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Unexpected non-Hoogsteen–based mutagenicity mechanism of FaPy-DNA lesions

Nature Chemical Biology volume 9, pages 455–461 (2013)Cite this article

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Abstract

8-Oxopurines (8-oxodG and 8-oxodA) and formamidopyrimidines (FaPydG and FaPydA) are major oxidative DNA lesions involved in cancer development and aging. Their mutagenicity is believed to result from a conformational shift of the N9-C1′ glycosidic bonds from anti to syn, which allows the lesions to form noncanonical Hoogsteen-type base pairs with incoming triphosphates during DNA replication. Here we present biochemical data and what are to our knowledge the first crystal structures of carbocyclic FaPydA and FaPydG containing DNA in complex with a high-fidelity polymerase. Crystallographic snapshots show that the cFaPy lesions keep the anti geometry of the glycosidic bond during error-free and error-prone replication. The observed dG·dC→dT·dA transversion mutations are the result of base shifting and tautomerization.

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Figure 1: Representation of the two main oxidation products of 2′-deoxyguanosine (8-oxodG, FaPydG) and FaPydA.
Figure 2: Nucleotide insertion and bypass of oxidative lesions.
Figure 3: Error-free reading of Bst Pol I through cFaPydA-containing template DNA.
Figure 4: Error-free reading of Bst Pol I through cFaPydG-containing template DNA.
Figure 5: Erroneous bypass and extension of cFaPydG.

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Acknowledgements

We are grateful to the beamline scientists at the Swiss Light Source and European Synchrotron Radiation Facility for setting up the beamlines. This research project was supported by the Deutsche Forschungsgemeinschaft through SFB 646 and SFB 749. Further support was obtained by the Volkswagen Foundation and in particular by the Excellence Cluster CiPSM. We thank K. Karaghiosoff and K. Lux for solving the crystal structures of the small molecules. We thank M. Müller for critical reading of the manuscript and many helpful discussions.

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Author notes

  1. Sabine Schneider

    Present address: Present address: Department of Chemistry, Technical University, Munich, Germany.,

  2. Tim H Gehrke, Ulrike Lischke, Karola L Gasteiger and Sabine Schneider: These authors contributed equally to the work.

Authors and Affiliations

  1. Center for Integrated Protein Science at the Department of Chemistry, Ludwig Maximilians University, Munich, Germany

    Tim H Gehrke, Ulrike Lischke, Karola L Gasteiger, Sabine Schneider, Simone Arnold, Heiko C Müller, David S Stephenson, Hendrik Zipse & Thomas Carell

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Contributions

T.C. conceived and directed the study. He wrote the manuscript and designed experiments. T.H.G. and U.L. designed experiments. T.H.G. performed the synthesis of the lesions and of the DNA strands. U.L. and T.H.G. performed the biochemical experiments. U.L. purified the protein. K.L.G. performed the synthesis of cdG. S.A. developed the synthesis of cFaPydA. H.C.M. developed the synthesis of cdG. S.S. conducted crystallographic data collection and solved the crystal structures. H.Z. performed the theoretical studies. D.S.S. performed the NMR studies.

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Correspondence to Thomas Carell.

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Gehrke, T., Lischke, U., Gasteiger, K. et al. Unexpected non-Hoogsteen–based mutagenicity mechanism of FaPy-DNA lesions. Nat Chem Biol 9, 455–461 (2013). https://doi.org/10.1038/nchembio.1254

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