Solution stability and degradation pathway of deoxyribonucleoside phosphoramidites in acetonitrile

Nucleosides Nucleotides Nucleic Acids. 2004 May;23(5):767-75. doi: 10.1081/NCN-120039215.

Abstract

The impuritiy profiles of acetonitrile solutions of the four standard O-cyanoethyl-N,N-diisopropyl-phosphoramidites of 5'-O-dimethoxytrityl (DMT) protected deoxyribonucleosides (dG(ib), dA(bz), dC(bz), T) were analyzed by HPLC-MS. The solution stability of the phosphoramidites decreases in the order T, dC>dA>dG. After five weeks storage under inert gas atmosphere the amidite purity was reduced by 2% (T, dC), 6% (dA), and 39% (dG), respectively. The main degradation pathways involve hydrolysis, elimination of acrylonitrile and autocatalytic acrylonitrile-induced formation of cyanoethyl phosphonoamidates. Consequently, the rate of degradation is reduced by reducing the water concentration in solution with molecular sieves and by lowering the amidite concentration. Acid-catalyzed hydrolysis could also be reduced by addition of small amounts of base.

MeSH terms

  • Acetonitriles / chemistry*
  • Deoxyribonucleosides / chemistry*
  • Deoxyribonucleosides / metabolism
  • Organophosphorus Compounds / chemistry*
  • Solutions

Substances

  • Acetonitriles
  • Deoxyribonucleosides
  • Organophosphorus Compounds
  • Solutions
  • phosphoramidite
  • acetonitrile