Single molecule fluorescence analysis of branch migration of holliday junctions: effect of DNA sequence.

Biophysical Journal
Mikhail A KarymovYuri L Lyubchenko

Abstract

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 ...Continue Reading

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Citations

Jul 6, 2010·Molecular BioSystems·Yann Gambin, Ashok A Deniz
Jun 10, 2009·Proceedings of the National Academy of Sciences of the United States of America·Yann GambinAshok A Deniz
Jul 20, 2010·Annual Review of Analytical Chemistry·J William Efcavitch, John F Thompson
Sep 23, 2010·Biophysical Journal·Dmytro PaletsYuri L Lyubchenko
Jan 22, 2019·Nature Chemical Biology·Ruobo ZhouTaekjip Ha
Jun 5, 2020·Journal of the American Chemical Society·Patrick IrmischRalf Seidel

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