This is one of the general observations linking recombination to replication fork repair. The replication defects that make bacterial growth recombination dependent are generally those that result in more frequent stalling of the replication fork.A similar phenomenon is seen in cells with a mutation in the holD gene, which encodes the subunit in the clamploading complex of DNA polymerase III. In rep recBC mutant cells, doublestrand breaks accumulate. How replication fork repair events are distributed between pathways that do or do not involve doublestrand breaks is not known, and probably varies depending on factors such as growth conditions and the associated spectrum of spontaneous DNA damage.While the list of potential repair pathways may already seem complicated, it is likely to grow.A determination of which repair pathways are most important may be difcult to achieve.A focus on one or a few pathways in individual research reports often reects the particulars of the investigation.In bacterial cells growing aerobically, most of the replication forks undergo repair, with the potential for use of a wide range of repair pathways.Most in vivo studies directed at the elucidation of these repair paths make use of some strategy to amplify the signal by increasing the frequency of fork stalling.The newly synthesized strands are displaced and then paired as the fork is regressed to create a branched structure, the chicken foot.Evidence for replication fork regression has been available in the literature for nearly three decades.The simplest path is nonenzymatic.The positive supercoiling that builds up ahead of a replication fork will lead to spontaneous fork regression to produce a chicken foot structure. Such spontaneous fork regression during sample preparation may be the origin of some of the early reports of regressed forks.The spontaneous process may also play a direct role in repair.When a stalled fork has few or no singlestrand gaps, this may be the principal enzymatic path to fork regression.This reaction has been demonstrated in vitro and is quite efcient. The in vitro efforts to date do not address the considerable topological complexities of the fork regression process.In the cell, fork regression is likely to require the action of helicases, topoisomerases, and other enzymes beyond those currently being investigated.Enzymes that specically cleave such structures to generate viable recombinant products have been found in many types of organisms. The reaction generally involves symmetric cleavage of two opposing strands of the intermediate so that two branches <a href="http://www.targetmol.com/compound/Carbimazole">Targetmol's
Carbimazole</a> remain with each product. The migration of DNA branches has been studied for several decades and has been a recognized part of recombination processes for a similar period of time.Spontaneous branch migration in isolate DNA proceeds in a random walk. With respect to replication fork repair, there is a need instead for directed branch migration.If the chicken foot structure is not cleaved, then this branch migration offers a conservative path to restoration of the replication fork.The short branch of the chicken foot is shown with thick lines so that the fate of these strands can be seen in the product of the branch migration reaction.