The stacked‐X DNA Holliday junction and protein recognition

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Abstract
The crystal structure of the four‐stranded DNA Holliday junction has now been determined in the presence and absence of junction binding proteins, with the extended open‐X form of the junction seen in all protein complexes, but the more compact stacked‐X structure observed in free DNA. The structures of the stacked‐X junction were crystallized because of an unexpected sequence dependence on the stability of this structure. Inverted repeat sequences that contain the general motif NCC or ANC favor formation of stacked‐X junctions, with the junction cross‐over occurring between the first two positions of the trinucleotides. This review focuses on the sequence dependent structure of the stacked‐X junction and how it may play a role in structural recognition by a class of dimeric junction resolving enzymes that themselves show no direct sequence recognition. Copyright © 2006 John Wiley & Sons, Ltd.