Synthesis of phosphorothioate oligonucleotides with stereodefined phosphorothioate linkages

Curr Protoc Nucleic Acid Chem. 2003 Oct:Chapter 4:Unit 4.17. doi: 10.1002/0471142700.nc0417s14.

Abstract

A method for solid-phase synthesis of stereodefined PS-oligos via an oxathiaphospholane approach using pure P-diastereomers of nucleoside oxathiaphospholane monomers is described. The oxathiaphospholane monomers are synthesized by phosphitylation of 5'-O-DMTr-N-protected deoxyribonucleosides with 2-chloro-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane followed by sulfurization. The procedure is general and may be applied to other analogs, depending on the aldehyde (or mercaptoalcohol) used. Starting from an 18O-labeled mercaptoalcohol, the corresponding 18O-labeled phosphitylating reagent and nucleoside monomers can be obtained and used for synthesis of labeled stereodefined PS-oligos, which are useful for studying mechanisms of enzymatic reactions. Details are provided for chromatographic separation of the 5'-O-DMTr-N-protected-deoxyribonucleoside-3'-O-(2-thio-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane)s into their P-diastereomers, and for manual solid-phase synthesis of PS-oligos. Oxidation of 5'-O-DMTr-N-protected-deoxyribonucleoside-3'-O-(2-thio-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane)s with selenium dioxide yields their 2-oxo-analogs, which are suitable either for elongation of stereodefined PS-oligos with segments consisting of unmodified nucleotide units possessing phosphate internucleotide linkages, or for generating isotopomeric 18O-labeled PO-oligos of predetermined P-chirality.

Publication types

  • Review

MeSH terms

  • Chemistry, Organic / instrumentation
  • Chemistry, Organic / methods
  • Cyclohexanecarboxylic Acids / chemical synthesis
  • Cyclohexanes / chemistry
  • Disulfides / chemical synthesis
  • Models, Biological
  • Nucleic Acid Conformation*
  • Nucleotides / chemical synthesis
  • Nucleotides / chemistry
  • Organothiophosphorus Compounds / chemical synthesis
  • Phosphates / chemistry*
  • Phosphates / metabolism
  • Phosphorothioate Oligonucleotides / chemical synthesis*
  • Phosphorothioate Oligonucleotides / chemistry*
  • Ribose / analogs & derivatives
  • Ribose / chemical synthesis
  • Ribose / chemistry
  • Sarcosine / chemistry
  • Solvents / chemistry
  • Solvents / pharmacology
  • Stereoisomerism
  • Succinic Acid / chemistry

Substances

  • Cyclohexanecarboxylic Acids
  • Cyclohexanes
  • Disulfides
  • Nucleotides
  • Organothiophosphorus Compounds
  • Phosphates
  • Phosphorothioate Oligonucleotides
  • Solvents
  • oxathiaphospholane
  • Cyclohexane
  • Ribose
  • phosphorodithioic acid
  • Succinic Acid
  • Sarcosine