The k-junction motif in RNA structure

Jia Wang, Peter Daldrop, Lin Huang, David M. J. Lilley (Lead / Corresponding author)

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    Abstract

    The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP riboswitch contains a related k-junction, and analysis of >11 000 sequences shows that the structure is common to these riboswitches. The k-junction exhibits all the key features of an N1-class k-turn, including the standard cross-strand hydrogen bonds. The third helix of the junction is coaxially aligned with the C (canonical) helix, while the k-turn loop forms the turn into the NC (non-canonical) helix. Analysis of ligand binding by ITC and global folding by gel electrophoresis demonstrates the importance of the k-turn nucleotides. Clearly the basic elements of k-turn structure are structurally well suited to generate a three-way helical junction, retaining all the key features and interactions of the k-turn.
    Original languageEnglish
    Pages (from-to)5322-5331
    Number of pages10
    JournalNucleic Acids Research
    Volume42
    Issue number8
    DOIs
    Publication statusPublished - Apr 2014

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