Reduction of Ribonucleosides to 2′‐Deoxyribonucleosides

Morris J. Robins1, Stanislaw F. Wnuk2

1 Brigham Young University, Provo, Utah, 2 Florida International University, Miami, Florida
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 1.11
DOI:  10.1002/0471142700.nc0111s21
Online Posting Date:  July, 2005
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Ribonucleosides are converted into 2′‐deoxyribonucleosides in good yields by a four‐step procedure. Selective protection of the 3′‐ and 5′‐hydroxyl groups with 1,3‐dichloro‐1,1,3,3‐tetraisopropyl‐1,3‐disiloxane is followed by functionalization of the 2′‐hydroxyl group with phenoxythiocarbonyl chloride. Free radical–mediated reductive C2′–O2′ bond cleavage of these 3′,5′‐O‐TPDS‐2′‐O‐PTC‐nucleoside derivatives with tributyltin hydride, followed by removal of the silyl protecting group with tetrabutylammonium fluoride, provides the 2′‐deoxyribonucleosides. Adenosine, cytidine, guanosine, and uridine are converted into dA, dC, dG, and dU in overall yields of 60% to 80%. Use of tributyltin deuteride in the reductive cleavage step gives 2′‐deuterio‐2′‐deoxyadenosine in 81% yield from adenosine with >85% retention of configuration at C2′. Application of this four‐step protocol with nucleoside analogs is straightforward.

Keywords: 2′‐deoxygenation of ribonucleosides; 2′‐deoxyribonucleosides; free radical‐mediated deoxygenation of ribonucleosides; protection–deprotection at O3′ and O5′ of ribonucleosides

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Table of Contents

  • Basic Protocol 1: Preparation of 2′‐Deoxyadenosine by Reduction of Adenosine
  • Alternate Protocol 1: Preparation of 2′‐Deuterio‐2′‐Deoxyadenosine by Reduction of Adenosine
  • Alternate Protocol 2: Preparation of 2′‐Deoxyguanosine by Reduction of Guanosine
  • Alternate Protocol 3: Preparation of 2′‐Deoxyuridine by Reduction of Uridine
  • Alternate Protocol 4: Preparation of 2′‐Deoxycytidine by Reduction of Cytidine
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
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Basic Protocol 1: Preparation of 2′‐Deoxyadenosine by Reduction of Adenosine

  • Adenosine ( S.1; Yamasa Shoyu or Aldrich)
  • Nitrogen gas
  • Dried pyridine (see recipe) or anhydrous pyridine in Sure/Seal bottles (Aldrich)
  • 1,3‐Dichloro‐1,1,3,3‐tetraisopropyl‐1,3‐disiloxane (Aldrich)
  • Chloroform
  • Methanol
  • Ethyl acetate
  • 1 M HCl, ice cold
  • Saturated NaHCO 3 solution
  • Saturated NaCl solution (brine)
  • Anhydrous sodium sulfate (Na 2SO 4)
  • Silica gel (Merck Kieselgel 60, 230 to 400 mesh)
  • Hot acetonitrile (∼70°C)
  • Dried acetonitrile (see recipe)
  • 4‐(Dimethylamino)pyridine (DMAP; Aldrich)
  • Phenoxythiocarbonyl chloride (phenyl chlorothionoformate; PTC‐Cl; Aldrich)
  • Dried toluene (see recipe)
  • α,α′‐Azobisisobutyronitrile (AIBN; Aldrich)
  • Tributyltin hydride (Aldrich)
  • Oxygen‐free nitrogen
  • Ethanol
  • Dried tetrahydrofuran (see recipe)
  • 1 M tetrabutylammonium fluoride (TBAF) in THF (solution purchased from Aldrich)
  • Diethyl ether
  • Dowex 1 × 2 (OH) ion‐exchange resin (see recipe)
  • Phosphorus pentoxide (P 2O 5)
  • Heating mantle
  • Reflux condensers
  • Vacuum drying pistol (Ace Glass)
  • Oven‐dried 100‐mL two‐ or three‐neck round‐bottom flasks with septa
  • Syringes and syringe needles
  • TLC plates (Merck Kieselgel 60 F 254 aluminum‐backed sheets or equivalent)
  • Ultraviolet lamp (254 nm)
  • Büchi rotary evaporator with Dewar dry ice condenser, connected to a “house” vacuum system or vacuum pump
  • 50‐ and 250‐mL separatory funnels
  • Glass funnel with Whatman no. 1 fluted filter paper
  • 3 × 40–cm, 2 × 30–cm, and 1 × 20–cm chromatography columns
  • Silicon oil bath
  • Wide‐mouth 50‐mL Erlenmeyer flask
  • Desiccator or other closed glass vessel
  • Additional reagents and equipment for thin‐layer chromatography (TLC; appendix 3D) and column chromatography ( appendix 3E)
NOTE: All evaporations are effected with a Büchi rotary evaporator equipped with a Dewar dry ice condenser. This is connected to a house vacuum system (≤15 Pa) when evaporating more volatile materials and to a mechanical oil pump (<1 Pa) when evaporating less volatile materials in vacuo. The heating bath for the evaporation flask is maintained at ≤40°C.
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Literature Cited

Literature Cited
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   Barton, D.H.R. and Subramanian, R. 1977. Reactions of relevance to the chemistry of aminoglycoside antibiotics. Part 7. Conversion of thiocarbonates into deoxy‐sugars. J. Chem. Soc., Perkin Trans. 1 1718‐1723.
   Chatgilialoglu, C. and Ferreri, C. 1993. Progress of the Barton‐McCombie methodology: From tin hydrides to silanes. Res. Chem. Intermed. 19:755‐775.
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   NRC (National Research Council, Committee on Prudent Practices for Handling, Storage, and Disposal of Chemicals in Laboratories). 1995. Prudent Practices in the Laboratory: Handling and Disposal of Chemicals. National Academy Press, Washington, D.C.
   Robins, M.J. and Wilson, J.S. 1981. Smooth and efficient deoxygenation of secondary alcohols. A general procedure for the conversion of ribonucleosides to 2′‐deoxynucleosides. J. Am. Chem. Soc. 103:932‐933.
   Robins, M.J. and Wilson, J.S. 1991. 2′‐Deoxy adenosine and 2′‐deoxy‐2′‐deuterioadenosine. Regiospecific and stereoselective 2′‐deoxy genation of a ribonucleoside. In Nucleic Acid Chemistry: Improved and New Synthetic Procedures, Methods and Techniques, Vol. 4 (L.B. Townsend and R.S. Tipson, eds.) pp. 194‐200. John Wiley & Sons, New York.
   Robins, M.J., Mengel, R., Jones, R.A., and Fouron, Y. 1976. Nucleic acid related compounds. 22. Transformation of ribonucleoside 2′,3′‐O‐ortho esters into halo, deoxy, and epoxy sugar nucleosides using acyl halides. Mechanism and structure of products. J. Am. Chem. Soc. 98:8204‐8213.
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   Robins, M.J., Wilson, J., Sawyer, L., and James, M.N.G. 1983b. Nucleic acid related compounds. 41. Restricted furanose conformations of 3′,5′‐O‐(1,1,3,3‐tetraisopropyldisilox‐1,3‐diyl)nucleosides provide a convenient evaluation of anomeric configuration. Can. J. Chem. 61:1911‐1920.
   Robins, M.J., Wnuk, S.F., Hernandez, A.E., and Samano, M.C. 1996. Nucleic acid related compounds. 91. Biomimetic reactions are in harmony with loss of 2′‐substituents as free radicals (rather than anions) during mechanism‐based inactivation of ribonucleotide reductases. Differential interactions of C2′ azide, halogen, and alkylthio groups with tributylstannane and triphenylsilane. J. Am. Chem. Soc. 118:11341‐11348.
   Robins, M.J., Sanker, S., Samano, V., and Wnuk, S.F. 1997. Nucleic acid related compounds. 94. Remarkably high stereoselective reductions of 2′‐ and 3′‐ketonucleoside derivatives to give arabino, ribo, and xylofuranosyl nucleosides with hydrogen isotopes at C2′ and C3′. Tetrahedron 53:447‐456.
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