Source: http://www.asmscience.org/content/book/10.1128/9781555817640.chap20
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Replication fork demise at the sites of DNA damage. (A) Encounter with a strand break leads to a double-strand break and dissociation of one arm of the fork. (B) Encounter with an unrepaired DNA lesion can result in the creation of a gap at a stalled fork. In either case, repair pathways involve recombination.
RecA protein structure. (A) A RecA filament is shown, with 24 RecA monomers, based on the 1992 structure by Story and Steitz ( 204 ) (see text). One monomer is colored in a darker gray. (B) A RecA monomer, with bound ADP. (C) An electron micrograph of one segment of a RecA filament formed on DNA.
Domain structures of RecA protein and its homologues in Saccharomyces cerevisiae and Sulfolobus solfataricus. The open box is the core domain shared by all four proteins. The RecA C-terminal domain is unique to bacterial RecA proteins. Homologies among other domain elements are indicated by shading patterns.
Assembly and disassembly pathways for RecA filaments. After nucleation, filament extension proceeds 5′ to 3′ relative to the ssDNA, and can encompass adjacent duplex regions. RecA dissociation occurs from the opposite filament end, and proceeds also 5′ to 3′.
RecA protein-mediated DNA strand exchange reactions. (A) The most common three-strand reaction used in many studies. (B) The standard four-strand reaction. RecA protein filaments are nucleated in the gap of the circular DNA substrate, and DNA pairing is also initiated in this gap. (C) Initiation of DNA strand exchange at a free duplex DNA end. (D) Initiation of DNA strand exchange at a free single-strand (RecA-bound) DNA end.
Unproductive complexes that can stall DNA strand exchange reactions. The formation of a joint molecule involves the uptake of a duplex DNA into the RecA filament and its alignment with the previously bound single-stranded DNA. Extension of the region of paired DNA requires a continued spooling of the duplex into the filament, as shown in the top panel. This extension can be blocked by a secondary DNA pairing involving another part of the duplex (leaving an external loop of DNA [middle panel]) or any unproductive interaction of the duplex and the filament (bottom panel) that halts the needed spooling process.
Model for RecA protein-mediated rotation of DNA to effect DNA strand exchange. Any duplex DNA external to the filament, perhaps as a result of the formation of external DNA loops as shown in Fig. 6 , would be rotated around the outside of the filament in a reaction coupled to ATP hydrolysis. Rotation in the direction of the curved arrows will result in branch movement in the direction of the black arrows.
Fork regression as might occur at a stalled replication fork. The product of this reaction is sometimes called a chicken foot.
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