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    New England Biolabs dnase i new england biolabs
    In situ assay specificity verified by DNase pretreatment. MT-CO1 sense DNA in situ hybridization assay on FFPE prostate tissues without <t>RNase</t> A ( A ), with RNase A ( B ), without <t>DNase</t> I ( C ), and with DNase I ( D ) pretreatments. Original magnification x40.
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    In situ assay specificity verified by DNase pretreatment. MT-CO1 sense DNA in situ hybridization assay on FFPE prostate tissues without RNase A ( A ), with RNase A ( B ), without DNase I ( C ), and with DNase I ( D ) pretreatments. Original magnification x40.

    Journal: bioRxiv

    Article Title: An in situ atlas of mitochondrial DNA in mammalian tissues reveals high content in stem/progenitor cells

    doi: 10.1101/2019.12.19.876144

    Figure Lengend Snippet: In situ assay specificity verified by DNase pretreatment. MT-CO1 sense DNA in situ hybridization assay on FFPE prostate tissues without RNase A ( A ), with RNase A ( B ), without DNase I ( C ), and with DNase I ( D ) pretreatments. Original magnification x40.

    Article Snippet: For DNase pretreatment, after steaming in Pretreatment II, the slides were treated with 100 μL DNase reaction buffer containing 10 μL DNase I Reaction Buffer (10X), 1 μL (2 units) DNAse I (M0303S, New England BioLabs, Ipswich, MA), and 89 μL nuclease-free H2 O.

    Techniques: In Situ, DNA In Situ Hybridization, Formalin-fixed Paraffin-Embedded

    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

    Journal: bioRxiv

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

    doi: 10.1101/852095

    Figure Lengend 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

    Article Snippet: RNA was treated with DNase I (NEB, Ipswich, MA, USA) according to the manufacturer’s instructions followed by re-precipitation.

    Techniques: Activity Assay, Binding Assay

    Association of nsp3a(1-183) and nsp3a(1-112) purified from E. coli with nucleic acids. (a) Nucleic acid was visualized with SYBR-gold staining before or after digestion with nucleases specific to DNA (DNase I or T7 endonuclease) or RNA (RNase I, RNase A, or RNase T 1 ). Cleavage assays were performed at 37°C for 1 h, and digested samples were analyzed by native electrophoresis on precast 6% polyacrylamide gels. Open arrowheads denote copurified nucleic acid species associated with nsp3a(1-112) or nsp3a(1-183), respectively. (b) EMSAs were performed to estimate the RNA binding affinity of nsp3a(1-112). Samples containing ssRNA1 or ssRNA2 were incubated at 37°C for 1 h with variable concentrations of protein and analyzed by native electrophoresis on precast 6% polyacrylamide gels. RNA was detected by SYPRO-gold poststain, and the fraction of bound RNA was calculated relative to the maximum binding observed in each experiment. Lane P, protein only; lanes 0, ssRNA only; lanes 1 to 7 (left panel), ssRNA with twofold dilutions of protein from a final concentration of 128 μM to 2 μM for ssRNA1; lanes 2, 4, 6, and 8 (right panel), ssRNA with fourfold dilutions of protein from 64 μM to 1 μM for ssRNA2. Electrophoretic mobilities of free (f) and bound (b) forms of each ssRNA species are indicated with arrowheads. (c) ssRNA1-binding at variable concentrations of nsp3a(1-112), as calculated from the EMSA data shown in panel b.

    Journal: Journal of Virology

    Article Title: Nuclear Magnetic Resonance Structure of the N-Terminal Domain of Nonstructural Protein 3 from the Severe Acute Respiratory Syndrome Coronavirus ▿

    doi: 10.1128/JVI.00969-07

    Figure Lengend Snippet: Association of nsp3a(1-183) and nsp3a(1-112) purified from E. coli with nucleic acids. (a) Nucleic acid was visualized with SYBR-gold staining before or after digestion with nucleases specific to DNA (DNase I or T7 endonuclease) or RNA (RNase I, RNase A, or RNase T 1 ). Cleavage assays were performed at 37°C for 1 h, and digested samples were analyzed by native electrophoresis on precast 6% polyacrylamide gels. Open arrowheads denote copurified nucleic acid species associated with nsp3a(1-112) or nsp3a(1-183), respectively. (b) EMSAs were performed to estimate the RNA binding affinity of nsp3a(1-112). Samples containing ssRNA1 or ssRNA2 were incubated at 37°C for 1 h with variable concentrations of protein and analyzed by native electrophoresis on precast 6% polyacrylamide gels. RNA was detected by SYPRO-gold poststain, and the fraction of bound RNA was calculated relative to the maximum binding observed in each experiment. Lane P, protein only; lanes 0, ssRNA only; lanes 1 to 7 (left panel), ssRNA with twofold dilutions of protein from a final concentration of 128 μM to 2 μM for ssRNA1; lanes 2, 4, 6, and 8 (right panel), ssRNA with fourfold dilutions of protein from 64 μM to 1 μM for ssRNA2. Electrophoretic mobilities of free (f) and bound (b) forms of each ssRNA species are indicated with arrowheads. (c) ssRNA1-binding at variable concentrations of nsp3a(1-112), as calculated from the EMSA data shown in panel b.

    Article Snippet: RNase-free DNase I (NEB), T7 endonuclease I (NEB), RNase If (NEB), RNase A (Invitrogen), and RNase T1 (Ambion) cleavage assays were thus performed at 37°C for 1 h with the manufacturer's recommended buffer conditions.

    Techniques: Purification, Staining, Electrophoresis, RNA Binding Assay, Incubation, Binding Assay, Concentration Assay

    Mutating of the major C-terminal CKII sites does not affect interaction of CTCF with c- myc CTSs assayed by EMSAs (A), methylation interference (B), and DNase I footprinting (C). Lanes: 1, full-length (FL) wtCTCF; 2, CTCF/2-mut; 3, CTCF/4-mut; 4, 11ZF protein. See the text for more details. F, free probe; B, protein-bound probe.

    Journal: Molecular and Cellular Biology

    Article Title: Functional Phosphorylation Sites in the C-Terminal Region of the Multivalent Multifunctional Transcriptional Factor CTCF

    doi: 10.1128/MCB.21.6.2221-2234.2001

    Figure Lengend Snippet: Mutating of the major C-terminal CKII sites does not affect interaction of CTCF with c- myc CTSs assayed by EMSAs (A), methylation interference (B), and DNase I footprinting (C). Lanes: 1, full-length (FL) wtCTCF; 2, CTCF/2-mut; 3, CTCF/4-mut; 4, 11ZF protein. See the text for more details. F, free probe; B, protein-bound probe.

    Article Snippet: For DNase I footprinting, 1 μl (1 Kunitz unit) of ultrapure DNase I (New England Biolabs) dissolved in phosphate-buffered saline supplemented with 1 mM CaCl2 and 1 mM MgCl2 was added to each of 10 32 P-DNA-CTCF binding mixtures, with 20-μl final volumes prepared as described for EMSA reactions, mixed at room temperature for 30 s, and immediately loaded on EMSA gels already running at 300 cV.

    Techniques: Methylation, Footprinting

    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

    DnaA bound to R5M, but not R1, is essential for DnaA assembly on the left-half DOR. (A–D) EMSA with the left-half DOR bearing R1non or R5Mnon mutations. Each DNA fragment (35 nM) was incubated with the indicated amount of DnaA in the absence ( A ) or presence ( C ) of 72 nM IHF, then analyzed by 2% agarose-gel electrophoresis. The amount of DNA complexed with DnaA relative to the input DNA is shown as ‘Complex formation (%)’ in ( B ) and ( D ). Two independent experiments were carried out, and both data, mean values, and representative gel images in a black-white inverted mode are shown. (E–G) DNase I-footprint assay with oriC fragments (346 bp) containing R1non or R5Mnon mutations. Indicated amounts of ATP–DnaA or ADP–DnaA were incubated for 10 min at 30°C with 2.4 nM 32 P-end-labeled oriC and 3 mM ATP or ADP in the absence ( E ) or presence ( F ) of 150–600 nM IHF, followed by DNase I digestion and gel-electrophoresis analysis. Positions of DNA motifs are indicated. The sequence of the region protected by IHF binding is shown in ( G ). The IBS consensus sequence and DNase I digestion-protected sites are indicated by bold lettering and asterisks, respectively.

    Journal: Nucleic Acids Research

    Article Title: Regulatory dynamics in the ternary DnaA complex for initiation of chromosomal replication in Escherichia coli

    doi: 10.1093/nar/gkx914

    Figure Lengend Snippet: DnaA bound to R5M, but not R1, is essential for DnaA assembly on the left-half DOR. (A–D) EMSA with the left-half DOR bearing R1non or R5Mnon mutations. Each DNA fragment (35 nM) was incubated with the indicated amount of DnaA in the absence ( A ) or presence ( C ) of 72 nM IHF, then analyzed by 2% agarose-gel electrophoresis. The amount of DNA complexed with DnaA relative to the input DNA is shown as ‘Complex formation (%)’ in ( B ) and ( D ). Two independent experiments were carried out, and both data, mean values, and representative gel images in a black-white inverted mode are shown. (E–G) DNase I-footprint assay with oriC fragments (346 bp) containing R1non or R5Mnon mutations. Indicated amounts of ATP–DnaA or ADP–DnaA were incubated for 10 min at 30°C with 2.4 nM 32 P-end-labeled oriC and 3 mM ATP or ADP in the absence ( E ) or presence ( F ) of 150–600 nM IHF, followed by DNase I digestion and gel-electrophoresis analysis. Positions of DNA motifs are indicated. The sequence of the region protected by IHF binding is shown in ( G ). The IBS consensus sequence and DNase I digestion-protected sites are indicated by bold lettering and asterisks, respectively.

    Article Snippet: DnaA was incubated for 10 min at 30°C in 10 μl buffer F containing 2.4 nM end-labeled oriC fragment (346 bp), 7 μg/ml poly (dA-dT), 7 μg/ml poly (dI-dC) and 3 mM ATP or ADP in the presence of absence of IHF, followed by further incubation with 2.5 mU DNase I (NEB) for 4 min. Purified DNA was analyzed by 5% sequencing-gel electrophoresis and a BAS-2500 image analyzer (Fuji).

    Techniques: Incubation, Immunohistofluorescence, Agarose Gel Electrophoresis, Labeling, Nucleic Acid Electrophoresis, Sequencing, Binding Assay

    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