Main content area

Ion-induced folding of a kink turn that departs from the conventional sequence

Schroeder, Kersten T., Lilley, David M.J.
Nucleic acids research 2009 v.37 no.21 pp. 7281-7289
RNA, Thermus thermophilus, geometry, hydrogen bonding, ions, magnesium, nucleotides, protein binding, protein subunits, ribosomal proteins, ribosomes, sodium
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 Mg²⁺ 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.