dnase i New England Biolabs Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    New England Biolabs dnase i new england biolabs
    <t>DNase</t> I footprint analysis of PpsR. Binding to the pucB promoter region under oxidizing (A) and reducing condition (B), and to the crtI promoter region under oxidizing (C) and reducing condition (D). Regions corresponding to the DNase I protection regions are shown in blue background. The possible PpsR-binding sites are boxed letters on the bottom of each figure. Sites for different protection patters observed in oxidized and reduced conditions are indicated with asterisks.
    Dnase I New England Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 427 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnase i new england biolabs/product/New England Biolabs
    Average 99 stars, based on 427 article reviews
    Price from $9.99 to $1999.99
    dnase i new england biolabs - by Bioz Stars, 2020-05
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher dnase i
    RPA subunits are differentially cross-linked when incubated alone or in combination with other repair factors. RPA was incubated with substrate DNA as described previously either alone or with other repair factors (at the same concentrations used to reconstitute excision repair) for 60 min and irradiated with black light, and then reaction mixtures were digested with DNase I. Following resolution in an SDS-10% polyacrylamide gel, the DNA-protein complexes were visualized by autoradiography (A). Lane 1 is a complete reaction, and lane 2 is RPA alone; to the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated with open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitation. Panel B is a graphic summarization of relative RPA70/RPA32 cross-linking values for RPA alone reactions ( n  = 8) and complete reactions ( n  = 16). Average values are plotted, and error bars represent the standard error. For each data set the relative RPA70 signal is defined as 1.
    Dnase I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 56198 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnase i/product/Thermo Fisher
    Average 99 stars, based on 56198 article reviews
    Price from $9.99 to $1999.99
    dnase i - by Bioz Stars, 2020-05
    99/100 stars
      Buy from Supplier

    84
    New England Biolabs recombinant proteins dnase i new england biolabs cat
    RPA subunits are differentially cross-linked when incubated alone or in combination with other repair factors. RPA was incubated with substrate DNA as described previously either alone or with other repair factors (at the same concentrations used to reconstitute excision repair) for 60 min and irradiated with black light, and then reaction mixtures were digested with DNase I. Following resolution in an SDS-10% polyacrylamide gel, the DNA-protein complexes were visualized by autoradiography (A). Lane 1 is a complete reaction, and lane 2 is RPA alone; to the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated with open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitation. Panel B is a graphic summarization of relative RPA70/RPA32 cross-linking values for RPA alone reactions ( n  = 8) and complete reactions ( n  = 16). Average values are plotted, and error bars represent the standard error. For each data set the relative RPA70 signal is defined as 1.
    Recombinant Proteins Dnase I New England Biolabs Cat, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/recombinant proteins dnase i new england biolabs cat/product/New England Biolabs
    Average 84 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    recombinant proteins dnase i new england biolabs cat - by Bioz Stars, 2020-05
    84/100 stars
      Buy from Supplier

    84
    New England Biolabs resource source identifier dnase i new england biolabs cat
    RPA subunits are differentially cross-linked when incubated alone or in combination with other repair factors. RPA was incubated with substrate DNA as described previously either alone or with other repair factors (at the same concentrations used to reconstitute excision repair) for 60 min and irradiated with black light, and then reaction mixtures were digested with DNase I. Following resolution in an SDS-10% polyacrylamide gel, the DNA-protein complexes were visualized by autoradiography (A). Lane 1 is a complete reaction, and lane 2 is RPA alone; to the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated with open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitation. Panel B is a graphic summarization of relative RPA70/RPA32 cross-linking values for RPA alone reactions ( n  = 8) and complete reactions ( n  = 16). Average values are plotted, and error bars represent the standard error. For each data set the relative RPA70 signal is defined as 1.
    Resource Source Identifier Dnase I New England Biolabs Cat, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/resource source identifier dnase i new england biolabs cat/product/New England Biolabs
    Average 84 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    resource source identifier dnase i new england biolabs cat - by Bioz Stars, 2020-05
    84/100 stars
      Buy from Supplier

    99
    New England Biolabs t7 endonuclase i m0302 new england biolabs
    RPA subunits are differentially cross-linked when incubated alone or in combination with other repair factors. RPA was incubated with substrate DNA as described previously either alone or with other repair factors (at the same concentrations used to reconstitute excision repair) for 60 min and irradiated with black light, and then reaction mixtures were digested with DNase I. Following resolution in an SDS-10% polyacrylamide gel, the DNA-protein complexes were visualized by autoradiography (A). Lane 1 is a complete reaction, and lane 2 is RPA alone; to the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated with open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitation. Panel B is a graphic summarization of relative RPA70/RPA32 cross-linking values for RPA alone reactions ( n  = 8) and complete reactions ( n  = 16). Average values are plotted, and error bars represent the standard error. For each data set the relative RPA70 signal is defined as 1.
    T7 Endonuclase I M0302 New England Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t7 endonuclase i m0302 new england biolabs/product/New England Biolabs
    Average 99 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    t7 endonuclase i m0302 new england biolabs - by Bioz Stars, 2020-05
    99/100 stars
      Buy from Supplier

    93
    New England Biolabs cas9 nickase
    RPA subunits are differentially cross-linked when incubated alone or in combination with other repair factors. RPA was incubated with substrate DNA as described previously either alone or with other repair factors (at the same concentrations used to reconstitute excision repair) for 60 min and irradiated with black light, and then reaction mixtures were digested with DNase I. Following resolution in an SDS-10% polyacrylamide gel, the DNA-protein complexes were visualized by autoradiography (A). Lane 1 is a complete reaction, and lane 2 is RPA alone; to the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated with open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitation. Panel B is a graphic summarization of relative RPA70/RPA32 cross-linking values for RPA alone reactions ( n  = 8) and complete reactions ( n  = 16). Average values are plotted, and error bars represent the standard error. For each data set the relative RPA70 signal is defined as 1.
    Cas9 Nickase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cas9 nickase/product/New England Biolabs
    Average 93 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    cas9 nickase - by Bioz Stars, 2020-05
    93/100 stars
      Buy from Supplier

    95
    New England Biolabs bspqi nickase
    RPA subunits are differentially cross-linked when incubated alone or in combination with other repair factors. RPA was incubated with substrate DNA as described previously either alone or with other repair factors (at the same concentrations used to reconstitute excision repair) for 60 min and irradiated with black light, and then reaction mixtures were digested with DNase I. Following resolution in an SDS-10% polyacrylamide gel, the DNA-protein complexes were visualized by autoradiography (A). Lane 1 is a complete reaction, and lane 2 is RPA alone; to the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated with open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitation. Panel B is a graphic summarization of relative RPA70/RPA32 cross-linking values for RPA alone reactions ( n  = 8) and complete reactions ( n  = 16). Average values are plotted, and error bars represent the standard error. For each data set the relative RPA70 signal is defined as 1.
    Bspqi Nickase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bspqi nickase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bspqi nickase - by Bioz Stars, 2020-05
    95/100 stars
      Buy from Supplier

    94
    New England Biolabs dnase i reaction buffer
    CbpA protects plasmid DNA from degradation by nucleases. A. The panel shows naked plasmid and complexes with CbpA run on a 1% agarose gel. Plasmid (30 ng) was pre-incubated with 0, 0.5, 1.0, or 2.0 µM CbpA. Note that only every other lane has been loaded on the gel. B. The panel shows plasmid run on a 1% agarose gel. Plasmids (77 ng) were treated with different combinations of DNase I, BSA (1, 2 or 3 µM) and CbpA (1, 2 or 3 µM).
    Dnase I Reaction Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 120 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnase i reaction buffer/product/New England Biolabs
    Average 94 stars, based on 120 article reviews
    Price from $9.99 to $1999.99
    dnase i reaction buffer - by Bioz Stars, 2020-05
    94/100 stars
      Buy from Supplier

    Image Search Results


    DNase I footprint analysis of PpsR. Binding to the pucB promoter region under oxidizing (A) and reducing condition (B), and to the crtI promoter region under oxidizing (C) and reducing condition (D). Regions corresponding to the DNase I protection regions are shown in blue background. The possible PpsR-binding sites are boxed letters on the bottom of each figure. Sites for different protection patters observed in oxidized and reduced conditions are indicated with asterisks.

    Journal: PLoS ONE

    Article Title: Evidence that Altered Cis Element Spacing Affects PpsR Mediated Redox Control of Photosynthesis Gene Expression in Rubrivivax gelatinosus

    doi: 10.1371/journal.pone.0128446

    Figure Lengend Snippet: DNase I footprint analysis of PpsR. Binding to the pucB promoter region under oxidizing (A) and reducing condition (B), and to the crtI promoter region under oxidizing (C) and reducing condition (D). Regions corresponding to the DNase I protection regions are shown in blue background. The possible PpsR-binding sites are boxed letters on the bottom of each figure. Sites for different protection patters observed in oxidized and reduced conditions are indicated with asterisks.

    Article Snippet: Initial binding reaction mixtures were incubated for 30 min at 22°C followed by a 15 min DNase I digestion that was initiated by adding 3 μl of DNase I (New England Biolabs) at an approximately 1:100 dilution (0.02 units/μl) in a footprint binding buffer, which gave partial probe digestion.

    Techniques: Binding Assay

    The β-gt can specifically modify 5hmC residues at a high efficiency. ( a ) Oligonucleotides that were either incubated in the presence or absence of the β-gt were digested with Taq I, treated with alkaline phosphatase, 5′-end labeled using T4 polynucleotide kinase and digested to 5′-mononucleotides using DNase I and Snake Venom Phosphodiesterase. Radiolabeled mononucleotides were analyzed by two-dimensional TLC. C, 3′-deoxyribocytosine-5′-monophosphate; T, 3′-deoxyribothymidine-5′-monophosphate; 5meC, 3′-deoxyribo-N5-methylcytosine-5′-monophosphate; 5hmC, 3′-deoxyribo-N5-hydroxymethylcytosine-5′-monophosphate. ( b ) HPLC coupled to tandem mass spectrometry was used to measure the efficiency of the β-gt reaction. Substrates analyzed were 2.7 kb linear PCR products of pUC18: the dC substrate contained only cytosine residues; the 5meC substrate was created by methylating the CpG dinucleotide of the cytosine substrate; the 5hmC substrate was created by using d5hmC in place of dCTP in the PCR reactions; the β-glu-5hmC substrate was created by incubating the 5hmC substrate with the β-gt in the presence of UDP-glucose. Control DNA was prepared from salmon sperm. LC/MS/MS chromatograms of the cytosine residues from each of the substrates are presented. Abbreviations: dC, 3′-deoxyribocytosine; 5me(dC), 3′-deoxyribo-N5-methylcytosine; 5hm(dC), 3′-deoxyribo-N5-hydroxymethylcytosine; 5-glu-hm(dC), 3′-deoxyribo-N5-(β- d -glucosyl(hydroxymethyl))cytosine. Asterisks indictes that cytosines are only 5meC modified at CpG sequences.

    Journal: Nucleic Acids Research

    Article Title: A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA

    doi: 10.1093/nar/gkr051

    Figure Lengend Snippet: The β-gt can specifically modify 5hmC residues at a high efficiency. ( a ) Oligonucleotides that were either incubated in the presence or absence of the β-gt were digested with Taq I, treated with alkaline phosphatase, 5′-end labeled using T4 polynucleotide kinase and digested to 5′-mononucleotides using DNase I and Snake Venom Phosphodiesterase. Radiolabeled mononucleotides were analyzed by two-dimensional TLC. C, 3′-deoxyribocytosine-5′-monophosphate; T, 3′-deoxyribothymidine-5′-monophosphate; 5meC, 3′-deoxyribo-N5-methylcytosine-5′-monophosphate; 5hmC, 3′-deoxyribo-N5-hydroxymethylcytosine-5′-monophosphate. ( b ) HPLC coupled to tandem mass spectrometry was used to measure the efficiency of the β-gt reaction. Substrates analyzed were 2.7 kb linear PCR products of pUC18: the dC substrate contained only cytosine residues; the 5meC substrate was created by methylating the CpG dinucleotide of the cytosine substrate; the 5hmC substrate was created by using d5hmC in place of dCTP in the PCR reactions; the β-glu-5hmC substrate was created by incubating the 5hmC substrate with the β-gt in the presence of UDP-glucose. Control DNA was prepared from salmon sperm. LC/MS/MS chromatograms of the cytosine residues from each of the substrates are presented. Abbreviations: dC, 3′-deoxyribocytosine; 5me(dC), 3′-deoxyribo-N5-methylcytosine; 5hm(dC), 3′-deoxyribo-N5-hydroxymethylcytosine; 5-glu-hm(dC), 3′-deoxyribo-N5-(β- d -glucosyl(hydroxymethyl))cytosine. Asterisks indictes that cytosines are only 5meC modified at CpG sequences.

    Article Snippet: Pellets were suspended in 5 µl DNase I buffer and 0.2 U DNase I (NEB) and 0.2 U snake venom phosphodiesterase (Worthington) was added to the reactions.

    Techniques: Incubation, Labeling, Thin Layer Chromatography, High Performance Liquid Chromatography, Mass Spectrometry, Polymerase Chain Reaction, Liquid Chromatography with Mass Spectroscopy, Modification

    hSWI/SNF remodeling of nucleosomes containing branched and nicked DNAs. (A) Analysis of hSWI/SNF remodeling of nucleosomes reconstituted with native, flap, hairpin, and nick templates by DNase I digestion. In each panel, lanes 1 show G-specific reaction markers of the native 5S DNA fragment, lanes 2 show DNase I digestion pattern of naked templates, lanes 3 are nucleosomes prior to DNase I digestion, lanes 4 show the DNase I cleavage pattern of nucleosomes incubated with hSWI/SNF without ATP, and lanes 5 show the DNase I cleavage patterns of nucleosomes incubated with hSWI/SNF and ATP for 15 min. (B) Effects of branched DNA structures on remodeling as determined by restriction enzyme accessibility assay. Glycerol-gradient-purified native, nicked, hairpin, and flap nucleosomes were incubated for the indicated times with hSWI/SNF in the presence or absence of ATP (open and solid symbols, respectively) and subjected to Eco RV digestion over a 45-min time course. The percent nucleosomes remaining uncut is plotted versus time of Eco RV digestion for native (diamonds), hairpin (squares), flap (triangles), and nicked (circles) nucleosomes.

    Journal: Molecular and Cellular Biology

    Article Title: hSWI/SNF-Catalyzed Nucleosome Sliding Does Not Occur Solely via a Twist-Diffusion Mechanism

    doi: 10.1128/MCB.22.21.7484-7490.2002

    Figure Lengend Snippet: hSWI/SNF remodeling of nucleosomes containing branched and nicked DNAs. (A) Analysis of hSWI/SNF remodeling of nucleosomes reconstituted with native, flap, hairpin, and nick templates by DNase I digestion. In each panel, lanes 1 show G-specific reaction markers of the native 5S DNA fragment, lanes 2 show DNase I digestion pattern of naked templates, lanes 3 are nucleosomes prior to DNase I digestion, lanes 4 show the DNase I cleavage pattern of nucleosomes incubated with hSWI/SNF without ATP, and lanes 5 show the DNase I cleavage patterns of nucleosomes incubated with hSWI/SNF and ATP for 15 min. (B) Effects of branched DNA structures on remodeling as determined by restriction enzyme accessibility assay. Glycerol-gradient-purified native, nicked, hairpin, and flap nucleosomes were incubated for the indicated times with hSWI/SNF in the presence or absence of ATP (open and solid symbols, respectively) and subjected to Eco RV digestion over a 45-min time course. The percent nucleosomes remaining uncut is plotted versus time of Eco RV digestion for native (diamonds), hairpin (squares), flap (triangles), and nicked (circles) nucleosomes.

    Article Snippet: For the DNase I assay, the bottom 215-mer strand was 3′ end labeled with the Klenow fragment (New England Biolabs) prior to the annealing reaction.

    Techniques: Incubation, Purification

    RPA subunits are differentially cross-linked when incubated alone or in combination with other repair factors. RPA was incubated with substrate DNA as described previously either alone or with other repair factors (at the same concentrations used to reconstitute excision repair) for 60 min and irradiated with black light, and then reaction mixtures were digested with DNase I. Following resolution in an SDS-10% polyacrylamide gel, the DNA-protein complexes were visualized by autoradiography (A). Lane 1 is a complete reaction, and lane 2 is RPA alone; to the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated with open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitation. Panel B is a graphic summarization of relative RPA70/RPA32 cross-linking values for RPA alone reactions ( n  = 8) and complete reactions ( n  = 16). Average values are plotted, and error bars represent the standard error. For each data set the relative RPA70 signal is defined as 1.

    Journal: Molecular and Cellular Biology

    Article Title: Molecular Anatomy of the Human Excision Nuclease Assembled at Sites of DNA Damage

    doi: 10.1128/MCB.22.16.5938-5945.2002

    Figure Lengend Snippet: RPA subunits are differentially cross-linked when incubated alone or in combination with other repair factors. RPA was incubated with substrate DNA as described previously either alone or with other repair factors (at the same concentrations used to reconstitute excision repair) for 60 min and irradiated with black light, and then reaction mixtures were digested with DNase I. Following resolution in an SDS-10% polyacrylamide gel, the DNA-protein complexes were visualized by autoradiography (A). Lane 1 is a complete reaction, and lane 2 is RPA alone; to the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated with open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitation. Panel B is a graphic summarization of relative RPA70/RPA32 cross-linking values for RPA alone reactions ( n = 8) and complete reactions ( n = 16). Average values are plotted, and error bars represent the standard error. For each data set the relative RPA70 signal is defined as 1.

    Article Snippet: T4 polynucleotide kinase and DNA ligase were purchased from New England BioLabs, DNase I was from Invitrogen, and the TnT Quick Coupled Transcription/Translation system was from Promega.

    Techniques: Recombinase Polymerase Amplification, Incubation, Irradiation, Autoradiography, Quantitation Assay

    Single-factor omission experiments for excision repair and cross-linking assays reveal that the third complex contains XPD. Repair factors (at the same concentrations used to reconstitute excision repair), with the omitted factor indicated, were incubated with psoralen-damaged DNA for 60 min and then either processed for detection of excised oligomers (A) or photo-cross-linked to detect DNA-protein complexes (B). To detect excision, deproteinized DNA was resolved in a 10% sequencing gel with  Hin fI digested DNA as size markers (mobility positions, in nucleotides, are shown to the left) and visualized by autoradiography (A). To detect DNA-protein complexes, reaction mixtures were resolved in an SDS-8% polyacrylamide gel with size markers (indicated to the left) and visualized by autoradiography (B). Only the portion of the gel corresponding to protein-DNA complexes greater than approximately 70 kDa is shown. Panel C illustrates in vitro-labeled proteins resolved in an SDS-10% polyacrylamide gel with a complete repair reaction that was cross-linked and treated with DNase I; only the relevant section of the gel is shown to illustrate the migration of the TFIIH and RPA70 complexes (lane 4) relative to  35 S-labeled XPB, RPA70, and XPD proteins (lanes 1 to 3).

    Journal: Molecular and Cellular Biology

    Article Title: Molecular Anatomy of the Human Excision Nuclease Assembled at Sites of DNA Damage

    doi: 10.1128/MCB.22.16.5938-5945.2002

    Figure Lengend Snippet: Single-factor omission experiments for excision repair and cross-linking assays reveal that the third complex contains XPD. Repair factors (at the same concentrations used to reconstitute excision repair), with the omitted factor indicated, were incubated with psoralen-damaged DNA for 60 min and then either processed for detection of excised oligomers (A) or photo-cross-linked to detect DNA-protein complexes (B). To detect excision, deproteinized DNA was resolved in a 10% sequencing gel with Hin fI digested DNA as size markers (mobility positions, in nucleotides, are shown to the left) and visualized by autoradiography (A). To detect DNA-protein complexes, reaction mixtures were resolved in an SDS-8% polyacrylamide gel with size markers (indicated to the left) and visualized by autoradiography (B). Only the portion of the gel corresponding to protein-DNA complexes greater than approximately 70 kDa is shown. Panel C illustrates in vitro-labeled proteins resolved in an SDS-10% polyacrylamide gel with a complete repair reaction that was cross-linked and treated with DNase I; only the relevant section of the gel is shown to illustrate the migration of the TFIIH and RPA70 complexes (lane 4) relative to 35 S-labeled XPB, RPA70, and XPD proteins (lanes 1 to 3).

    Article Snippet: T4 polynucleotide kinase and DNA ligase were purchased from New England BioLabs, DNase I was from Invitrogen, and the TnT Quick Coupled Transcription/Translation system was from Promega.

    Techniques: Incubation, Sequencing, Autoradiography, In Vitro, Labeling, Migration

    Repair factor binding is preferentially located 5′ to the psoralen damage. Panel A is a schematic diagram of the psoralen 140-bp duplex, highlighting the central 20 nt; the substrate extends 60 nt in both the 5′ and 3′ directions, and the locations of 32 P radiolabel are indicated by arrows above the sequence. Panel B is an autoradiograph of an SDS-10% polyacrylamide gel. The complete complement of repair factors was incubated with either the 3′ labeled substrate (lane 1) or the 5′ labeled substrate (lane 2), irradiated with black light, and reaction mixtures were digested with DNase I prior to electrophoresis and autoradiography. To the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated by open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitative analyses.

    Journal: Molecular and Cellular Biology

    Article Title: Molecular Anatomy of the Human Excision Nuclease Assembled at Sites of DNA Damage

    doi: 10.1128/MCB.22.16.5938-5945.2002

    Figure Lengend Snippet: Repair factor binding is preferentially located 5′ to the psoralen damage. Panel A is a schematic diagram of the psoralen 140-bp duplex, highlighting the central 20 nt; the substrate extends 60 nt in both the 5′ and 3′ directions, and the locations of 32 P radiolabel are indicated by arrows above the sequence. Panel B is an autoradiograph of an SDS-10% polyacrylamide gel. The complete complement of repair factors was incubated with either the 3′ labeled substrate (lane 1) or the 5′ labeled substrate (lane 2), irradiated with black light, and reaction mixtures were digested with DNase I prior to electrophoresis and autoradiography. To the left are shown the positions of molecular mass markers resolved in the same gel. The fainter bands migrating between RPA70-DNA and RPA32-DNA complexes (indicated by open arrows) result from cross-linking proteolytic fragments of RPA70 to the substrate and were not included in quantitative analyses.

    Article Snippet: T4 polynucleotide kinase and DNA ligase were purchased from New England BioLabs, DNase I was from Invitrogen, and the TnT Quick Coupled Transcription/Translation system was from Promega.

    Techniques: Binding Assay, Sequencing, Autoradiography, Incubation, Labeling, Irradiation, Electrophoresis

    CbpA protects plasmid DNA from degradation by nucleases. A. The panel shows naked plasmid and complexes with CbpA run on a 1% agarose gel. Plasmid (30 ng) was pre-incubated with 0, 0.5, 1.0, or 2.0 µM CbpA. Note that only every other lane has been loaded on the gel. B. The panel shows plasmid run on a 1% agarose gel. Plasmids (77 ng) were treated with different combinations of DNase I, BSA (1, 2 or 3 µM) and CbpA (1, 2 or 3 µM).

    Journal: Molecular Microbiology

    Article Title: Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA

    doi: 10.1111/j.1365-2958.2010.07292.x

    Figure Lengend Snippet: CbpA protects plasmid DNA from degradation by nucleases. A. The panel shows naked plasmid and complexes with CbpA run on a 1% agarose gel. Plasmid (30 ng) was pre-incubated with 0, 0.5, 1.0, or 2.0 µM CbpA. Note that only every other lane has been loaded on the gel. B. The panel shows plasmid run on a 1% agarose gel. Plasmids (77 ng) were treated with different combinations of DNase I, BSA (1, 2 or 3 µM) and CbpA (1, 2 or 3 µM).

    Article Snippet: DNase I protection assays Purified plasmid DNA (77 ng) was pre-incubated with CbpA or BSA, at 37°C, in DNase I reaction buffer (NEB) in a final volume of 10 µl.

    Techniques: Plasmid Preparation, Agarose Gel Electrophoresis, Incubation