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Crystal structure of a DNA Holliday junction

Abstract

DNA recombination is a universal biological event responsible both for the generation of genetic diversity and for the maintenance of genome integrity. A four-way DNA junction, also termed Holliday junction, is the key intermediate in nearly all recombination processes. This junction is the substrate of recombination enzymes that promote branch migration or catalyze its resolution. We have determined the crystal structure of a four-way DNA junction by multiwavelength anomalous diffraction, and refined it to 2.16 Å resolution. The structure has two-fold symmetry, with pairwise stacking of the double-helical arms, which form two continuous B-DNA helices that run antiparallel, cross in a right-handed way, and contain two G-A mismatches. The exchanging backbones form a compact structure with strong van der Waals contacts and hydrogen bonds, implying that a conformational change must occur for the junction to branch-migrate or isomerize. At the branch point, two phosphate groups from one helix occupy the major groove of the other one, establishing sequence-specific hydrogen bonds. These interactions, together with different stacking energies and steric hindrances, explain the preference for a particular junction stacked conformer.

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Figure 1: Global structure of the Holliday junction.
Figure 2: Electron density maps.
Figure 3: Structural details of the four-way junction.
Figure 4: Scheme of the conformational changes required for the four-way junction to migrate or isomerize.

References

  1. Holliday, R. Genet. Res. 5, 282–304 ( 1964).

    Article  Google Scholar 

  2. Broker, T.R. J. Mol. Biol. 81, 1–16 ( 1973).

    Article  CAS  Google Scholar 

  3. Duckett, D.R. et al. Cell 55, 79–89 (1988).

    Article  CAS  Google Scholar 

  4. Cooper, J.P. & Hagerman, P.J. J. Mol. Biol. 198 , 711–719 (1987).

    Article  CAS  Google Scholar 

  5. Murchie, A.I.H. et al. Nature 341, 763–766 (1989).

    Article  CAS  Google Scholar 

  6. Miick, S.M., Fee, R.S., Millar, D.P. & Chazin, W.J. Proc. Natl. Acad. Sci. USA 94, 9080–9084 ( 1997).

    Article  CAS  Google Scholar 

  7. Chen, S.M. & Chazin, W.J. Biochemistry 33, 11453–11459 (1994).

    Article  CAS  Google Scholar 

  8. Overmars, F.J. & Altona, C. J. Mol. Biol. 273, 519–524 (1997).

    Article  CAS  Google Scholar 

  9. Churchill, M.E.A., Tullius, T.D., Kallenbach, N.R. & Seeman, N.C. Proc. Natl. Acad. Sci. USA 85, 4653– 4656 (1988).

    Article  CAS  Google Scholar 

  10. Grainger, R.J., Murchie, A.I.H. & Lilley, D.M.J. Biochemistry 37, 23– 32 (1998).

    Article  CAS  Google Scholar 

  11. Panyutin, I.G., Biswas, I. & Hsieh, P. EMBO J. 14, 1819– 1826 (1995).

    Article  CAS  Google Scholar 

  12. Sigal, N. & Alberts, B. J. Mol. Biol. 71, 789–793 (1972).

    Article  CAS  Google Scholar 

  13. von Kitzing, E., Lilley, D.M.J. & Dikmann, S. Nucleic Acids Res. 18, 2671– 2683 (1990).

    Article  CAS  Google Scholar 

  14. Timsit, Y. & Moras, D. J. Mol. Biol. 221, 919–940 (1991).

    Article  CAS  Google Scholar 

  15. Goodsell, D.S., Grzezkowiak, K. & Dickerson, R.E. Biochemistry 34, 1022– 1029 (1995).

    Article  CAS  Google Scholar 

  16. Wood, A.A., Nunn, C.M., Trent, J.O. & Neidle, S. J. Mol. Biol. 269, 827–841 (1997).

    Article  CAS  Google Scholar 

  17. Seeman, N.C. & Kallenbach, N.R. Annu. Rev. Biophys. Biomol. Struct. 23, 53–86 ( 1994).

    Article  CAS  Google Scholar 

  18. Lilley, D.M.J. In Nucleic acid structure (ed. Neidle, S.) 471– 498 (Oxford University Press, Oxford; 1999).

    Google Scholar 

  19. Hargreaves, D. et al. Nature Struct. Biol. 5, 441– 446 (1998).

    Article  CAS  Google Scholar 

  20. Roe, S.M. et al. Mol. Cell 2, 361–372 (1998).

    Article  CAS  Google Scholar 

  21. Gopaul, D.N., Guo, F. & Van Duyne, G.D. EMBO J. 17, 4175– 4187 (1998).

    Article  CAS  Google Scholar 

  22. Nowakowski, J., Shim, P.J., Prasad, G.S., Stout, C.D. & Joyce, G.F. Nature Struct. Biol. 6, 151 –156 (1999).

    Article  CAS  Google Scholar 

  23. Taylor, R. & Kennard, O. J. Am. Chem. Soc. 104 , 5063–5070 (1982).

    Article  CAS  Google Scholar 

  24. Duckett, D.R., Murchie, A.I.H. & Lilley, D.M.J. EMBO J. 9, 583– 590 (1990).

    Article  CAS  Google Scholar 

  25. Privé, G.G. et al. Science 238, 498–504 (1987).

    Article  Google Scholar 

  26. Duckett, D.R. & Lilley, D.M.J. J. Mol. Biol. 221 , 147–161 (1991).

    Article  CAS  Google Scholar 

  27. Azaro, M.A. & Landy, A. EMBO J. 16, 3744–3755 (1997).

    Article  CAS  Google Scholar 

  28. Raaijmakers, H. et al. EMBO J. 18, 1447–1458 (1999).

    Article  CAS  Google Scholar 

  29. Otwinowski, Z. & Minor, W. Methods Enzymol. 276, 307–326 ( 1997).

    Article  CAS  Google Scholar 

  30. Leslie, A.G.W. In Crystallographic computing 5: from chemistry to biology (eds Moras, D., Podjanry, A.D. & Thierry, J.C.) 27–38 (Oxford University Press, Oxford, United Kingdom; 1991).

    Google Scholar 

  31. Collaborative Computational Project, Number 4. Acta Crystallogr. D 50, 760– 763 (1994).

  32. Navaza, J. Acta Crystallogr. A 50 , 157–163 (1994).

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from the Ministerio de Educación y Cultura of Spain, the Generalitat de Catalunya, the Centre de Referència en Biotecnologia and the European Union. Synchrotron data collection was supported by the EU program for access to large installations.

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Correspondence to Miquel Coll.

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Ortiz-Lombardía, M., González, A., Eritja, R. et al. Crystal structure of a DNA Holliday junction. Nat Struct Mol Biol 6, 913–917 (1999). https://doi.org/10.1038/13277

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