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The crystal structure of Z-DNA with untypically coordinated Ca2+ ions

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Abstract

DNA oligomer duplexes with alternating cytosines and guanines in their sequence tend to form helices of the Z-DNA type, where the sugar and phosphate backbone forms a left-handed helix in a zigzag fashion with a repeat of two successive Watson–Crick pairs of nucleotides. Z-DNA duplexes often crystallize in complexes with diverse metal ions interacting with polar DNA atoms in various ways. This work describes the high-resolution crystal structure of a Z-DNA d(CGCGCG)2 duplex in complex with Ca2+ ions, unusually coordinated as an approximate pentagonal bipyramid by two neighboring guanines through their O6 and N7 atoms and a water molecule in the equatorial plane and a phosphate oxygen atom and another water molecule in the apical positions.

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References

  1. Wang AH-J, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A (1979) Nature 282:680–686

    Article  CAS  PubMed  Google Scholar 

  2. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucl Acid Res 28:235–242

    Article  CAS  Google Scholar 

  3. Ho PS, Mooers BHM (1997) Biopolymers 14:65–90

    Article  CAS  PubMed  Google Scholar 

  4. Mandal K, Venkadesh S, Gautham N (2008) J Indian Inst Sci 88:73–93

    CAS  Google Scholar 

  5. Otwinowski Z, Minor W (1997) Methods Enzymol 276:307–326

    Article  CAS  Google Scholar 

  6. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) J Appl Cryst 40:658–674

    Article  CAS  Google Scholar 

  7. Brzezinski K, Brzuszkiewicz A, Dauter M, Kubicki M, Jaskolski M, Dauter Z (2011) Nucl Acid Res 39:6238–6248

    Article  CAS  Google Scholar 

  8. Murshudov GN, Vagin AA, Dodson EJ (1997) Acta Cryst D53:240–255

    CAS  Google Scholar 

  9. Emsley P, Cowtan K (2004) Acta Cryst D60:2126–2132

    CAS  Google Scholar 

  10. Kowiel M, Brzezinski D, Jaskolski M (2016) Nucl Acids Res 44:8479–8489

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kowiel M, Jaskolski M, Dauter Z (2014) Acta Cryst D70:3290–3298

    Google Scholar 

  12. Wang AH-J, Quigley GJ, Kolpak FJ, van der Marel G, van Boom JH, Rich A (1981) Science 211:171–176

    Article  CAS  PubMed  Google Scholar 

  13. Neidle S (2008) Principles of nucleic acid structure. Academic Press, London

    Google Scholar 

  14. Harding MM (2006) Acta Cryst D62:678–682

    CAS  Google Scholar 

  15. Cramer DT (1983) J Appl Cryst 16:437–438

    Article  Google Scholar 

  16. Jaskolski M (1983) Acta Cryst A40:364–366

    Google Scholar 

Download references

Acknowledgements

We thank Dr. Mirek Gilski for helpful advice on the stereochemical restraints of Z-DNA. This work was supported by the Intramural Research Program of the National Cancer Institute, Center for Cancer Research. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Science, under Contract No. W-31-109-Eng-38.

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Authors and Affiliations

  1. Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL, 60439, USA

    Zhipu Luo & Zbigniew Dauter

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  1. Zhipu Luo
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  2. Zbigniew Dauter
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Correspondence to Zbigniew Dauter.

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PDB accession code: 6BST.

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Luo, Z., Dauter, Z. The crystal structure of Z-DNA with untypically coordinated Ca2+ ions. J Biol Inorg Chem 23, 253–259 (2018). https://doi.org/10.1007/s00775-017-1526-4

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  • DOI: https://doi.org/10.1007/s00775-017-1526-4

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