dnase  (New England Biolabs)


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  • 99
    Name:
    DNase I RNase free
    Description:
    DNase I RNase free 5 000 units
    Catalog Number:
    M0303L
    Price:
    282
    Category:
    Deoxyribonucleases DNase
    Size:
    5 000 units
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    Structured Review

    New England Biolabs dnase
    DNase I RNase free
    DNase I RNase free 5 000 units
    https://www.bioz.com/result/dnase/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dnase - by Bioz Stars, 2021-06
    99/100 stars

    Images

    1) Product Images from "Holliday junction affinity of the base excision repair factor Endo III contributes to cholera toxin phage integration"

    Article Title: Holliday junction affinity of the base excision repair factor Endo III contributes to cholera toxin phage integration

    Journal: The EMBO Journal

    doi: 10.1038/emboj.2012.219

    Endo III blocks XerC-catalysis on pseudo-HJ and displaces it from them. ( A ) Scheme of the suicide pseudo-HJ indicating the mismatch engineered to slow down re-ligation after XerC-cleavage. KMnO 4 sensitive residues in the XerC- and XerD-binding att P(+) arms are indicated by a star. ( B ) Resolution of att P(+)/ dif suicide pseudo-HJs. Legend as in Figure 4D . ( C ) DNase I protection and ( D ) KMnO 4 sensitivity assays of the att P(+)/ dif 1 pseudo-HJ substrate. The analysed strand was labelled on its 5′ end. A scheme of the analysed strand is drawn on the left of the gels. KMnO 4 sensitive residues in the XerC- and XerD-binding sites are indicated by a star.
    Figure Legend Snippet: Endo III blocks XerC-catalysis on pseudo-HJ and displaces it from them. ( A ) Scheme of the suicide pseudo-HJ indicating the mismatch engineered to slow down re-ligation after XerC-cleavage. KMnO 4 sensitive residues in the XerC- and XerD-binding att P(+) arms are indicated by a star. ( B ) Resolution of att P(+)/ dif suicide pseudo-HJs. Legend as in Figure 4D . ( C ) DNase I protection and ( D ) KMnO 4 sensitivity assays of the att P(+)/ dif 1 pseudo-HJ substrate. The analysed strand was labelled on its 5′ end. A scheme of the analysed strand is drawn on the left of the gels. KMnO 4 sensitive residues in the XerC- and XerD-binding sites are indicated by a star.

    Techniques Used: Ligation, Binding Assay

    2) Product Images from "Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis"

    Article Title: Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis

    Journal: bioRxiv

    doi: 10.1101/852095

    AcNPM1 co-occupies with RNA Pol II, chromatin remodeling factors and transcription factors at transcriptional regulatory elements. (A) Plot showing the percent number of AcNPM1 peaks overlapped with ChromHMM + Segway combined segmentation for HeLa S3 genome from the UCSC genome browser. (Key: TSS, predicted promoter region including TSS; PF, predicted promoter flanking region; E, enhancer; WE, predicted weak enhancer or open chromatin cis-regulatory element; CTCF, CTCF enriched element; T, predicted transcribed region; R, predicted repressed or low activity region; None, unclassified). (B) Percent number of TSS and enhancer regions identified by ChromHMM + Segway combined segmentation for HeLa S3, overlapped with AcNPM1 peaks. (C) UCSC genome browser snapshot showing AcNPM1 enrichment at TSS and enhancer regions defined by ChromHMM + Segway combined segmentation for HeLa S3 genome. (Key: TSS, predicted promoter region including TSS; E, enhancer). (D) Boxplots showing AcNPM1 read density on AcNPM1 peaks that overlap or do not overlap DNase I hypersensitive sites (DHSs). (E) Boxplots showing AcNPM1 read density on AcNPM1 peaks with high or low enrichment of H3K27ac. (F-G) Boxplots showing AcNPM1 read density on AcNPM1 peaks that overlap or do not overlap (F) p300 and (G) RNA Pol II (Pol2). (H) Transcription factor binding motifs enriched in AcNPM1 peaks and broadly grouped by transcription factor family. P -value
    Figure Legend Snippet: AcNPM1 co-occupies with RNA Pol II, chromatin remodeling factors and transcription factors at transcriptional regulatory elements. (A) Plot showing the percent number of AcNPM1 peaks overlapped with ChromHMM + Segway combined segmentation for HeLa S3 genome from the UCSC genome browser. (Key: TSS, predicted promoter region including TSS; PF, predicted promoter flanking region; E, enhancer; WE, predicted weak enhancer or open chromatin cis-regulatory element; CTCF, CTCF enriched element; T, predicted transcribed region; R, predicted repressed or low activity region; None, unclassified). (B) Percent number of TSS and enhancer regions identified by ChromHMM + Segway combined segmentation for HeLa S3, overlapped with AcNPM1 peaks. (C) UCSC genome browser snapshot showing AcNPM1 enrichment at TSS and enhancer regions defined by ChromHMM + Segway combined segmentation for HeLa S3 genome. (Key: TSS, predicted promoter region including TSS; E, enhancer). (D) Boxplots showing AcNPM1 read density on AcNPM1 peaks that overlap or do not overlap DNase I hypersensitive sites (DHSs). (E) Boxplots showing AcNPM1 read density on AcNPM1 peaks with high or low enrichment of H3K27ac. (F-G) Boxplots showing AcNPM1 read density on AcNPM1 peaks that overlap or do not overlap (F) p300 and (G) RNA Pol II (Pol2). (H) Transcription factor binding motifs enriched in AcNPM1 peaks and broadly grouped by transcription factor family. P -value

    Techniques Used: Activity Assay, Binding Assay

    3) Product Images from "Transposase assisted tagmentation of RNA/DNA hybrid duplexes"

    Article Title: Transposase assisted tagmentation of RNA/DNA hybrid duplexes

    Journal: bioRxiv

    doi: 10.1101/2020.01.29.926105

    Tagmentation activity of Tn5 transposome on RNA/DNA hybrids. (a) Denaturing (8 M urea) polyacrylamide gel analysis of reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 1: ssRNA marker. Lane 2: in vitro transcribed mRNA (IRF9). Lane 3 4: reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 5: reverse transcription product treated with DNase I. Lane 6: reverse transcription product treated with RNase H. ssRNA and ssDNA is marked with a red asterisk and a blue pound sign, respectively. (b) Gel picture showing size distribution of RNA/DNA hybrids products of 50 μl reaction systems without Tn5 transposome, and with 5 μl, 10 μl, and 15 μl Tn5 transposome, respectively. The blue and orange patches denote small and large fragments, respectively. (c) qPCR amplification curve of tagmentation products without Tn5 treatment or with Tn5 treatment in three different buffers (see methods). Average Ct values are 26.41, 18.39, 18.33 and 18.34, respectively. (d) Sanger sequencing chromatograms of PCR products following RNA/DNA hybrid tagmentation and strand extension. Adaptor A and B sequences are highlighted with blue background color and insert sequences are highlighted with yellow background.
    Figure Legend Snippet: Tagmentation activity of Tn5 transposome on RNA/DNA hybrids. (a) Denaturing (8 M urea) polyacrylamide gel analysis of reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 1: ssRNA marker. Lane 2: in vitro transcribed mRNA (IRF9). Lane 3 4: reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 5: reverse transcription product treated with DNase I. Lane 6: reverse transcription product treated with RNase H. ssRNA and ssDNA is marked with a red asterisk and a blue pound sign, respectively. (b) Gel picture showing size distribution of RNA/DNA hybrids products of 50 μl reaction systems without Tn5 transposome, and with 5 μl, 10 μl, and 15 μl Tn5 transposome, respectively. The blue and orange patches denote small and large fragments, respectively. (c) qPCR amplification curve of tagmentation products without Tn5 treatment or with Tn5 treatment in three different buffers (see methods). Average Ct values are 26.41, 18.39, 18.33 and 18.34, respectively. (d) Sanger sequencing chromatograms of PCR products following RNA/DNA hybrid tagmentation and strand extension. Adaptor A and B sequences are highlighted with blue background color and insert sequences are highlighted with yellow background.

    Techniques Used: Activity Assay, In Vitro, Marker, Real-time Polymerase Chain Reaction, Amplification, Sequencing, Polymerase Chain Reaction

    4) Product Images from "Transcriptome analysis of root‐knot nematode (Meloidogyne incognita)‐infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both host and nematode during susceptible and resistance responses"

    Article Title: Transcriptome analysis of root‐knot nematode (Meloidogyne incognita)‐infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both host and nematode during susceptible and resistance responses

    Journal: Molecular Plant Pathology

    doi: 10.1111/mpp.12547

    (a) Distribution of significant differentially expressed genes (DEGs) in tomato at different stages during the susceptible response. (b) Comparative expression profile of tomato DEGs detected during the susceptible (Pusa Ruby, PR) and resistance (transgenic Money Maker, M36) responses at stage 2. Differential expression was calculated with respect to the corresponding uninfected controls. Each row of the heatmap represents a gene and each column represents a stage of disease development. The colour key is given in the top‐left corner of the figure. (c, d) Quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR) validation of RNA sequencing (RNA‐seq) data for the tomato genes, receptor‐like kinase and glucan endo‐1,3‐β‐glucosidase, during resistance and susceptible responses, respectively. The y axes represent the relative fold change (calculated using the ΔΔ Ct method) in gene expression at various stages relative to the corresponding uninfected controls. The data are representative of two technical replicates and three independent biological replicates. Bars indicate standard errors. I, infected; UI, uninfected.
    Figure Legend Snippet: (a) Distribution of significant differentially expressed genes (DEGs) in tomato at different stages during the susceptible response. (b) Comparative expression profile of tomato DEGs detected during the susceptible (Pusa Ruby, PR) and resistance (transgenic Money Maker, M36) responses at stage 2. Differential expression was calculated with respect to the corresponding uninfected controls. Each row of the heatmap represents a gene and each column represents a stage of disease development. The colour key is given in the top‐left corner of the figure. (c, d) Quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR) validation of RNA sequencing (RNA‐seq) data for the tomato genes, receptor‐like kinase and glucan endo‐1,3‐β‐glucosidase, during resistance and susceptible responses, respectively. The y axes represent the relative fold change (calculated using the ΔΔ Ct method) in gene expression at various stages relative to the corresponding uninfected controls. The data are representative of two technical replicates and three independent biological replicates. Bars indicate standard errors. I, infected; UI, uninfected.

    Techniques Used: Expressing, Transgenic Assay, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, RNA Sequencing Assay, Infection

    5) Product Images from "Transposase-assisted tagmentation of RNA/DNA hybrid duplexes"

    Article Title: Transposase-assisted tagmentation of RNA/DNA hybrid duplexes

    Journal: eLife

    doi: 10.7554/eLife.54919

    Tagmentation activity of Tn5 transposome on RNA/DNA hybrids. ( a ) Denaturing (8 M urea) polyacrylamide gel analysis of reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 1: ssRNA marker. Lane 2: in vitro transcribed mRNA (IRF9). Lane 3 and 4: reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 5: reverse transcription product treated with DNase I. Lane 6: reverse transcription product treated with RNase H. ssRNA and ssDNA is marked with a red asterisk and a blue pound sign, respectively. ( b ) Gel picture showing size distribution of RNA/DNA hybrids products of 50 μl reaction systems without Tn5 transposome, and with 5 μl, 10 μl, and 15 μl Tn5 transposome, respectively. The blue and orange patches denote small and large fragments, respectively. ( c ) qPCR amplification curve of tagmentation products without Tn5 treatment or with Tn5 treatment in three different buffers (see Methods). Average Ct values of two technical replicates are 26.41, 18.39, 18.33 and 18.34, respectively. ( d ) Sanger sequencing chromatograms of PCR products following RNA/DNA hybrid tagmentation and strand extension. Adaptor A and B sequences are highlighted with blue background color and insert sequences are highlighted with yellow background. ( e ) Assessment of gDNA contamination by qPCR of represented genes. ( f ) Dot blot analysis of a series of diluted samples using the anti-hybrid S9.6 antibody. S9.6 antibody showed no cross-reactivity with dsDNA and the successful hybrids productions were confirmed in CLuc annealed products and mRNA RT products. ( g ) Native PAGE analysis of 150 bp CLuc annealed products under different annealing conditions. (Annealed hybrids 1: RNA:DNA = 2:1; Annealed hybrids 2: RNA:DNA = 1.2:1; Annealed dsDNA 1: ssDNA:ssDNA-rev = 2:1; Annealed dsDNA 2: ssDNA:ssDNA-rev = 1.2:1; See Methods). ( h ) qPCR amplification curve of tagmentation products of CLuc annealed RNA/DNA hybrid and dsDNA products with Tn5 treatment or without Tn5 treatment. Average Ct values of three technical replicates of annealed hybrid products are 22.68 and 30.4, respectively. Average Ct values of three technical replicates of annealed dsDNA products are 18.08 and 30.83, respectively.
    Figure Legend Snippet: Tagmentation activity of Tn5 transposome on RNA/DNA hybrids. ( a ) Denaturing (8 M urea) polyacrylamide gel analysis of reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 1: ssRNA marker. Lane 2: in vitro transcribed mRNA (IRF9). Lane 3 and 4: reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 5: reverse transcription product treated with DNase I. Lane 6: reverse transcription product treated with RNase H. ssRNA and ssDNA is marked with a red asterisk and a blue pound sign, respectively. ( b ) Gel picture showing size distribution of RNA/DNA hybrids products of 50 μl reaction systems without Tn5 transposome, and with 5 μl, 10 μl, and 15 μl Tn5 transposome, respectively. The blue and orange patches denote small and large fragments, respectively. ( c ) qPCR amplification curve of tagmentation products without Tn5 treatment or with Tn5 treatment in three different buffers (see Methods). Average Ct values of two technical replicates are 26.41, 18.39, 18.33 and 18.34, respectively. ( d ) Sanger sequencing chromatograms of PCR products following RNA/DNA hybrid tagmentation and strand extension. Adaptor A and B sequences are highlighted with blue background color and insert sequences are highlighted with yellow background. ( e ) Assessment of gDNA contamination by qPCR of represented genes. ( f ) Dot blot analysis of a series of diluted samples using the anti-hybrid S9.6 antibody. S9.6 antibody showed no cross-reactivity with dsDNA and the successful hybrids productions were confirmed in CLuc annealed products and mRNA RT products. ( g ) Native PAGE analysis of 150 bp CLuc annealed products under different annealing conditions. (Annealed hybrids 1: RNA:DNA = 2:1; Annealed hybrids 2: RNA:DNA = 1.2:1; Annealed dsDNA 1: ssDNA:ssDNA-rev = 2:1; Annealed dsDNA 2: ssDNA:ssDNA-rev = 1.2:1; See Methods). ( h ) qPCR amplification curve of tagmentation products of CLuc annealed RNA/DNA hybrid and dsDNA products with Tn5 treatment or without Tn5 treatment. Average Ct values of three technical replicates of annealed hybrid products are 22.68 and 30.4, respectively. Average Ct values of three technical replicates of annealed dsDNA products are 18.08 and 30.83, respectively.

    Techniques Used: Activity Assay, In Vitro, Marker, Real-time Polymerase Chain Reaction, Amplification, Sequencing, Polymerase Chain Reaction, Dot Blot, Clear Native PAGE

    Related Articles

    Footprinting:

    Article Title: The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding
    Article Snippet: After incubation at 22°C for 10 min, the binding reaction mixtures were loaded on 5% (w/v) native polyacrylamide gels and run in TBE buffer at 100 V for 45 min. EMSA data were collected and analysed on a PhosphoImager (FujiFilm) using Multi Gauge image analysis software (FujiFilm). .. DNase I footprinting Templates for DNase I footprinting were amplified by PCR using one unlabelled primer and one primer 5′-end labelled using [γ32 -P] ATP and T4 polynucleotide kinase (New England Biolabs). ..

    Amplification:

    Article Title: The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding
    Article Snippet: After incubation at 22°C for 10 min, the binding reaction mixtures were loaded on 5% (w/v) native polyacrylamide gels and run in TBE buffer at 100 V for 45 min. EMSA data were collected and analysed on a PhosphoImager (FujiFilm) using Multi Gauge image analysis software (FujiFilm). .. DNase I footprinting Templates for DNase I footprinting were amplified by PCR using one unlabelled primer and one primer 5′-end labelled using [γ32 -P] ATP and T4 polynucleotide kinase (New England Biolabs). ..

    Polymerase Chain Reaction:

    Article Title: The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding
    Article Snippet: After incubation at 22°C for 10 min, the binding reaction mixtures were loaded on 5% (w/v) native polyacrylamide gels and run in TBE buffer at 100 V for 45 min. EMSA data were collected and analysed on a PhosphoImager (FujiFilm) using Multi Gauge image analysis software (FujiFilm). .. DNase I footprinting Templates for DNase I footprinting were amplified by PCR using one unlabelled primer and one primer 5′-end labelled using [γ32 -P] ATP and T4 polynucleotide kinase (New England Biolabs). ..

    Lysis:

    Article Title: Detecting RNA-RNA interactions in E. coli using a modified CLASH method
    Article Snippet: Identification of ligated RNAs This study (Fig. ) employed in vivo crosslinking of RNA duplexes with the AMT molecule, which can, upon 365 nm UV irradiation, generate inter-strand adducts between juxtaposed uridine bases [ ]. .. Following cell lysis and RNA extraction, DNA residues were digested by DNase I, and single strand RNAs and free RNA overhangs adjacent to duplexes were digested by RNase T1. .. Then, the residual single strand RNAs were hybridized with 20 nt oligonucleotides and digested by RNase H three times.

    RNA Extraction:

    Article Title: Detecting RNA-RNA interactions in E. coli using a modified CLASH method
    Article Snippet: Identification of ligated RNAs This study (Fig. ) employed in vivo crosslinking of RNA duplexes with the AMT molecule, which can, upon 365 nm UV irradiation, generate inter-strand adducts between juxtaposed uridine bases [ ]. .. Following cell lysis and RNA extraction, DNA residues were digested by DNase I, and single strand RNAs and free RNA overhangs adjacent to duplexes were digested by RNase T1. .. Then, the residual single strand RNAs were hybridized with 20 nt oligonucleotides and digested by RNase H three times.

    Binding Assay:

    Article Title: Evidence that Altered Cis Element Spacing Affects PpsR Mediated Redox Control of Photosynthesis Gene Expression in Rubrivivax gelatinosus
    Article Snippet: Individual footprint reactions were initiated with a 22 μl binding reaction mixture that contained 12.5 mM HEPES (pH 7.8), 5 mM K-acetate (pH 8.0), 2.5 mM Mg-acetate, 1 mM CaCl2 , 12.5 μg/ml bovine serum albumin [ ], 0.3 mg/ml heparin, 200 nM of fluorescence-labeled DNA probe and various amounts of purified protein. .. 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. ..

    Incubation:

    Article Title: Evidence that Altered Cis Element Spacing Affects PpsR Mediated Redox Control of Photosynthesis Gene Expression in Rubrivivax gelatinosus
    Article Snippet: Individual footprint reactions were initiated with a 22 μl binding reaction mixture that contained 12.5 mM HEPES (pH 7.8), 5 mM K-acetate (pH 8.0), 2.5 mM Mg-acetate, 1 mM CaCl2 , 12.5 μg/ml bovine serum albumin [ ], 0.3 mg/ml heparin, 200 nM of fluorescence-labeled DNA probe and various amounts of purified protein. .. 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. ..

    Article Title: Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription
    Article Snippet: .. Nuclei were incubated with various concentrations of Dnase I (0–1.5 units, NEB) for 10 minutes at 37°C. .. Reactions were stopped by adding an equal volume of 2× Lysis Buffer (1% SDS, 200 mM NaCl, 10 mM EDTA, 20 mM Tris pH 7.5, 0.4 mg/ml proteinase K) and incubated overnight at 37°C.

    Synthesized:

    Article Title: Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae
    Article Snippet: The quantity of 5′-methylguanosine-capped RNA was measured by NanoDrop (Thermo Fisher) analysis and its integrity was determined with an Agilent 2100 Bioanalyzer. .. 3′-RACE analysis of CPA-sRNAs using 5′-capped RNA 5′-methylguanosine-capped RNA was treated with DNase I (NEB) to remove any contaminating genomic DNA. cDNA was synthesized in 20 µl reactions by adding the following reagents: 1 µg of 5′-methylguanosine-capped RNA, 50 picomole of 3′-oligo(dT) 20 VN primer, 5 mM of dNTPs, 1 U of RNaseOut (Invitrogen) and 5 U of Superscript III (Invitrogen). ..

    other:

    Article Title: Campylobacter-Induced Interleukin-8 Secretion in Polarized Human Intestinal Epithelial Cells Requires Campylobacter-Secreted Cytolethal Distending Toxin- and Toll-Like Receptor-Mediated Activation of NF-?B ▿
    Article Snippet: However, treatment of the basolateral conditioned supernatant with DNase I did not significantly change its ability to induce IL-8 secretion (Fig. ).

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    New England Biolabs dnase i
    Non-overlapping regulatory modules within angptl4 intron 3 confer liver, islet, and enterocyte-specific reporter expression. (A) Depiction of the 6 dpf zebrafish showing liver (li, green), intestine (in, blue), swim bladder (sb, grey), and muscle (mu, grey), with the fish oriented anterior (a) to the left and posterior (p) to the right. The opposite orientation reveals the exocrine pancreas (pa, yellow) and islet (is, orange). (B) Scaled schematic of the zebrafish angptl4 locus and non-coding DNA assayed for regulatory potential. Modules are color coded according to the tissues in which they confer expression. Ratios of islet or intestine positive fish versus total fish expressing gfp are shown in parentheses next to truncation labels. (C–N) Representative images of GFP reporter expression in mosaic (column 1) and F 1 stable (column 2) animals driven by each non-coding DNA region (rows). Scale bars = 100 µm; li = liver, is = islet, in = intestine, sb = swim bladder. Colored arrowheads indicate tissue with specific reporter expression. (C–D) Full-length intron 3 (in3; 2,136 bp) is sufficient to promote expression of the reporter in the liver, islet (D, inset, scale bar = 50 µm), and intestine. (E–F) Truncation in3.1 (1,219 bp) confers expression in the liver. (G–H) Truncation in3.2 (701 bp) confers expression in both the intestine and islet (H, inset). Inset scale bar = 50 µm. (I–J) Truncation in3.3 (387 bp) confers islet expression. A transverse section (inset, J) reveals islet expression (nuclei stained with DAPI). Inset scale bar = 50 µm. (K–L) Truncation in3.4 (316 bp) confers intestinal expression. Insets in panels K and L contain transverse sections showing expression localized to the intestinal epithelium (nuclei stained with DAPI). Inset scale bar = 25 µm. The dotted lines in panels D, G, H, and I outline the pancreas. The white arrows in panels H, K, and L mark the boundary between the anterior intestine (segment 1) and mid-intestine (segment 2). (M–N) Cells expressing GFP driven by the in3.4 regulatory module colocalize with a marker (4E8, red, white arrow) of the brush border of absorptive enterocytes, but fail to co-localize with marker for secretory cells (2F11, red, asterisk). Nuclei stained with DAPI. Scale bars = 5 µm. (O) Intercross of Tg(in3.2-Mmu.Fos:tdTomato) with β-cell specific reporter line ( Tg(ins:CFP-NTR) s892 ) show colocalization of tdTomato and CFP in the islet. Scale bars = 10 µm. (P) Quantitative PCR shows that the in3.4 module and the angptl4 promoter (TATA box), but not the in3.3 module, are hypersensitive to <t>DNase</t> I cleavage in intestinal epithelial cells isolated from adult zebrafish. Asterisks denote P-value
    Dnase I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnase i/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dnase i - by Bioz Stars, 2021-06
    99/100 stars
      Buy from Supplier

    Image Search Results


    Non-overlapping regulatory modules within angptl4 intron 3 confer liver, islet, and enterocyte-specific reporter expression. (A) Depiction of the 6 dpf zebrafish showing liver (li, green), intestine (in, blue), swim bladder (sb, grey), and muscle (mu, grey), with the fish oriented anterior (a) to the left and posterior (p) to the right. The opposite orientation reveals the exocrine pancreas (pa, yellow) and islet (is, orange). (B) Scaled schematic of the zebrafish angptl4 locus and non-coding DNA assayed for regulatory potential. Modules are color coded according to the tissues in which they confer expression. Ratios of islet or intestine positive fish versus total fish expressing gfp are shown in parentheses next to truncation labels. (C–N) Representative images of GFP reporter expression in mosaic (column 1) and F 1 stable (column 2) animals driven by each non-coding DNA region (rows). Scale bars = 100 µm; li = liver, is = islet, in = intestine, sb = swim bladder. Colored arrowheads indicate tissue with specific reporter expression. (C–D) Full-length intron 3 (in3; 2,136 bp) is sufficient to promote expression of the reporter in the liver, islet (D, inset, scale bar = 50 µm), and intestine. (E–F) Truncation in3.1 (1,219 bp) confers expression in the liver. (G–H) Truncation in3.2 (701 bp) confers expression in both the intestine and islet (H, inset). Inset scale bar = 50 µm. (I–J) Truncation in3.3 (387 bp) confers islet expression. A transverse section (inset, J) reveals islet expression (nuclei stained with DAPI). Inset scale bar = 50 µm. (K–L) Truncation in3.4 (316 bp) confers intestinal expression. Insets in panels K and L contain transverse sections showing expression localized to the intestinal epithelium (nuclei stained with DAPI). Inset scale bar = 25 µm. The dotted lines in panels D, G, H, and I outline the pancreas. The white arrows in panels H, K, and L mark the boundary between the anterior intestine (segment 1) and mid-intestine (segment 2). (M–N) Cells expressing GFP driven by the in3.4 regulatory module colocalize with a marker (4E8, red, white arrow) of the brush border of absorptive enterocytes, but fail to co-localize with marker for secretory cells (2F11, red, asterisk). Nuclei stained with DAPI. Scale bars = 5 µm. (O) Intercross of Tg(in3.2-Mmu.Fos:tdTomato) with β-cell specific reporter line ( Tg(ins:CFP-NTR) s892 ) show colocalization of tdTomato and CFP in the islet. Scale bars = 10 µm. (P) Quantitative PCR shows that the in3.4 module and the angptl4 promoter (TATA box), but not the in3.3 module, are hypersensitive to DNase I cleavage in intestinal epithelial cells isolated from adult zebrafish. Asterisks denote P-value

    Journal: PLoS Genetics

    Article Title: Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription

    doi: 10.1371/journal.pgen.1002585

    Figure Lengend Snippet: Non-overlapping regulatory modules within angptl4 intron 3 confer liver, islet, and enterocyte-specific reporter expression. (A) Depiction of the 6 dpf zebrafish showing liver (li, green), intestine (in, blue), swim bladder (sb, grey), and muscle (mu, grey), with the fish oriented anterior (a) to the left and posterior (p) to the right. The opposite orientation reveals the exocrine pancreas (pa, yellow) and islet (is, orange). (B) Scaled schematic of the zebrafish angptl4 locus and non-coding DNA assayed for regulatory potential. Modules are color coded according to the tissues in which they confer expression. Ratios of islet or intestine positive fish versus total fish expressing gfp are shown in parentheses next to truncation labels. (C–N) Representative images of GFP reporter expression in mosaic (column 1) and F 1 stable (column 2) animals driven by each non-coding DNA region (rows). Scale bars = 100 µm; li = liver, is = islet, in = intestine, sb = swim bladder. Colored arrowheads indicate tissue with specific reporter expression. (C–D) Full-length intron 3 (in3; 2,136 bp) is sufficient to promote expression of the reporter in the liver, islet (D, inset, scale bar = 50 µm), and intestine. (E–F) Truncation in3.1 (1,219 bp) confers expression in the liver. (G–H) Truncation in3.2 (701 bp) confers expression in both the intestine and islet (H, inset). Inset scale bar = 50 µm. (I–J) Truncation in3.3 (387 bp) confers islet expression. A transverse section (inset, J) reveals islet expression (nuclei stained with DAPI). Inset scale bar = 50 µm. (K–L) Truncation in3.4 (316 bp) confers intestinal expression. Insets in panels K and L contain transverse sections showing expression localized to the intestinal epithelium (nuclei stained with DAPI). Inset scale bar = 25 µm. The dotted lines in panels D, G, H, and I outline the pancreas. The white arrows in panels H, K, and L mark the boundary between the anterior intestine (segment 1) and mid-intestine (segment 2). (M–N) Cells expressing GFP driven by the in3.4 regulatory module colocalize with a marker (4E8, red, white arrow) of the brush border of absorptive enterocytes, but fail to co-localize with marker for secretory cells (2F11, red, asterisk). Nuclei stained with DAPI. Scale bars = 5 µm. (O) Intercross of Tg(in3.2-Mmu.Fos:tdTomato) with β-cell specific reporter line ( Tg(ins:CFP-NTR) s892 ) show colocalization of tdTomato and CFP in the islet. Scale bars = 10 µm. (P) Quantitative PCR shows that the in3.4 module and the angptl4 promoter (TATA box), but not the in3.3 module, are hypersensitive to DNase I cleavage in intestinal epithelial cells isolated from adult zebrafish. Asterisks denote P-value

    Article Snippet: Nuclei were incubated with various concentrations of Dnase I (0–1.5 units, NEB) for 10 minutes at 37°C.

    Techniques: Expressing, Fluorescence In Situ Hybridization, Staining, Marker, Real-time Polymerase Chain Reaction, Isolation

    Characterization of PfaF binding to the pfaA promoter. (A) Electrophoretic mobility shift assay demonstrating PfaF binding to the pfaA promoter in a concentration dependent manner. (B) Binding of FAM-labeled probe (+FAM) is partially inhibited by the inclusion of molar excess of unlabeled probe (-FAM) indicating that PfaF binding is specific. (C) Addition of oleoyl-CoA at the indicated concentrations reverses the binding of PfaF to the probe in a concentration dependent manner. (D) DNase I footprinting analysis of PfaF binding to pfaA promoter. Purified PfaF was added at the indicated concentrations and subjected to DNase I digestion as described in Materials and Methods. Chromatograms and sequencing traces shown correspond to the coding strand and the box indicates the region protected from digestion by PfaF. (E) DNA sequence of pfaA probe used in mobility shift and footprinting assays. Putative promoter elements (−35 and −10 sites) and transcriptional start site (arrow) were previously determined ( 25 ). Region protected by PfaF indicated in bold, green, underlined font.

    Journal: bioRxiv

    Article Title: Genetic regulation of the bacterial omega-3 polyunsaturated fatty acid biosynthesis pathway

    doi: 10.1101/2020.01.28.924217

    Figure Lengend Snippet: Characterization of PfaF binding to the pfaA promoter. (A) Electrophoretic mobility shift assay demonstrating PfaF binding to the pfaA promoter in a concentration dependent manner. (B) Binding of FAM-labeled probe (+FAM) is partially inhibited by the inclusion of molar excess of unlabeled probe (-FAM) indicating that PfaF binding is specific. (C) Addition of oleoyl-CoA at the indicated concentrations reverses the binding of PfaF to the probe in a concentration dependent manner. (D) DNase I footprinting analysis of PfaF binding to pfaA promoter. Purified PfaF was added at the indicated concentrations and subjected to DNase I digestion as described in Materials and Methods. Chromatograms and sequencing traces shown correspond to the coding strand and the box indicates the region protected from digestion by PfaF. (E) DNA sequence of pfaA probe used in mobility shift and footprinting assays. Putative promoter elements (−35 and −10 sites) and transcriptional start site (arrow) were previously determined ( 25 ). Region protected by PfaF indicated in bold, green, underlined font.

    Article Snippet: Digestion reactions were stopped by the addition of DNase I stop buffer (NEB) and were extracted with phenol:chloroform:isoamyl alcohol (25:24:1, Thermo Scientific).

    Techniques: Binding Assay, Electrophoretic Mobility Shift Assay, Concentration Assay, Labeling, Footprinting, Purification, Sequencing, Mobility Shift

    Endo III blocks XerC-catalysis on pseudo-HJ and displaces it from them. ( A ) Scheme of the suicide pseudo-HJ indicating the mismatch engineered to slow down re-ligation after XerC-cleavage. KMnO 4 sensitive residues in the XerC- and XerD-binding att P(+) arms are indicated by a star. ( B ) Resolution of att P(+)/ dif suicide pseudo-HJs. Legend as in Figure 4D . ( C ) DNase I protection and ( D ) KMnO 4 sensitivity assays of the att P(+)/ dif 1 pseudo-HJ substrate. The analysed strand was labelled on its 5′ end. A scheme of the analysed strand is drawn on the left of the gels. KMnO 4 sensitive residues in the XerC- and XerD-binding sites are indicated by a star.

    Journal: The EMBO Journal

    Article Title: Holliday junction affinity of the base excision repair factor Endo III contributes to cholera toxin phage integration

    doi: 10.1038/emboj.2012.219

    Figure Lengend Snippet: Endo III blocks XerC-catalysis on pseudo-HJ and displaces it from them. ( A ) Scheme of the suicide pseudo-HJ indicating the mismatch engineered to slow down re-ligation after XerC-cleavage. KMnO 4 sensitive residues in the XerC- and XerD-binding att P(+) arms are indicated by a star. ( B ) Resolution of att P(+)/ dif suicide pseudo-HJs. Legend as in Figure 4D . ( C ) DNase I protection and ( D ) KMnO 4 sensitivity assays of the att P(+)/ dif 1 pseudo-HJ substrate. The analysed strand was labelled on its 5′ end. A scheme of the analysed strand is drawn on the left of the gels. KMnO 4 sensitive residues in the XerC- and XerD-binding sites are indicated by a star.

    Article Snippet: E. coli Endo III, T7 endo I and Dnase I were purchased from New England Biolabs.

    Techniques: Ligation, Binding Assay

    IL-8 secretion induced by conditioned supernatants generated from Campylobacter -T84 cell coculture. (A) Polarized T84 cells were incubated for 24 h either with bacterium-free conditioned supernatants generated from the apical or basolateral supernatant of polarized T84 cells that had been inoculated with C. jejuni 81-176 for 4 h or with C. jejuni 81-176 alone cultured in the invasion medium for 4 h (bacterial). T84 cells were incubated with the bacterial culture medium in the apical chamber, with the apical conditioned supernatant in the apical chamber, or with the basolateral conditioned supernatant in the basolateral chamber. Polarized T84 cells inoculated apically with live C. jejuni 81-176 for 4 h and 24 h were used as controls. (B) The basolateral conditioned supernatant generated from C. jejuni 81-176-T84 cell coculture either was not pretreated (−) or was pretreated with either DNase I (10 U/ml) at 37°C for 2 h, polymyxin B (20 μg/ml) at 37°C for 30 min (PLXB), protease K (100 μg/ml) overnight followed by a 20-min incubation at 100°C (ProtK), or a 20-min incubation at 100°C without protease K (Boiling). Polarized T84 cells were incubated with the pretreated or untreated conditioned supernatants from wt C. jejuni 81-176-T84 cell coculture in the basolateral chamber at 37°C for 24 h. (C) Polarized T84 cells were treated basolaterally with a C. jejuni 81-176 DNA extract (25 μg/ml) (DNA) and DNase I-treated C. jejuni 81-176 DNA (DNA + DNase) at 37°C for 24 h. (D) Polarized T84 cells were incubated basolaterally with different concentrations of E. coli LPS in the presence or absence of 20 μg/ml PLXB. (E) Polarized T84 cells were incubated with conditioned supernatants from a coculture of T84 cells with wt C. jejuni 81-176 or its flaA , pflA , cdtB , or flaA cdtB mutant in the basolateral chamber at 37°C for 24 h. After different treatments, the apical (filled bars) and basolateral (open bars) media were collected. IL-8 concentrations were determined by ELISA. The data are means for three independent experiments; error bars, standard deviations. The data in panels B and E are expressed as the ratio of the IL-8 level induced by a treated basolateral conditioned supernatant to that induced by an untreated supernatant and as the ratio of the IL-8 level induced by a mutant basolateral conditioned supernatant to that induced by a wt supernatant. *, P

    Journal: Infection and Immunity

    Article Title: Campylobacter-Induced Interleukin-8 Secretion in Polarized Human Intestinal Epithelial Cells Requires Campylobacter-Secreted Cytolethal Distending Toxin- and Toll-Like Receptor-Mediated Activation of NF-?B ▿

    doi: 10.1128/IAI.01317-07

    Figure Lengend Snippet: IL-8 secretion induced by conditioned supernatants generated from Campylobacter -T84 cell coculture. (A) Polarized T84 cells were incubated for 24 h either with bacterium-free conditioned supernatants generated from the apical or basolateral supernatant of polarized T84 cells that had been inoculated with C. jejuni 81-176 for 4 h or with C. jejuni 81-176 alone cultured in the invasion medium for 4 h (bacterial). T84 cells were incubated with the bacterial culture medium in the apical chamber, with the apical conditioned supernatant in the apical chamber, or with the basolateral conditioned supernatant in the basolateral chamber. Polarized T84 cells inoculated apically with live C. jejuni 81-176 for 4 h and 24 h were used as controls. (B) The basolateral conditioned supernatant generated from C. jejuni 81-176-T84 cell coculture either was not pretreated (−) or was pretreated with either DNase I (10 U/ml) at 37°C for 2 h, polymyxin B (20 μg/ml) at 37°C for 30 min (PLXB), protease K (100 μg/ml) overnight followed by a 20-min incubation at 100°C (ProtK), or a 20-min incubation at 100°C without protease K (Boiling). Polarized T84 cells were incubated with the pretreated or untreated conditioned supernatants from wt C. jejuni 81-176-T84 cell coculture in the basolateral chamber at 37°C for 24 h. (C) Polarized T84 cells were treated basolaterally with a C. jejuni 81-176 DNA extract (25 μg/ml) (DNA) and DNase I-treated C. jejuni 81-176 DNA (DNA + DNase) at 37°C for 24 h. (D) Polarized T84 cells were incubated basolaterally with different concentrations of E. coli LPS in the presence or absence of 20 μg/ml PLXB. (E) Polarized T84 cells were incubated with conditioned supernatants from a coculture of T84 cells with wt C. jejuni 81-176 or its flaA , pflA , cdtB , or flaA cdtB mutant in the basolateral chamber at 37°C for 24 h. After different treatments, the apical (filled bars) and basolateral (open bars) media were collected. IL-8 concentrations were determined by ELISA. The data are means for three independent experiments; error bars, standard deviations. The data in panels B and E are expressed as the ratio of the IL-8 level induced by a treated basolateral conditioned supernatant to that induced by an untreated supernatant and as the ratio of the IL-8 level induced by a mutant basolateral conditioned supernatant to that induced by a wt supernatant. *, P

    Article Snippet: However, treatment of the basolateral conditioned supernatant with DNase I did not significantly change its ability to induce IL-8 secretion (Fig. ).

    Techniques: Generated, Incubation, Cell Culture, Mutagenesis, Enzyme-linked Immunosorbent Assay