Holliday junction

What are known as Holliday junctions are believed to occur as intermediates in some genetic recombination processes involving changes to DNA. These junctions involve four arms of DNA in which two of the strands undergo sharp changes in direction. 

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Yet another super family, the nucleotidyl-transferase family, also utilizes two-metal-ion-dependent catalysis the members include transposases, retrovirus integrases and Holliday junction resolvases4. Whereas in the nucleases, the Mg2+ ions are asymmetrically coordinated, and play distinct roles, in activating the nucleophile and stabilizing the transition state, respectively, in the transposases, they are symmetrically coordinated and exchange roles to alternatively activate a water molecule and a 3 -OH for successive strand cleavage and transfer. 

The three-way DNA junction (also called Holliday junction) has been studied by single molecule AFM analysis [48]. DNA molecules have been dispersed in saline buffer injected in a fluid cell mounted on the top of the APTES mica. Fig. 10 presents two consecutive AFM scans (separated by approximately 3 min) of 301 bp DNA molecules containing a 7 bp hairpin. Also Fig. 11 presents the AFM images of representative slipped strand DNA structures. The 3D projections of the (CGGjso (CCGjso slipped strand structures... 

Crossover junction endoribonuclease [EC 3.1.22.4], also referred to as Holliday junction nuclease, catalyzes the endonucleolytic hydrolysis of a bond(s) in DNA at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). 

Selected entries from Methods in Enzymology [vol, page(s)] Analysis of GTP-binding/GTPase cycle of G protein, 237, 411-412 applications, 240, 216-217, 247 246, 301-302 [diffusion rates, 246, 303 distance of closest approach, 246, 303 DNA (Holliday junctions, 246, 325-326 hybridization, 246, 324 structure, 246, 322-324) dye development, 246, 303, 328 reaction kinetics, 246, 18, 302-303, 322] computer programs for testing, 240, 243-247 conformational distribution determination, 240, 247-253 decay evaluation [donor fluorescence decay, 240, 230-234, 249-250, 252 exponential approximation of exact theoretical decay, 240, 222-229 linked systems, 240, 234-237, 249-253 randomly distributed fluorophores, 240, 237-243] diffusion coefficient determination, 240, 248, 250-251 diffusion-enhanced FRET, 246, 326-328 distance measurement [accuracy, 246, 330 effect of dye orientation, 246, 305, 312-313 limitations, 246,... 

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. 

Re combinational DNA repair of a circular bacterial chromosome, while essential, sometimes generates deleterious byproducts. The resolution of a Holliday junction at a replication fork by a nuclease such as RuvC, followed by completion of replication, can give rise to one of two products the usual two monomeric chromosomes or a contiguous dimeric chromosome (Fig. 25-41). In the latter case, the covalently linked chromosomes cannot be segregated to daughter cells at cell division and the dividing cells become stuck. A specialized site-specific recombination system in E. coli, the XerCD system, converts the dimeric chromosomes to monomeric chromosomes so that cell division can proceed. The reaction is a site-specific deletion reaction (Fig. 25-39b). This is another example of the close coordination between DNA recombination processes and other aspects of DNA metabolism. 

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. 

Double-crossover molecules have been used extensively to characterize the properties of Holliday junctions. The strong torsional coupling between their crossover points has been exploited to construct symmetric immobile junctions (S. Zhang et al. 1993), junctions in which one of the crossovers is flanked by homology, but is nevertheless unable to branch migrate. Symmetric immobile junctions have been used to characterize crossover isomerization thermodynamics (S. Zhang and Seeman 1994) and, more recently, the sequence dependence of the branch point stability (W. Sun et al., 1998). Double crossover molecules have also been employed to establish the cleavage patterns of endonuclease VII, an enzyme that resolves branched junctions (Fu et al. 1994 a). 

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

Zhang, S., Seeman, N.C. (1994) Symmetric Holliday junction crossover isomers. J. Mol. BioL 238, 658-668. 

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... 

An important characteristic of Holliday junctions formed from homologous duplexes is that they can move by a process called branch migration.295 Because of the twofold symmetry of the branched structure the hydrogen bonds of one base pair can be broken while those of a new base pair are formed, the branch moving as shown in Fig. 5-28. Notice that, in this example, the nonhomo-logous (boxed) base pairs TA and GC have become mispaired as TG and AC after branch migration. More significantly, the junction may be cut by a resolvase at the points marked... 

Figure 5-28 (A) Abbreviated reaction sequence for formation of a four-way Holliday junction between two homologous DNA duplexes. In step a strands are cut and rejoined with movement of the strands to a roughly antiparallel orientation. The resulting structure is thought to resemble that shown below the four-stranded representation.

A few recent NMR investigations of polynucleotides include studies of triple-helical DNA,689 Holliday junctions,290 double-stranded oligonucleotides containing adducts of carcinogens,690 691 of hairpin loops with sheared A A and G G pairs,692 and of proton exchange in both imino and amino groups.693... 

H-DNA, proposed structure 226 helical twist 216 helix parameters 216 Holliday junction 228 - 230 hydration of 216 hydrolysis of 249, 251 hypersensitive sites 266 interaction with spermidine and... 

RuvC is an endonuclease that is highly specific for Holliday junctions. It is a resolvase that cuts at either points a,a or b,b of Eq. 27-11 to form either "patched" or "spliced" recombinant DNA (Fig. 27-26C). Similar resolvases process bacteriophage DNA562-564 and have also been found in yeasts and in mammals.565 566 All are dimeric metal ion-dependent proteins.567... 

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