The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion

Nucleic Acids Res. 2012 Oct;40(18):9329-39. doi: 10.1093/nar/gks672. Epub 2012 Jul 14.


We report here the first structure of double helical arabino nucleic acid (ANA), the C2'-stereoisomer of RNA, and the 2'-fluoro-ANA analogue (2'F-ANA). A chimeric dodecamer based on the Dickerson sequence, containing a contiguous central segment of arabino nucleotides, flanked by two 2'-deoxy-2'F-ANA wings was studied. Our data show that this chimeric oligonucleotide can adopt two different structures of comparable thermal stabilities. One structure is a monomeric hairpin in which the stem is formed by base paired 2'F-ANA nucleotides and the loop by unpaired ANA nucleotides. The second structure is a bimolecular duplex, with all the nucleotides (2'F-ANA and ANA) forming Watson-Crick base pairs. The duplex structure is canonical B-form, with all arabinoses adopting a pure C2'-endo conformation. In the ANA:ANA segment, steric interactions involving the 2'-OH substituent provoke slight changes in the glycosidic angles and, therefore, in the ANA:ANA base pair geometry. These distortions are not present in the 2'F-ANA:2'F-ANA regions of the duplex, where the -OH substituent is replaced by a smaller fluorine atom. 2'F-ANA nucleotides adopt the C2'-endo sugar pucker and fit very well into the geometry of B-form duplex, allowing for favourable 2'F···H8 interactions. This interaction shares many features of pseudo-hydrogen bonds previously observed in 2'F-ANA:RNA hybrids and in single 2'F-ANA nucleotides.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabinonucleotides / chemistry*
  • Arabinose / chemistry*
  • Base Pairing
  • Carbohydrate Conformation
  • DNA / chemistry
  • Fluorine / chemistry
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Oligonucleotides / chemistry


  • Arabinonucleotides
  • Oligonucleotides
  • Fluorine
  • DNA
  • Arabinose

Associated data

  • PDB/2LSC