Ion-induced folding of a kink turn that departs from the conventional sequence.
Kink turns (k-turns) are important structural motifs that create a sharp axial bend in RNA. Most conform to a consensus in which a three-nucleotide bulge is followed by consecutive G*A and A*G base pairs, and when these G*A pairs are modified in vitro this generally leads to a failure to adopt the k-turn conformation. Kt-23 in the 30S ribosomal subunit of Thermus thermophilus is a rare exception in which the bulge-distal A*G pair is replaced by a non-Watson-Crick A*U pair. In the context of the ribosome, Kt-23 adopts a completely conventional k-turn geometry. We show here that this sequence is induced to fold into a k-turn structure in an isolated RNA duplex by Mg(2+) or Na(+) ions. Therefore, the Kt-23 is intrinsically stable despite lacking the key A*G pair; its formation requires neither tertiary interactions nor protein binding. Moreover, the Kt-23 k-turn is stabilized by the same critical hydrogen-bonding interactions within the core of the structure that are found in more conventional sequences such as the near-consensus Kt-7. T. thermophilus Kt-23 has two further non-Watson-Crick base pairs within the non-canonical helix, three and four nucleotides from the bulge, and we find that the nature of these pairs influences the ability of the RNA to adopt k-turn conformation, although the base pair adjacent to the A*U pair is more important than the other.
Schroeder
Kersten T
KT
Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
Lilley
David M J
DM
D020029:Base Pairing; D001483:Base Sequence; D002412:Cations / Q000737:chemistry; D031541:Fluorescence Resonance Energy Transfer; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry; D008670:Metals / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012335:RNA, Ribosomal / Q000737:chemistry*; D054680:Ribosome Subunits, Small, Bacterial / Q000737:chemistry; D012964:Sodium / Q000737:chemistry; D016963:Thermus thermophilus / Q000235:genetics
D002412:Cations; D008670:Metals; D012335:RNA, Ribosomal; D012964:Sodium; D008274:Magnesium