Chemical Synthesis of Oligodeoxyribonucleotides Using <i>N</i>-Unprotected <i>H</i>-Phosphonate Monomers and Carbonium and Phosphonium Condensing Reagents:  <i>O</i>-Selective Phosphonylation and Condensation

Abstract

Oligodeoxyribonucleotides were synthesized using H -phosphonate monomers without amino protection. The H -phosphonate monomers of deoxyadenosine, deoxycytidine, and deoxyguanosine bearing the free amino groups were synthesized in good yields by O -selective phosphonylation of the parent 5‘- O -(dimethoxytrityl)deoxyribonucleosides. It was found that the amino groups of the nucleosides were not modified during internucleotidic bond formation where (benzotriazol-1-yloxy)carbonium and -phosphonium compounds were employed as condensing reagents. The most effective condensing reagent for rapid internucleotidic bond formation was found to be 2-(benzotriazol-1-yloxy)-1,1-dimethyl-2-pyrrolidin-1-yl-1,3,2-diazaphospholidinium hexafluorophosphate (BOMP). In the present H -phosphonate method, 2-(phenylsulfonyl)-3-(3-nitrophenyl)oxaziridine (PNO) was employed as a new oxidizing reagent for the oxidation of internucleotidic H -phosphonate linkages under anhydrous conditions in the presence of N,O -bis(trimethylsilyl)acetamide. The reaction mechanism for the O -selective condensation was investigated in detail by means of 31 P NMR spectroscopy. Unprecedented oxidation of the H -phosphonate monomers was observed during activation of the monomers with (benzotriazol-1-yloxy)phosphonium and -carbonium condensing reagents in the absence of the 5‘-hydroxyl components. A mechanism for the O -selective condensation was proposed on the basis of ab initio molecular orbital calculations for the model compounds at the HF/6-31G* level.