Recombination-related reactions promoted by the RecA protein of E. coli. (a) Strand invasion involving a 3′ single-stranded extension to form a D-loop. Here, RecA is promoting the strand invasion reaction outlined in Figure 13-2. (b) A DNA strand exchange involving three DNA strands. The substrates shown here are often used in research because the products are readily separated and visualized by agarose gel electrophoresis. The initial step is a strand invasion of the single-stranded DNA into one end of the duplex. Once strand invasion occurs, RecA also promotes a unidirectional (5′→3′ relative to the single-stranded circle) branch migration that completes an exchange of strands between the two DNA substrates. (c) DNA strand exchange involving a single-strand gap. Reactions of this sort also begin with strand invasion of the single strand into the duplex and are often facilitated by topoisomerases. (d) Strand exchange involving a single-strand gap and four DNA strands. The reaction begins with a strand invasion of the DNA in the single-strand gap into another duplex DNA. RecA then promotes a directional branch migration that carries the reaction into the adjacent duplex.