DMT-2′Fluoro-dU Phosphoramidite Chemical Properties

storage temp. 

Sealed in dry,Store in freezer, under -20°C

solubility 

DMSO: Sparingly soluble: 1-10 mg/ml
Ethanol: Sparingly soluble: 1-10 mg/ml

form 

powder

pka

9.39±0.10(Predicted)

color 

white to off-white

biological source

non-animal source (no BSE/TSE risk)

InChI

InChI=1/C39H46FN4O8P/c1-26(2)44(27(3)4)53(50-24-10-22-41)52-36-33(51-37(35(36)40)43-23-21-34(45)42-38(43)46)25-49-39(28-11-8-7-9-12-28,29-13-17-31(47-5)18-14-29)30-15-19-32(48-6)20-16-30/h7-9,11-21,23,26-27,33,35-37H,10,24-25H2,1-6H3,(H,42,45,46)/t33-,35-,36-,37-,53?/s3

InChIKey

HQHQPAYRJJMYQX-YOKGOYKLNA-N

SMILES

N1(C=CC(=O)NC1=O)[C@@H]1O[C@H](COC(C2=CC=CC=C2)(C2C=CC(=CC=2)OC)C2=CC=C(C=C2)OC)[C@@H](OP(OCCC#N)N(C(C)C)C(C)C)[C@H]1F |&1:8,10,36,51,r|

Safety Information

WGK Germany 

3

DMT-2′Fluoro-dU Phosphoramidite Usage And Synthesis

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).

References

[1] Patent: EP2816053, 2014, A1. Location in patent: Paragraph 0371
[2] Patent: US9371353, 2016, B2. Location in patent: Page/Page column 78
[3] DR. MUTHIAH MANOHARAN. Unique Gene-Silencing and Structural Properties of 2′-Fluoro-Modified siRNAs†[J]. Angewandte Chemie, 2011, 123 10: 2332-2336. DOI: 10.1002/ange.201006519

DMT-2′Fluoro-dU Phosphoramidite(146954-75-8)Related Product Information

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