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Transient Hoogsteen base pairs in canonical duplex DNA

Abstract

Sequence-directed variations in the canonical DNA double helix structure that retain Watson–Crick base-pairing have important roles in DNA recognition, topology and nucleosome positioning. By using nuclear magnetic resonance relaxation dispersion spectroscopy in concert with steered molecular dynamics simulations, we have observed transient sequence-specific excursions away from Watson–Crick base-pairing at CA and TA steps inside canonical duplex DNA towards low-populated and short-lived A•T and G•C Hoogsteen base pairs. The observation of Hoogsteen base pairs in DNA duplexes specifically bound to transcription factors and in damaged DNA sites implies that the DNA double helix intrinsically codes for excited state Hoogsteen base pairs as a means of expanding its structural complexity beyond that which can be achieved based on Watson–Crick base-pairing. The methods presented here provide a new route for characterizing transient low-populated nucleic acid structures, which we predict will be abundant in the genome and constitute a second transient layer of the genetic code.

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Figure 1: Detection of base-pair-specific excited states in CA/TG steps of duplex DNA.
Figure 2: Kinetic-thermodynamic analysis of ground-to-excited state transitions.
Figure 3: Chemical shift assignment of excited state Hoogsteen base pairs.
Figure 4: Watson–Crick to Hoogsteen base pair transition simulations.

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Acknowledgements

We thank A. L. Hansen, S. Horowitz and J. Feigon for valuable discussions and suggestions, A. V. Kurochkin for NMR expertise, and C.L. Brooks III for access to a supercomputing cluster. We gratefully acknowledge the Michigan Economic Development Cooperation and the Michigan Technology Tri-Corridor for support in the purchase of a 600 MHz spectrometer. This work was supported by NSF CAREER awards (MCB 0644278 to HMA and CHE-0918817 to I.A.) and an NIH grant (R01GM089846). E.N.N. acknowledges support by a Rackham International and Predoctoral Fellowship awarded by the University of Michigan.

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Contributions

E.N.N. prepared DNA samples assisted by A.A.W. and performed/analysed all NMR experiments and DFT calculations; E.N.N. and H.M.A. conceived the idea of an HG excited state base pair and approaches to investigate its formation; I.A. and E.K. performed and analysed the MD/CPR simulations; P.J.O. provided expertise and guidance for damaged DNA studies along with critical manuscript revisions; H.M.A. and E.N.N. with help from P.J.O, E.K. and I.A. wrote the paper.

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Correspondence to Ioan Andricioaei or Hashim M. Al-Hashimi.

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Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-8 with legends, Supplementary Tables 1-6, a Supplementary Discussion, Supplementary References and legends for Supplementary Movies 1-2. (PDF 5534 kb)

Supplementary Movie 1

This movie shows An A•T WC-to-HG base pair transition in duplex B-DNA (see Supplementary Information file for full legend). (MOV 625 kb)

Supplementary Movie 2

This movie shows A G•C WC-to-HG base pair transition in duplex B-DNA (see Supplementary Information file for full legend). (MOV 503 kb)

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Nikolova, E., Kim, E., Wise, A. et al. Transient Hoogsteen base pairs in canonical duplex DNA. Nature 470, 498–502 (2011). https://doi.org/10.1038/nature09775

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