Genetics: Branch Migration and Isomerization

Branch Migration and Isomerization

Evidence mentioned in the previous section suggests that DNA duplexes engaged in recombination are likely to involve heteroduplexes consisting of one DNA strand from each parent. The problem we will address here is one way these heteroduplexes might be formed and what steps might be necessary to convert them to recombinants. As a glance at any genetics book will show, there are many schemes consisting of more or less reasonable steps that conceivably could be catalyzed by enzymes and that would ultimately lead to the generation of genetic recombina-tion. We will outline one of these.

A single-stranded end of a DNA molecule can invade a DNA duplex in a region of homology and form a DNA heteroduplex by displacing one of the strands of the invaded parent. This can occur because

negatively supercoiled DNA is under torsion to untwist, and thereby melt a portion of duplex. Displacement of a portion of the original duplex by an invading single strand of DNA is energetically favored. Thus, once this has started, additional nucleotides from the invading strand are free to base pair because for each base pair broken in the parental duplex, a new pair forms in the heteroduplex. Then the cross-over point is free to drift in either direction along the DNA by this branch migration process.

Before proceeding with the recombination mechanism, we must consider a diversion. For simplicity we will examine a double crossover and then apply the principles to the situation described in the previous paragraph. The strands that appear to cross from one duplex over to the other are not fixed! What is the basis of this remarkable assertion? By a simple reshuffling of the DNA in the crossover region, the other strands can be made to appear to be the ones crossing over (Fig. 8.14). This reshuffling is called isomerization. To understand, consider the more dramatic transformations as shown in the Figure. These result in a change in the pair of strands that cross from one duplex to the other. In reality, however, they amount to little more than looking at the DNA from a different angle. Isomerization requires only minor structural shifts in the crossover region and therefore is free to occur during genetic recombination.

Figure 8.15 One possible pathway for genetic recombination. A nick is con-verted to a crossover region, which isomerizes and branch migrates, and finally the strands crossing over are cleaved.

Now let us return to the crossover mechanism. At the one crossover stage, an isomerization yields a two strand crossover (Fig. 8.15). Branch migration followed by cleavage of these strands then produces a cross-over between the two parental duplexes with a heteroduplex region near the crossover point.