dnase  (New England Biolabs)


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    Structured Review

    New England Biolabs dnase
    <t>Endo</t> 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 ) <t>DNase</t> 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.
    Dnase, 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
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    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

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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
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    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

    Extrachromosomal nucleic acids within P. membranifaciens are double stranded RNA molecules. Agarose gel electrophoresis of cellulose column purified nucleic acids from P. membranifaciens NCYC333 with DNase I (lane 1) and ShortCut® RNase III (lane 2).

    Journal: bioRxiv

    Article Title: A Novel Virus Discovered in the Yeast Pichia membranifaciens

    doi: 10.1101/2022.01.05.475065

    Figure Lengend Snippet: Extrachromosomal nucleic acids within P. membranifaciens are double stranded RNA molecules. Agarose gel electrophoresis of cellulose column purified nucleic acids from P. membranifaciens NCYC333 with DNase I (lane 1) and ShortCut® RNase III (lane 2).

    Article Snippet: DNase I (New England Biolabs) digestion was performed as directed by the manufacturer in 1X reaction buffer for 10 min at 37°C. the reaction was stopped by incubation at 75°C for 10 min. All digested products were analyzed by agarose gel electrophoresis with ethidium bromide staining.

    Techniques: Agarose Gel Electrophoresis, Purification

    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

    Identification of dorsal root ganglion (DRG)‐specifically‐enriched lncRNA ( DS‐lncRNA ) in DRG neurons. a) A long and highly expressed splice isoform transcript I ( SIT1 ) and a short and weakly expressed splice isoform transcript II ( SIT2 ) of  DS‐lncRNA  were detected in mouse DRG and one  DS‐lncRNA  (DS) transcript was detected in human DRG using reverse transcription (RT)‐PCR with strand‐specific primers. To exclude genomic DNA contamination, the extracted RNA samples were pretreated with excess DNase I. GAPDH was used as a control. Without RT primers, neither  Gapdh  nor  DS‐lncRNA  PCR products were detected in the DNase I‐treated samples. n = 3 biological repeats/species. Lane C: H 2 O. M: DNA ladder marker. b) Expression of  SIT1  and  SIT2  in different tissues from normal mice. Lane 1: dorsal root ganglion (DRG). Lane 2: trigeminal ganglion (TG). Lane 3: brainstem (BS). Lane 4: spinal cord (SC). Lane 5: cerebellum (Cere). Lane 6: hippocampus (Hip). Lane 7: Frontal cortex (FC). Lane 8: heart. Lane 9: lung. Lane 10: kidney. Lane 11: liver. Lane 12: spleen. Lane 13: no‐template control (NC).  Tuba‐1 α  is used as an internal control. n = 4 mice. M: DNA ladder marker. c) Schematic diagrams of full‐length  SIT1  and  SIT2  constructions analyzed by 5′ and 3′ RACE assay. Blue‐highlighted boxes indicate exons and the linked thin lines introns. d) Northern blot analysis of  DS‐lncRNA  ( DS ) expression (lane 3) in mouse DRG. ‐: no RNA. +: with RNA. n = 3 mice. M: RNA marker. e)  In vitro  translation of  DS‐lncRNA  using the Transcend Non‐Radioactive Translation Detection Systems.  H19  is used as a control for noncoding RNA. Luciferase and  Creb1  are used as controls for coding RNA. M: protein molecular weight marker. n = 3 mice. f) Ratios of nucleus to cytoplasm for  Gapdh  mRNA,  Tuba‐1α  mRNA,  DS‐lncRNA ,  Malat1 ,  Neat1 , and  H19  in cultured DRG neurons. n = 4 mice. g)  DS‐lncRNA  (red) was co‐expressed with  β ‐tubulin III (green, left) in individual DRG cells and undetected in cellular nuclei (labeled by 4′, 6‐diamidino‐2‐phenylindole (DAPI), blue, right) of glutamine synthetase (GS, green, right)‐labeled DRG cells. n = 5 mice. Scale bar: 50 µm. h) Histogram showing the distribution of  DS‐lncRNA ‐positive somata in the normal mouse L4 DRG: small, 77%; medium, 18%; large, 5%. n = 3 mice.

    Journal: Advanced Science

    Article Title: Downregulation of a Dorsal Root Ganglion‐Specifically Enriched Long Noncoding RNA is Required for Neuropathic Pain by Negatively Regulating RALY‐Triggered Ehmt2 Expression, Downregulation of a Dorsal Root Ganglion‐Specifically Enriched Long Noncoding RNA is Required for Neuropathic Pain by Negatively Regulating RALY‐Triggered Ehmt2 Expression

    doi: 10.1002/advs.202004515

    Figure Lengend Snippet: Identification of dorsal root ganglion (DRG)‐specifically‐enriched lncRNA ( DS‐lncRNA ) in DRG neurons. a) A long and highly expressed splice isoform transcript I ( SIT1 ) and a short and weakly expressed splice isoform transcript II ( SIT2 ) of DS‐lncRNA were detected in mouse DRG and one DS‐lncRNA (DS) transcript was detected in human DRG using reverse transcription (RT)‐PCR with strand‐specific primers. To exclude genomic DNA contamination, the extracted RNA samples were pretreated with excess DNase I. GAPDH was used as a control. Without RT primers, neither Gapdh nor DS‐lncRNA PCR products were detected in the DNase I‐treated samples. n = 3 biological repeats/species. Lane C: H 2 O. M: DNA ladder marker. b) Expression of SIT1 and SIT2 in different tissues from normal mice. Lane 1: dorsal root ganglion (DRG). Lane 2: trigeminal ganglion (TG). Lane 3: brainstem (BS). Lane 4: spinal cord (SC). Lane 5: cerebellum (Cere). Lane 6: hippocampus (Hip). Lane 7: Frontal cortex (FC). Lane 8: heart. Lane 9: lung. Lane 10: kidney. Lane 11: liver. Lane 12: spleen. Lane 13: no‐template control (NC). Tuba‐1 α is used as an internal control. n = 4 mice. M: DNA ladder marker. c) Schematic diagrams of full‐length SIT1 and SIT2 constructions analyzed by 5′ and 3′ RACE assay. Blue‐highlighted boxes indicate exons and the linked thin lines introns. d) Northern blot analysis of DS‐lncRNA ( DS ) expression (lane 3) in mouse DRG. ‐: no RNA. +: with RNA. n = 3 mice. M: RNA marker. e) In vitro translation of DS‐lncRNA using the Transcend Non‐Radioactive Translation Detection Systems. H19 is used as a control for noncoding RNA. Luciferase and Creb1 are used as controls for coding RNA. M: protein molecular weight marker. n = 3 mice. f) Ratios of nucleus to cytoplasm for Gapdh mRNA, Tuba‐1α mRNA, DS‐lncRNA , Malat1 , Neat1 , and H19 in cultured DRG neurons. n = 4 mice. g) DS‐lncRNA (red) was co‐expressed with β ‐tubulin III (green, left) in individual DRG cells and undetected in cellular nuclei (labeled by 4′, 6‐diamidino‐2‐phenylindole (DAPI), blue, right) of glutamine synthetase (GS, green, right)‐labeled DRG cells. n = 5 mice. Scale bar: 50 µm. h) Histogram showing the distribution of DS‐lncRNA ‐positive somata in the normal mouse L4 DRG: small, 77%; medium, 18%; large, 5%. n = 3 mice.

    Article Snippet: Total RNA was extracted by the RNeasy Mini Kit (Qiagen, Valencia, CA) and treated with excess DNase I (New England Biolabs, Ipswich, MA).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Marker, Expressing, Mouse Assay, Northern Blot, In Vitro, Luciferase, Molecular Weight, Cell Culture, Labeling