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

Nucleic Acids Res. 2009 Nov;37(21):7281-9. doi: 10.1093/nar/gkp791.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • Cations / chemistry
  • Fluorescence Resonance Energy Transfer
  • Hydrogen Bonding
  • Magnesium / chemistry
  • Metals / chemistry*
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA, Ribosomal / chemistry*
  • Ribosome Subunits, Small, Bacterial / chemistry
  • Sodium / chemistry
  • Thermus thermophilus / genetics

Substances

  • Cations
  • Metals
  • RNA, Ribosomal
  • Sodium
  • Magnesium