Four-way junctions

Proposed structure of a complex of the HMGB1 A-domain with a four-way junction... 

Webb, M. and Thomas, J.O. (1999) Structure-specific-binding of the HMGl didomain to four-way junction DNA is mediated by the A domain. J. Mol. Biol. 294, 373-387. 

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... 

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"... 

An additional benefit of this purification method is that different RNA species can be separated, if the charge per molecule is significantly different, as for instance between mono- and multimeric RNA species. During purification of a 74-nt RNA, four-way junction from the... 

Figure 7.1 The principle of the long-short arm method for the electrophoretic analysis of a four-way junction. The six species can be considered to be derived from the central junction comprising four long arms (e.g., 40 bp). These are named sequentially A, B, C, and D. The long—short arm species are generated by shortening two helical arms, to give the six species shown, named by their long arms.

Figure 7 A Analysis of the 2HSj2HS2 four-way junction of the HCV IRES by comparative gel electrophoresis. The sequence of the junction around the point of strand exchange is shown. Comparative gel electrophoresis in a 10% polyacrylamide gel was performed in the presence of 90 mM Tris-borate (pH 8.3), 1 mM Mg2+, using the six long-short arm species, where arms were extended with DNA sections as before. The observed pattern of mobilities is interpreted in terms of a rapid exchange between approximately equal populations of parallel and antiparallel conformations as shown, with strand polarities indicated for clarity.

Figure 8.7 Steady-state FRET analysis of a 4H four-way junction derived from the 2HSj2HS2 junction of the HCV IRES (Melcher et al., 2003). The central sequence of the junction is shown. The four arms are sequentially named A, B, C and S. Donor-acceptor-labeled vectors for FRET analysis are constructed with. -terminally attached fluorescein (donor) and Cy3 (acceptor) on selected helical arms, named according to those arms in that order. Thus, BA is labeled with donor on the end of arm B, and acceptor on A. (A) Fiistogram of the FRET efficiencies of the six end-to-end vectors.

Sdf-assembly Two oligonucleotides spontaneously organize themselves in duplex structures as encoded by the DNA base sequence. Even complex supramolecular arrangements can be realized, e.g. polyhedra or four-way junctions [2],... 

A four-way junction from hairpin ribozyme exhibits two types of ion binding [3], At low concentrations of monovalent ions, binding of magnesium to the junction is diffuse [3], In contrast, at high concentrations of monovalent ions, site binding of magnesium occurs at low magnesium concentration [3]. Other nucleic acids exhibit similar characteristics [6]. 

The number of counterions associated with the tetrahedral junction was less than sensitive not only to parameters that define the junction region, but also to the interbranch angle between 90° and 109.5° [74] The number of associated counterions is substantially larger in the four-way junction than other junction geometries and constructs studied [74]. As salt concentration is increased, the stability of the junction is enhanced over a linear polyelectrolyte molecule of identical length as the junction [74], For junctions with symmetrical branches, the counterions associated with the junction in excess of that of a linear construct increases with the length of the branches and then saturates [74],... 

Odom DT, Dill EA, Barton JK. Charge transport through DNA four-way junctions. Nucleic Acids Res 2001 29 2026-33. 

One more interesting structure, also representing an unusual metal-binding center, is the DNA cruciform (or four-way junction) structure. This type of structure results from rearrangement of palindromes (inverted repeat sequences) and may be formed reversibly under certain conditions (e.g. to relax strain in supercoiled DNA). The relative efficiency of different divalent metal ions in promoting the formation of DNA cruciform structures is Mg + > Mn + > Co + >... 

Electron transfer has primarily been studied with DNA duplexes, but there are higher order structures that have been examined. Triplexes have been studied where it was shown that transfer to the third strand occurs. In quadruplex structures more damage occurs at the external tetrads, and quad-ruplex guanines are more effective traps than when in a duplex. Charge transfer has also been examined with three-way " and four-way junctions. DNA bound to electrode surfaces has been used to study the electrochemical... 

The crystal structure of a 108-nucleotide RNA-DNA Holliday junction has been solved at 3.1 and differs from a previously solved stacked-X conformation. The present structure differs due to a 135° rotation of the branches, and comparison of the two structures gives an insight into factors contributing to the flexibility of four-way junctions. 

Figure 4.34. Schematic of the four-way junction. [From Fig. 5 of Ref. 210, with permission.]...

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