3'-C-Branched LNA-type nucleosides locked in an N-type furanose ring conformation: synthesis, incorporation into oligodeoxynucleotides, and hybridization studies

J Org Chem. 2004 Sep 17;69(19):6310-22. doi: 10.1021/jo049159a.

Abstract

Three protected 3'-C-branched LNA-type phosphoramidite building blocks 17, 27, and 38, containing furanose rings locked in an N-type conformation, were synthesized from a known 3-C-allyl allofuranose derivative using strategies relying on the introduction of the branching alkyl chain before condensation with the nucleobase. Synthesis of 3'-C-hydroxypropyl derivatives proved superior to synthesis of the 3'-C-hydroxyethyl derivatives, and the former was converted into the corresponding 3'-C-aminopropyl derivatives. Phosphoramidites 27 and 38 were subsequently applied on an automated DNA synthesizer leading to the introduction of three novel 3'-C-branched LNA-type monomers X, Y, and Z into oligodeoxynucleotides and studies of their effect on the hybridization properties. A duplex-stabilizing effect of introducing 3'-C-aminopropyl-LNA monomer Y, relative to 3'-C-hydroxypropyl-LNA monomer X, was observed, especially at low salt conditions. This indicates that the primary amino group of monomer Y is protonated under the hybridization conditions applied and that positioning of this positively charged group in the major groove has a significant duplex stabilizing effect. Monomer Y was by an on-column conjugation method further functionalized by a glycyl unit to give monomer Z that showed a less stabilizing effect than monomer Y.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Furans / chemistry*
  • Magnetic Resonance Spectroscopy
  • Molecular Conformation
  • Nucleic Acid Hybridization
  • Nucleosides / chemical synthesis
  • Nucleosides / chemistry*
  • Oligonucleotides / chemistry*
  • Spectrometry, Mass, Fast Atom Bombardment

Substances

  • Furans
  • Nucleosides
  • Oligonucleotides