Pentopyranosyl oligonucleotide systems. Part 11: Systems with shortened backbones: (D)-beta-ribopyranosyl-(4'-->3')- and (L)-alpha-lyxopyranosyl-(4'-->3')-oligonucleotides

Bioorg Med Chem. 2001 Sep;9(9):2411-28. doi: 10.1016/s0968-0896(01)00220-6.

Abstract

The (L)-alpha-lyxopyranosyl-(4'-->3')-oligonucleotide system-a member of a pentopyranosyl oligonucleotide family containing a shortened backbone-is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding (D)-beta-ribopyransoyl-(4'-->3')-oligonucleotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the 'six-bonds-per-backbone-unit' rule by having five bonds instead, if their vicinally bound phosphodiester bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the (L)-alpha-lyxopyranosyl-(4'-->3')-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system's capability to cross-pair with DNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Chromatography, High Pressure Liquid
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nucleic Acid Denaturation
  • Oligoribonucleotides / chemical synthesis
  • Oligoribonucleotides / chemistry*
  • Oligoribonucleotides / metabolism
  • Pentoses
  • Ribose
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Temperature

Substances

  • Oligoribonucleotides
  • Pentoses
  • lyxose
  • Ribose