Insights into the RNA quadruplex binding specificity of DDX21

• Published in: Biochimica et biophysica acta. General subjects Vol. 1862; no. 9; pp. 1973 - 1979
• Main Authors: McRae, Ewan K.S., Davidson, David E., Dupas, Steven J., McKenna, Sean A.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.09.2018
• Subjects: Binding Sites; DEAD-box RNA helicases; DEAD-box RNA Helicases - chemistry; DEAD-box RNA Helicases - genetics; DEAD-box RNA Helicases - metabolism; DNA; G-Quadruplexes; guanine; heterochromatin; Humans; nuclear magnetic resonance spectroscopy; Nucleic Acid Conformation; nucleotides; Protein Binding; Protein Domains; RNA; RNA - chemistry; RNA - genetics; RNA - metabolism; Telomere; telomeres
• ISSN: 0304-4165; 1872-8006
• DOI: 10.1016/j.bbagen.2018.06.009

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. •DDX21's C terminal domain can interact directly with TERRA RNA G4.•DDX21-TERRA G4 interaction is mediated by electrostatic interactions.•2′OH is a requirement for G4 binding by DDX21's C terminal domain.•DDX21's C terminal domain interacts with the ribose sugars of both quadruplex forming guanines and loop nucleotides.