Synthesis, nucleic acid hybridization properties and molecular modelling studies of conformationally restricted 3'-O,4'-C-methylene-linked alpha-L-ribonucleotides

Carbohydr Res. 2006 Jul 24;341(10):1398-407. doi: 10.1016/j.carres.2006.04.010. Epub 2006 May 18.

Abstract

Nucleotides with conformationally restricted carbohydrate rings such as locked nucleic acid (LNA), alpha-L-LNA or 2',5'-linked 3'-O,4'-C-methyleribonucleotides exhibit significant potential as building blocks for antigene and antisense strategies. 2',5'-Linked alpha-L-ribo configured monomer X (termed alpha-L-ONA) was designed as a potential structural mimic of alpha-L-LNA. The corresponding phosphoramidite building block of monomer X was obtained in five steps (10% overall yield) from the easily obtainable thymine derivative 1. Incorporation of monomer X into oligodeoxyribonucleotides (ONs) results in dramatically decreased thermal stabilities with DNA/RNA complements (DeltaTm/mod=-11.5 to -17.0 degrees C) compared to unmodified reference ONs. Less pronounced decreases (DeltaTm/mod=-4.5 to -8.5 degrees C) are observed when monomer X is incorporated into triplex forming ONs and targeted against double-stranded DNA (parallel orientation, pyrimidine motif). This biophysical data, together with modelling studies, suggest that 2',5'-linked alpha-L-ONA is a poor structural mimic of alpha-L-LNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Models, Molecular
  • Nucleic Acid Conformation / drug effects
  • Nucleic Acid Denaturation
  • Nucleic Acid Hybridization / methods*
  • Oligonucleotides
  • Oligonucleotides, Antisense / chemistry*
  • Ribonucleotides / chemical synthesis*
  • Ribonucleotides / chemistry*

Substances

  • Oligonucleotides
  • Oligonucleotides, Antisense
  • Ribonucleotides
  • locked nucleic acid