The plasticity of a structural motif in RNA: Structural polymorphism of a kink turn as a function of its environment

Peter Daldrop, David M. J. Lilley

    Research output: Contribution to journalArticlepeer-review

    25 Citations (Scopus)

    Abstract

    The k-turn is a widespread structural motif that introduces a tight kink into the helical axis of double-stranded RNA. The adenine bases of consecutive G.A pairs are directed toward the minor groove of the opposing helix, hydrogen bonding in a typical A-minor interaction. We show here that the available structures of k-turns divide into two classes, depending on whether N3 or N1 of the adenine at the 2b position accepts a hydrogen bond from the O2' at the -1n position. There is a coordinated structural change involving a number of hydrogen bonds between the two classes. We show here that Kt-7 can adopt either the N3 or N1 structures depending on environment. While it has the N1 structure in the ribosome, on engineering it into the SAM-I riboswitch, it changes to the N3 structure, resulting in a significant alteration in the trajectory of the helical arms.

    Original languageEnglish
    Pages (from-to)357-364
    Number of pages8
    JournalRNA: a Publication of the RNA Society
    Volume19
    Issue number3
    DOIs
    Publication statusPublished - 2013

    Keywords

    • SEQUENCE
    • BINDING
    • SAM-I riboswitch
    • ANGSTROM RESOLUTION
    • PROTEIN
    • LARGE RIBOSOMAL-SUBUNIT
    • k-turn
    • RNA structure
    • COMPLEX
    • RNA-protein interaction
    • L7AE
    • APTAMER
    • TERTIARY INTERACTIONS
    • RIBOSWITCH

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