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TCI Practical Example: Construction of the Nucleic Acid Monomer Using a Phosphordiamidite

We are proud to introduce the synthesis of thymidine phosphoramidite by using 2-cyanoethyl N,N,N',N'-tetraisopropylphosphordiamidite as a phosphitylation reagent.

Used Chemicals

• 2-Cyanoethyl N,N,N',N'-Tetraisopropylphosphordiamidite [C2228]
• 1H-Tetrazole
• Acetonitrile
• DMF

Procedure

To an acetonitrile (1 mL) solution of 2-cyanoethyl N,N,N',N'-tetraisopropylphosphordiamidite (0.21 g, 0.69 mmol) and 1H-tetrazole (40 mg, 0.58 mmol) were added a DMF solution of 1 (0.20 g, 0.58 mmol) at room temperature. The reaction mixture was stirred overnight at room temperature, then diluted with TBME and washed with water, DMF:H₂O (1:1) solution, H₂O, and brine. The organic layer was concentrated under reduced pressure. The resulting crude product was purified by column chromatography (hexane:ethyl acetate:triethylamine = 1:2:0.03, on silica gel) to give 2 as a white powder (0.23 g, 72% yield).

Experimenter’s Comments

The reaction mixtures were monitored by LCMS.

Analytical Data

Compound 2

¹H NMR (400 MHz, DMSO-d6); δ 11.36 (brs, 1H), 8.05-7.96 (m, 2H), 7.73-7.64 (m, 1H), 7.59-7.51 (m, 2H), 7.45-7.37 (m, 1H), 6.25-6.17 (m, 1H), 4.72-4.62 (m, 1H), 4.62-4.52 (m, 1H), 4.51-4.38 (m, 1H), 4.32-4.15 (m, 1H), 3.84-3.66 (m, 2H), 3.66-3.51 (m, 2H), 2.84-2.73 (m, 2H), 2.47-2.22 (m, 2H), 1.67-1.53 (m, 3H), 1.27-1.03 (m, 12H).

¹³C NMR (101 MHz, DMSO-d6); δ 165.5, 163.6, 150.4, 135.8, 133.7, 129.3 (3C), 128.9 (2C), 119.0, 109.9, 84.1, 82.8, 72.8, 64.9, 58.3 (2C), 42.7, 37.7, 24.3 (4C), 19.8, 11.9.

³¹P NMR (162 MHz, DMSO-d6); δ 147.89.

Lead Reference

• Synthesis of DNA Oligomers Containing Modified Uracil Possessing Electron-Accepting Benzophenone Chromophore
• • K. Nakatani, C. Dohno, I. Saito. J. Org. Chem. 1999, 64, 6901.