The Structure of the Four-Way Junction in DNA

Lilley, David M. J.; Clegg, Robert M.

doi:10.1146/annurev.bb.22.060193.001503

Cited by 172 publications

(141 citation statements)

References 66 publications

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“…1c, for example, the pair of helices form an acute angle of 60Њ, with the backbone of one helix fitting snugly into the grooves of the other; this type of structure was seen in several crystals, with the acute angle ranging from 43Њ to 77Њ (6). A pair of DNA helices with a backbone-groove fit was also deduced earlier through a variety of measurements in solution for the Holliday junction, a four-way DNA junction involved in DNA recombination (7)(8)(9)(10).…”

mentioning

confidence: 58%

Chirality of DNA trefoils: Implications in intramolecular synapsis of distant DNA segments

Shaw

Wang

1997

Proc. Natl. Acad. Sci. U.S.A.

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We show that supercoiling of a DNA trefoil, the simplest knotted ring, perturbs differently the spatial writhe of its two chiral forms. As a consequence, the negativenoded and positive-noded DNA trefoils can be resolved by gel electrophoresis. Analysis of the chirality of trefoils produced by cyclization of two linear DNAs demonstrates that the two chiral trefoils are produced in equal amounts, suggesting that these DNAs do not prefer intrinsic writhe of one chirality or the other. In contrast, knotting of nicked DNA rings by a molar excess of Saccharomyces cerevisiae DNA topoisomerase II produces more negative-noded than positive-noded trefoils, indicating an asymmetry in the interaction between the enzyme and DNA crossovers of different signs. These results suggest that asymmetry in DNA crossovers and intrinsic or ligand-induced writhe in a DNA might be detectable from an analysis of trefoil chirality.Crossovers or nodes between two duplex DNA segments are a common motif in higher order structures of DNA and DNA-protein complexes. When two segments along a DNA are brought into proximity, they may form a positive or negative node, as illustrated in Fig. 1 a and b. In topological transformations of DNA rings catalyzed by DNA topoisomerases and site-specific recombinases, the topology of the final products are often critically dependent on the nodes present in the DNA and their signs.A question that often arises in the study of reactions involving intramolecular synapsis of two remote DNA segments is whether the structure of DNA might impose a bias for nodes of a particular sign. In general, two factors may affect the nodal sign. First, a DNA of a particular sequence might have a preferred writhe in solution and thus favor the formation of a node of a particular sign: positive writhe or preferential formation of a right-handed loop would favor the formation of a positive node, and negative writhe or preferential formation of a left-handed loop would favor the formation of a negative node. Second, if the crossing segments are in close contact, then interactions between the pair of DNA double helices might favor one geometry over another. A number of studies have revealed the structures of DNA helices in close contact. In several crystals, a pair of contacting DNA segments were found to form crossovers with unique structures (1-6). In the crossover illustrated in Fig. 1c, for example, the pair of helices form an acute angle of 60Њ, with the backbone of one helix fitting snugly into the grooves of the other; this type of structure was seen in several crystals, with the acute angle ranging from 43Њ to 77Њ (6). A pair of DNA helices with a backbone-groove fit was also deduced earlier through a variety of measurements in solution for the Holliday junction, a four-way DNA junction involved in DNA recombination (7-10).The crossover exemplified by the structure shown in Fig. 1c is chiral, and inverting its chirality by pushing the upper helix through the lower one would destroy the backbone-groove fit. The formati...

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mentioning

confidence: 58%

Chirality of DNA trefoils: Implications in intramolecular synapsis of distant DNA segments

Shaw

Wang

1997

Proc. Natl. Acad. Sci. U.S.A.

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“…This effect is maximized at 4° C, where the observed increase in friction constant is about 38%, compared with 23% at 25° C. Thus, there is a preferred pair of stacking domains for both domains of the 4-arm junction, which is well known. 25,26 This double stacking dominance seems to be unique to the 4-arm junction.…”

Section: Ferguson Analysismentioning

confidence: 91%

Assembly and Characterization of 8-Arm and 12-Arm DNA Branched Junctions

2007

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Branched DNA molecules can be assembled into objects and networks directed by sticky-ended cohesion. The connectivity of these species is limited by the number of arms flanking the branch point. To date, the only branched junctions constructed contain six or fewer arms. We report the construction of DNA branched junctions that contain either 8 or 12 double helical arms surrounding a branch point. The design of the 8-arm junction expoits the limits of a previous approach to thwart branch migration, but the design of the 12-arm junction uses a new to principle achieve this end. The 8-arm junction is stable with 16 nucleotide pairs per arm, but the 12-arm junction has been stabilized by 24 nucleotide pairs per arm. Ferguson analysis of these junctions in combination with three, four, five, and six-arm junctions indicates a linear increase in friction constant as the number of arms increases; the four-arm junction migrates anomalously at 4°C., suggesting stacking of its domains. All strands in both the 8-arm and 12-arm junctions show similar responses to hydroxyl radical autofootprinting analysis, indicating that they lack any dominant stacking structures. The stability of the 12-arm junction demonstrates that the number of arms in a junction is not limited to the case of having adjacent identical base pairs flanking the junction. The ability to construct eight-arm and twelve-arm junctions increases the number of objects, graphs and networks that can be built from branched DNA components. In principle, the stick structure corresponding to cubic close packing is now a possible target for assembly by DNA nanotechnology. KeywordsBranched DNA Motifs; N-Connected DNA-Networks; N-Connected DNA Graphs; Hydroxyl Radical Autofootprinting; Gel Electrophoresis; Ferguson Plots DNA branched junctions containing 3 or 4 arms around a single point are seen as ephemeral intermediates in the biological processes of replication 1 and recombination. 2 In addition, immobile versions of these junctions have served as the basis for virtually all of the work done in structural DNA nanotechnology. 3 A variety of DNA structures and motifs have been created using these components, 4 including stick figures whose edges are DNA double helices and whose vertices are the branch points of branched junctions; these include molecules with the connectivities of a cube 5 and a truncated octahedron, 6 as well as an irregular graph. 7 The connectivity of DNA structures of this sort is limited by the number of double helical DNA arms that can flank a branch point.

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“…Junction C is an immobile junction, and it serves as a control for the patterns seen there. Crossover residues [123, 124] of strand II are protected, as are residues [12,13] of strand I, but helical residues [9,10], and [83, 84] of strand II show no protection. These data confirm that the molecule constructed has the conformation indicated at the top of Figure 2, and it is poised to branch migrate following restriction.…”

Section: Hydroxyl Radical Autofootprintingmentioning

confidence: 99%

“…In the new numbering scheme, the crossover the crossover at junction B occurred before restriction at [14,15] on strand ii and at [30,31] on strand iii. Figure 6a shows that the key protection on strand ii has shifted to [9,10] and the major protection on strand iii has shifted to [25,26]; these crossover sites correspond to junction B′ (Figure 2). Thus, this junction has also migrated 5 positions through the symmetric region; however, the crossover strands have migrated in the 5′ direction, rather than the 3′ direction, as in junction A′.…”

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confidence: 99%

Direct Evidence for Spontaneous Branch Migration in Antiparallel DNA Holliday Junctions

2000

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The Holliday junction is a central intermediate in genetic recombination. It contains four strands of DNA that are paired into four double helical arms flanking a branch point. In naturallyoccurring Holliday junctions, the sequence flanking the branch point contains twofold (homologous) symmetry. As a consequence of this symmetry, the junction can undergo a conformational isomerization known as branch migration, which relocates the site of branching. In the absence of proteins and in the presence of Mg 2+ , the four arms are known to stack in pairs, forming two helical domains whose orientations are antiparallel. Nevertheless, the mechanistic models proposed for branch migration are all predicated on a parallel alignment of helical domains. Here, we have used antiparallel DNA double crossover molecules to demonstrate that branch migration can occur in antiparallel Holliday junctions. We have constructed a DNA double crossover molecule with three crossover points. Two adjacent branch points in this molecule are flanked by symmetric sequences. The symmetric crossover points are held immobile by the third crossover point, which is flanked by asymmetric sequences. Restriction of the helices that connect the immobile junction to the symmetric junctions releases this constraint. The restricted molecule undergoes branch migration, even though it is constrained to an antiparallel conformation. KeywordsBranch migration; DNA double crossover molecules; Branched junction conformational isomerizations; Hydroxyl radical autofootprinting; DNA topology The Holliday (1) junction is the most prominent DNA intermediate in genetic recombination. It is known to be involved in site specific recombination (2-4), and it is likely to be involved in homologous recombination (5). The life cycle of the Holliday junction in recombination is illustrated in Figure 1, which depicts the process in junctions with both parallel and antiparallel conformations. The first step, shown at the left of the drawing, is the formation of the junction (II) from two pieces of DNA containing homology (I). The branch point of the Holliday junction is flanked typically by regions of dyad (homologous) sequence symmetry; this symmetry enables the branch point to relocate through an isomerization known as branch migration (e.g., 6). Branch migration (III) is illustrated in the next step to the right of formation. Proceeding to the right, the Holliday junction may undergo another conformational change, known as crossover isomerization. This rearrangement reverses the helical and crossover strands (IV), and it is known to be spontaneous (7). The junctions may then be cleaved (V) by resolvases, such as endonuclease VII (8) or RuvC (9), and religated (VI). It is clear from Figure 1 that the extent of branch migration and the number of crossover isomerizations will influence the products of recombination; the extent of branch migration will determine the site of resolution, and (for * Address Correspondence to this Author: ned.seeman@nyu.edu; NIH-PA Author Ma...

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The Structure of the Four-Way Junction in DNA

Cited by 172 publications

References 66 publications

Chirality of DNA trefoils: Implications in intramolecular synapsis of distant DNA segments

Chirality of DNA trefoils: Implications in intramolecular synapsis of distant DNA segments

Assembly and Characterization of 8-Arm and 12-Arm DNA Branched Junctions

Direct Evidence for Spontaneous Branch Migration in Antiparallel DNA Holliday Junctions

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