Holliday recombination intermediate

Holliday recombination intermediate (Fig. 27-22, Fig. 5-28, Eq. 27-11).521,528 530a Such four-way junctions can arise in several ways.530a d For example, a 3 or 5 single-stranded tail in a piece of dsDNA can "invade"... 

Churchill MEA, Tullius TD, Kallenbach NR, Seeman NC (1988) A Holliday recombination intermediate is twofold symmetric. Proc Natl Acad Sci USA 85 4653-4656 Clark EP, Michaels HB, Peterson EC, Epp ER (1983) Irradiation of mammalian cells in the presence of diamide and low concentrations of oxygen at conventional and at ultrahigh dose rates. Radiat Res 93 479-491... 

The Holliday recombination intermediate. In 1964, Holliday suggested a recombination process that would give rise to characteristic H-shaped intermediates. Recombination could be inibated at special points on the duplexes, recognizable by a recombinabon enzyme (Fig. 27-... 

Gopaul, D. N., Guo, F. and Van Duyne, G. D. (1998). Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17, 4175-4187. 

Recombination Reactions Proceed Through Holliday Junction Intermediates... 

Describe the Holliday model for homologous recombination. Explain how resolution of the Holliday Junction intermediate can form different recombinant DNA products. 

In this double-strand break repair model for recombination, the 3 ends are used to initiate the genetic exchange. Once paired with the complementary strand on the intact homolog, a region of hybrid DNA is created that contains complementary strands from two different parent DNAs (the product of step (2)in Fig. 25-31a). Each of the 3 ends can then act as a primer for DNA replication. The structures thus formed, Holliday intermediates (Fig. 25 31b), are a feature of homologous genetic recombination pathways in all organisms. 

S) Cleavage of the Holliday intermediates by specialized nucleases generates either of the two recombination products. In product set 2, the DNA on either side of the region undergoing repair is recombined. 

I or III, and DNA ligase—are required to complete recombination. The RuvC protein (Mr 20,000) of E. coli cleaves Holliday intermediates to generate full-length, unbranched chromosome products. 

To complete the reaction, the process must be repeated at a second point within each of the two recombination sites (steps (3) and (4)). In some systems, both strands of each recombination site are cut concurrently and rejoined to new partners without the Holliday intermediate. The exchange is always reciprocal and precise, regenerating the recombination sites when the reaction is complete. We can view a recombinase as a site-specific endonuclease and ligase in one package. 

FIGURE 25-41 DNA deletion to undo a deleterious effect of re-combinational DNA repair. The resolution of a Holliday intermediate during recombinational DNA repair (if cut at the points indicated by red arrows) can generate a contiguous dimeric chromosome. A specialized site-specific recombinase in E. coli, XerCD, converts the dimer to monomers, allowing chromosome segregation and cell division to proceed. 

Site-specific recombination occurs only at specific target sequences, and this process can also involve a Holliday intermediate. Recombinases cleave the DNA at specific points and ligate the strands to new partners. This type of recombination is found in virtually all cells, and its many functions include DNA integration and regulation of gene expression. 

Holliday intermediates in homologous genetic recombination differ from their formation in site-specific recombination ... 

The Holliday junction is a well-known intermediate in recombination, but it is not the only one. Another species is the DNA double-crossover molecule, termed DX. The DX molecule consists of two four-arm branched junctions that have been joined at two adjacent arms, to create a molecule containing two helical domains joined by two crossover points (Fu and Seeman 1993). There are five different motifs of the DX molecule these are illustrated in Figure 14, with a modification of one of them. The names of the DX molecules all begin with D, for double crossover . Those in the top row have P for their second letter, indicating that their helix axes are parallel hence, there is a dyad axis, vertical in the plane of the page and parallel to the helix axes, relating each helical domain of the DP molecules to the other domain. 

Schwacha, A., Kleckner, N. (1995) Identification of double Holliday junctions as intermediates in meiotic recombination. Cell 83, 783-791. 

Special structural features may be found at junctions between different types of DNA, e.g., between A-DNA and B-DNA.284-286 However, the most interesting junctions are branched.287 29° For example, Fig. 5-28 shows a four-way junction in which all of the bases form Watson-Crick pairs. This junction is better known as a Holliday junction because it was proposed by Holliday in 1964 as an intermediate in genetic recombination.291 As shown at the top of Fig. 5-28A the junction is formed from two homologous DNA duplexes. These are identical except for the boxed and shaded base pairs. The ends of the first duplex are marked I and II and those of the second III and IV. The Holliday junction appears to arise by cleavage of one strand of each duplex with rejoining of the strands as indicated by the green arrows. Rotation gives the untwisted Holliday junction structure... 

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