Branch migration through DNA sequence heterology

Journal of Molecular Biology
I BiswasP Hsieh

Abstract

Branch migration of a DNA Holliday junction is a key step in genetic recombination. Previously, it was shown that a single base-pair heterology between two otherwise identical DNA sequences is a substantial barrier to passage of a Holliday junction during spontaneous branch migration. Here, we exploit this inhibitory effect of sequence heterology to estimate the step size of branch migration. We also devise a simulation of branch migration through mismatched base-pairs to arrive at the underlying molecular basis for the block to branch migration imposed by sequence heterology. Based on the observation that two adjacent sequence heterologies exert their effects on branch migration more or less independently, we conclude that the step size of branch migration is quite small, of the order of one or two base-pairs per migratory step. Comparison of branch migration experiments through a single base-pair heterology with simulations of a random walk through sequence heterology suggests that the inhibition of branch migration is largely attributable to a thermodynamic barrier arising from the formation of unpaired or mispaired bases in heteroduplex DNAs.

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Citations

Apr 11, 2000·Nucleic Acids Research·A LishanskiE F Ullman
May 25, 2004·Nucleic Acids Research·Noëlle PougetLaurence Salomé
Aug 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·A DawidF Heslot
Mar 29, 2007·Proceedings of the National Academy of Sciences of the United States of America·Nader PourmandRonald W Davis
May 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Mikhail KarymovYuri L Lyubchenko
Nov 11, 2014·Nature Communications·Robert R F MachinekAndrew J Turberfield
Oct 2, 2015·Journal of the Royal Society, Interface·Casey GrunPeng Yin
Apr 28, 2009·FEMS Microbiology Reviews·Stuart A Hill, John K Davies
Sep 2, 2003·The Journal of Biological Chemistry·Alexander Y LushnikovYuri L Lyubchenko
Mar 9, 2002·Journal of Molecular Biology·Vidya P PrabhuJunghuei Chen
Dec 7, 2002·Journal of Theoretical Biology·Michael F Bruist, Eric Myers
Jun 12, 2013·Journal of the American Chemical Society·Jeffrey R ViereggNiles A Pierce
May 16, 2018·ACS Nano·Denis SelnihhinEbbe Sloth Andersen

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