Article | Published:

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

Nature Chemical Biology volume 9, pages 455461 (2013) | Download Citation

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.

  • Compound C60H66N7O6P

    (1'S,2'R,4'R)-2-((Bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-4-((5-formamido-6-(tritylamino)pyrimidin-4-yl)amino)cyclopentyl-(2-cyanoethyl)diisopropylphosphoramidite

  • Compound C43H54N7O8P

    (1'S,2'R,4'R)-4-((2-Acetamido-5-formamido-6-oxo-1,6-dihydropyrimidin-4-yl)-amino)-2-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)cyclopentyl(2-cyanoethyl)diisopropylphosphoramidite

  • Compound C8H14F3NO4

    (1S,2R,4R)-4-Ammonium-2-(hydroxymethyl)cyclopentanol-trifluoroacetate

  • Compound C11H21NO4

    tert-Butyl ((1R,3S,4R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl)carbamate

  • Compound C4H3ClN4O2

    4-Amino-6-chloro-5-nitropyrimidine

  • Compound C4H4N2O2

    Pyrimidine-4,6-diol

  • Compound C4H3N3O4

    4,6-Dihydroxy-5-nitropyrimidine

  • Compound C4HCl2N3O2

    4,6-Dichloro-5-nitropyrimidine

  • Compound C10H15N5O4

    N-4-{[(1'R,3'S,4'R)-3'-Hydroxy-4'-(hydroxymethyl)cyclopentyl]amino}-5-nitro-6-aminopyrimidine

  • Compound C22H43N5O4Si2

    N-4-{[(1'R,3'S,4'R)-3'-[(tert-Butyldimethylsilyl)oxy]-4'-{[(tert-butyldimethylsilyl)oxy]methyl}cyclopentyl]amino}-5-nitro-6-aminopyrimidine

  • Compound C23H45N5O3Si2

    N-4-{[(1'R,3'S,4'R)-3'-[(tert-Butyldimethylsilyl)oxy]-4'-{[(tert-butyldimethylsilyl)oxy]methyl}cyclopentyl]amino}-5-formylamino-6-aminopyrimidine

  • Compound C42H59N5O3Si2

    N-4-{[(1'R,3'S,4'R)-3'-[(tert-Butyldimethylsilyl)oxy]-4'-{[(tert-butyldimethylsilyl)oxy]methyl}cyclopentyl]amino}-5-formylamino-6-tritylaminopyrimidine

  • Compound C30H31N5O3

    N-4-{[(1'R,3'S,4'R)-3'-Hydroxy-4'-(hydroxymethyl)cyclopentyl]amino}-5-formylamino-6-tritylaminopyrimidine

  • Compound C51H49N5O5

    N-4-{[(1'R,3'S,4'R)-4'-{[(Dimethoxytrityl)oxy]methyl}-3'-hydroxycyclopentyl]amino}-5-(formylamino)-6-tritylaminopyrimidine

  • Compound C11H17N5O3

    N-(5-(Formylamino)-4-{[(1'R,3'S,4'R)-3'-hydroxy-4'-(hydroxymethyl)cyclopentyl]amino}-6-aminopyrimidine

  • Compound C24H45N5O6Si2

    N-(4-(((1'R,3'S,4'R)-3-((tert-Butyldimethylsilyl)oxy)-4-(((tert-butyldimethylsilyl)oxy)methyl)cyclopentyl)amino)-5-nitro-6-oxo-1,6-dihydropyrimidin-2-yl)acetamide

  • Compound C25H45N5O4Si2

    N-[9-[(1'R,3'S,4'R)-3'-[(tert-Butyldimethylsilyl)oxy]-4'-[[(tert-butyldimethylsilyl)oxy]methyl]cyclopentyl]-6-oxo-6,9-dihydro-1H-purin-2-yl]acetamide

  • Compound C23H43N5O3Si2

    2-Amino-9-[(1'R,3'S,4'R)-3'-[(tert-butyldimethylsilyl)oxy]-4'-[[(tert-butyldimethylsilyl)oxy]methyl]cyclopentyl]-1,9-dihydropurine-6-one

  • Compound C11H15N5O3

    2-Amino-9-((1'R,3'S,4'R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl)-1,9-dihydro-6H-purin-6-one

  • Compound C10H13N5O4

    2'-Desoxyguanosine

  • Compound C10H15N5O5

    N-(2-Amino-4-(((2'R,5'R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)amino)-6-oxo-1,6-dihydropyrimidin-5-yl)formamide)

  • Compound C11H17N5O4

    N-(2-Amino-4-(((1'R,4'R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl)amino)-6-oxo-1,6-dihydropyrimidin-5-yl)formamide

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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.

Author information

Author notes

    • Sabine Schneider

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

    • Tim H Gehrke
    • , Ulrike Lischke
    • , Karola L Gasteiger
    •  & Sabine Schneider

    These authors contributed equally to the work.

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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Thomas Carell.

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DOI

https://doi.org/10.1038/nchembio.1254

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