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5'-O-DMT-3'-O-tert-Butyldimethylsilyl-uridine-2'-CE phosphoramidite
5'-O-DMT-3'-O-tert-Butyldimethylsilyl-uridine-2'-CE phosphoramidite is a phosphoramidite reagent used in the synthesis of oligonucleotides. It features a dimethoxytrityl (DMT) protecting group at the 5'-hydroxyl position, a tert-butyldimethylsilyl (TBDMS) protecting group at the 3'-hydroxyl position, and a cyanoethyl (CE) protecting group on the phosphoramidite at the 2' position. These protective groups ensure efficient incorporation of uridine into oligonucleotides while enhancing the stability and accuracy of synthesis. This reagent is important for creating modified oligonucleotides for research and therapeutic applications.
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Catalog
BRP-02169
Synonyms
3'-O-tert-Butyldimethylsilyl-5'-O-DMT-uridine 2'-CE phosphoramidite; 3'-TBDMS-rU Phosphoramidite; 5-O-(4,4'-dimethoxytrityl)-2-O-(diisopropylamino-2-cyanoethoxyphosphanyl)-3-O-(tert-butyl-dimethyl-silyl)-1-deoxy-1-uracil-1-yl-beta-D-ribo-pentofuranose; Uridine, 5'-O-[bis(4-methoxyphenyl)phenylmethyl]-3'-O-[(1,1-dimethylethyl)dimethylsilyl]-, 2'-[2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite]; 3'-OTBS U 2'-amidite; 3'-O-TBDMS-5'-O-DMT-rU CED phosphoramidite; DMT-3'-O-TBDMS-U-2'-CE-Phosphoramidite
CAS
129451-77-0
IUPAC Name
3-[[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[tert-butyl(dimethyl)silyl]oxy-2-(2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile
Molecular Weight
861.05
Molecular Formula
C45H61N4O9PSi
Canonical SMILES
CC(C)N(C(C)C)P(OCCC#N)OC1C(C(OC1N2C=CC(=O)NC2=O)COC(C3=CC=CC=C3)(C4=CC=C(C=C4)OC)C5=CC=C(C=C5)OC)O[Si](C)(C)C(C)(C)C
InChI
InChI=1S/C45H61N4O9PSi/c1-31(2)49(32(3)4)59(55-29-15-27-46)57-41-40(58-60(10,11)44(5,6)7)38(56-42(41)48-28-26-39(50)47-43(48)51)30-54-45(33-16-13-12-14-17-33,34-18-22-36(52-8)23-19-34)35-20-24-37(53-9)25-21-35/h12-14,16-26,28,31-32,38,40-42H,15,29-30H2,1-11H3,(H,47,50,51)/t38-,40-,41-,42-,59?/m1/s1
InChIKey
UZVSHRLVIXPYEZ-ZMHKPELYSA-N
Purity
≥97% by HPLC
Storage
Store at -20 °C
Chemical Structure:
Reference Reading
1. Novel method of synthesis of 5''-phosphate 2'-O-ribosyl-ribonucleosides and their 3'-phosphoramidites
Marcin K Chmielewski, Wojciech T Markiewicz. Molecules. 2013 Nov 29;18(12):14780-96. doi: 10.3390/molecules181214780.
Synthesis of 5''-phosphate 2'-O-ribosylribonucleosides [Nr(p)] of four common ribonucleosides, and 3'-phosphoramidites of 5''-phosphate 2'-O-ribosyladenosine and 2'-O-ribosylguanosine using the H-phosphonate chemistry is described. An additional ring protected by benzoyl groups was incorporated into the main ribosyl ring in the reaction with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose in the presence of SnCl4. The obtained 2'-O-ribosylribonucleosides (Nr) were applied in the subsequent transformations with selective deprotection. Ethanolamine was applied as a very convenient reagent for selective removal of benzoyl groups. Additionally, the tetraisopropyldisiloxane-1,3-diyl (TIPDSi) group was found to be stable under these deprotection conditions. Thus, the selectively deprotected 5''-hydroxyl group of Nr was transformed into an H-phosphonate monoester which was found to be stable under the following conditions: the removal of the TIPDSi group with triethylammonium fluoride and the dimethoxytritylation of the 5''-hydroxyl function. The 5''-H-phosphonate of Nr precursors was easily transformed to the corresponding dicyanoethyl 5''-O-phosphotriesters before phosphitylation, which gave 3'-phosphoramidite units of Nr(p) in high yield. The derived phosphoramidite units were used in an automated oligonucleotide synthesizer to produce dimer Ar(p)T via the phosphoramidite approach. The obtained products were fully deprotected under standard deprotection conditions giving dimers with a 5''-phosphate monoester function. Application of an alkaline phosphatase to prove the presence of an additional phosphate group was described.
2. Synthesis of an Atom-Specifically 2 H/13 C-Labeled Uridine Ribonucleoside Phosphoramidite
Lukasz T Olenginski, Owen B Becette, Serge L Beaucage, Theodore K Dayie. Curr Protoc. 2022 Jul;2(7):e481. doi: 10.1002/cpz1.481.
A combined enzymatic and chemical synthesis of a 2'-O-cyanoethoxymethyl (CEM) protected [1',6-13 C2 , 5-2 H]-uridine phosphoramidite is described herein. This is the first report of an atom-specific nucleobase and ribose labeled 2'-O-CEM protected ribonucleoside phosphoramidite. Importantly, the CEM 2'-OH protecting group permits the efficient solid-phase synthesis of large (>60 nucleotides) RNAs with good yield and purity. The new isotope-labeled phosphoramidite can therefore be applied to nuclear magnetic resonance (NMR) spectroscopy studies. Specifically, the [1',6-13 C2 , 5-2 H]-uridine phosphoramidite can be used to make position-specifically labeled RNAs for NMR analysis without complications from resonance overlap and scalar and dipolar couplings. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of the ribonucleoside 6 Basic Protocol 2: Synthesis of the ribonucleoside phosphoramidite 11.
3. Synthesis of 5'-Thio-3'-O-ribonucleoside Phosphoramidites
Nan-Sheng Li, Jun Lu, Joseph A Piccirilli. J Org Chem. 2017 Dec 1;82(23):12003-12013. doi: 10.1021/acs.joc.7b01484.
The chemical synthesis of phosphoramidite derivatives of all four 5'-deoxy-5'-thioribonucleosides is described. These phosphoramidites contained trityl (A, G, C, and U), dimethoxytrityl (A and G), or tert-butyldisulfanyl (G) as the 5'-S-protecting group. The application of several of these phosphoramidites for solid-phase synthesis of oligoribonucleotides containing a 2'-O-photocaged 5'-S-phosphorothiolate linkage or 5'-thiol-labeled RNAs is also further investigated.
