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Nucleic Acids Research 2004 32(22):6683-6695; doi:10.1093/nar/gkh1006
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Published online 21 December 2004

Nucleic Acids Research, Vol. 32 No. 22 © Oxford University Press 2004; all rights reserved

Conformational model of the Holliday junction transition deduced from molecular dynamics simulations

Jin Yu1,2, Taekjip Ha2 and Klaus Schulten1,2,*

1 Beckman Institute and 2 Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

* To whom correspondence should be addressed at Beckman Institute, 405 N. Mathews, Urbana, IL 61801, USA. Tel: +1 217 244 1604; Fax: +1 217 244 6078; Email: kschulte{at}ks.uiuc.edu

Received August 13, 2004; Revised November 3, 2004; Accepted November 29, 2004

Homologous recombination plays a key role in the restart of stalled replication forks and in the generation of genetic diversity. During this process, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction. In the presence of metal ions, the Holliday junction folds into the stacked-X structure that has two alternative conformers. Experiments have revealed the spontaneous transitions between these conformers, but their detailed pathways are not known. Here, we report a series of molecular dynamics simulations of the Holliday junction at physiological and elevated (400 K) temperatures. The simulations reveal new tetrahedral intermediates and suggest a schematic framework for conformer transitions. The tetrahedral intermediates bear resemblance to the junction conformation in complex with a junction-resolving enzyme, T7 endonuclease I, and indeed, one intermediate forms a stable complex with the enzyme as demonstrated in one simulation. We also describe free energy minima for various states of the Holliday junction system, which arise during conformer transitions. The results show that magnesium ions stabilize the stacked-X form and destabilize the open and tetrahedral intermediates. Overall, our study provides a detailed dynamic model of the Holliday junction undergoing a conformer transition.


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