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

Kersten T. Schroeder, David M. J. Lilley

    Research output: Contribution to journalArticle

    22 Citations (Scopus)

    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 languageEnglish
    Pages (from-to)7281-7289
    Number of pages9
    JournalNucleic Acids Research
    Volume37
    Issue number21
    DOIs
    Publication statusPublished - Nov 2009

    Keywords

    • LARGE RIBOSOMAL-SUBUNIT
    • A-MINOR MOTIF
    • ANGSTROM RESOLUTION
    • MOLECULAR-BASIS
    • BASE-PAIRS
    • RNA
    • PROTEIN
    • BINDING
    • L7AE
    • NUCLEOTIDES

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