Figure 1

(a) Side view of the s-ray structure of the dsDNA poststrand exchange (final) state with complementary (on the right at the arrow) and incoming strands shown as black and silver stick renderings. The arrow points to a few rises between two triplets in the dsDNA structure. The VMD (32) renderings of RecA crystal structure 3CMX (8) show site II residues with charged nitrogen atoms. (b) Top view of the same structure with circles indicating the radii occupied by the incoming (silver), outgoing (dark gray), and complementary strands (black). The dashed circle shows the complementary strand's position in the intermediate state, and the solid circle shows the final state. (c) Top view showing the base pairing in the homology recognition–strand exchange process superimposed on the actual x-ray structure.Reuse & Permissions

Figure 2

Schematic of interactions between dsDNA and the ssDNA-RecA filament as strand exchange progresses for a homolog with side views shown in the central part of each panel and top views shown in the right part of each panel where the gray region indicates the space occupied by the protein DNA–protein and the circles indicate the radii occupied by the three strands in their final poststrand exchange positions. In the schematic, the filament consisting of three RecA proteins, showing site I (pale red/left shaded area), site II (pale orange/right shaded area), and the support for the rises provided by the L1 and L2 loops (magenta/dark shaded triangle), with (i) unbound ssDNA, (ii) ssDNA bound in site I and unbound B-form dsDNA, and (iii) ssDNA bound in site I and dsDNA bound in site II. The outgoing strand (far left), complementary strand (bound to the outgoing strand), and incoming strand (bound to the protein on the right) are shown in blue (on the left), red (in the middle), and green (on the right), respectively. (iv) Central triplet has undergone strand exchange, resulting in a decrease in lattice mismatch and a decrease in the stress on the bp (v) all three triplets shown have undergone strand exchange (vi) ssDNA bound in site II and dsDNA bound in site I in the final assembled state which has even less bp stress than the strand exchanged state due to increase mechanical support for the rises.Reuse & Permissions

Figure 3

Schematic of dsDNA bound to site II of the protein showing the model parameters.Reuse & Permissions

Figure 4

Effects of adding triplets to the initial bound state as calculated by the model. (a) Three triplets shown in the bound state with an arrow pointing to the second one. (b) Adding a triplet to the initial state changes the tension in the other triplets. (c) Again tension on the triplets change as a fifth triplet is added to the initial state.Reuse & Permissions

Figure 5

The dashed, solid gray, and solid black lines show the absolute value of $v_i-u_i$ for the outer triplet, central triplet, and the first triplet out from the center, respectively, when the number of bound triplets is odd.Reuse & Permissions

Figure 6

Total energy as a function of bound base pairs all in the initial bound state (dashed line), the intermediate state (solid gray line), and the final poststrand exchange state (solid black line).Reuse & Permissions

Figure 7

For a completely homologous dsDNA with all triplets in the intermediate strand exchanged state, the free-energy penalty for a single triplet reversing strand exchange by making a transition from the intermediate strand exchanged state to the initial bound state as a function of then number of base pairs when the base flipping triplet is in the center of the filament (solid line) or at the end of the filament (dashed line).Reuse & Permissions

Figure 8

The free-energy penalty for adding another triplet in the initial bound state as a function of the number of base pairs in the strand exchanged state. The dashed black line shows the penalty when all of the triplets are homologous. The dashed gray line shows the penalty for adding an additional triplet to the initial bound state after a triplet that is nonhomologous. The solid gray line shows the penalty for adding a second triplet after a nonhomolog where the first triplet after the nonhomolog was homologous. The solid black line shows the energetic favorability of strand exchanging a homologous triplet in the initial bound state.Reuse & Permissions