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The inherent properties of DNA four-way junctions: Comparing the crystal structures of holliday junctions

AuthorsEichman, Brandt F.; Ortiz-Lombardía, Miguel; Aymamí, Joan; Coll, Miquel ; Ho, Puishing
Holliday junctions
DNA structure
Four-way junction
Issue Date26-Jul-2002
PublisherAcademic Press
CitationJournal of Molecular Biology 320(5): 1037-1051 (2002)
AbstractHolliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. Much work has focused on the overall structure and properties of four-way junctions in solution, but we are just now beginning to understand these complexes at the atomic level. The crystal structures of two all-DNA Holliday junctions have been determined recently from the sequences d(CCGGGACCGG) and d(CCGGTACCGG). A detailed comparison of the two structures helps to distinguish distortions of the DNA conformation that are inherent to the cross-overs of the junctions in this crystal system from those that are consequences of the mismatched dG·dA base-pair in the d(CCGGGACCGG) structure. This analysis shows that the junction itself perturbs the sequence-dependent conformational features of the B-DNA duplexes and the associated patterns of hydration in the major and minor grooves only minimally. This supports the idea that a DNA four-way junction can be assembled at relatively low energetic cost. Both structures show a concerted rotation of the adjacent duplex arms relative to B-DNA, and this is discussed in terms of the conserved interactions between the duplexes at the junctions and further down the helical arms. The interactions distant from the strand cross-overs of the junction appear to be significant in defining its macroscopic properties, including the angle relating the stacked duplexes across the junction. © 2002 Elsevier Science Ltd. All rights reserved.
Publisher version (URL)http://dx.doi.org/10.1016/S0022-2836(02)00540-5
Identifiersdoi: 10.1016/S0022-2836(02)00540-5
issn: 0022-2836
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