ϕx174 replicative Search Results


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  • 95
    Qiagen plasmid giga kit
    Plasmid Giga Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 95/100, based on 587 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs apali
    Apali, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 150 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs ϕx174 replicative
    DIDS disrupts the DNA binding activity of eh Rad51. (A) Time course analysis of eh Rad51 ATPase activity in the presence or absence of DIDS (67 μM), with and without <t>ϕX174</t> ssDNA or linearized ϕX174 dsDNA. Reactions were stopped with the addition of EDTA at the indicated times prior to separation with thin-layer chromatography and phosphorimager analysis. (B) eh Rad51 (7 μM) incubated with 32 P-radiolabeled ssDNA and increasing amounts of DIDS (5 μM, 10 μM, 15 μM, 20 μM, 30 μM, 40 μM; lanes 3–8 respectively). Lane 1 contained no protein or DIDS. Lane 2 contained no DIDS. Lane 9 contained 40 μM DIDS without eh Rad51. (C) eh Rad51 (35 μM) incubated with the 32 P-radiolabled dsDNA and increasing concentrations of DIDS (20 μM, 40 μM, 80 μM, 100 μM, 150 μM, 200 μM; lanes 3–8 respectively). Lane 1 lacked protein and DIDS, lane 2 contained no DIDS and lane 9 contained 200 μM DIDS and no protein. (D) eh Rad51 (7 μM) was incubated with radiolabeled ssDNA in the absence (lane 3) and presence of increasing concentrations of DIDS (5 μM, 10 μM, 15 μM, 20 μM, 30 μM, and 40 μM; lanes 4–9) prior to the addition of DNase I. The reaction were deproteinized, and the products were separated using non-denaturing PAGE. Lane 1 contained radiolabeled ssDNA alone, lane 2 contained DNase with radiolabeled ssDNA, and lane 10 contained radiolabeled ssDNA in the presence of 40 μM DIDS and DNase I. Error bars represent SEM (n = 3).
    ϕx174 Replicative, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 81/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche t4 polynucleotide kinase
    DIDS disrupts the DNA binding activity of eh Rad51. (A) Time course analysis of eh Rad51 ATPase activity in the presence or absence of DIDS (67 μM), with and without <t>ϕX174</t> ssDNA or linearized ϕX174 dsDNA. Reactions were stopped with the addition of EDTA at the indicated times prior to separation with thin-layer chromatography and phosphorimager analysis. (B) eh Rad51 (7 μM) incubated with 32 P-radiolabeled ssDNA and increasing amounts of DIDS (5 μM, 10 μM, 15 μM, 20 μM, 30 μM, 40 μM; lanes 3–8 respectively). Lane 1 contained no protein or DIDS. Lane 2 contained no DIDS. Lane 9 contained 40 μM DIDS without eh Rad51. (C) eh Rad51 (35 μM) incubated with the 32 P-radiolabled dsDNA and increasing concentrations of DIDS (20 μM, 40 μM, 80 μM, 100 μM, 150 μM, 200 μM; lanes 3–8 respectively). Lane 1 lacked protein and DIDS, lane 2 contained no DIDS and lane 9 contained 200 μM DIDS and no protein. (D) eh Rad51 (7 μM) was incubated with radiolabeled ssDNA in the absence (lane 3) and presence of increasing concentrations of DIDS (5 μM, 10 μM, 15 μM, 20 μM, 30 μM, and 40 μM; lanes 4–9) prior to the addition of DNase I. The reaction were deproteinized, and the products were separated using non-denaturing PAGE. Lane 1 contained radiolabeled ssDNA alone, lane 2 contained DNase with radiolabeled ssDNA, and lane 10 contained radiolabeled ssDNA in the presence of 40 μM DIDS and DNase I. Error bars represent SEM (n = 3).
    T4 Polynucleotide Kinase, supplied by Roche, used in various techniques. Bioz Stars score: 97/100, based on 1330 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    New England Biolabs i dna
    <t>DNA-binding</t> and RAD51-binding activities of the PSF domains. <t>ϕX174</t> ssDNA (20 µM) ( A ) or ϕX174 linear dsDNA (20 µM) ( B ) was incubated with PSF, PSF(1–266) or PSF(267–468) at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer and were visualized by ethidium bromide staining. The protein concentrations for panel A were 0 µM (lane 1), 0.15 µM (lanes 2, 5 and 8), 0.3 µM (lanes 3, 6 and 9) and 0.6 µM (lanes 4, 7 and 10). The protein concentrations for panel B were 0 µM (lane 1), 0.1 µM (lanes 2, 5 and 8), 0.2 µM (lanes 3, 6 and 9) and 0.4 µM (lanes 4, 7 and 10). ( C ) The pull-down assay with Ni–NTA beads. Lanes 2–5 represent purified RAD51, His 6 -tagged PSF, His 6 -tagged PSF(1–266) and His 6 -tagged PSF(267–468), respectively. His 6 -tagged PSF, His 6 -tagged PSF(1–266) or His 6 -tagged PSF(267–468) (3.8 µg) was mixed with RAD51 (7.4 µg). The RAD51 bound to the His 6 -tagged proteins was pulled down by the Ni–NTA agarose beads, and was analyzed by 12% SDS–PAGE. Bands were visualized by Coomassie Brilliant Blue staining.
    I Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 73 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs i dsdna
    DNA binding activity of wild type and Walker A variants of hDMC1. (panel I) hDMC1 WT (1.4 μM, lane 2; 2.8 μM, lane 3; 5.6 μM, lane 4; 11.2 μM, lanes 5–11) was incubated with <t>ϕX174</t> (+) ssDNA DNA (ss) and linearized ϕX174 RF (I) <t>dsDNA</t> (ds) in the absence (lane 9) or presence of ATP (lanes 1–5 and 10) and nucleotide analogs (ATP-γ-S, lane 6; AMP–PNP, lane 7; and ADP, lane 8). The reaction products were analyzed on 1% agarose gels. Lane 11, the reaction was deproteinized prior loading on the agarose gel. The hDMC1 K132R (panel II) and hDMC1 K132A (panel III) were analyzed as described for hDMC1 WT .
    I Dsdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 77/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs ϕx174 viral
    DNA binding activity of wild type and Walker A variants of hDMC1. (panel I) hDMC1 WT (1.4 μM, lane 2; 2.8 μM, lane 3; 5.6 μM, lane 4; 11.2 μM, lanes 5–11) was incubated with <t>ϕX174</t> (+) ssDNA DNA (ss) and linearized ϕX174 RF (I) <t>dsDNA</t> (ds) in the absence (lane 9) or presence of ATP (lanes 1–5 and 10) and nucleotide analogs (ATP-γ-S, lane 6; AMP–PNP, lane 7; and ADP, lane 8). The reaction products were analyzed on 1% agarose gels. Lane 11, the reaction was deproteinized prior loading on the agarose gel. The hDMC1 K132R (panel II) and hDMC1 K132A (panel III) were analyzed as described for hDMC1 WT .
    ϕx174 Viral, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 77/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs new england biolabs ϕx174 dsdna
    BCCIPβ binds DNA. ( A ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) incubated with <t>ϕX174</t> (+) ssDNA (ss; 30 μM nucleotides). ( B ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) was incubated with ϕX174 RF (I) <t>dsDNA</t> (ds; 30 μM base pairs). The reaction products were separated on a 1.0% agarose gel, and were stained with ethidium bromide. Lane 1 contained no protein, and lane 8 was deproteinized with SDS and Proteinase K (S/P) prior to loading.
    New England Biolabs ϕx174 Dsdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 79/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs viral strand dna
    Homologous <t>DNA</t> pairing and strand exchange by rad51 mutants. A , scheme of the homologous DNA pairing and strand exchange reaction. Pairing between the circular <t>ϕX174</t> (+) ssDNA and linear ϕX174 dsDNA yields a joint molecule ( jm ), which
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    Thermo Fisher calf thymus topoisomerase i
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
    Calf Thymus Topoisomerase I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 130 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MACHEREY NAGEL standard miniprep kit macherey nagel
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
    Standard Miniprep Kit Macherey Nagel, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 80/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen standard miniprep kit
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
    Standard Miniprep Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 90/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it picogreen dsdna broad range assay kit
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
    Quant It Picogreen Dsdna Broad Range Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher phusion high fidelity dna polymerase
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    Millipore dids
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    Millipore thin layer chromatography
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    Millipore edta
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    Millipore polyethyleneimine cellulose plates
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    New England Biolabs quick ligation kit
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
    Quick Ligation Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 3587 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Avantor polyethyleneimine plate
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    GE Healthcare γ 32 p atp
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    New England Biolabs ddei restriction endonuclease
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    Thermo Fisher rapid dna ligation kit
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    PerkinElmer liquid scintillation analyzer
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    GE Healthcare typhoon 9400 laser scanner
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    Bethyl rpa1 a300 241a antibodies
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    ecori  (Roche)
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    Roche ecori
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    Roche template pcr system
    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or
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    Image Search Results


    DIDS disrupts the DNA binding activity of eh Rad51. (A) Time course analysis of eh Rad51 ATPase activity in the presence or absence of DIDS (67 μM), with and without ϕX174 ssDNA or linearized ϕX174 dsDNA. Reactions were stopped with the addition of EDTA at the indicated times prior to separation with thin-layer chromatography and phosphorimager analysis. (B) eh Rad51 (7 μM) incubated with 32 P-radiolabeled ssDNA and increasing amounts of DIDS (5 μM, 10 μM, 15 μM, 20 μM, 30 μM, 40 μM; lanes 3–8 respectively). Lane 1 contained no protein or DIDS. Lane 2 contained no DIDS. Lane 9 contained 40 μM DIDS without eh Rad51. (C) eh Rad51 (35 μM) incubated with the 32 P-radiolabled dsDNA and increasing concentrations of DIDS (20 μM, 40 μM, 80 μM, 100 μM, 150 μM, 200 μM; lanes 3–8 respectively). Lane 1 lacked protein and DIDS, lane 2 contained no DIDS and lane 9 contained 200 μM DIDS and no protein. (D) eh Rad51 (7 μM) was incubated with radiolabeled ssDNA in the absence (lane 3) and presence of increasing concentrations of DIDS (5 μM, 10 μM, 15 μM, 20 μM, 30 μM, and 40 μM; lanes 4–9) prior to the addition of DNase I. The reaction were deproteinized, and the products were separated using non-denaturing PAGE. Lane 1 contained radiolabeled ssDNA alone, lane 2 contained DNase with radiolabeled ssDNA, and lane 10 contained radiolabeled ssDNA in the presence of 40 μM DIDS and DNase I. Error bars represent SEM (n = 3).

    Journal: Molecular and biochemical parasitology

    Article Title: Characterization of the recombination activities of the Entamoeba histolytica Rad51 recombinase

    doi: 10.1016/j.molbiopara.2016.09.001

    Figure Lengend Snippet: DIDS disrupts the DNA binding activity of eh Rad51. (A) Time course analysis of eh Rad51 ATPase activity in the presence or absence of DIDS (67 μM), with and without ϕX174 ssDNA or linearized ϕX174 dsDNA. Reactions were stopped with the addition of EDTA at the indicated times prior to separation with thin-layer chromatography and phosphorimager analysis. (B) eh Rad51 (7 μM) incubated with 32 P-radiolabeled ssDNA and increasing amounts of DIDS (5 μM, 10 μM, 15 μM, 20 μM, 30 μM, 40 μM; lanes 3–8 respectively). Lane 1 contained no protein or DIDS. Lane 2 contained no DIDS. Lane 9 contained 40 μM DIDS without eh Rad51. (C) eh Rad51 (35 μM) incubated with the 32 P-radiolabled dsDNA and increasing concentrations of DIDS (20 μM, 40 μM, 80 μM, 100 μM, 150 μM, 200 μM; lanes 3–8 respectively). Lane 1 lacked protein and DIDS, lane 2 contained no DIDS and lane 9 contained 200 μM DIDS and no protein. (D) eh Rad51 (7 μM) was incubated with radiolabeled ssDNA in the absence (lane 3) and presence of increasing concentrations of DIDS (5 μM, 10 μM, 15 μM, 20 μM, 30 μM, and 40 μM; lanes 4–9) prior to the addition of DNase I. The reaction were deproteinized, and the products were separated using non-denaturing PAGE. Lane 1 contained radiolabeled ssDNA alone, lane 2 contained DNase with radiolabeled ssDNA, and lane 10 contained radiolabeled ssDNA in the presence of 40 μM DIDS and DNase I. Error bars represent SEM (n = 3).

    Article Snippet: All oligonucleotides indicated as radiolabeled were done so using T4 polynucleotide kinase and [32 P-γ]-ATP as described [ ]. ϕX174 (+) virion ssDNA and ϕX174 replicative form I dsDNA were purchased from New England BioLabs; the ϕX174 replicative form I dsDNA was linearized with Apa LI (New England BioLabs). pBluescript was purified from E. coli using a Plasmid Giga kit (Qiagen).

    Techniques: Binding Assay, Activity Assay, Thin Layer Chromatography, Incubation, Polyacrylamide Gel Electrophoresis

    eh Rad51 hydrolyzes ATP and binds DNA. (A) Purified recombinant eh Rad51 (0.5 μg) on a 12% SDS-polyacrylamide gel stained with Coomassie blue. (B) Time course analysis of eh Rad51 ATPase activity in the absence and presence of ϕX174 ssDNA or linearized ϕX174 dsDNA. (C) Increasing concentrations of eh Rad51 (lanes 2–6) were incubated with 32 P-labeled ssDNA, and were resolved on a 12% polyacrylamide gel. (D) Increasing concentrations of eh Rad51 (lanes 2–6) were incubated with 32 P-labeled dsDNA. The samples were resolved on a 12% polyacrylamide gel. The results for B, C and D were quantified using a phosphorimager and graphed. Lane 1 for C and D contained no protein, and lane 7 for C and D was treated with SDS/PK (S/P). Error bars represent SEM (n = 3).

    Journal: Molecular and biochemical parasitology

    Article Title: Characterization of the recombination activities of the Entamoeba histolytica Rad51 recombinase

    doi: 10.1016/j.molbiopara.2016.09.001

    Figure Lengend Snippet: eh Rad51 hydrolyzes ATP and binds DNA. (A) Purified recombinant eh Rad51 (0.5 μg) on a 12% SDS-polyacrylamide gel stained with Coomassie blue. (B) Time course analysis of eh Rad51 ATPase activity in the absence and presence of ϕX174 ssDNA or linearized ϕX174 dsDNA. (C) Increasing concentrations of eh Rad51 (lanes 2–6) were incubated with 32 P-labeled ssDNA, and were resolved on a 12% polyacrylamide gel. (D) Increasing concentrations of eh Rad51 (lanes 2–6) were incubated with 32 P-labeled dsDNA. The samples were resolved on a 12% polyacrylamide gel. The results for B, C and D were quantified using a phosphorimager and graphed. Lane 1 for C and D contained no protein, and lane 7 for C and D was treated with SDS/PK (S/P). Error bars represent SEM (n = 3).

    Article Snippet: All oligonucleotides indicated as radiolabeled were done so using T4 polynucleotide kinase and [32 P-γ]-ATP as described [ ]. ϕX174 (+) virion ssDNA and ϕX174 replicative form I dsDNA were purchased from New England BioLabs; the ϕX174 replicative form I dsDNA was linearized with Apa LI (New England BioLabs). pBluescript was purified from E. coli using a Plasmid Giga kit (Qiagen).

    Techniques: Purification, Recombinant, Staining, Activity Assay, Incubation, Labeling

    eh Rad51 facilitates plasmid length homologous DNA pairing and DNA strand exchange. (A) Schematic of plasmid length strand exchange assay. Css, circular ssDNA; lds, linearized dsDNA; jm, joint-molecule; nc, nicked-circular; lss, linearized ssDNA. (B) Increasing concentrations of eh Rad51 (lanes 2–8) were incubated with circular ϕX174 ssDNA (css). The reaction was initiated with the introduction of linearized ϕX174 dsDNA (lds) and was deproteinized after 90 min. Reaction products were resolved on an agarose gel and stained with ethidium bromide. Lane 1 contained no protein. (C) The percent product of nicked-circular and total product (jm + nc) were graphed.

    Journal: Molecular and biochemical parasitology

    Article Title: Characterization of the recombination activities of the Entamoeba histolytica Rad51 recombinase

    doi: 10.1016/j.molbiopara.2016.09.001

    Figure Lengend Snippet: eh Rad51 facilitates plasmid length homologous DNA pairing and DNA strand exchange. (A) Schematic of plasmid length strand exchange assay. Css, circular ssDNA; lds, linearized dsDNA; jm, joint-molecule; nc, nicked-circular; lss, linearized ssDNA. (B) Increasing concentrations of eh Rad51 (lanes 2–8) were incubated with circular ϕX174 ssDNA (css). The reaction was initiated with the introduction of linearized ϕX174 dsDNA (lds) and was deproteinized after 90 min. Reaction products were resolved on an agarose gel and stained with ethidium bromide. Lane 1 contained no protein. (C) The percent product of nicked-circular and total product (jm + nc) were graphed.

    Article Snippet: All oligonucleotides indicated as radiolabeled were done so using T4 polynucleotide kinase and [32 P-γ]-ATP as described [ ]. ϕX174 (+) virion ssDNA and ϕX174 replicative form I dsDNA were purchased from New England BioLabs; the ϕX174 replicative form I dsDNA was linearized with Apa LI (New England BioLabs). pBluescript was purified from E. coli using a Plasmid Giga kit (Qiagen).

    Techniques: Plasmid Preparation, Incubation, Agarose Gel Electrophoresis, Staining

    DNA-binding and RAD51-binding activities of the PSF domains. ϕX174 ssDNA (20 µM) ( A ) or ϕX174 linear dsDNA (20 µM) ( B ) was incubated with PSF, PSF(1–266) or PSF(267–468) at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer and were visualized by ethidium bromide staining. The protein concentrations for panel A were 0 µM (lane 1), 0.15 µM (lanes 2, 5 and 8), 0.3 µM (lanes 3, 6 and 9) and 0.6 µM (lanes 4, 7 and 10). The protein concentrations for panel B were 0 µM (lane 1), 0.1 µM (lanes 2, 5 and 8), 0.2 µM (lanes 3, 6 and 9) and 0.4 µM (lanes 4, 7 and 10). ( C ) The pull-down assay with Ni–NTA beads. Lanes 2–5 represent purified RAD51, His 6 -tagged PSF, His 6 -tagged PSF(1–266) and His 6 -tagged PSF(267–468), respectively. His 6 -tagged PSF, His 6 -tagged PSF(1–266) or His 6 -tagged PSF(267–468) (3.8 µg) was mixed with RAD51 (7.4 µg). The RAD51 bound to the His 6 -tagged proteins was pulled down by the Ni–NTA agarose beads, and was analyzed by 12% SDS–PAGE. Bands were visualized by Coomassie Brilliant Blue staining.

    Journal: Nucleic Acids Research

    Article Title: Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities

    doi: 10.1093/nar/gkp298

    Figure Lengend Snippet: DNA-binding and RAD51-binding activities of the PSF domains. ϕX174 ssDNA (20 µM) ( A ) or ϕX174 linear dsDNA (20 µM) ( B ) was incubated with PSF, PSF(1–266) or PSF(267–468) at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer and were visualized by ethidium bromide staining. The protein concentrations for panel A were 0 µM (lane 1), 0.15 µM (lanes 2, 5 and 8), 0.3 µM (lanes 3, 6 and 9) and 0.6 µM (lanes 4, 7 and 10). The protein concentrations for panel B were 0 µM (lane 1), 0.1 µM (lanes 2, 5 and 8), 0.2 µM (lanes 3, 6 and 9) and 0.4 µM (lanes 4, 7 and 10). ( C ) The pull-down assay with Ni–NTA beads. Lanes 2–5 represent purified RAD51, His 6 -tagged PSF, His 6 -tagged PSF(1–266) and His 6 -tagged PSF(267–468), respectively. His 6 -tagged PSF, His 6 -tagged PSF(1–266) or His 6 -tagged PSF(267–468) (3.8 µg) was mixed with RAD51 (7.4 µg). The RAD51 bound to the His 6 -tagged proteins was pulled down by the Ni–NTA agarose beads, and was analyzed by 12% SDS–PAGE. Bands were visualized by Coomassie Brilliant Blue staining.

    Article Snippet: The 5′ ends of the oligonucleotide were labeled with T4 polynucleotide kinase (New England Biolabs, Ipswich, MA, USA) in the presence of [γ-32 P]ATP at 37°C for 30 min. Single-stranded ϕX174 viral (+) strand DNA and double-stranded ϕX174 replicative form I DNA were purchased from New England Biolabs.

    Techniques: Binding Assay, Incubation, Agarose Gel Electrophoresis, Staining, Pull Down Assay, Purification, SDS Page

    DNA binding activity of wild type and Walker A variants of hDMC1. (panel I) hDMC1 WT (1.4 μM, lane 2; 2.8 μM, lane 3; 5.6 μM, lane 4; 11.2 μM, lanes 5–11) was incubated with ϕX174 (+) ssDNA DNA (ss) and linearized ϕX174 RF (I) dsDNA (ds) in the absence (lane 9) or presence of ATP (lanes 1–5 and 10) and nucleotide analogs (ATP-γ-S, lane 6; AMP–PNP, lane 7; and ADP, lane 8). The reaction products were analyzed on 1% agarose gels. Lane 11, the reaction was deproteinized prior loading on the agarose gel. The hDMC1 K132R (panel II) and hDMC1 K132A (panel III) were analyzed as described for hDMC1 WT .

    Journal: DNA repair

    Article Title: Role of the conserved lysine within the Walker A motif of human DMC1

    doi: 10.1016/j.dnarep.2012.10.005

    Figure Lengend Snippet: DNA binding activity of wild type and Walker A variants of hDMC1. (panel I) hDMC1 WT (1.4 μM, lane 2; 2.8 μM, lane 3; 5.6 μM, lane 4; 11.2 μM, lanes 5–11) was incubated with ϕX174 (+) ssDNA DNA (ss) and linearized ϕX174 RF (I) dsDNA (ds) in the absence (lane 9) or presence of ATP (lanes 1–5 and 10) and nucleotide analogs (ATP-γ-S, lane 6; AMP–PNP, lane 7; and ADP, lane 8). The reaction products were analyzed on 1% agarose gels. Lane 11, the reaction was deproteinized prior loading on the agarose gel. The hDMC1 K132R (panel II) and hDMC1 K132A (panel III) were analyzed as described for hDMC1 WT .

    Article Snippet: The ϕX174 viral (+) strand (ssDNA) and ϕX174 replicative form I (dsDNA) was purchased from New England Biolabs.

    Techniques: Binding Assay, Activity Assay, Incubation, Agarose Gel Electrophoresis

    BCCIPβ binds DNA. ( A ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) incubated with ϕX174 (+) ssDNA (ss; 30 μM nucleotides). ( B ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) was incubated with ϕX174 RF (I) dsDNA (ds; 30 μM base pairs). The reaction products were separated on a 1.0% agarose gel, and were stained with ethidium bromide. Lane 1 contained no protein, and lane 8 was deproteinized with SDS and Proteinase K (S/P) prior to loading.

    Journal: Nucleic Acids Research

    Article Title: The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing

    doi: 10.1093/nar/gkw877

    Figure Lengend Snippet: BCCIPβ binds DNA. ( A ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) incubated with ϕX174 (+) ssDNA (ss; 30 μM nucleotides). ( B ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) was incubated with ϕX174 RF (I) dsDNA (ds; 30 μM base pairs). The reaction products were separated on a 1.0% agarose gel, and were stained with ethidium bromide. Lane 1 contained no protein, and lane 8 was deproteinized with SDS and Proteinase K (S/P) prior to loading.

    Article Snippet: All oligonucleotides were purchased from Integrated DNA Technologies. pBluescript was purified from E. coli using a Giga Kit (Qiagen). ϕX174 (+) virion ssDNA and ϕX174 replicative form I double-stranded DNA (dsDNA) were purchased from New England BioLabs—ϕX174 dsDNA was linearized with ApaLI (New England BioLabs).

    Techniques: Incubation, Agarose Gel Electrophoresis, Staining

    Homologous DNA pairing and strand exchange by rad51 mutants. A , scheme of the homologous DNA pairing and strand exchange reaction. Pairing between the circular ϕX174 (+) ssDNA and linear ϕX174 dsDNA yields a joint molecule ( jm ), which

    Journal: The Journal of Biological Chemistry

    Article Title: Regulation of Rad51 Recombinase Presynaptic Filament Assembly via Interactions with the Rad52 Mediator and the Srs2 Anti-recombinase *

    doi: 10.1074/jbc.M109.032953

    Figure Lengend Snippet: Homologous DNA pairing and strand exchange by rad51 mutants. A , scheme of the homologous DNA pairing and strand exchange reaction. Pairing between the circular ϕX174 (+) ssDNA and linear ϕX174 dsDNA yields a joint molecule ( jm ), which

    Article Snippet: The ϕX174 replicative form I DNA and viral (+) strand DNA were purchased from New England Biolabs.

    Techniques:

    Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in  panel I. Panel II  shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or

    Journal: The Journal of Biological Chemistry

    Article Title: Regulation of Rad51 Recombinase Presynaptic Filament Assembly via Interactions with the Rad52 Mediator and the Srs2 Anti-recombinase *

    doi: 10.1074/jbc.M109.032953

    Figure Lengend Snippet: Resistance of the rad51 Y388H and rad51 G393D presynaptic filaments to Srs2. A , the schematic of the topoisomerase I-linked assay is shown in panel I. Panel II shows the results obtained when presynaptic filaments of Rad51, rad51 A320V, rad51 Y388H, or

    Article Snippet: Topologically relaxed ϕX174 DNA was prepared by treating the replicative form I DNA with calf thymus topoisomerase I (Invitrogen) as described previously ( ).

    Techniques: