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Modulation of Hoogsteen dynamics on DNA recognition

Author

Listed:
  • Yu Xu

    (Duke University
    Duke University School of Medicine)

  • James McSally

    (University of California Irvine)

  • Ioan Andricioaei

    (University of California Irvine)

  • Hashim M. Al-Hashimi

    (Duke University
    Duke University School of Medicine)

Abstract

In naked duplex DNA, G–C and A–T Watson-Crick base pairs exist in dynamic equilibrium with their Hoogsteen counterparts. Here, we used nuclear magnetic resonance (NMR) relaxation dispersion and molecular dynamics (MD) simulations to examine how Watson-Crick/Hoogsteen dynamics are modulated upon recognition of duplex DNA by the bisintercalator echinomycin and monointercalator actinomycin D. In both cases, DNA recognition results in the quenching of Hoogsteen dynamics at base pairs involved in intermolecular base-specific hydrogen bonds. In the case of echinomycin, the Hoogsteen population increased 10-fold for base pairs flanking the chromophore most likely due to intermolecular stacking interactions, whereas actinomycin D minimally affected Hoogsteen dynamics at other sites. Modulation of Hoogsteen dynamics at binding interfaces may be a general phenomenon with important implications for DNA–ligand and DNA–protein recognition.

Suggested Citation

  • Yu Xu & James McSally & Ioan Andricioaei & Hashim M. Al-Hashimi, 2018. "Modulation of Hoogsteen dynamics on DNA recognition," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03516-1
    DOI: 10.1038/s41467-018-03516-1
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    Cited by:

    1. Xiaoyu Zhang & Tianyi Ding & Fan Yang & Jixing Zhang & Haowen Xu & Yiran Bai & Yibing Shi & Jiaqi Yang & Chaoqun Chen & Chengbo Zhu & He Zhang, 2024. "Peptidylprolyl isomerase A guides SENP5/GAU1 DNA-lncRNA triplex generation for driving tumorigenesis," Nature Communications, Nature, vol. 15(1), pages 1-20, December.

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