Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structural dynamics of individual Holliday junctions

Nature Structural Biology volume 10, pages 93–97 (2003)Cite this article

Abstract

The four-way DNA (Holliday) junction is the central intermediate of genetic recombination, but the dynamic aspects of this important structure are presently unclear. Although transitions between alternative stacking conformers have been predicted, conventional kinetic studies are precluded by the inability to synchronize the junction in a single conformer in bulk solution. Using single-molecule fluorescence methodology we have been able to detect these transitions. The sequence dependence, the influence of counterions and measured energetic barriers indicate that the conformer transition and branch migration processes share the unstacked, open structure as the common intermediate but have different rate-limiting steps. Relative rates indicate that multiple conformer transitions occur at each intermediate step of branch migration, allowing the junction to reach conformational equilibrium. This provides a mechanism whereby the sequence-dependent conformational bias could determine the extent of genetic exchange upon junction resolution.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Holliday junction structure.
Figure 2: Single-molecule time records and analysis
Figure 3: Na+ and Mg2+ influence the conformer transition rates differently.
Figure 4: Energetics of Holliday junction dynamics.

Similar content being viewed by others

References

  1. Cox, M.M. et al. The importance of repairing stalled replication forks. Nature 404, 37–41 (2000).

    Article  CAS  Google Scholar 

  2. Holliday, R. A mechanism for gene conversion in fungi. Genet. Res. 5, 282–304 (1964).

    Article  Google Scholar 

  3. Potter, H. & Dressler, D. On the mechanism of genetic recombination: electron microscopic obervation of recombination intermediates. Proc. Natl. Acad. Sci. USA 73, 3000–3004 (1978).

    Article  Google Scholar 

  4. Schwacha, A. & Kleckner, N. Identification of double Holliday junctions as intermediates in meiotic recombination. Cell 83, 783–791 (1995).

    Article  CAS  Google Scholar 

  5. Lilley, D.M.J. & White, M.F. The junction-resolving enzymes. Nat. Rev. Mol. Cell. Biol. 2, 433–443 (2001).

    Article  CAS  Google Scholar 

  6. Lilley, D.M.J. Structure of helical junctions in nucleic acids. Q. Rev. Biophys. 33, 109–159 (2000).

    Article  CAS  Google Scholar 

  7. Clegg, R.M., Murchie, A.I.H. & Lilley, D.M.J. The solution structure of the four-way DNA junction at low-salt conditions — a fluorescence resonance energy transfer analysis. Biophys. J. 66, 99–109 (1994).

    Article  CAS  Google Scholar 

  8. Duckett, D.R. et al. The structure of the Holliday junction, and its resolution. Cell 55, 79–89 (1988).

    Article  CAS  Google Scholar 

  9. Murchie, A.I. et al. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 341, 763–766 (1989).

    Article  CAS  Google Scholar 

  10. Nowakowski, J., Shim, P.J., Prasad, G.S., Stout, C.D. & Joyce, G.F. Crystal structure of an 82-nucleotide RNA–DNA complex formed by the 10–23 DNA enzyme. Nat. Struct. Biol. 6, 151–156 (1999).

    Article  CAS  Google Scholar 

  11. Ortiz-Lombardia, M. et al. Crystal structure of a DNA Holliday junction. Nat. Struct. Biol. 6, 913–917 (1999).

    Article  CAS  Google Scholar 

  12. Eichman, B.F., Vargason, J.M., Mooers, B.H.M. & Ho, P.S. The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Proc. Natl. Acad. Sci. USA 97, 3971–3976 (2000).

    Article  CAS  Google Scholar 

  13. Mueller, J.E., Kemper, B., Cunningham, R.P., Kallenbach, N.R. & Seeman, N.C. T4 endonuclease VII cleaves the crossover strands of Holliday junction analogs. Proc. Natl. Acad. Sci. USA 85, 9441–9445 (1988).

    Article  CAS  Google Scholar 

  14. Bennett, R.J. & West, S.C. RuvC protein resolves Holliday junctions via cleavage of the continuous (noncrossover) strands. Proc. Natl. Acad. Sci. USA 92, 5635–5639 (1995).

    Article  CAS  Google Scholar 

  15. Miick, S.M., Fee, R.S., Millar, D.P. & Chazin, W.J. Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions. Proc. Natl. Acad. Sci. USA 94, 9080–9084 (1997).

    Article  CAS  Google Scholar 

  16. Grainger, R.J., Murchie, A.I.H. & Lilley, D.M.J. Exchange between stacking conformers in a four-way DNA junction. Biochemistry 37, 23–32 (1998).

    Article  CAS  Google Scholar 

  17. Chen, J.H., Churchill, M.E., Tullius, T.D., Kallenbach, N.R. & Seeman, N.C. Construction and analysis of monomobile DNA junctions. Biochemistry 27, 6032–6038 (1988).

    Article  CAS  Google Scholar 

  18. Carlstrom, G. & Chazin, W.J. Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy. Biochemistry 35, 3534–3544 (1996).

    Article  CAS  Google Scholar 

  19. Overmars, F.J.J. & Altona, C. NMR study of the exchange rate between two stacked conformers of a model Holliday junction. J. Mol. Biol. 273, 519–524 (1997).

    Article  CAS  Google Scholar 

  20. Weiss, S. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat. Struct. Biol. 7, 724–729 (2000).

    Article  CAS  Google Scholar 

  21. Zhuang, X.W. et al. Correlating structural dynamics and function in single ribozyme molecules. Science 296, 1473–1476 (2002).

    Article  CAS  Google Scholar 

  22. Ha, T. et al. Initiation and reinitiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419, 638–641 (2002).

    Article  CAS  Google Scholar 

  23. Johnson, R.D. & Symington, L.S. Crossed-stranded DNA structures for investigating the molecular dynamics of the Holliday junction. J. Mol. Biol. 229, 812–820 (1993).

    Article  CAS  Google Scholar 

  24. Panyutin, I.G. & Hsieh, P. The kinetics of spontaneous DNA branch migration. Proc. Natl. Acad. Sci. USA 91, 2021–2025 (1994).

    Article  CAS  Google Scholar 

  25. Mulrooney, S.B., Fishel, R.A., Hejna, J.A. & Warner, R.C. Preparation of figure 8 and cruciform DNAs and their use in studies of the kinetics of branch migration. J. Biol. Chem. 271, 9648–9659 (1996).

    Article  CAS  Google Scholar 

  26. Panyutin, I.G., Biswas, I. & Hsieh, P. A pivotal role for the structure of the Holliday junction in DNA branch migration. EMBO J. 14, 1819–1826 (1995).

    Article  CAS  Google Scholar 

  27. Parson, C.A., Stasiak, A., Bennett, R.J. & West, S.C. Structure of a multisubunit complex that promotes DNA branch migration. Nature 374, 375–378 (1995).

    Article  Google Scholar 

  28. Ha, T.J. et al. Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism. Proc. Natl. Acad. Sci. USA 96, 893–898 (1999).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank I. Rasnik for experimental help. Funding was provided by the NIH, NSF, Searle Scholars Award (T.H.) and by Cancer Research UK (D.M.J.L.). S.A.M. was partially supported by the NIH molecular biophysics training grant.

Author information

Authors and Affiliations

  1. Physics department, University of Illinois, Urbana-Champaign, Urbana, 61801, Illinois, USA

    Sean A. McKinney & Taekjip Ha

  2. Department of Biochemistry, Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, DD1 5EH, UK

    Anne-Cécile Déclais & David M.J. Lilley

Authors
  1. Sean A. McKinney
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anne-Cécile Déclais
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David M.J. Lilley
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Taekjip Ha
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Taekjip Ha.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

McKinney, S., Déclais, AC., Lilley, D. et al. Structural dynamics of individual Holliday junctions. Nat Struct Mol Biol 10, 93–97 (2003). https://doi.org/10.1038/nsb883

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb883

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing