Synthesis of 5′‐O‐DMT‐2′‐O‐TBS Mononucleosides Using an Organic Catalyst

Sunggi Lee1, Thomas P. Blaisdell1, Pinar Kasaplar2, Xixi Sun1, Kian L. Tan1

1 Boston College, Chestnut Hill, 2 Institute of Chemical Research of Catalonia, Tarragona
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 2.17
DOI:  10.1002/0471142700.nc0217s57
Online Posting Date:  June, 2014
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Abstract

This unit describes a highly effective method to produce 5′‐O‐DMT‐2′‐O‐TBS mononucleosides selectively using a small organic catalyst. This methodology avoids the tedious protection/deprotection strategy necessary to differentiate the 2′‐ and 3′‐hydroxyl groups in a ribonucleoside. The catalyst was synthesized in two steps, starting from the condensation of valinol and cyclopentyl aldehyde, followed by anionic addition of N‐methylimidazole. Ring closure of the amino alcohol with N,N‐dimethylformamide dimethyl acetal in methanol furnishes the catalyst. All four 2′‐O‐TBS protected mono‐nucleosides, U, ABz, GIb, and CAc, were produced in a single step using 10 to 20 mol% of the catalyst at room temperature with excellent yields and selectivity. Further transformation to phosphoramidite demonstrates the utility of this protocol in the preparation of monomers useful for automated synthesis of RNA. Curr. Protoc. Nucleic Acid Chem. 57.2.17.1‐2.17.11. © 2014 by John Wiley & Sons, Inc.

Keywords: 2′‐O‐TBS ribonucleosides; protection by site‐selective functionalization; organocatalyst; phosphoramidation

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Two‐Step Preparation of Organocatalyst
  • Basic Protocol 2: TBS Protection of 2′‐Hydroxyl Group in Presence of Free 3′‐Hydroxyl Group
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Two‐Step Preparation of Organocatalyst

  Materials
  • Cyclopentene
  • Tris(2,4‐di‐tert‐butylphenyl)phosphite (Aldrich, cat. no. 441791)
  • Rh(acac)(CO) 2 (Aldrich, cat. no. 288101)
  • Anhydrous benzene
  • 1:1 H 2/CO (“syn” gas)
  • (S)‐Valinol (Combi‐Blocks, cat. no. HC‐6495)
  • Anhydrous tetrahydrofuran
  • Anhydrous magnesium sulfate
  • N‐methylimidazole (Aldrich, cat. no. M50834)
  • Dry ice/acetone bath
  • n‐Butyllithium (10 M in hexanes; Aldrich, cat. no. 230715)
  • Saturated aqueous ammonium chloride
  • Diethyl ether
  • Anhydrous methanol
  • Nitrogen source
  • N,N‐dimethylformamide dimethyl acetal (AK Scientific, cat. no. 168056)
  • Anhydrous pentane
  • Silica gel (EMD Silica Gel 60, 230‐400 mesh)
  • Hexane
  • Ethyl acetate
  • Pressurized bomb reactor
  • Glovebox with balance, −40°C freezer, and vacuum ports
  • 500‐mL round‐bottom flask
  • PTFE syringe‐driven filter
  • Cannula
  • 500‐mL separatory funnel
  • Rotary evaporator
  • 3.8 × 46‐cm chromatography column
  • High‐vacuum pump
  • Additional reagents and equipment for column chromatography ( ) and thin‐layer chromatography (TLC; ).

Basic Protocol 2: TBS Protection of 2′‐Hydroxyl Group in Presence of Free 3′‐Hydroxyl Group

  Materials
  • 5′‐O‐DMTr‐uridine (5a; Jena Bioscience, cat. no. N‐PM‐2205)
  • Catalyst (4; protocol 1, step 18)
  • N,N‐diisopropylethylamine hydrochloride (see recipe)
  • Tetrahydrofuran (anhydrous)
  • N,N‐diisopropylethylamine (distilled from CaH 2)
  • Tert‐butyldimethylsilyl chloride
  • Methanol (MeOH)
  • Silica gel (EMD Silica Gel 60, 230‐400 mesh)
  • Ethyl acetate
  • Hexane
  • Dichloromethane (CH 2Cl 2)
  • 2‐cyanoethyl N,N‐diisopropylchlorophosphordiamidite
  • N‐methylimidazole
  • Triethylamine (TEA)
  • N6‐Bz‐5′‐O‐DMTr‐adenosine (5b; Jena Bioscience, cat. no. N‐PM‐2109)
  • N4‐Ac‐5′‐ODMTr‐cytidine (5c; Jena Bioscience, cat. no. N‐PM‐2114)
  • N2‐5′‐O‐DMTr‐guanosine (5d; Jena Bioscience, cat. no. N‐PM‐2111)
  • Glove box equipped with balance
  • Round‐bottom flask (10 mL)
  • Magnetic stirring bar
  • Rubber septa for 14/20 glass joint
  • 3.0 mL disposable syringe (Norm‐Ject)
  • 3.8 × 46–, 2.5 × 41–, and 1.0 × 30–cm chromatography columns
  • Rotary evaporator
  • Vacuum pump and high‐vacuum pump
  • Additional reagents and equipment for column chromatography ( ) and thin‐layer chromatography (TLC; )
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Figures

Videos

Literature Cited

Literature Cited
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