Severe axial bending of RNA induced by the U1A binding element present in the 3' untranslated region of the U1A mRNA

Richard J. Grainger, Alastair I.H. Murchie, David G. Norman, David M. J. Lilley (Lead / Corresponding author)

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    16 Citations (Scopus)


    The 3' untranslated region of the U1A mRNA contains a binding site for the U1A protein that consists of two asymmetric internal bulges. The bulges each comprise a loop of seven unpaired bases opposing a single base (termed a U1A box). The seven-base loops are located on opposite strands, distributed in a symmetrical manner about the intervening four-base duplex. We have investigated the global conformation of this binding element. Comparison of electrophoretic mobilities of RNA duplexes interrupted by a single U1A box with a series of duplexes of the same length containing oligoadenine bulges indicates that the individual boxes cause a substantial kinking of the helix axis, estimated to be 90 (± 10)°. A series of RNA duplexes were constructed containing a U1A box separated from an A5 bulge by a duplex section of length between 3 and 21 bp. It was found that the electrophoretic mobilities of these species varied sinusoidally, indicating that the U1A box introduces a defined kink into the RNA helix, rather than a point of flexibility. Electrophoretic experiments with the complete U1A binding element suggest that the axial trajectories of the two U1A boxes combine to give an approximately in-line, 180°change in duplex direction.

    Original languageEnglish
    Pages (from-to)84-92
    Number of pages9
    JournalJournal of Molecular Biology
    Issue number1
    Publication statusPublished - 17 Oct 1997


    • Base bulges
    • RNA processing
    • RNA structure
    • Splicing
    • U1A protein

    ASJC Scopus subject areas

    • Biophysics
    • Structural Biology
    • Molecular Biology


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