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  • 95
    New England Biolabs apali
    Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with <t>BamHI-HindIII</t> ( A ), BamHI-EcoRI ( B ), and <t>ApaLI</t> ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.
    Apali, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 194 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher lipofectamine 2000 reagent
    Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with <t>BamHI-HindIII</t> ( A ), BamHI-EcoRI ( B ), and <t>ApaLI</t> ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.
    Lipofectamine 2000 Reagent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 73405 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs ecori
    Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with <t>BamHI-HindIII</t> ( A ), BamHI-EcoRI ( B ), and <t>ApaLI</t> ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.
    Ecori, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 10938 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs t4 dna ligase
    Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with <t>BamHI-HindIII</t> ( A ), BamHI-EcoRI ( B ), and <t>ApaLI</t> ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.
    T4 Dna Ligase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 49148 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs nebuilder hifi dna assembly master mix
    Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with <t>BamHI-HindIII</t> ( A ), BamHI-EcoRI ( B ), and <t>ApaLI</t> ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.
    Nebuilder Hifi Dna Assembly Master Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2302 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs smai
    Alterations of restriction enzyme accessibility in the juxtaposed region of Crabp1 promoter along the course of adipocyte differentiation. ( A ) Detection of nucleosome array. Chromatin of MNase partially digested nuclei was separated on agarose gels followed by Southern blot analysis (left panel) and EtBr staining (right panel). A probe used covering the TIS (HinfI-PvuII) was used for Southern blot analysis. ( B–F ) Nuclei (differentiation Days 0, 4, 8) were digested with the indicated restriction enzymes and the recovered chromatin DNAs were completely re-digested with ApaI ( B–D ) or <t>PstI</t> ( E and F ) (the relationship of specific restriction site and each individual nucleosome was depicted in panel G), followed by Southern blot analyses using probe 1 ( D ) or probe 2 (B–C and E–F). ( G ) Schematic description of restriction enzyme digestion, nucleosomes, and predicted fragments detected with probes on the Southern blots. Complete digestion with ApaI produced 1.3 kb, and complete digestion with PstI produced 1.65 kb fragments. The generated fragments by digestion with XhoI, PstI, <t>SmaI,</t> SpeI and ApaLI for the corresponding nucleosome are 0.93, 0.67, 0.86, 0.55 and 0.65 kb, respectively. Nucleosomes on this array were named N5 to N-1, from the 5′- to the 3′-ends of this chromatin segment. Experiments were performed for least three times.
    Smai, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1694 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs t4 polynucleotide kinase
    Alterations of restriction enzyme accessibility in the juxtaposed region of Crabp1 promoter along the course of adipocyte differentiation. ( A ) Detection of nucleosome array. Chromatin of MNase partially digested nuclei was separated on agarose gels followed by Southern blot analysis (left panel) and EtBr staining (right panel). A probe used covering the TIS (HinfI-PvuII) was used for Southern blot analysis. ( B–F ) Nuclei (differentiation Days 0, 4, 8) were digested with the indicated restriction enzymes and the recovered chromatin DNAs were completely re-digested with ApaI ( B–D ) or <t>PstI</t> ( E and F ) (the relationship of specific restriction site and each individual nucleosome was depicted in panel G), followed by Southern blot analyses using probe 1 ( D ) or probe 2 (B–C and E–F). ( G ) Schematic description of restriction enzyme digestion, nucleosomes, and predicted fragments detected with probes on the Southern blots. Complete digestion with ApaI produced 1.3 kb, and complete digestion with PstI produced 1.65 kb fragments. The generated fragments by digestion with XhoI, PstI, <t>SmaI,</t> SpeI and ApaLI for the corresponding nucleosome are 0.93, 0.67, 0.86, 0.55 and 0.65 kb, respectively. Nucleosomes on this array were named N5 to N-1, from the 5′- to the 3′-ends of this chromatin segment. Experiments were performed for least three times.
    T4 Polynucleotide Kinase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 29387 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs bglii
    Confirmation of chromatin looping by 3C assay with <t>BglII</t> and/or <t>ApaLI</t> restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII
    Bglii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2543 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Corning Life Sciences cm2 culture flasks
    Confirmation of chromatin looping by 3C assay with <t>BglII</t> and/or <t>ApaLI</t> restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII
    Cm2 Culture Flasks, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 93/100, based on 568 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs cutsmart buffer
    Confirmation of chromatin looping by 3C assay with <t>BglII</t> and/or <t>ApaLI</t> restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII
    Cutsmart Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2628 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs klenow fragment
    Confirmation of chromatin looping by 3C assay with <t>BglII</t> and/or <t>ApaLI</t> restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII
    Klenow Fragment, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 7893 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs i dna
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    I Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs pcii
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    Pcii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 222 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick gel extraction kit
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    Qiaquick Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 113321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs acci
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    Acci, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 156 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs acli
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    Acli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs afl iii
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    Afl Iii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GE Healthcare amersham hybond n membrane
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    Amersham Hybond N Membrane, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 99/100, based on 1060 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GE Healthcare amersham hybond xl membrane
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    Amersham Hybond Xl Membrane, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 99/100, based on 197 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher apali
    Stimulation of the Dmc1-mediated <t>DNA</t> strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with <t>φX174</t> circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.
    Apali, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 51 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with BamHI-HindIII ( A ), BamHI-EcoRI ( B ), and ApaLI ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.

    Journal: The Journal of Biological Chemistry

    Article Title: Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

    doi: 10.1074/jbc.M117.780239

    Figure Lengend Snippet: Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with BamHI-HindIII ( A ), BamHI-EcoRI ( B ), and ApaLI ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.

    Article Snippet: Probing with restriction enzymes The cleavage reactions of the H-NS nucleoprotein complexes were carried out for 5 min with BamHI-EcoRI and BamHI-HindIII and for 10 min with ApaLI at 37 °C in the same standard New England BioLabs CutSmart buffer.

    Techniques: Footprinting, Construct, Plasmid Preparation, Binding Assay, Sequencing

    Confirmation of chromatin looping by 3C assay with BglII and/or ApaLI restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII

    Journal: The Journal of Biological Chemistry

    Article Title: Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells *

    doi: 10.1074/jbc.M109.058586

    Figure Lengend Snippet: Confirmation of chromatin looping by 3C assay with BglII and/or ApaLI restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII

    Article Snippet: SDS was then sequestered from the samples by the addition of 1.8% Triton X-100 (Fisher), and the samples were incubated at 37 °C for 1 h. The samples were digested with BglII and/or ApaLI restriction enzyme (New England Biolabs) at 37 °C for 16 h. Restriction enzymes were inactivated by the addition of 1.6% SDS and further incubation at 65 °C for 20 min.

    Techniques:

    Alterations of restriction enzyme accessibility in the juxtaposed region of Crabp1 promoter along the course of adipocyte differentiation. ( A ) Detection of nucleosome array. Chromatin of MNase partially digested nuclei was separated on agarose gels followed by Southern blot analysis (left panel) and EtBr staining (right panel). A probe used covering the TIS (HinfI-PvuII) was used for Southern blot analysis. ( B–F ) Nuclei (differentiation Days 0, 4, 8) were digested with the indicated restriction enzymes and the recovered chromatin DNAs were completely re-digested with ApaI ( B–D ) or PstI ( E and F ) (the relationship of specific restriction site and each individual nucleosome was depicted in panel G), followed by Southern blot analyses using probe 1 ( D ) or probe 2 (B–C and E–F). ( G ) Schematic description of restriction enzyme digestion, nucleosomes, and predicted fragments detected with probes on the Southern blots. Complete digestion with ApaI produced 1.3 kb, and complete digestion with PstI produced 1.65 kb fragments. The generated fragments by digestion with XhoI, PstI, SmaI, SpeI and ApaLI for the corresponding nucleosome are 0.93, 0.67, 0.86, 0.55 and 0.65 kb, respectively. Nucleosomes on this array were named N5 to N-1, from the 5′- to the 3′-ends of this chromatin segment. Experiments were performed for least three times.

    Journal: Nucleic Acids Research

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation

    doi: 10.1093/nar/gkp780

    Figure Lengend Snippet: Alterations of restriction enzyme accessibility in the juxtaposed region of Crabp1 promoter along the course of adipocyte differentiation. ( A ) Detection of nucleosome array. Chromatin of MNase partially digested nuclei was separated on agarose gels followed by Southern blot analysis (left panel) and EtBr staining (right panel). A probe used covering the TIS (HinfI-PvuII) was used for Southern blot analysis. ( B–F ) Nuclei (differentiation Days 0, 4, 8) were digested with the indicated restriction enzymes and the recovered chromatin DNAs were completely re-digested with ApaI ( B–D ) or PstI ( E and F ) (the relationship of specific restriction site and each individual nucleosome was depicted in panel G), followed by Southern blot analyses using probe 1 ( D ) or probe 2 (B–C and E–F). ( G ) Schematic description of restriction enzyme digestion, nucleosomes, and predicted fragments detected with probes on the Southern blots. Complete digestion with ApaI produced 1.3 kb, and complete digestion with PstI produced 1.65 kb fragments. The generated fragments by digestion with XhoI, PstI, SmaI, SpeI and ApaLI for the corresponding nucleosome are 0.93, 0.67, 0.86, 0.55 and 0.65 kb, respectively. Nucleosomes on this array were named N5 to N-1, from the 5′- to the 3′-ends of this chromatin segment. Experiments were performed for least three times.

    Article Snippet: Isolated nuclei from differentiating 3T3-L1 cells were digested with 100 U of PstI, XhoI, SmaI, SpeI and ApaLI (New England Biolabs) for 30 min.

    Techniques: Southern Blot, Staining, Produced, Generated

    Confirmation of chromatin looping by 3C assay with BglII and/or ApaLI restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII

    Journal: The Journal of Biological Chemistry

    Article Title: Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells *

    doi: 10.1074/jbc.M109.058586

    Figure Lengend Snippet: Confirmation of chromatin looping by 3C assay with BglII and/or ApaLI restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII

    Article Snippet: SDS was then sequestered from the samples by the addition of 1.8% Triton X-100 (Fisher), and the samples were incubated at 37 °C for 1 h. The samples were digested with BglII and/or ApaLI restriction enzyme (New England Biolabs) at 37 °C for 16 h. Restriction enzymes were inactivated by the addition of 1.6% SDS and further incubation at 65 °C for 20 min.

    Techniques:

    Stimulation of the Dmc1-mediated DNA strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.

    Journal: Nucleic Acids Research

    Article Title: Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein

    doi: 10.1093/nar/gkl562

    Figure Lengend Snippet: Stimulation of the Dmc1-mediated DNA strand exchange activity by Rad54B. ( A ) Schematic representation of the DNA strand exchange assay. The nucleoprotein filament is formed by incubating Dmc1 with circular ssDNA. The filament is paired with homologous linear dsDNA to yield a joint molecule. A nicked circular duplex (nc) and linear ssDNA are then generated by completing strand exchange over the length of the DNA molecules. ( B ) Dmc1-mediated DNA strand exchange activity with Rad54B. A constant amount of Dmc1 (7.5 µM) was incubated for 2 h with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM), KCl (200 mM) and increasing concentrations of Rad54B (0, 0.025, 0.1, 0.4 and 1.6 µM in lanes 2–6, respectively), in the order described for the procedure at 37°C. In lane 1, ssDNA and dsDNA were incubated in buffer with RPA and KCl, but without other recombinant proteins, and in lane 7, ssDNA and dsDNA were incubated in buffer with RPA, KCl and Rad54B (1.6 µM), but no Dmc1. The reaction mixtures were deproteinized, fractionated on a 1% agarose gel and stained with ethidium bromide. ( C ) Graphic representation of the experiments shown in (B). The amounts of nicked circular duplex are presented. ( D ) Time course experiments for DNA strand exchange. Dmc1 (7.5 µM) was incubated with φX174 circular ssDNA (30 µM), φX174 linear dsDNA (22 µM), RPA (2 µM) and KCl (200 mM), in the presence (open squares) or absence (closed squares) of Rad54B (0.4 µM), in the order described for the procedure at 37°C, for the indicated times. ( E ) Graphic representation of the experiments shown in (D). The amounts of nicked circular duplex are graphically presented.

    Article Snippet: DNA substrates The φX174 circular ssDNA (5386 bases) and replicative form I DNA were purchased from New England Biolabs and Life Technologies.

    Techniques: Activity Assay, Generated, Incubation, Recombinase Polymerase Amplification, Recombinant, Agarose Gel Electrophoresis, Staining

    Pull down assay for the protein transfer between ssDNA molecules. ( A ) A schematic diagram of the pull down assay. Dmc1 and biotinylated DNA form a complex in the absence or presence of Rad54B. Then, circular ssDNA is added as a competitor, and protein transfer occurs. Biotinylated DNA is immobilized on streptavidin beads, and the reaction mixture is divided into the beads and supernatant. ( B ) Dmc1 (5 µM) was incubated with SAT-120 (20 µM) labeled with biotin at the 5′ end in the absence (lane 2) or presence (lane 3) of Rad54B (200 nM), followed by an incubation with φX174 circular ssDNA (2 mM). After immobilization on streptavidin beads for 1 h at 4°C, the reaction mixture was divided into the beads and the supernatant by centrifugation. Then, one-tenth of the supernatant was fractionated on a 4–20% gradient SDS–PAGE gel. Lane 1 is one-tenth of the input protein. ( C ) Graphic representation of the experiments shown in (B). The amounts of Dmc1 within the supernatant are presented.

    Journal: Nucleic Acids Research

    Article Title: Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein

    doi: 10.1093/nar/gkl562

    Figure Lengend Snippet: Pull down assay for the protein transfer between ssDNA molecules. ( A ) A schematic diagram of the pull down assay. Dmc1 and biotinylated DNA form a complex in the absence or presence of Rad54B. Then, circular ssDNA is added as a competitor, and protein transfer occurs. Biotinylated DNA is immobilized on streptavidin beads, and the reaction mixture is divided into the beads and supernatant. ( B ) Dmc1 (5 µM) was incubated with SAT-120 (20 µM) labeled with biotin at the 5′ end in the absence (lane 2) or presence (lane 3) of Rad54B (200 nM), followed by an incubation with φX174 circular ssDNA (2 mM). After immobilization on streptavidin beads for 1 h at 4°C, the reaction mixture was divided into the beads and the supernatant by centrifugation. Then, one-tenth of the supernatant was fractionated on a 4–20% gradient SDS–PAGE gel. Lane 1 is one-tenth of the input protein. ( C ) Graphic representation of the experiments shown in (B). The amounts of Dmc1 within the supernatant are presented.

    Article Snippet: DNA substrates The φX174 circular ssDNA (5386 bases) and replicative form I DNA were purchased from New England Biolabs and Life Technologies.

    Techniques: Pull Down Assay, Incubation, Labeling, Centrifugation, SDS Page

    Model of Rad54B converting the Dmc1–DNA complex from the octameric ring form to the helical filament form. Rad54B interacts with terminus of the stacked octameric rings of the Dmc1–DNA complex, causing a conversion into the helical-filament form. This conversion results in the stabilization of the Dmc1–ssDNA complex, and the stimulation of the DNA strand exchange promoted by Dmc1.

    Journal: Nucleic Acids Research

    Article Title: Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein

    doi: 10.1093/nar/gkl562

    Figure Lengend Snippet: Model of Rad54B converting the Dmc1–DNA complex from the octameric ring form to the helical filament form. Rad54B interacts with terminus of the stacked octameric rings of the Dmc1–DNA complex, causing a conversion into the helical-filament form. This conversion results in the stabilization of the Dmc1–ssDNA complex, and the stimulation of the DNA strand exchange promoted by Dmc1.

    Article Snippet: DNA substrates The φX174 circular ssDNA (5386 bases) and replicative form I DNA were purchased from New England Biolabs and Life Technologies.

    Techniques: