5'-DMT-2'O-TBDMS-rU Phosphoramidite is a classic 2-OTBDMS phosphoramidite used to incorporate U into synthetic oligonucleotides.
Reference Reading
1. 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.
2. 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.
3. Solution-Phase Chemical Synthesis of Modified RNA Dinucleotides
Annamalai Senthilvelan, Muthian Shanmugasundaram, Anilkumar R Kore. Curr Protoc. 2022 Nov;2(11):e583. doi: 10.1002/cpz1.583.
This article describes a simple, reliable, efficient, and improved solution-phase method for the gram-scale chemical synthesis of RNA dinucleotides such as pAm pA, pAm pG, and pAm pU that utilizes phosphoramidite chemistry. The overall synthetic strategy involves three steps. The first step involves the coupling reaction between 5'-O-MMT protected nucleoside-3'-O-phosphoramidite and a protected nucleoside containing a free 5'-OH group in the presence of tetrazole, followed by the oxidation of phosphite triester using tert-butyl hydroperoxide to give the corresponding protected Nm pN. Next, the 5'-O-MMT is cleaved under 3% trichloroacetic acid in dichloromethane conditions. Finally, the 5'-hydroxyl group is phosphorylated by the use of an activated bis(2-cyanoethyl)-N,N-diisopropyl phosphoramidite using tetrazole, followed by the oxidation of trivalent to pentavalent phosphorus using tert-butyl hydroperoxide and subsequent deprotection using ammonium hydroxide to afford the corresponding RNA dinucleotide, pNm pN, in good yields with high purity (>99.5%).
