DNA branching

The repair of stalled replication forks entails a coordinated transition from replication to recombination and back to replication. The recombination steps function to fill the DNA gap or rejoin the broken DNA branch to recreate the branched DNA structure at the replication fork. Lesions left behind in what is now duplex DNA are repaired by pathways such as base-excision or nucleotide-excision repair. Thus a wide range of enzymes encompassing every aspect of DNA metabolism ultimately take part in the repair of a stalled replication fork. This type of repair process is clearly a primary function of the homologous recombination system of every cell, and defects in recombinational DNA repair play an important role in human disease (Box 25-1). 

Figure 2. A stable DNA-branched junction. The junction shown is composed of four strands of DNA, labeled with Arabic numerals arms are labeled with Roman numerals. The 3 end of each strand is indicated by the half-arrows. Each strand is paired with two other strands to form a double helical arm. There is no homologous twofold sequence symmetry flanking the central branch point, thereby stabilizing its position.

What about the outer nodes Whereas this is a topological diagram, it is useful to think about distorting it. One way to do so would be to wrap it around a sphere. If that were done, the three-arm B-DNA-branched junction at the middle could correspond to the north pole, and the three outer nodes would each flank the south pole. Hence, they, too, could be coalesced to form a DNA-branched junction. However, this junction would need to be constructed from Z-DNA, because the signs of the outer nodes are positive. 

Du, S.M., Seeman, N.C. (1994) The construction of a trefoil knot from a DNA branched junction motif. Biopolymers 34, 31-37. 

In living cells, DNA is found almost exclusively in the form of linear duplex molecules they may be supercoiled, stressed, or even knotted (White et al., 1987), but the helical axis is unbranched. DNA branched junction structures occur as intermediates in the process of recombination, but they are inherently unstable because of the twofold sequence symmetry, which occurs in natural DNAs. Oligonucleotides with stable branchings can, however, be made if the sequence symmetry is minimized. Solid-state synthesis (Chen and Seeman, 1991 Zhang and Seeman, 1992, 1994) then allows the construction of complex supramolecules with the 2-nm-thick DNA double strands. The procedure contains the following steps ... 

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