The k-junction motif in RNA structure

Nucleic Acids Res. 2014 Apr;42(8):5322-31. doi: 10.1093/nar/gku144. Epub 2014 Feb 14.

Abstract

The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP riboswitch contains a related k-junction, and analysis of >11 000 sequences shows that the structure is common to these riboswitches. The k-junction exhibits all the key features of an N1-class k-turn, including the standard cross-strand hydrogen bonds. The third helix of the junction is coaxially aligned with the C (canonical) helix, while the k-turn loop forms the turn into the NC (non-canonical) helix. Analysis of ligand binding by ITC and global folding by gel electrophoresis demonstrates the importance of the k-turn nucleotides. Clearly the basic elements of k-turn structure are structurally well suited to generate a three-way helical junction, retaining all the key features and interactions of the k-turn.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Escherichia coli / genetics
  • Hydrogen Bonding
  • Models, Molecular
  • Nucleotide Motifs
  • RNA Folding
  • RNA, Double-Stranded / chemistry*
  • Riboswitch*
  • Thiamine Pyrophosphate / metabolism

Substances

  • RNA, Double-Stranded
  • Riboswitch
  • Thiamine Pyrophosphate