Synthesis of nonnatural oligonucleotides made exclusively of alkynyl C-nucleosides with nonnatural bases

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Abstract

This unit describes detailed procedures for the preparation of nonnatural C-nucleosides comprising seven types of nonnatural nucleobases attached to 1'-position of 2'-deoxyribose through an acetylene bond with the β-configuration. In addition, derivatization of these alkynyl C-nucleosides into the corresponding phosphoramidites and the subsequent oligonucleotide synthesis are also presented. The processes are depicted in three parts. The first basic protocol deals with the synthesis of a key intermediate, 5-O-DMTr-protected 1-ethynyl-2-deoxy-β-d-ribofuranoside. The second basic protocol mentions the procedures of the preparation of nonnatural C-nucleosides by a palladium-catalyzed coupling reaction of the ethynyl intermediate and halogen-attached nonnatural nucleobases. The synthetic procedures of the corresponding nonnatural phosporamidites are also described. The third basic protocol presents the solid-phase, automated synthesis of nonnatural oligonucleotides composed exclusively of the nonnatural C-nucleotides.

Original languageEnglish
Pages (from-to)4.62.1-4.62.22
JournalCurrent Protocols in Nucleic Acid Chemistry
Volume2015
DOIs
StatePublished - 2015

Keywords

  • Alkynyl C-nucleosides
  • Nonnatural nucleobases
  • Oligonucleotides

ASJC Scopus subject areas

  • Biochemistry
  • Organic Chemistry

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