title: RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn.
abstract: The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G⋅A and A⋅G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure.
authors: Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK.
authors: Kersten T
authors: KT
authors: Schroeder
authors: Peter
authors: P
authors: Daldrop
authors: David M J
authors: DM
authors: Lilley
mesh_terms: D001483:Base Sequence; D002151:Calorimetry; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D020871:RNA Stability; D058928:Riboswitch; D013816:Thermodynamics
chemical_list: D058928:Riboswitch; D012313:RNA; D008274:Magnesium