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Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)

Author

Listed:
  • Xiaolin Niu

    (Tsinghua University)

  • Qiuhan Liu

    (Tsinghua University)

  • Zhonghe Xu

    (Tsinghua University)

  • Zhifeng Chen

    (Tsinghua University)

  • Linghui Xu

    (Tsinghua University)

  • Lilei Xu

    (Tsinghua University)

  • Jinghong Li

    (Tsinghua University)

  • Xianyang Fang

    (Tsinghua University)

Abstract

Mechanical anisotropy is an essential property for many biomolecules to assume their structures, functions and applications, however, the mechanisms for their direction-dependent mechanical responses remain elusive. Herein, by using a single-molecule nanopore sensing technique, we explore the mechanisms of directional mechanical stability of the xrRNA1 RNA from ZIKA virus (ZIKV), which forms a complex ring-like architecture. We reveal extreme mechanical anisotropy in ZIKV xrRNA1 which highly depends on Mg2+ and the key tertiary interactions. The absence of Mg2+ and disruption of the key tertiary interactions strongly affect the structural integrity and attenuate mechanical anisotropy. The significance of ring structures in RNA mechanical anisotropy is further supported by steered molecular dynamics simulations in combination with force distribution analysis. We anticipate the ring structures can be used as key elements to build RNA-based nanostructures with controllable mechanical anisotropy for biomaterial and biomedical applications.

Suggested Citation

  • Xiaolin Niu & Qiuhan Liu & Zhonghe Xu & Zhifeng Chen & Linghui Xu & Lilei Xu & Jinghong Li & Xianyang Fang, 2020. "Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19260-4
    DOI: 10.1038/s41467-020-19260-4
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    Cited by:

    1. Guiquan Zhang & Yao Liu & Shisheng Huang & Shiyuan Qu & Daolin Cheng & Yuan Yao & Quanjiang Ji & Xiaolong Wang & Xingxu Huang & Jianghuai Liu, 2022. "Enhancement of prime editing via xrRNA motif-joined pegRNA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Xiaolin Niu & Ruirui Sun & Zhifeng Chen & Yirong Yao & Xiaobing Zuo & Chunlai Chen & Xianyang Fang, 2021. "Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs," Nature Communications, Nature, vol. 12(1), pages 1-14, December.

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