]⁺, 786.34918 [M+Na]⁺.