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    New England Biolabs buffer iii a
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    New England Biolabs 10x dnase reaction buffer
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    New England Biolabs factor xa protease
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    New England Biolabs micrococcal nuclease buffer
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    New England Biolabs reaction buffer
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    New England Biolabs lysis buffer
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    New England Biolabs nuclear extraction buffer
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    New England Biolabs dnase i buffer
    Biochemical and bioinformatic analyses of PobR, a negative regulator of pobA . ( A ) Predicted domains organization of PobR protein. Both N-terminal domain and C-terminal domains of PobR are homologous to intact IclR family transcription factors. ( B ) The overall view of the region upstream of the pobA open reading frame (ORF), highlighting the transcription start site of pobA (turquoise), putative -35 and -10 pobA promoter elements (underlined and highlighted in orange) and the PobR regulator binding site sequence (in bold and boxed). ( C ) DNA binding of PobR was assessed using agarose electrophoretic mobility shift assays (EMSAs). A PCR-amplified DNA fragment spanning the entire region between the transcription and translation start sites (5′-untranslated region) was titrated with PobR. In comparison with the unbound DNA probe in the electrophoresis, retarded migration of the DNA probe was observed upon addition of PobR. Bands representing the PobR-DNA probe complex and the unbound DNA probe are highlighted by arrows. For a negative control, a 486-bp fragment amplified from hrdB ORF, which does not contain the PobR binding site, was used. ( D ) The PobR binding site upstream of the pobA ORF was mapped using <t>DNase</t> I footprinting analysis. A 5′- 32 P end-labeled 118-bp DNA fragment was digested with DNase I in the absence and presence of heterologously produced and purified PobR. In comparison with the DNA digest in the absence of PobR, a protected region was observed when DNA was incubated with PobR before digestion. Sequencing ladders indicated by lanes C/T and A/G were generated via Maxam-Gilbert reactions. The reactions were performed in duplicate. ( E ) Sequence alignment of the regions upstream of the pobA ORFs in various streptomycetes. Putative –35 and –10 pobA promoter elements and PobR binding site sequence (boxed) identified in DNase I footprinting reaction are conserved in several members of the Streptomyces genus. A conserved PobR binding site was also identified using the Gibbs Motif Sampler ( 47 ). Sequence logo images ( 51 ) depict the sequence conservation of PobR binding site.
    Dnase I Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 188 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs nuclei extraction buffer
    Biochemical and bioinformatic analyses of PobR, a negative regulator of pobA . ( A ) Predicted domains organization of PobR protein. Both N-terminal domain and C-terminal domains of PobR are homologous to intact IclR family transcription factors. ( B ) The overall view of the region upstream of the pobA open reading frame (ORF), highlighting the transcription start site of pobA (turquoise), putative -35 and -10 pobA promoter elements (underlined and highlighted in orange) and the PobR regulator binding site sequence (in bold and boxed). ( C ) DNA binding of PobR was assessed using agarose electrophoretic mobility shift assays (EMSAs). A PCR-amplified DNA fragment spanning the entire region between the transcription and translation start sites (5′-untranslated region) was titrated with PobR. In comparison with the unbound DNA probe in the electrophoresis, retarded migration of the DNA probe was observed upon addition of PobR. Bands representing the PobR-DNA probe complex and the unbound DNA probe are highlighted by arrows. For a negative control, a 486-bp fragment amplified from hrdB ORF, which does not contain the PobR binding site, was used. ( D ) The PobR binding site upstream of the pobA ORF was mapped using <t>DNase</t> I footprinting analysis. A 5′- 32 P end-labeled 118-bp DNA fragment was digested with DNase I in the absence and presence of heterologously produced and purified PobR. In comparison with the DNA digest in the absence of PobR, a protected region was observed when DNA was incubated with PobR before digestion. Sequencing ladders indicated by lanes C/T and A/G were generated via Maxam-Gilbert reactions. The reactions were performed in duplicate. ( E ) Sequence alignment of the regions upstream of the pobA ORFs in various streptomycetes. Putative –35 and –10 pobA promoter elements and PobR binding site sequence (boxed) identified in DNase I footprinting reaction are conserved in several members of the Streptomyces genus. A conserved PobR binding site was also identified using the Gibbs Motif Sampler ( 47 ). Sequence logo images ( 51 ) depict the sequence conservation of PobR binding site.
    Nuclei Extraction Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 96 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Biochemical and bioinformatic analyses of PobR, a negative regulator of pobA . ( A ) Predicted domains organization of PobR protein. Both N-terminal domain and C-terminal domains of PobR are homologous to intact IclR family transcription factors. ( B ) The overall view of the region upstream of the pobA open reading frame (ORF), highlighting the transcription start site of pobA (turquoise), putative -35 and -10 pobA promoter elements (underlined and highlighted in orange) and the PobR regulator binding site sequence (in bold and boxed). ( C ) DNA binding of PobR was assessed using agarose electrophoretic mobility shift assays (EMSAs). A PCR-amplified DNA fragment spanning the entire region between the transcription and translation start sites (5′-untranslated region) was titrated with PobR. In comparison with the unbound DNA probe in the electrophoresis, retarded migration of the DNA probe was observed upon addition of PobR. Bands representing the PobR-DNA probe complex and the unbound DNA probe are highlighted by arrows. For a negative control, a 486-bp fragment amplified from hrdB ORF, which does not contain the PobR binding site, was used. ( D ) The PobR binding site upstream of the pobA ORF was mapped using DNase I footprinting analysis. A 5′- 32 P end-labeled 118-bp DNA fragment was digested with DNase I in the absence and presence of heterologously produced and purified PobR. In comparison with the DNA digest in the absence of PobR, a protected region was observed when DNA was incubated with PobR before digestion. Sequencing ladders indicated by lanes C/T and A/G were generated via Maxam-Gilbert reactions. The reactions were performed in duplicate. ( E ) Sequence alignment of the regions upstream of the pobA ORFs in various streptomycetes. Putative –35 and –10 pobA promoter elements and PobR binding site sequence (boxed) identified in DNase I footprinting reaction are conserved in several members of the Streptomyces genus. A conserved PobR binding site was also identified using the Gibbs Motif Sampler ( 47 ). Sequence logo images ( 51 ) depict the sequence conservation of PobR binding site.

    Journal: Nucleic Acids Research

    Article Title: A peculiar IclR family transcription factor regulates para-hydroxybenzoate catabolism in Streptomyces coelicolor

    doi: 10.1093/nar/gkx1234

    Figure Lengend Snippet: Biochemical and bioinformatic analyses of PobR, a negative regulator of pobA . ( A ) Predicted domains organization of PobR protein. Both N-terminal domain and C-terminal domains of PobR are homologous to intact IclR family transcription factors. ( B ) The overall view of the region upstream of the pobA open reading frame (ORF), highlighting the transcription start site of pobA (turquoise), putative -35 and -10 pobA promoter elements (underlined and highlighted in orange) and the PobR regulator binding site sequence (in bold and boxed). ( C ) DNA binding of PobR was assessed using agarose electrophoretic mobility shift assays (EMSAs). A PCR-amplified DNA fragment spanning the entire region between the transcription and translation start sites (5′-untranslated region) was titrated with PobR. In comparison with the unbound DNA probe in the electrophoresis, retarded migration of the DNA probe was observed upon addition of PobR. Bands representing the PobR-DNA probe complex and the unbound DNA probe are highlighted by arrows. For a negative control, a 486-bp fragment amplified from hrdB ORF, which does not contain the PobR binding site, was used. ( D ) The PobR binding site upstream of the pobA ORF was mapped using DNase I footprinting analysis. A 5′- 32 P end-labeled 118-bp DNA fragment was digested with DNase I in the absence and presence of heterologously produced and purified PobR. In comparison with the DNA digest in the absence of PobR, a protected region was observed when DNA was incubated with PobR before digestion. Sequencing ladders indicated by lanes C/T and A/G were generated via Maxam-Gilbert reactions. The reactions were performed in duplicate. ( E ) Sequence alignment of the regions upstream of the pobA ORFs in various streptomycetes. Putative –35 and –10 pobA promoter elements and PobR binding site sequence (boxed) identified in DNase I footprinting reaction are conserved in several members of the Streptomyces genus. A conserved PobR binding site was also identified using the Gibbs Motif Sampler ( 47 ). Sequence logo images ( 51 ) depict the sequence conservation of PobR binding site.

    Article Snippet: After a 20 min incubation at 30°C, 5 μL of DNase I buffer [100 mM Tris pH 7.6, 25 mM MgCl2 , and 5 mM CaCl2 ] and 0.2 unit of DNase I (New England Biolabs) were added.

    Techniques: Binding Assay, Sequencing, Electrophoretic Mobility Shift Assay, Polymerase Chain Reaction, Amplification, Electrophoresis, Migration, Negative Control, Footprinting, Labeling, Produced, Purification, Incubation, Generated

    Rate of transfer of DNA from UvrA to UvrB DNase I footprinting of Bca UvrA and Bca UvrB-DNA complexes. Reaction mixtures contained UvrA 2 (10 nM), ± 100 nM UvrB, 2 nM F 26 50/NDB duplex with the radiolabel on the damaged strand. The reactions were incubated at 37 °C then DNase I was added for 30 sec at RT. Then the samples were processed as described in the methods. The time indicated in the figure includes the time for DNase I digestion. Panel a , Gel image showing the transition of the WT UvrA footprint to WT UvrB footprint. The right side of the gel contains a graphic representation of the DNase I footprints observed. Panel b , Gel image showing the transition of the KRAA UvrA footprint to the WT UvrB footprint. The position of the adduct and the 3′ and 5′ incision sites are noted on the left-hand side of the gels. Asterisks indicate the position of the band used to quantify the gels, p1. Panel c , Graphic representation of the band intensities of p1 relative to the band intensity observed in lane 4, DNase I digestion in the absence of proteins. The average of 3 independent experiments was plotted with the standard deviation at each point. Data were fit to a single or double exponential using Excel.

    Journal: DNA repair

    Article Title: Cooperative damage recognition by UvrA and UvrB: Identification of UvrA residues that mediate DNA binding

    doi: 10.1016/j.dnarep.2007.11.013

    Figure Lengend Snippet: Rate of transfer of DNA from UvrA to UvrB DNase I footprinting of Bca UvrA and Bca UvrB-DNA complexes. Reaction mixtures contained UvrA 2 (10 nM), ± 100 nM UvrB, 2 nM F 26 50/NDB duplex with the radiolabel on the damaged strand. The reactions were incubated at 37 °C then DNase I was added for 30 sec at RT. Then the samples were processed as described in the methods. The time indicated in the figure includes the time for DNase I digestion. Panel a , Gel image showing the transition of the WT UvrA footprint to WT UvrB footprint. The right side of the gel contains a graphic representation of the DNase I footprints observed. Panel b , Gel image showing the transition of the KRAA UvrA footprint to the WT UvrB footprint. The position of the adduct and the 3′ and 5′ incision sites are noted on the left-hand side of the gels. Asterisks indicate the position of the band used to quantify the gels, p1. Panel c , Graphic representation of the band intensities of p1 relative to the band intensity observed in lane 4, DNase I digestion in the absence of proteins. The average of 3 independent experiments was plotted with the standard deviation at each point. Data were fit to a single or double exponential using Excel.

    Article Snippet: After incubation at 37 °C for the indicated amount of time, DNase I (1 µL of 0.03 U/µL in 50 mM CaCl2 and 100 nM bovine serum albumin, New England BioLabs) was added and after digestion for 30 sec at room temperature the reactions were stopped by the addition of sarkosyl (0.5%) and EDTA (15 mM).

    Techniques: Footprinting, BIA-KA, Incubation, Size-exclusion Chromatography, Standard Deviation

    DNase I Footprinting DNase I footprint of the WT and KRAA UvrA proteins bound to the 50 bp F 26 50/NBD duplex with the 32 P on the 5′ end of the damaged strand. The indicated proteins were incubated with 2 nM duplex in the presence of 50 mM Tris-HCl, pH 7.5, 50 mM KCl, 10 MgCl 2 , 1 mM ATP, 10 mM DTT, 100 nM bovine serum albumin for 15 min at 37 °C then DNase I treated and processed as described in the methods. Panel a , WT UvrA DNase I footprint. Panel b , KRAA UvrA DNase I footprint. Both gels are loaded in the same order. The lanes contained the following: lane 1, no protein and no DNase I; lane 2, UvrA 2 , 10 nM and no DNase I; lane 3, no protein plus DNase I; lanes 4–7, increasing concentrations of UvrA 2 , 10 – 80 nM, plus DNase I; lane 8, UvrA 2 , 10 nM, WT UvrB, 100 nM, plus DNase I; lane 9, WT UvrB, 100 nM, plus DNase I. The position of the adduct and the 3′ and 5′ incision sites are noted on the left-hand side of the gels. The bands that were quantified for the graph in panel c are denoted by the arrows, p1 and p2. Panel c ]. For more details see the Materials and Methods.

    Journal: DNA repair

    Article Title: Cooperative damage recognition by UvrA and UvrB: Identification of UvrA residues that mediate DNA binding

    doi: 10.1016/j.dnarep.2007.11.013

    Figure Lengend Snippet: DNase I Footprinting DNase I footprint of the WT and KRAA UvrA proteins bound to the 50 bp F 26 50/NBD duplex with the 32 P on the 5′ end of the damaged strand. The indicated proteins were incubated with 2 nM duplex in the presence of 50 mM Tris-HCl, pH 7.5, 50 mM KCl, 10 MgCl 2 , 1 mM ATP, 10 mM DTT, 100 nM bovine serum albumin for 15 min at 37 °C then DNase I treated and processed as described in the methods. Panel a , WT UvrA DNase I footprint. Panel b , KRAA UvrA DNase I footprint. Both gels are loaded in the same order. The lanes contained the following: lane 1, no protein and no DNase I; lane 2, UvrA 2 , 10 nM and no DNase I; lane 3, no protein plus DNase I; lanes 4–7, increasing concentrations of UvrA 2 , 10 – 80 nM, plus DNase I; lane 8, UvrA 2 , 10 nM, WT UvrB, 100 nM, plus DNase I; lane 9, WT UvrB, 100 nM, plus DNase I. The position of the adduct and the 3′ and 5′ incision sites are noted on the left-hand side of the gels. The bands that were quantified for the graph in panel c are denoted by the arrows, p1 and p2. Panel c ]. For more details see the Materials and Methods.

    Article Snippet: After incubation at 37 °C for the indicated amount of time, DNase I (1 µL of 0.03 U/µL in 50 mM CaCl2 and 100 nM bovine serum albumin, New England BioLabs) was added and after digestion for 30 sec at room temperature the reactions were stopped by the addition of sarkosyl (0.5%) and EDTA (15 mM).

    Techniques: Footprinting, Incubation