Uses
5'-O-DMT-2'-F-Deoxyuridine-CE Phosphoramidite (DMT-2′Fluoro-dU Phosphoramidite) is a uridine phosphoramidite consisting of a fluorine in the 2' position, and the compound is used in the synthesis of DNA.
Definition
DMT-2′Fluoro-dU Phosphoramidite is also known as 2'-F-U CE-Phosphoramidite. 2'-F-RNA oligonucleotides adopt an A-form helix on hybridisation to a target. Whereas a hydroxyl group of RNA is a hydrogen bond donor, fluorine appears to be a weak acceptor. These features of 2'-F-RNA oligonucleotides lead to certain interesting properties. For example, it was demonstrated that oligonucleotides hybridise to a RNA oligonucleotide in the following order of increasing stability: DNA < RNA < 2'-OMe-RNA < 2'-F-RNA
Synthesis
5'-O-(4,4'-Dimethoxytrityl)-2'-deoxy-2'-fluorouridine (3.00 g, 5.47 mmol) was dissolved in anhydrous dichloromethane (50 ml) under an argon atmosphere, N,N-diisopropylethylamine (0.55 ml,3.18 mmol), 1H-tetrazole (0.45 g, 6.45 mmol) and 2-cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite (1.92 g, 6.36mmol) were added. And the mixture was stirred at room temperature overnight. The completion of the reaction was confirmed, 5 percent aqueous sodium hydrogen carbonate solution (20 ml) was added to the reaction mixture to allow layer separation, and the organic layer was washed with saturated brine (20 ml). The organic layer was dried over sodium sulfate, the filtrate was concentrated and the obtained crude product was purified by silica gel chromatography (hexane:ethyl acetate=75:25 - 30/70(v/v), containing 3percent triethylamine). The object fractions were collected and concentratedto give DMT-2′Fluoro-dU Phosphoramidite (2.76 g, 67.3 percent).
