Nature Structural Biology10, 93 - 97 (2002)
Published online: 23 December 2002; | doi:10.1038/nsb883
Structural dynamics of individual Holliday junctions
Sean A. McKinney1, Anne-Cécile Déclais2, David M.J. Lilley2
& Taekjip Ha1
1
Physics department, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA.
2
Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, UK.
Correspondence should be addressed to Taekjip Ha tjha@uiuc.edu
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.
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