title: The k-junction motif in RNA structure.
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.
authors: Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors: Jia
authors: J
authors: Wang
authors: Peter
authors: P
authors: Daldrop
authors: Lin
authors: L
authors: Huang
authors: David M J
authors: DM
authors: Lilley
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D006860:Hydrogen Bonding; D008958:Models, Molecular; D059372:Nucleotide Motifs; D059370:RNA Folding; D012330:RNA, Double-Stranded / Q000737:chemistry*; D058928:Riboswitch; D013835:Thiamine Pyrophosphate / Q000378:metabolism
chemical_list: D012330:RNA, Double-Stranded; D058928:Riboswitch; D013835:Thiamine Pyrophosphate