Insights into the RNA quadruplex binding specificity of DDX21

Ewan K.S. McRae, David E. Davidson, Steven J. Dupas, Sean A. McKenna

    Research output: Contribution to journalArticlepeer-review

    18 Scopus citations

    Abstract

    Guanine quadruplexes can form in both DNA and RNA and influence many biological processes through various protein interactions. The DEAD-box RNA helicase protein DDX21 has been shown to bind and remodel RNA quadruplexes but little is known about its specificity for different quadruplex species. Previous reports have suggested DDX21 may interact with telomeric repeat containing RNA quadruplex (TERRA), an integral component of the telomere that contributes to telomeric heterochromatin formation and telomere length regulation. Here we report that the C-terminus of DDX21 directly interacts with TERRA. We use, for the first time, 2D saturation transfer difference NMR to map the protein binding site on a ribonucleic acid species and show that the quadruplex binding domain of DDX21 interacts primarily with the phosphoribose backbone of quadruplexes. Furthermore, by mutating the 2′OH of loop nucleotides we can drastically reduce DDX21's affinity for quadruplex, indicating that the recognition of quadruplex and specificity for TERRA is mediated by interactions with the 2′OH of loop nucleotides.

    Original languageEnglish (US)
    Pages (from-to)1973-1979
    Number of pages7
    JournalBiochimica et Biophysica Acta - General Subjects
    Volume1862
    Issue number9
    DOIs
    StatePublished - Sep 2018

    ASJC Scopus subject areas

    • Biophysics
    • Biochemistry
    • Molecular Biology

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