Article | Published:

Visualizing transient Watson–Crick-like mispairs in DNA and RNA duplexes

Nature volume 519, pages 315320 (19 March 2015) | Download Citation

Abstract

Rare tautomeric and anionic nucleobases are believed to have fundamental biological roles, but their prevalence and functional importance has remained elusive because they exist transiently, in low abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show here that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson–Crick-like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson–Crick fidelity checkpoints and form with probabilities (10−3 to 10−5) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases.

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Acknowledgements

We thank S. Horowitz, H. Zhou, J. Lee, A. M. Mustoe, and E. N. Nikolova for assistance and critical comments. We are grateful for technical support and resources from the Duke Magnetic Resonance Spectroscopy Center and University of Michigan Flux HPC Cluster. This work was supported by an NIH grant (R01GM089846) and an Agilent Thought Leader Award given to H.M.A.

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Affiliations

  1. Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, North Carolina 27710, USA

    • Isaac J. Kimsey
    • , Bharathwaj Sathyamoorthy
    •  & Hashim M. Al-Hashimi
  2. Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden

    • Katja Petzold
  3. Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA

    • Zachary W. Stein

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Contributions

I.J.K. and H.M.A. conceived the project and experimental design. I.J.K. prepared NMR samples as well as performed and analysed all NMR RD experiments. I.J.K. assigned resonances in all nucleic acid constructs with assistance from B.S.; K.P. prepared the hp-GU-24 sample and carried out additional NMR RD experiments. I.J.K. performed all DFT calculations. Z.W.S. assisted I.J.K. with numerical Bloch–McConnell simulations. I.J.K. and H.M.A. wrote the manuscript with critical input from B.S. and K.P.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hashim M. Al-Hashimi.

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    Supplementary Information

    This file contains Supplementary Discussions 1-10 and additional references.

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    Supplementary Table 1

    This file contains relaxation dispersion related fit parameters and spinlock powers and offsets used for all constructs and nuclei reported in the manuscript.

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https://doi.org/10.1038/nature14227

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