Figure 7.

Illustrations showing how the speed of D-loop extension could influence the N dependence of the extension of the invading strand in a D-loop created by RecA-mediated formation of a heteroduplex product. The invading, complementary, and outgoing strands are shown in pink, dark blue, and light blue, respectively. Regions in which all three DNA strands are bound to a RecA nucleoprotein filament are indicated by the yellow rectangles with black outlines. The DNA polymerase synthesis is represented in green. The direction of polymerization is indicated by the green arrow, and the newly synthesized extension of the invading strand is shown in red. A, case in which no polymerase is present, so extension of the invading strand in a D-loop due to strand displacement DNA synthesis is not possible. Without synthesis, all products remain reversible. Some transient melting of the dsDNA may occur near the 3′ end of the invading strand. B, case in which the extension of the invading strand in a D-loop is so rapid that every heteroduplex that includes N > N_min and reaches the 3′ end of the invading strand creates an irreversible product by triggering DNA synthesis that progresses forever even if the heteroduplex partially reverses on the 5′ side of the invading strand. Thus, once the D-loop forms, it never completely collapses. This system cannot distinguish between N values ≥N_min. If N < N_min, then S remains less than S_min, so the D-loop can completely collapse. Thus, the system can distinguish between N values if N < N_min. C, case in which S is always less than S_min. Thus, the D-loop can always completely collapse, and extension is always influenced by the behavior of the heteroduplex because synthesis proceeds slowly enough that the heteroduplex product reverses before the polymerase synthesizes S_min bases. The black arrow pointing to the lower left indicates a case in which only 1 base is synthesized before the D-loop collapses. The arrow pointing to the lower right shows a case in which a second base can be synthesized before the D-loop collapses. The time required for the heteroduplex to collapse depends on N, so S increases with N. After the D-loop collapses, restarting synthesis may require formation of another heteroduplex.