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 center dot A and A center dot G base pairs, and when these G center dot 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 center dot G pair is replaced by a non-Watson-Crick A center dot 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 center dot 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 center dot U pair is more important than the other.
Original language | English |
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Pages (from-to) | 7281-7289 |
Number of pages | 9 |
Journal | Nucleic Acids Research |
Volume | 37 |
Issue number | 21 |
DOIs | |
Publication status | Published - Nov 2009 |
Keywords
- LARGE RIBOSOMAL-SUBUNIT
- A-MINOR MOTIF
- ANGSTROM RESOLUTION
- MOLECULAR-BASIS
- BASE-PAIRS
- RNA
- PROTEIN
- BINDING
- L7AE
- NUCLEOTIDES