Synthesis of the Tellurium‐Derivatized Phosphoramidites and Their Incorporation into DNA Oligonucleotides

Sibo Jiang1, Jia Sheng1, Zhen Huang1

1 Department of Chemistry, Georgia State University, Atlanta, Georgia
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 1.25
DOI:  10.1002/0471142700.nc0125s47
Online Posting Date:  December, 2011
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In this unit, an efficient method for the synthesis of 2′‐tellerium‐modified phosphoramidite and its incorporation into oligonucleotide are presented. We choose 5′‐O‐DMTr‐2,2′‐anhydro‐uridine and ‐thymidine nucleosides (S.1, S.2) as starting materials due to their easy preparation. The 5′‐O‐DMTr‐2,2′‐anhydro‐uridine and ‐thymidine can be converted to the corresponding 2′‐tellerium‐derivatized nucleosides by treating with the telluride nucleophiles. Subsequently, the 2′‐Te‐nucleosides can be transformed into 3′‐phosphoramidites, which are the building blocks for DNA/RNA synthesis. The DNA synthesis, purification, and applications of oligonucleotides containing 2′‐Te‐U or 2′‐Te‐T are described in the protocol. Curr. Protoc. Nucleic Acid Chem. 47:1.25.1‐1.25.16. © 2011 by John Wiley & Sons, Inc.

Keywords: tellurium nucleic acid; nucleic acid modification; Te‐derivatized DNA; nucleic acid X‐ray crystallography; DNA damaging; conductive DNA; DNA imaging

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Table of Contents

  • Introduction
  • Basic Protocol 1: Preparation of the 2′‐Phenyltellanyl Phosphoramidite
  • Basic Protocol 2: Preparation of the 2′‐Methyltellanyl Phosphoramidite
  • Basic Protocol 3: Synthesis, Purification, and Characterization of Oligonucleotides Containing 2′‐Tellurium Functionality
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: Preparation of the 2′‐Phenyltellanyl Phosphoramidite

  • Sodium borohydride (NaBH 4; Sigma)
  • Dry argon (Ar)
  • Anhydrous tetrahydrofuran (THF)
  • Diphenylditelluride (PhTeTePh; TCI America)
  • Anhydrous ethanol (EtOH)
  • 5′‐DMTr‐2, 2′‐anhydrouridine S.1 (SeNA Research)
  • 5′‐DMTr‐2, 2′‐anhydrothymidine S.2 (SeNA Research)
  • Anhydrous DCM (methylene chloride, CH 2Cl 2)
  • Methanol (MeOH)
  • Anhydrous MgSO 4
  • Silica gel 60 (230 to 400 mesh)
  • N,N‐diisopropylethylamine (Chemgene)
  • 2‐cyanoethyl N,N‐diisopropyl‐chlorophosphoramidite (Chemgene)
  • Saturated NaHCO 3 aqueous solution
  • Saturated NaCl aqueous solution
  • Anhydrous Na 2SO 4
  • Petroleum ether
  • Al 2O 3
  • Hexane
  • Ethyl acetate
  • 250‐, 100‐, 50‐, 25‐, 5‐mL round‐bottom flasks
  • 8 × 1.5–mm magnetic stir bar
  • Vacuum pump
  • 1‐, 3‐, 5‐, and 10‐mL disposable syringes
  • Ice bath
  • Magnetic stirring plate
  • 18‐G needles
  • Oil bath
  • 125‐mL separatory funnel
  • 100‐mL oven‐dried beakers
  • 125‐mL Erlenmeyer flasks
  • Additional reagents and equipment for thin‐layer chromatography (TLC; appendix 3D)
NOTE: All reactions are performed in Ar atmosphere. An Ar atmosphere can be carried out through a rubber septum that seals the flask and connects to balloon filled with Ar. A slightly positive pressure is maintained in the system to provide dry and oxygen‐free atmosphere. Liquid chemical is added using a syringe through a rubber septum.

Basic Protocol 2: Preparation of the 2′‐Methyltellanyl Phosphoramidite

  • Dry argon (Ar)
  • Anhydrous tetrahydrofuran (THF)
  • Dimethyl ditelluride (CH 3TeTeCH 3; Organometallics)
  • 1 M LiAlH 4 solution in THF
  • 12‐crown‐4 (1,4,7,10‐tetraoxacyclododecane)
  • Anhydrous DCM (methylene chloride, CH 2Cl 2)
  • Methanol (MeOH)
  • Saturated NaCl aqueous solution
  • Anhydrous MgSO 4
  • Magnetic stir bars
  • 25‐mL round‐bottom flasks
  • Vacuum pump
  • 125‐mL separatory funnels
  • 100‐mL oven‐dried beakers
  • Rotary evaporator
  • Additional reagents and equipment for TLC ( appendix 3D)

Basic Protocol 3: Synthesis, Purification, and Characterization of Oligonucleotides Containing 2′‐Tellurium Functionality

  • 2′‐Te‐modified U and T phosphoramidites ( protocol 1 or protocol 2)
  • Acetonitrile (CH 3CN), anhydrous (Glen Research)
  • DNA CPG (controlled‐pore glass) support
  • Argon
  • 0.05 M K 2CO 3 in methanol
  • 2 M triethylammonium acetate (TEAA) buffer, pH 7.0
  • Acetonitrile (CH 3CN), HPLC grade
  • 30% aqueous trichloroacetic acid (TCA)
  • 3‐hydroxypicolinic acid (3‐HPA)
  • Diammonium citrate
  • ABI3400 DNA/RNA synthesizer
  • DNA synthesis column
  • 2‐ mL microcentrifuge tubes
  • Vortex mixer
  • Microcentrifuge
  • SpeedVac
  • HPLC system (optional) with detector at 260 and/or 369 nm
  • HPLC column: 21.2 × 250–mm Zorbax RX‐C8 (Agilent Technology) or 21 × 250–mm XB‐C18 (Welch Materials)
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Literature Cited

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