Figure 1. Homologous joint formation by RecA involves two reactions

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Figure 1. Homologous joint formation by RecA involves two reactions Figure 1. Homologous joint formation by RecA involves two reactions. (A) Homologous joint formation by normal RecA. (i) ... Figure 1. Homologous joint formation by RecA involves two reactions. (A) Homologous joint formation by normal RecA. (i) Homologous (DNA) pairing is an ATP-dependent but ATP-hydrolysis-independent reaction. RecA forms spiral filaments around ssDNA, after which free dsDNA interacts with the filaments. Homologous sequences between dsDNA and ssDNA in the filaments are searched for by reiterative association and dissociation and scanning to a limited length, and a homologous-joint nucleus (nascent homologous joint) is formed. The minimum detectable homologous joint is 6–8 bp in length. (ii) Branch migration is an ATP-hydrolysis-dependent reaction. The nascent homologous joints are extended by RecA/Rad51 and can be thousands of base pairs long. (B) Assumed homologous joint formation by a pair of adjacent RecA protomers without involvement of the RecA filament. When substrate dsDNA has negative supercoils like natural dsDNA, if a nascent homologous joint is formed, the relaxation of the supercoils promotes the extension of the nascent homologous joints in a protein-independent manner to stabilize the joint. The red lines and the double blue lines represent ssDNA and dsDNA, respectively. RecA is represented by the white balls. The DNA topology is abbreviated in these diagrams. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 46, Issue 20, 04 October 2018, Pages 10855–10869, https://doi.org/10.1093/nar/gky877 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. Design of RecA variants and the absence of polymer formation in free forms of npRecA variants. (A) Domain ... Figure 2. Design of RecA variants and the absence of polymer formation in free forms of npRecA variants. (A) Domain structure of RecA variants.The RecA and RecA variants are: RecA-wt (wild-type RecA), RecA-wt<sub>ΔC</sub> (the RecA variant with the C-terminal 16 amino-acid deletion that is part of the C-terminal 25 amino-acid-disordered region; 34), RecA-3m<sub>ΔC</sub> (RecA-wt<sub>ΔC</sub> variant which bears the 3m three-residue replacement [C116M, S117V, Q118R]), the nonpolymerizing (np) RecA monomer, the npRecA dimer (the nonpolymerizing head-to-tail-fused RecA dimer) and Δ33RecA (truncated RecA lacking the N-terminal 33 amino-acid residues; Mikawa et al. (1995), see ref. 35). The concentration of npRecA dimers was expressed as the concentration of RecA subunits. Thus, 1 mol of the npRecA dimer is expressed as 2 mols in this paper. (B) Gel-filtration profiles of the RecA variants. RecA variants (10 μM 100 μl) were analyzed by chromatography on a Superdex200 10/300 GL column. Molecular-sized markers: conalbumin (CO, 75 kDa), ovalbumin (OV, 44 kDa) and carbonic anhydrase (CA, 29 kDa). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 46, Issue 20, 04 October 2018, Pages 10855–10869, https://doi.org/10.1093/nar/gky877 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. NpRecA dimers binds to DNA but does not form filaments Figure 3. NpRecA dimers binds to DNA but does not form filaments. (A, B and C) ssDNA-binding activities of npRecA ... Figure 3. NpRecA dimers binds to DNA but does not form filaments. (A, B and C) ssDNA-binding activities of npRecA dimers detected by electrophoretic mobility-shift assay. FAM-labeled 90-mer ssDNA (4.5 μM) was incubated in a standard reaction buffer with the indicated amounts of RecA variants in the absence of nucleotide cofactor (A), the presence of ATP (1.3 mM) (B), or ATPγS (1.3 mM) (C). DNA samples without fixation were electrophoresed through an agarose gel. FAM-labeled DNA was detected using a biomolecular imager. (D) dsDNA-binding activities of npRecA dimers and npRecA monomers detected by electrophoretic mobility-shift assay. Unlabeled pUC119 dsDNA linearized by HindIII (9.0 μM) was incubated as in A to C in the presence of ATPγS (1.3 mM). After electrophoresis, dsDNA was detected by ethidium bromide-staining using a biomolecular imager. (E and F) NpRecA dimers form beads-on-string structures instead of filaments upon DNA binding. RecA-wt (E) and npRecA dimers (F) at 0.2 μM (RecA subunit) were allowed to form a complex with linearized pUC119 dsDNA (2.0 μM) in the presence of ATPγS (0.5 mM) and MgCl<sub>2</sub> (10 mM). After 3-fold dilution, the complexes were fixed with glutaraldehyde (0.2%) on a mica surface and visualized by DFM (a scanning-probe microscope in dynamic force mode). (G) Beads-on-string structures formed by the npRecA monomer bound to dsDNA. The npRecA monomer at 0.8 μM was allowed to form a complex with dsDNA as described above. After 12-fold dilution, the complexes were visualized by DFM as described above. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 46, Issue 20, 04 October 2018, Pages 10855–10869, https://doi.org/10.1093/nar/gky877 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 4. ATP/dATP hydrolyzing activities of RecA variants Figure 4. ATP/dATP hydrolyzing activities of RecA variants. All incubation was carried out in a standard reaction ... Figure 4. ATP/dATP hydrolyzing activities of RecA variants. All incubation was carried out in a standard reaction buffer (20 μl). (A–C) DNA-independent ATP/dATP hydrolysis. The amount of ATP (A and C) or dATP (B) hydrolyzed during incubation (15 min) in the presence of sodium acetate (1.5 M) was plotted against the indicated amounts of RecA variants. The white symbols represent a complete system for DNA-independent hydrolysis of ATP or dATP by the RecA variants; the black symbols represent the absence of sodium acetate. Circles represent RecA-wt; triangles represent the npRecA dimer; squares represent the npRecA monomer; and diamonds represent RecA-3m<sub>ΔC</sub>. Each value is the average of data from at least three independent experiments. (D and E) ssDNA-dependent ATP hydrolysis with various amounts of RecA variants and ssDNA. ATP hydrolysis was carried out by a 30 min incubation at 37°C with circular ssDNA (10 μM) and the indicated amounts of RecA variants (D), or with RecA variants (2.0 μM) and the indicated amounts of circular ssDNA (E). Circles represent RecA-wt; triangles represent the npRecA dimer; squares represent the npRecA monomer. Values represent the average of data from at least three independent experiments. (F) ssDNA-dependent ATP/dATP hydrolysis. The amount of ATP/dATP hydrolyzed during incubation (30 min) in the presence of circular ssDNA (10 μM) and RecA-wt or the RecA variants (2.0 μM) was plotted. We chose the concentrations of RecA variants and ssDNA within the limits of those in which ATP hydrolysis linearly depended in the concentrations of RecA variants (D) and ssDNA (E). In contrast with (A) to (E), the observed amounts of ADP and dADP in the controls without DNA were subtracted from the values obtained in the presence of DNA in each experiment. The observed values of the control without DNA were 0.8 and 0.2 nmol for ADP and dADP, respectively, for RecA-wt, and 0.12 and 0.14 nmol for ADP and dADP, respectively, for the npRecA dimer. White squares represent RecA-wt, diagonally striped squares represent the npRecA dimer and black squares represent the npRecA monomer. Each value represents the average of data from at least three independent experiments. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 46, Issue 20, 04 October 2018, Pages 10855–10869, https://doi.org/10.1093/nar/gky877 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. Homologous joint formation by the npRecA dimer as shown by D-loop assay. 90-mer [33P] oligo-ssDNA ... Figure 5. Homologous joint formation by the npRecA dimer as shown by D-loop assay. 90-mer [<sup>33</sup>P] oligo-ssDNA (0.05 μM) and RecA variant (2 μM) were incubated in a standard reaction buffer at 37°C in the presence of ATPγS or dATP (1.3 mM) for 5–15 min, following which homologous negatively supercoiled dsDNA (18 μM) was added to initiate the reaction. Mixtures were incubated at 37°C for the indicated times. (A) Formation of D-loops as represented by gel profile. OL2 ssDNA and homologous pBluescript SK(–) negatively supercoiled dsDNA were incubated with (i) RecA-wt, (ii) the npRecA monomer or no protein added and (iii) the npRecA dimer for the indicated times. (B) Quantitative representation of D-loop formation. (i) D-loop formation by RecA variants in the presence of ATPγS or dATP. OL2 ssDNA and homologous pBluescript SK(–) negatively supercoiled dsDNA were incubated with the indicated RecA variants. White symbols represent the presence of ATPγS; black symbols represent the presence of dATP. Circles represent RecA-wt; triangles represent the npRecA dimer; squares represent the npRecA monomer; the X represents without protein. (ii) D-loop formation by the npRecA dimer in the presence of ATPγS. (iii) D-loop formation by the npRecA dimer in the presence of dATP. In (ii) and (iii), the white symbols represent homologous combination of ssDNA and negatively supercoiled dsDNA and the black symbols represent heterologous combination of ssDNA and negatively supercoiled dsDNA. Triangles represent the npRecA dimer, OL2 ssDNA and homologous or heterologous dsDNA and inverted triangles represent the npRecA dimer, Km90 ssDNA and homologous or heterologous ssDNA. OL2 ssDNA is homologous to pBluescript SK(–) dsDNA, but heterologous to pKF18 dsDNA. Km90 ssDNA is homologous to pKF18 dsDNA, but heterologous to pBluescript SK(–) dsDNA. Each value represents the average of data from at least three independent experiments. The values for the npRecA dimer, OL2 ssDNA and pBluescript SK(–) dsDNA shown in (ii) and (iii) are identical to those shown in (i) for the presence of ATPγS and dATP, respectively. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 46, Issue 20, 04 October 2018, Pages 10855–10869, https://doi.org/10.1093/nar/gky877 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. Homologous joint formation by the npRecA dimer as shown by D-loop assay. 90-mer [33P] oligo-ssDNA ... Figure 5. Homologous joint formation by the npRecA dimer as shown by D-loop assay. 90-mer [<sup>33</sup>P] oligo-ssDNA (0.05 μM) and RecA variant (2 μM) were incubated in a standard reaction buffer at 37°C in the presence of ATPγS or dATP (1.3 mM) for 5–15 min, following which homologous negatively supercoiled dsDNA (18 μM) was added to initiate the reaction. Mixtures were incubated at 37°C for the indicated times. (A) Formation of D-loops as represented by gel profile. OL2 ssDNA and homologous pBluescript SK(–) negatively supercoiled dsDNA were incubated with (i) RecA-wt, (ii) the npRecA monomer or no protein added and (iii) the npRecA dimer for the indicated times. (B) Quantitative representation of D-loop formation. (i) D-loop formation by RecA variants in the presence of ATPγS or dATP. OL2 ssDNA and homologous pBluescript SK(–) negatively supercoiled dsDNA were incubated with the indicated RecA variants. White symbols represent the presence of ATPγS; black symbols represent the presence of dATP. Circles represent RecA-wt; triangles represent the npRecA dimer; squares represent the npRecA monomer; the X represents without protein. (ii) D-loop formation by the npRecA dimer in the presence of ATPγS. (iii) D-loop formation by the npRecA dimer in the presence of dATP. In (ii) and (iii), the white symbols represent homologous combination of ssDNA and negatively supercoiled dsDNA and the black symbols represent heterologous combination of ssDNA and negatively supercoiled dsDNA. Triangles represent the npRecA dimer, OL2 ssDNA and homologous or heterologous dsDNA and inverted triangles represent the npRecA dimer, Km90 ssDNA and homologous or heterologous ssDNA. OL2 ssDNA is homologous to pBluescript SK(–) dsDNA, but heterologous to pKF18 dsDNA. Km90 ssDNA is homologous to pKF18 dsDNA, but heterologous to pBluescript SK(–) dsDNA. Each value represents the average of data from at least three independent experiments. The values for the npRecA dimer, OL2 ssDNA and pBluescript SK(–) dsDNA shown in (ii) and (iii) are identical to those shown in (i) for the presence of ATPγS and dATP, respectively. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 46, Issue 20, 04 October 2018, Pages 10855–10869, https://doi.org/10.1093/nar/gky877 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 6. Base unstacking of ssDNA by RecA variants Figure 6. Base unstacking of ssDNA by RecA variants. (A) Fluorescence-emission spectra of 6-MI oligo ssDNA in the ... Figure 6. Base unstacking of ssDNA by RecA variants. (A) Fluorescence-emission spectra of 6-MI oligo ssDNA in the presence or absence of RecA-wt<sub>ΔC</sub> and ATPγS. Fluorescence of 6-MI oligo ssDNA (3.0 μM) was measured at 25°C in the presence of RecA-wt<sub>ΔC</sub> (1.0 μM) in the absence or presence of ATPγS (0.04 mM). Fluorescence is expressed in arbitrary units (a.u.). (B) Relief of fluorescence quenching of 6-MI oligo ssDNA by RecA variants in the presence or absence of ATPγS. Fluorescence at 425 nm was measured at 25°C in the presence of 6-MI labeled oligo-ssDNA (3.0 μM) and the indicated amounts of RecA variants, with or without ATPγS. Fluorescence enhancement of 6-MI oligo ssDNA was defined as the fluorescence of a sample minus the fluorescence of the 6-MI oligo ssDNA control without RecA. White symbols represent the presence of ATPγS (0.04 mM) and black symbols represent the absence of ATPγS. Circles represent RecA-wt<sub>ΔC</sub>, triangles represent the npRecA dimer and squares represent the npRecA monomer. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 46, Issue 20, 04 October 2018, Pages 10855–10869, https://doi.org/10.1093/nar/gky877 The content of this slide may be subject to copyright: please see the slide notes for details.