Synthesis and hybridization studies of alpha-configured arabino nucleic acids

Org Biomol Chem. 2009 Jun 7;7(11):2389-401. doi: 10.1039/b905019c. Epub 2009 Apr 15.

Abstract

Synthesis of alpha-L-arabino- and alpha-D-arabino-configured pentofuranosyl nucleosides of four of the natural bases [thymine (ara-T), adenine (ara-A), cytosine (ara-C) and guanine (ara-G)] is reported together with hybridization properties of oligonucleotides containing alpha-L-ara-T and -A, alpha-D-ara-T and -A, and 2'-amino-alpha-L-ara-T monomers. 2'-O-Acetylated alpha-L-ara-T, -A, -C and -G, alpha-D-ara-T, -A, -C and -G, and N2'-acylated-alpha-L-ara-T phosphoramidite building blocks were synthesized and used together with standard DNA phosphoramidites for solid-phase synthesis of 18-mer oligonucleotides. Thermal denaturation experiments showed that incorporation of three or six of the arabino-configured monomers into DNA-oligonucleotides reduced the binding affinity towards antiparallel DNA/RNA complements. Fully modified alpha-L-ara-oligonucleotides did not hybridize with DNA/RNA complements, whereas hybridization of fully modified alpha-D-ara-oligonucleotides with complementary DNA/RNA in parallel strand orientation was confirmed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabinonucleosides / chemical synthesis*
  • Arabinonucleosides / chemistry
  • Arabinonucleosides / metabolism*
  • DNA / metabolism
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization
  • Nucleic Acids / chemical synthesis*
  • Nucleic Acids / chemistry
  • Nucleic Acids / metabolism*
  • RNA / metabolism
  • Stereoisomerism

Substances

  • Arabinonucleosides
  • Nucleic Acids
  • RNA
  • DNA