Formation of N-branched oligonucleotides as by-products in solid-phase oligonucleotide synthesis

Oligonucleotides. 2006 Summer;16(2):181-5. doi: 10.1089/oli.2006.16.181.

Abstract

During the synthesis of oligonucleotides by the standard phosphoramidite method using 2'-deoxycytidine- derivatized solid support, a side reaction was observed that gave rise to the formation of high molecular weight N-branched oligomers having two identical chains linked to the 3'-terminal 2'-deoxycytidine. Postsynthesis treatment with neat triethylamine trihydrofluoride selectively cleaved the phosphoramidate linkage and converted the N-branched oligomers back to the expected oligonucleotides.

MeSH terms

  • Base Sequence
  • Deoxycytidine / chemistry
  • Oligonucleotides / chemical synthesis*
  • Organophosphorus Compounds / chemistry*
  • Polyamines / chemistry*

Substances

  • Oligonucleotides
  • Organophosphorus Compounds
  • Polyamines
  • phosphoramidite
  • diethylenetriamine
  • Deoxycytidine