Intramolecular triple helix as a model for regular polyribonucleotide (CAA)(n)

Biochem Biophys Res Commun. 2009 Oct 9;388(1):127-30. doi: 10.1016/j.bbrc.2009.07.133. Epub 2009 Jul 30.

Abstract

The regular (CAA)(n) polyribonucleotide, as well as the omega leader sequence containing (CAA)-rich core, have recently been shown to form cooperatively melted and compact structures. In this report, we propose a structural model for the (CAA)(n) sequence in which the polyribonucleotide chain is folded upon itself, so that it forms an intramolecular triple helix. The triple helix is stabilized by hydrogen bonding between bases thus forming coplanar triads, and by stacking interactions between the base triads. A distinctive feature of the proposed triple helix is that it does not contain the canonical double-helix elements. The difference from the known triple helices is that Watson-Crick hydrogen bond pairings do not take place in the interactions between the bases within the base triads.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions*
  • Adenine / chemistry*
  • Base Sequence
  • Cytosine / chemistry*
  • Hydrogen Bonding
  • Models, Chemical*
  • Nucleic Acid Conformation*
  • Polyribonucleotides / chemistry*
  • RNA, Viral / chemistry

Substances

  • 5' Untranslated Regions
  • Polyribonucleotides
  • RNA, Viral
  • Cytosine
  • Adenine