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Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts

Author

Listed:
  • Fabio D. Steffen

    (University of Zurich)

  • Mokrane Khier

    (University of Zurich)

  • Danny Kowerko

    (University of Zurich
    Technical University Chemnitz)

  • Richard A. Cunha

    (University of Zurich)

  • Richard Börner

    (University of Zurich
    University of Applied Sciences Mittweida)

  • Roland K. O. Sigel

    (University of Zurich)

Abstract

The fidelity of group II intron self-splicing and retrohoming relies on long-range tertiary interactions between the intron and its flanking exons. By single-molecule FRET, we explore the binding kinetics of the most important, structurally conserved contact, the exon and intron binding site 1 (EBS1/IBS1). A comparison of RNA-RNA and RNA-DNA hybrid contacts identifies transient metal ion binding as a major source of kinetic heterogeneity which typically appears in the form of degenerate FRET states. Molecular dynamics simulations suggest a structural link between heterogeneity and the sugar conformation at the exon-intron binding interface. While Mg2+ ions lock the exon in place and give rise to long dwell times in the exon bound FRET state, sugar puckering alleviates this structural rigidity and likely promotes exon release. The interplay of sugar puckering and metal ion coordination may be an important mechanism to balance binding affinities of RNA and DNA interactions in general.

Suggested Citation

  • Fabio D. Steffen & Mokrane Khier & Danny Kowerko & Richard A. Cunha & Richard Börner & Roland K. O. Sigel, 2020. "Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-019-13683-4
    DOI: 10.1038/s41467-019-13683-4
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    Cited by:

    1. Leonie Vollmar & Julia Schimpf & Bianca Hermann & Thorsten Hugel, 2024. "Cochaperones convey the energy of ATP hydrolysis for directional action of Hsp90," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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