The Holliday junction is a central intermediate in various genetic processes including homologous, site-specific recombination and DNA replication. Recent single molecule FRET experiments led to the model for branch migration as a stepwise stochastic process in which the branch migration hop is terminated by the folding of the junction. In this article, we studied the effect of the sequence on Holliday junction dynamics and branch migration process. We show that a GC pair placed at the border of the homologous region almost prevents the migration into this position. At the same time, insertion of a GC pair into the middle of the AT tract does not show this effect, however when the junction folds at this position, it resides at this position much longer time in comparison to the folding at AT pairs. Two contiguous GC pairs do not block migration as well and generally manifest the same effect as one GC pair - the junction when it folds resides at these positions for a relatively long time. The same elevated residence time was obtained for the design with the homology region that consists of only GC pairs. These data suggest a model for branch migration in which the sequence modulates the overall stochastic process of the junction dynamics and branch migration by the variability of the time that the junction dwells before making a migration hop.
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