5′‐O‐(4,4′‐Dimethoxytrityl)‐2′‐O‐methyl‐3‐N‐methyluridine (2): 2′‐O‐Methyluridine (1) (0.2 g, 0.77 mmol) was dissolved in dry dimethyl sulfoxide (2 mL). Sodium hydride (18.6 mg, 0.77 mmol) was added to the reaction mixture and stirred at room temperature under argon atmosphere until bubbling stopped. Then, methyl iodide (0.05 mL, 0.77 mmol) was added dropwise. The solution was stirred for another 5 h. All volatiles were evaporated under high vacuum. The residue was co‐evaporated once with methanol and twice with pyridine before it was dissolved in anhydrous pyridine (1 mL). Dimethoxytrityl chloride (0.32 g, 0.93 mmol) and 4‐dimethylaminopyridine (14.2 mg, 0.12 mmol) were added. The reaction solution was stirred under argon at room temperature overnight before the reaction was quenched by adding methanol. All volatiles were evaporated, the residue was diluted in methylene chloride and was washed three times with a solution of 5 % citric acid, once with a saturated sodium bicarbonate solution, and once with a saturated sodium chloride solution. The product was isolated after column chromatography (100:0.1 to 100:0.5 methylene chloride/methanol). Yield: 0.24 g (54 %) of 2 as white foam. 1H NMR (300 MHz, [D6]DMSO): δ=3.15 (s, 3 H; H3C‐N), 3.24–3.36 (m, 2 H; Ha,b‐C(5′)), 3.44 (s, 3 H; H3C‐O(2′)), 3.75 (s, 6 H; 2×H3C‐O(DMT)), 3.80–3.58 (m, 1 H; H‐C(2′)), 3.94–4.00 (m, 1 H; H‐C(4′)), 4.19–4.255 (dd, J=12, 7.0 Hz, 1 H; H‐C(3′)), 5.22 (d, J=5.1 Hz, 1 H; H‐O(3′)), 5.39 (d, J=8.1 Hz, 1 H; H‐C(5′)), 5.84 (d, J=2.7 Hz, 1 H; H‐C(1′)), 6.90 (d, 4 H; Har‐C (DMT)), 7.21–737 (m, 9 H; Har‐C (DMT)), 7.80 ppm (d, J=8.1 Hz, 1 H; H‐C(6)); 13C NMR (75 MHz, [D6]DMSO): δ=27.3 (1 C, H3C‐N), 55.0 (1 C, H3C‐O (DMT)), 58.0 (1 C, H3C‐O(2′)), 62.3 (C(5′)), 68.4 (1 C, C(2′)), 82.4 (1 C, C(4′)), 82.8 (1 C, C(3′)), 88.7 (1 C, C(1′)), 100.5 (1 C, C(5)), 113.4 (4C, Car(DMT)), 127.0 (1 C, Car(DMT)), 127.61 (2 C, Car(DMT)), 127.80 (2 C, Car(DMT)), 129.9 (4 C, Car), 138.4 (1 C, C(6)); HRMS (ESI) m/z calcd: 597.2207 [M+Na]+; found: 597.2219.
5′‐O‐Dimethoxytrityl‐2′‐O‐methyl‐3‐N‐methyluridine‐3′‐(2‐cyanoethyl‐diisopropylphosporamidite) (3): Compound 2 (0.24 g, 0.41 mmol) was dried under high vacuum and vented with argon. The solid was dissolved in dry methylene chloride (6 mL) and treated with N,N‐diisopropylethylamine (0.28 mL, 1.66 mmol) and 2‐cyanoethyl‐N,N‐diisopropyl‐chlorophosphoramidite (0.20 g, 0.83 mmol). The reaction solution was stirred for 4 h at room temperature. Afterward, the reaction was quenched by adding 1 mL of methanol. It then was diluted with methylene chloride (1:10), washed with saturated sodium bicarbonate solution and with a saturated sodium chloride solution. The product was isolated by column chromatography (1 % triethylamine, 35 % ethyl acetate and 64 % n‐hexane). Yield: 0.27 g (84 %) of 3 as white foam. 1H NMR (700 MHz, CDCl3): δ=0.96 (d, J=6.8 Hz, 3 H; CH‐NCH3), 1.08–1.12 (m, 9 H; 3.15 CH‐NCH3), 2.33 (t, J=6.38, 7.08 Hz, 1 H; NC‐CH), 2.57 (m, J=6.35, 7.08 Hz, 1 H; NC‐CH), 3.25 (s, 3 H; H3C‐N), 3.35–3.6 (m, 4 H; H‐C(5′)(a,b), NCH‐(CH3)2, PO‐CH), 3.53 (2 s, 3 H; H3C‐O(2′)), 3.73 (2 s, 6 H; 2×H3C‐O(DMT)), 3.68–3.71 (m, 2 H; PO‐CH, H‐C(2′)), 4.15–4.19 (m, 1 H; H‐C(4′)), 4.36–4.42 (m, 1 H; H‐C(3′)), 4.51–4.56 (m, 1 H; H‐C(3′)), 5.21–5.26 (dd, J=8.02, 8.30 Hz, 1 H; H‐C(5′)), 5.93–5.97 (dd, J=1.7, 2.7 Hz, 1 H; H‐C(1′)), 6.74–6.79 (m, 4 H; H‐Car(DMT)), 7.16–7.35 (m, 9 H; H‐Car(DMT)), 7.88–7.99 ppm (dd, J=8.07, 8.07 Hz, 1 H; H‐C(6)); 31P NMR (162 MHz, CDCl3, 25 °C): δ=150.17; 150.73 ppm; HRMS (ESI): m/z calcd: 775.3466 [M+H]+; found: 775.3472.
3′,5′‐Diacetyl‐2′‐O‐methyladenosine (5): 2′‐O‐Methyladenosine (4; 0.50 g, 1.78 mmol) was co‐evaporated with pyridine, before dimethylformamide (1.4 mL), dry pyridine (0.7 mL), acetic anhydride (0.7 mL, 7.41 mol) and 4‐dimethylaminopyridine (8 mg, 0.065 mmol) were added. The reaction solution was stirred at 0 °C for 3 hours. The reaction progress was controlled by TLC (5 % methanol in methylene chloride). Methanol (0.5 mL) was added to quench the reaction. Then all volatiles were removed by distillation under high vacuum (70 °C) before the residue was co‐evaporated once with pyridine and three times with toluene. This crude product was directly used for the next reaction. For analytical analysis the product was further purified by column chromatography (1 % methanol in methylene chloride). Yield: 0.64 g (98 %) of 5 as white solid. 1H NMR (300 MHz, [D6]DMSO): δ=2.04, 2.14 (2 s, 6 H; O(5′)CO‐CH3, O(3′)CO‐CH3)), 3.28 (s, 3 H; H3C‐O(2′)), 4.21–4.38 (m, 3 H; C(4′)‐H, Ha,b‐C(5′)), 4.88 (ddt, J=6, 5.7 Hz, 1 H; H‐C(2′)), 5.49–5.51 (dd, J=2.4, 4.8 Hz, 1 H; H‐C(3′)), 6.03 (d, J=6 Hz, 1 H; H‐C(1′)), 7.34 (br s, 2 H; NH2), 8.16 (s, 1 H; H‐C(8) or H‐C(2)), 8.38 ppm (s, 1 H; H‐C(2) or H‐C(8)); 13C NMR (75 MHz,CDCl3): δ=20.9, 21.0 (2 C, O(5′)‐CO‐CH3, O(3′)‐CO‐CH3), 59.5 (1 C, C(5′)), 63.2 (1 C, C(4′)), 80.3 (1 H; C(2′)), 81.2 (1 H; C(3′)), 87.7 (1 C, C(1′)), 139.5 (1 C, C(8) or C(2)), 153.5 ppm (1 C, C(2) or C(8)); HRMS (ESI): m/z calcd: 366.1408 [M+H]+; found: 366.1414.
9‐(3′,5′‐Diacetyl‐2′‐O‐methylfuranosyl)‐6‐(1,2,4‐triazol‐4‐yl)purine (6): Compound 5 (0.54 g, 1.48 mmol) was co‐evaporated with pyridine and treated with N,N‐bis[(dimethylamino)methylene]hydrazine dihydrochloride (5.16 g, 2.15 mmol; prepared as described below following ref. 28) which was previously dried over phosphorpentoxide under high vacuum for 2 h. This solid was diluted in dry pyridine (8 mL) and stirred under argon atmosphere in the dark at 85 °C for 48 h. Then all volatiles were removed under vacuum and the residue was co‐evaporated twice with toluene. The residue was filtrated and washed with methylene chloride. The solid N,N‐dimethylformamide‐azine dihydrochloride can be recycled. The filtrate was washed with a solution of 5 % citric acid, a saturated solution of sodium bicarbonate and a saturated solution of sodium chloride. The organic fractions were united and the volatiles were removed under vacuum. The residue was then purified by column chromatography (silica, 0.5–1.5 % methanol in methylene chloride). Yield: 0.47 g (76 %) of 6 as white foam. 1H NMR (300 MHz, [D6]DMSO): δ=2.05, 2.16 (s, 3 H; H3C‐CO‐O(5′), H3C‐CO‐OO(3′)), 3.31 (s, 3 H; H3C‐O(2′)), 4.28–4.44 (m, 3 H; H‐C(4′), Ha,b‐C(5′)), 4.92 (ddt, J=6, 5.4 Hz, 1 H; H‐C(2′)), 5.53–5.56 (dd, J=3.9, 4.8 Hz, 1 H; H‐C(3′)), 6.24 (d, J=6 Hz, 1 H; H‐C(1′)), 7.34 (br s, 2 H; NH2), 8.96 (s, 1 H; H‐C(8) or H‐C(2)), 9.03(s, 1 H; H‐C(2) or H‐C(8)), 9.63 ppm (s, 2 H; N=CH−N); 13C NMR (75 MHz, [D6]DMSO): δ=21.16, 21.19 (2 C, O(5′)‐CO‐CH3, O(3′)‐CO‐CH3), 59.0 (1 C, H3C‐O(2′)), 63.7 (1 C, C(5′)), 71.3 (1 H; C(3′)), 80.4 (1 H; C(2′)), 80.8 (1 C, C(4′)), 86.8 (1 C, C(1′)), 141.9 (2 C, N=CH−N), 146.8 (1 C, C(2) or C(8)), 152.8 ppm (1 C, C(8) or C(2)); HRMS (ESI): m/z calcd: 418.1470 [M+H]+; found: 418.1475.
6‐(N,N‐Dimethyl)‐2′‐O‐methyladenosine (7): Compound 6 (0.47 g, 1.12 mmol) was suspended in 33 % dimethylamine solution in ethanol (3 mL) and stirred under argon atmosphere at room temperature for 48 h. During that time, the white suspension turned into a clear solution. All volatiles were removed under vacuum. Further processing was done without further purification. For analytical reasons the crude product was purified by column chromatography (silica, 1–3 % methanol in methylene chloride). Yield: 0.34 g (98 %) of 7 as white foam. 1H NMR (300 MHz, [D6]DMSO): δ=3.31 (s, 3 H; H3C‐O(2′)), 3.46 (br s, 6 H; (CH3)2‐N), 3.53–3.71 (m, 3 H; H‐C(4′), Ha,b‐C(5′)), 3.98 (s, 1 H; O(3′)), 4.33–4.34 (br, 2 H; H‐C(2′), H‐O(5′)), 5.24 (d, J=4.2 Hz, 1 H; H‐C(3′)), 5.33–537 (ddt, J=4.8, 5.0 Hz, 1 H; H‐C(4′)), 6.03 (d, J=4,2 Hz, 1 H; H‐C(1′)), 8.22 (s, 1 H; H‐C(8) or H‐C(2)), 8.40 ppm (s, 1 H; H‐C(2) or H‐C(8)); 13C NMR (75 MHz, [D6]DMSO): δ=37.8 (1 C, H3C‐N), 57.4 (1 C, H3C‐O(2′)), 61.3 (1 C, C(5′)), 68.7 (1 H; C(3′)), 82.4 (1 H; C(2′)), 85.6 (1 C, C(1′)), 86.3 (1 C, C(4′)), 138.3 (1 C, C(2) or C(8)), 151.9 ppm (1 C, C(8) or C(2)); HRMS (ESI): m/z calcd: 310.1510 [M+H]+; found: 310.1515.
5′‐O‐Dimethoxytrityl‐6‐(N,N‐dimethyl)‐2′‐O‐methyladenosine (8): Compound 7 (0.24 g, 0.77 mmol) together with 4‐(dimethylamino)‐pyridine (14 mg, 0.12 mmol) were co‐evaporated with pyridine. The residue was diluted in dry pyridine (8 mL). 4,4′‐O‐Dimethoxytrityl chloride (0.32 g, 0.92 mmol) was dried for 2 h on high vacuum before it was added to the reaction solution, and the mixture was stirred overnight at room temperature together with molecular sieves under argon atmosphere. The reaction was quenched with methanol (0.5 mL) before all volatiles were removed under reduced pressure. The residue was co‐evaporated three times with toluene. Afterward the product was purified by column chromatography (silica, 0–3 % methanol in methylene chloride). Another column chromatography (12–25 % acetone in toluene) can be necessary to further improve purity. Yield: 0.382 g (81 %) of 8 as white foam. 1H NMR (300 MHz, [D6]DMSO): δ=3.20 (m, 2 H; C(5′)‐Ha,b), 3.31–3.59 (br s, 6 H; H3C−N), 3.73 (s, 6 H; 2×H3C‐O‐(DMT)), 4.06 (m, 1 H; H‐C(4′)), 4.41 (s, 2 H; H‐C(3′), H‐C(2′)), 5.25 (s, 1 H; H‐O(3′)), 6.06 (s, 1 H; H‐C(1′)), 6.78–6.88 (m, 4 H; HCar(DMT)), 7.16–7.40 (m, 9 H; Char(DMT)), 8.18 (s, 1 H; H‐C(8) or H‐C(2)), 8.26 ppm (s, 1 H; H‐C(2) or H‐C(8)); 13C NMR (75 MHz, [D6]DMSO): δ=38.8 (1 C, N‐CH3), 55.5 (2 C, O‐CH3(DMT)), 59.3 (1 C, H3C‐O(2′)), 63.4 (1 C, C(5′)), 70.1 (1 C; C(3′)), 83.5 (1 C; C(2′)), 83.9 (1 C; C(4′)), 86.6 (1 C, C(1′)), 113.4 (4 C, Car(DMT)), 127.0 (1 C, Car(DMT)), 128.1 (2 C, Car(DMT)), 128.4 (2 C, Car(DMT)), 130.4 (4 C, Car(DMT)), 136.0 (1 C, C(2) or C(8)), 152.8 ppm (1 C, C(8) or C(2)); HRMS (ESI): m/z calcd: 612.2817 [M+H]+; found: 612.2822.
5′‐O‐Dimethoxytrityl‐6‐(N,N‐dimethyl)‐2′‐O‐methyladenosine‐3′‐(2‐cyanoethyl)‐N,N‐diisopropylphosphoramidite) (9): Compound 8 (0.54 g, 0.88 mmol) was dried under high vacuum for several hours and ventilated with argon. The solid was dissolved in dry methylene chloride (10 mL), and treated with N,N‐diisopropylethylamine (0.61 mL, 3.53 mmol) and 2‐cyanoethyl N,N‐diisopropylchlorophosphoramidite (0.42 g, 1.76 mmol). The reaction solution was stirred under argon atmosphere for 3.5 hours at room temperature. Then methanol (2 mL) was added and the solution was stirred for another 20 minutes. The solution was diluted with methylene chloride (1:10) and washed with saturated sodium bicarbonate solution and saturated sodium chloride solution. The product was isolated by column chromatography (1 % triethylamine, 35 % ethyl acetate and 64 % n‐hexane). Yield: 551 mg (77 %) of white foam. 1H NMR (600 MHz, CDCl3): δ=1.06–1.07 (d, J=6.6 Hz, 3 H; N‐CH‐(CH3)2), 1.19–1.22 (m, 9 H; N‐CH‐(CH3)2), 2.38–2.40 (m, 1 H; H‐C‐CN), 2.65–2.68 (m, 1 H; H‐C‐CN), 3.31–3.35 (m, H‐C(5′)), 3.48–3.69 (m, 12 H; N‐CH; H2‐C(5′), H3C‐O(2′), N‐(CH3)2, N‐CH, P‐O‐CH2), 3.80–3.79 (2 s, O‐CH3(DMT)), 3.87–3.98 (mP‐O‐CH2‐), 4.33–4.39 (m, 1 H; H‐C(4′)), 4.55–4.67 (m, 2 H; H‐C(2′)), H‐C(3′)), 6.13–6.15 (m, 1 H; H‐C(1′)), 6.80–6.84 (m, 4 H; CH(ar, DMT)), 7.20–7.35 (m, 7 H; HC(ar, DMT)), 7.44–7.47 (m, 2 H; HC(ar, DMT)), 7.92–7.97 (2 s, 1 H; H‐C(8) or H‐C(2)), 8.30–8.28 ppm (2 s, 1 H; H‐C(2) or H‐C(8)); 31P NMR (162 MHz, CDCl3, 25 °C): δ=150.21, 150.91 ppm; HRMS (ESI): m/z calcd: 812.3895 [M+H]+; found: 812.3901.
N,N‐bis[(Dimethylamino)methylene]hydrazine dihydrochloride:28 Thionyl chloride (1.4 mL, 19.3 mmol) was added dropwise to dry DMF (7 mL) under cooling with ice water. This transparent, slightly yellow solution was stirred for 20 h under argon. A solution of hydrazine monohydrate (0.24 mL, 1 equiv, 5.0 mmol) in dry DMF (7 mL) was added in drops and under cooling. This slightly yellow suspension was stirred for another 24 h under argon atmosphere. After the filtration the filter cake was washed with 10 mL DMF and 15 mL ethyl acetate and dried under high vacuum. Yield: 1.94 g (99 %) of white powder. 1H NMR (300 MHz, [D6]DMSO): δ=3.00 (s, 12 H; 4×NCH3), 8.36 ppm (s, 2 H; 2×N=CH−N).
Guanosine 5′‐diphosphate di‐tributylammonium salt: DOWEX‐50WX8 200–400 resin (H+ form) was filtered with nanopure water using a glass frit (pore size 16–40 μm) to remove small particles. Afterward, guanosine 5′‐diphosphate disodium salt (0.5 g, 1 mmol) was dissolved in water (4 mL) and eluted through a column (1,5 cm) packed with 2 cm of wet DOWEX‐50WX8 200–400 for 10 minutes. After filtration into a flask with 25 mL ethanol at 0 °C, tributylamine (0.5 mL, 2 mmol) was added. The solution was stirred while the column was rinsed with water until pH was about 7–8 before all volatiles were removed under high vacuum. To preserve a dry powder further co‐evaporations (three times with ethanol and two times with dioxane) were performed. The resulting white solid was directly used without further purifications. Yield: 0.70 g (86 %) of a white solid. 1H NMR (400 MHz, [D6]DMSO): δ=0.89 (t, J=7.4 Hz, 9 H; CH3), 1.29 (m, 6 H; CH2‐CH3), 1.55 (m, 6 H; N‐CH2‐CH2), 2.86 (br s, J=7.6 Hz, 6 H; N‐CH2), 3.92–4.05 (m, 3 H; H‐C(4′), H2‐C(5′)), 4.27 (t, J=4 Hz, 1 H; H‐C(3′)), 4.47 (t, J=4.95 Hz, 1 H; H‐C(2′)), 5.68 (d, J=5.3 Hz, 1 H; H‐C(1′)), 6.62 (br s, NH2), 7.89 (s, 1 H; H‐C(8)), 10.6 ppm (br s, NH); 31P NMR (162 MHz, DMSO, 25 °C): δ=−10.20 (d), −10.85 ppm (d).
RNA solid‐phase synthesis: All RNAs were assembled on an ABI392 synthesizer using 2′‐O‐TOM nucleoside phosphoramidites (ChemGenes Corporation) and CPG supports (2′‐tBDSilyl Guanosine (n‐PAC) 3′‐lcaa CPG 1000 Å, 2′‐tBDSilyl Adenosine (n‐PAC) 3′‐lcaa CPG 1000 Å, ≈40 μmol g−1 ChemGenes Corporation). Standard RNA synthesis cycle: detritylation (120 s) with dichloroacetic acid/1,2‐dichloroethane (4:96); coupling (2.0 min) with phosphoramidites/acetonitrile (0.1 m) and benzylthiotetrazole/acetonitrile (0.3 m); capping (2×0.25 min, Cap A/Cap B=1:1) with Cap A: 4‐(dimethylamino)pyridine in acetonitrile (0.5 m) and Cap B: acetic anhydride/sym‐collidine/acetonitrile (2:3:5); oxidation (1.0 min) with iodine (20 mm) in tetrahydrofuran (THF)/pyridine/H2O (35:10:5). Commercially available modified nucleoside building blocks: 2′‐O‐methyl adenosine and 2′‐O‐methyl cytidine (ChemGenes Corporation), were incorporated using modified synthesis cycles with longer coupling times (6 min).
RNA phosphitylation, hydrolysis, oxidative amidation was performed in analogy to ref. 29a, while Gpp attachment was performed in analogy to ref. 29b. Construction of the triphosphate‐bridged inverted guanosine to the RNA on the solid phase involved four steps, all of them performed under argon atmosphere. RNA phosphitylation was carried out by applying 0.5 mL of phosphitylation solution (2 mL diphenylphosphite, 8 mL anhydrous pyridine) over 300 s. This treatment was repeated twice. After washing the beads with acetonitrile, hydrolysis was performed using 0.5 mL of hydrolysis solution (1.0 mL of 1 m aqueous triethylammonium bicarbonate, 5 mL water and 4 mL acetonitrile) over a period of 5 min. This treatment was repeated four times. The solid support was then rinsed with 20 mL of acetonitrile before being dried under vacuum for several hours. Oxidative amidation was done by incubation with 0.5 mL of a solution containing 600 mg imidazole, 2 mL N,O‐bis(trimethylsilyl)acetamide, 4 mL anhydrous acetonitrile, 4 mL bromotrichloromethane and 0.4 mL trimethylamine for 30 min. This treatment was repeated four times. The solid support was intensively rinsed with dry acetonitrile. Finally, Gpp attachment was achieved by application of 0.5 mL of coupling solution (0.28 m guanosine 5′‐diphosphate di‐tributylammonium salt [preparation see above] in dry DMF, 500 mm zinc chloride) over 8 h at room temperature. This treatment was repeated three times.
Gppp‐capped RNA deprotection: The solid supports with the Gppp‐capped and otherwise fully protected oligos were rinsed with DBU in acetonitrile (6 mL; 1 m), then washed with acetonitrile and dried. Cleavage from the support and base deprotection was effected by treating the solid support with a 1:1 mixture of 40 % aqueous methylamine and 30 % aqueous ammonia (AMA) in a screw‐cap vial for 2 h at 40 °C. The resulting suspensions were filtered and the filtrates dried. Removal of 2′‐O silyl protecting groups was carried out with of 1 m tetrabutylammonium fluoride trihydrate in THF (1 mL) for 6 h at 40 °C. The reaction was quenched by the addition of 1 m triethylammonium acetate solution (pH 7.4, 1 mL) and then concentrated to approximately 1 mL. This viscous solution was desalted by size exclusion chromatography on a HiPrep 26/10 Sephadex G25 column (GE Healthcare). The crude products were evaporated and re‐dissolved in water (1 mL). Quality assessment of the crude Gppp‐capped RNAs via anion‐exchange HPLC on a Dionex DNAPac PA‐100 column (4×250 mm); conditions: flow 1 mL min−1; eluent A: 25 mm Tris hydrochloride, 6 m urea, pH 8.0, eluent B: 500 mm sodium perchlorate, 25 mm Tris hydrochloride, 6 m urea, pH 8.0; gradient: 0–60 % B in 45 minutes; temperature: 40 °C, UV detection at 260 nm. The Gppp‐capped RNAs were isolated by anion‐exchange HPLC on a Dionex DNAPac PA‐100 column (4×250 mm); Conditions: flow 1 mL min−1; eluents: see above; temperature 40 °C; UV detection at 260 nm. The product fractions were diluted with an equal amount of triethylammonium bicarbonate buffer (100 mm, pH 7.4) and loaded onto equilibrated C18 Sep‐Pak (Waters Corporation). The cartridge was washed with water and the RNA was eluted with acetonitrile/water (1:1). All volatiles were evaporated and the residue re‐dissolved in water (1 mL). Yields were determined UV photometrically. The quality of the product was analyzed via anion‐exchange HPLC as described above and by reversed‐phase LC–ESI‐MS.
Enzymatic N7 methylation of Gppp‐RNA: The enzymatic transformation was conducted in analogy to refs. 31 and 32. In short, lyophilized Gppp‐RNA 10 (4 nmol) was dissolved in buffer (8.0 μL, 1.5 m NaCl, 200 mm Na2HPO4, pH 7.4) followed by the addition of an aqueous solution of S‐adenosylmethionine (2.0 μL, 12 nmol), and the addition of water to obtain a total volume of 68.8 μL. To the mixed solution, enzymes were added successively (1.6 μL of 50 μm MTAN, 1.6 μL of 50 μm LuxS, 8 μL of 50 μm Ecm1 (Figures S1 and S2 in the Supporting Information)). The mixture was incubated for 45 min at 37 °C. The solution was extracted twice with an equal volume of chloroform/isoamyl alcohol solution (24:1, v/v). The organic layers were rewashed twice with an equal volume of water. The aqueous layers were combined and lyophilized, to eliminate remaining organic solvents. Analysis of the methylation reaction and purification of the product was performed by anion‐exchange chromatography (conditions see above). The integrity of the product was confirmed by LC–ESI mass spectrometry (conditions see below).
Enzymatic ligation of cap‐4 RNA. The 38‐nt T. cruzi cap‐4 RNA was prepared by splinted enzymatic ligation of an 11‐nt cap‐4 RNA and a chemically synthesized 5′‐phosphorylated 27‐nt RNA by using T4 DNA ligase (Thermo Fisher) in analogy to ref. 34. Briefly, 10 μm of RNA fragment 10 (8 nmol), 12.5 μm of RNA fragment 11 (10 nmol), and 12.5 μm of a 20‐nt DNA splint oligonucleotide (IDT, 10 nmol) were heated at 70 °C for 2 min and passively cooled to room temperature. Afterward water was added up to a total volume of 560 μL before 10× ligation buffer (80 μL, Thermo Fisher) and PEG (80 μL, Thermo Fisher) was added. T4 DNA ligase (80 μL; Thermo Fisher, 5 U μL−1) was added to a final concentration of 0.5 U μL−1 in a total volume of 0.8 mL before the mixture was incubated for 2 h at 37 °C. Ligation was stopped by chloroform/isoamyl alcohol (24:1, v/v) extraction. After lyophilization and re‐dissolving, analysis of the ligation reaction and purification of the ligation products were performed by anion‐exchange chromatography (conditions see above). The integrity of product was confirmed by LC–ESI mass spectrometry (conditions see below).
Mass spectrometry of cap‐4 RNA. All experiments were performed on a Finnigan LCQ Advantage MAX ion trap instrument connected to a Thermo Fisher Ultimate 3000 system. RNA sequences were analyzed in negative‐ion mode with a potential of −4 kV applied to the spray needle. LC: sample (200 pmol RNA dissolved in 30 μL of 20 mm EDTA solution; average injection volume: 30 μL), column (Waters XTerraMS, C18 2.5 μm; 2.1×50 mm) at 21 °C; flow rate: 0.1 mL min−1; eluent A: Et3N (8.6 mm), 1,1,1,3,3,3‐hexafluoroisopropanol (100 mm) in H2O (pH 8.0); eluent B: MeOH; gradient: 0–100 % B in A within 20 min; UV detection at 254 nm.
Leiter J., Reichert D., Rentmeister A, & Micura R. (2019). Practical Synthesis of Cap‐4 RNA. Chembiochem, 21(1-2), 265-271.