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m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

Nature Structural & Molecular Biology volume 23, pages 803810 (2016) | Download Citation

Abstract

The B-DNA double helix can dynamically accommodate G-C and A-T base pairs in either Watson–Crick or Hoogsteen configurations. Here, we show that G-C+ (in which + indicates protonation) and A-U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result,N1-methyladenosine and N1-methylguanosine, which occur in DNA as a form of alkylation damage and in RNA as post-transcriptional modifications, have dramatically different consequences. Whereas they create G-C+ and A-T Hoogsteen base pairs in duplex DNA, thereby maintaining the structural integrity of the double helix, they block base-pairing and induce local duplex melting in RNA. These observations provide a mechanism for disrupting RNA structure through post-transcriptional modifications. The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.

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Acknowledgements

We thank M. Juen (University of Innsbruck, Austria), N. Orlovsky, Y. Xue, A. Shakya, M. Clay, A. Rangadurai, E. Szymanski, members of the Al-Hashimi laboratory, and T. Mustoe (UNC–Chapel Hill) for assistance and critical input. We acknowledge technical support and resources from the Duke Magnetic Resonance Spectroscopy Center, the Duke Compute Cluster and the Shared Materials Instrumentation Facility at Duke University. This work was supported by NIH grants (R01GM089846 to I.A. and H.M.A.; 5P50GM103297 to H.M.A.) and Austrian Science Fund (FWF) grants (P26550 and P28725 to C.K.). H.Z. acknowledges support from the China Scholarship Council.

Author information

Author notes

    • Bharathwaj Sathyamoorthy

    Present address: Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

Affiliations

  1. Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.

    • Huiqing Zhou
    • , Isaac J Kimsey
    • , Bharathwaj Sathyamoorthy
    • , Tianyu Bai
    •  & Hashim M Al-Hashimi
  2. Department of Molecular Biology, The Scripps Research Institute, La Jolla, California USA.

    • Evgenia N Nikolova
  3. Department of Chemistry, University of California Irvine, Irvine, California USA.

    • Gianmarc Grazioli
    • , James McSally
    •  & Ioan Andricioaei
  4. Bachem Americas, Torrance, California USA.

    • Christoph H Wunderlich
  5. Institute of Organic Chemistry, University of Innsbruck, Innsbruck, Austria.

    • Christoph Kreutz
  6. Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria.

    • Christoph Kreutz
  7. Department of Chemistry, Duke University, Durham, North Carolina, USA.

    • Hashim M Al-Hashimi

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Contributions

H.Z., E.N.N., and H.M.A. conceived the project and experimental design. H.Z. prepared NMR samples, with assistance from I.J.K. and E.N.N., and performed NMR experiments and analyzed NMR data, with assistance from I.J.K. and B.S. H.Z. performed DFT calculations and modeling of steric analysis. H.Z., I.J.K., and E.N.N. performed the structure-based survey of RNA Hoogsteen base pairs. I.A., G.G., and J.M. performed and analyzed the MD simulations. C.H.W. and C.K. prepared the 13C-C8-adenosine phosphoramidite. H.Z. and T.B. carried out the UV melting experiments and performed the data analysis. H.M.A., H.Z., and I.A. wrote the manuscript with critical input from I.J.K., B.S., E.N.N., G.G., J.M., T.B., C.H.W., and C.K.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Ioan Andricioaei or Hashim M Al-Hashimi.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–6, Supplementary Tables 1–5 and Supplementary Note

Videos

  1. 1.

    dA–dT WC→HG transition in B-DNA

    Shown is the transition of dA16-dT9 bp (in green and purple) from WC to HG bp in a B-DNA duplex (A6-DNA) from the biased MD simulation. dA16 is being flipped around the glycosidic bond under the biasing force. The purple sphere keeps track of dA16-H2, which has a close contact with the 5′-neighbouring bp (dC15-dG10). The steric contact is effectively accommodated by minimal structural adjustment of dC15-dG10 without disrupting hydrogen-bonding.

  2. 2.

    rA–rU WC→HG transition in A-RNA

    Shown is a representative transition of rA16-rU9 bp (rA16 in green) from WC to HG bp in an A-RNA hairpin construct (hp-A6-RNA) from the biased MD simulation. In this case, although the biasing force is eventually able to force the rA16 residue shown in bright green to flip 180° around the X angle, it does so at the cost of disrupting the hydrogen bonding of the 5′- neighboring base pair shown in orange and cyan.

  3. 3.

    Stable Hoogsteen base pair during unbiased MD simulations for dA-dT HG bp in A6-DNA duplex

  4. 4.

    Stable Hoogsteen base pair during unbiased MD simulations for rA-dT HG bp in A6-DNA duplex

  5. 5.

    Stable Hoogsteen base pair during unbiased MD simulations for m1dA-dT HG bp in A6-DNA duplex

  6. 6.

    m1rA–rU induced melting in hp-A6-RNA

    In stark contrast to the stably accommodated m1dA-dT bp in B-DNA (Supplementary Movie 5), m1rA (in grey) leads to the melting of most bps in the unbiased MD simulation. The melting starts near the m1rA -rU bp and then propagates through both sides of the strand, thus leading to melting of almost the entire helix.

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https://doi.org/10.1038/nsmb.3270

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