dnase i  (Worthington Biochemical)


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    Name:
    Deoxyribonuclease I
    Description:
    Chromatographically purified A lyophilized powder with glycine as a stabilizer
    Catalog Number:
    ls002004
    Price:
    33
    Size:
    5 mg
    Source:
    Bovine Pancreas
    Cas Number:
    9003.98.9
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    Structured Review

    Worthington Biochemical dnase i
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Chromatographically purified A lyophilized powder with glycine as a stabilizer
    https://www.bioz.com/result/dnase i/product/Worthington Biochemical
    Average 99 stars, based on 675 article reviews
    Price from $9.99 to $1999.99
    dnase i - by Bioz Stars, 2020-08
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    Images

    1) Product Images from "Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter"

    Article Title: Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter

    Journal: Molecular and Cellular Biology

    doi: 10.1128/MCB.21.22.7682-7695.2001

    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution DNase I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Figure Legend Snippet: Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution DNase I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.

    Techniques Used: Binding Assay

    Locations of probes and primers for analysis of the HPRT promoter region. Horizontal line bounded by Bcl I sites, 4.3-kb Bcl I fragment containing the HPRT promoter; gray box, potential AP-2 site; five black boxes, cluster of GC boxes in the HPRT promoter; white box, first exon of the HPRT gene including the region of multiple transcription initiation sites in the promoter; ATG, translation initiation site; Bam HI, position of a reference Bam HI site in the first intron 100 bp downstream of the translation initiation site; hatched box, position of the 400-bp hybridization probe used to map DNase I and MNase cleavage sites in the HPRT promoter by indirect end labeling; black rectangles above and below the line, positions of the LMPCR primer sets used to map the high-resolution DNase I cleavage pattern of the HPRT minimal promoter; arrows extending from the black boxes, strand and region analyzed with each primer set.
    Figure Legend Snippet: Locations of probes and primers for analysis of the HPRT promoter region. Horizontal line bounded by Bcl I sites, 4.3-kb Bcl I fragment containing the HPRT promoter; gray box, potential AP-2 site; five black boxes, cluster of GC boxes in the HPRT promoter; white box, first exon of the HPRT gene including the region of multiple transcription initiation sites in the promoter; ATG, translation initiation site; Bam HI, position of a reference Bam HI site in the first intron 100 bp downstream of the translation initiation site; hatched box, position of the 400-bp hybridization probe used to map DNase I and MNase cleavage sites in the HPRT promoter by indirect end labeling; black rectangles above and below the line, positions of the LMPCR primer sets used to map the high-resolution DNase I cleavage pattern of the HPRT minimal promoter; arrows extending from the black boxes, strand and region analyzed with each primer set.

    Techniques Used: Hybridization, End Labeling

    DNase I in vivo footprint analysis of the human HPRT promoter. Active, samples from cells containing an active HPRT gene on the active human X chromosome; inactive, samples from cells containing an inactive HPRT gene on the inactive human X chromosome; DNA , naked DNA treated with DNase I; cells, DNA from permeabilized cells treated with DNase I; GC boxes, position of a DNase I in vivo footprint over the five GC boxes in the human HPRT promoter; AP-2, position of a DNase I in vivo footprint over a putative consensus AP-2 site in the human HPRT promoter. All position numbers (left and right) are relative to the translation initiation site of the HPRT gene. (A) DNase I in vivo footprint analysis of the upper strand of the HPRT promoter using LMPCR primer set E. Ladder of arrows, apparent 10-bp ladder of DNase I cleavages in permeabilized cells consistent with rotationally positioned nucleosomes on the inactive HPRT promoter. (B) DNase I in vivo footprinting analysis of the lower strand of the HPRT promoter using LMPCR primer set A. All designations and symbols are as described above. This analysis identifies footprints over both a cluster of five GC boxes and a putative AP-2 site in the active HPRT promoter. (C) DNase I in vivo footprinting analysis of the upper strand using LMPCR primer set C. All designations and symbols are as described above. This analysis identifies a DNase in vivo footprint over a putative AP-2 site on the active HPRT promoter.
    Figure Legend Snippet: DNase I in vivo footprint analysis of the human HPRT promoter. Active, samples from cells containing an active HPRT gene on the active human X chromosome; inactive, samples from cells containing an inactive HPRT gene on the inactive human X chromosome; DNA , naked DNA treated with DNase I; cells, DNA from permeabilized cells treated with DNase I; GC boxes, position of a DNase I in vivo footprint over the five GC boxes in the human HPRT promoter; AP-2, position of a DNase I in vivo footprint over a putative consensus AP-2 site in the human HPRT promoter. All position numbers (left and right) are relative to the translation initiation site of the HPRT gene. (A) DNase I in vivo footprint analysis of the upper strand of the HPRT promoter using LMPCR primer set E. Ladder of arrows, apparent 10-bp ladder of DNase I cleavages in permeabilized cells consistent with rotationally positioned nucleosomes on the inactive HPRT promoter. (B) DNase I in vivo footprinting analysis of the lower strand of the HPRT promoter using LMPCR primer set A. All designations and symbols are as described above. This analysis identifies footprints over both a cluster of five GC boxes and a putative AP-2 site in the active HPRT promoter. (C) DNase I in vivo footprinting analysis of the upper strand using LMPCR primer set C. All designations and symbols are as described above. This analysis identifies a DNase in vivo footprint over a putative AP-2 site on the active HPRT promoter.

    Techniques Used: In Vivo, Footprinting

    Summary of the 10-base DNase I cleavage ladders of chromatin from the active and inactive HPRT promoters. Boldface letters, protein-coding region of the first exon; lowercase letters, nucleotides within the first intron; partial ovals, approximate positions of the translationally positioned nucleosomes on the active HPRT promoter as determined by MNase cleavage; open boxes, positions of transcription factor (TF) binding sites. From top to bottom, left to right, the TF binding sites are a putative AP-1 site (−271 to −264), five GC boxes (centered at −213, −201, −187, −177, and −166), and a putative initiator element (−94 to −86). Bent arrows, positions of the two major transcription initiation sites identified by Kim et al. (16); line between the nucleotide sequence of the upper and lower strands, region of multiple transcription initiation sites described by Patel et al. (32); black triangles above the sequence, positions of DNase I cleavage sites on the upper strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; gray triangles below the sequence, positions of DNase I cleavages on the lower strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; white triangles, positions of DNase I cleavages on the lower strand making up the 10-bp ladder, suggestive of rotational positioning of a nucleosome on the active promoter region in permeabilized cells; vertical ovals, positions of three CpG dinucleotides whose methylation is strongly correlated with transcriptional repression of the HPRT ).
    Figure Legend Snippet: Summary of the 10-base DNase I cleavage ladders of chromatin from the active and inactive HPRT promoters. Boldface letters, protein-coding region of the first exon; lowercase letters, nucleotides within the first intron; partial ovals, approximate positions of the translationally positioned nucleosomes on the active HPRT promoter as determined by MNase cleavage; open boxes, positions of transcription factor (TF) binding sites. From top to bottom, left to right, the TF binding sites are a putative AP-1 site (−271 to −264), five GC boxes (centered at −213, −201, −187, −177, and −166), and a putative initiator element (−94 to −86). Bent arrows, positions of the two major transcription initiation sites identified by Kim et al. (16); line between the nucleotide sequence of the upper and lower strands, region of multiple transcription initiation sites described by Patel et al. (32); black triangles above the sequence, positions of DNase I cleavage sites on the upper strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; gray triangles below the sequence, positions of DNase I cleavages on the lower strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; white triangles, positions of DNase I cleavages on the lower strand making up the 10-bp ladder, suggestive of rotational positioning of a nucleosome on the active promoter region in permeabilized cells; vertical ovals, positions of three CpG dinucleotides whose methylation is strongly correlated with transcriptional repression of the HPRT ).

    Techniques Used: Binding Assay, Sequencing, Methylation

    2) Product Images from "Development of a Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry Method for Analysis of Stable 4-Hydroxyequilenin-DNA Adducts in Human Breast Cancer Cells"

    Article Title: Development of a Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry Method for Analysis of Stable 4-Hydroxyequilenin-DNA Adducts in Human Breast Cancer Cells

    Journal: Chemical research in toxicology

    doi: 10.1021/tx900063g

    Optimization of hydrolysis conditions for detecting stable 4-OHEN-DNA adducts. A) Method I, incubation with NP1 and ALP together in 25 mM ammonium acetate (pH 5.3) for 45 min at 37 °C. Method II, the DNA solutions were incubated with NP1 for 4 h in ammonium acetate at 55 °C, and then ALP and VPH were added to mixture for 4 h at 37 °C after pH adjustment to 9.8 by 0.1 M diethanolamine. B) Equal amounts of calf thymus DNA were hydrolyzed using Method I and Method II. The hydrolysates were analyzed by LC-MS/MS and compared by total relative intensity of each adduct peak.
    Figure Legend Snippet: Optimization of hydrolysis conditions for detecting stable 4-OHEN-DNA adducts. A) Method I, incubation with NP1 and ALP together in 25 mM ammonium acetate (pH 5.3) for 45 min at 37 °C. Method II, the DNA solutions were incubated with NP1 for 4 h in ammonium acetate at 55 °C, and then ALP and VPH were added to mixture for 4 h at 37 °C after pH adjustment to 9.8 by 0.1 M diethanolamine. B) Equal amounts of calf thymus DNA were hydrolyzed using Method I and Method II. The hydrolysates were analyzed by LC-MS/MS and compared by total relative intensity of each adduct peak.

    Techniques Used: Incubation, ALP Assay, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    3) Product Images from "Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter"

    Article Title: Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter

    Journal: Molecular and Cellular Biology

    doi: 10.1128/MCB.21.22.7682-7695.2001

    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution DNase I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Figure Legend Snippet: Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution DNase I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.

    Techniques Used: Binding Assay

    Locations of probes and primers for analysis of the HPRT promoter region. Horizontal line bounded by Bcl I sites, 4.3-kb Bcl I fragment containing the HPRT promoter; gray box, potential AP-2 site; five black boxes, cluster of GC boxes in the HPRT promoter; white box, first exon of the HPRT gene including the region of multiple transcription initiation sites in the promoter; ATG, translation initiation site; Bam HI, position of a reference Bam HI site in the first intron 100 bp downstream of the translation initiation site; hatched box, position of the 400-bp hybridization probe used to map DNase I and MNase cleavage sites in the HPRT promoter by indirect end labeling; black rectangles above and below the line, positions of the LMPCR primer sets used to map the high-resolution DNase I cleavage pattern of the HPRT minimal promoter; arrows extending from the black boxes, strand and region analyzed with each primer set.
    Figure Legend Snippet: Locations of probes and primers for analysis of the HPRT promoter region. Horizontal line bounded by Bcl I sites, 4.3-kb Bcl I fragment containing the HPRT promoter; gray box, potential AP-2 site; five black boxes, cluster of GC boxes in the HPRT promoter; white box, first exon of the HPRT gene including the region of multiple transcription initiation sites in the promoter; ATG, translation initiation site; Bam HI, position of a reference Bam HI site in the first intron 100 bp downstream of the translation initiation site; hatched box, position of the 400-bp hybridization probe used to map DNase I and MNase cleavage sites in the HPRT promoter by indirect end labeling; black rectangles above and below the line, positions of the LMPCR primer sets used to map the high-resolution DNase I cleavage pattern of the HPRT minimal promoter; arrows extending from the black boxes, strand and region analyzed with each primer set.

    Techniques Used: Hybridization, End Labeling

    DNase I in vivo footprint analysis of the human HPRT promoter. Active, samples from cells containing an active HPRT gene on the active human X chromosome; inactive, samples from cells containing an inactive HPRT gene on the inactive human X chromosome; DNA , naked DNA treated with DNase I; cells, DNA from permeabilized cells treated with DNase I; GC boxes, position of a DNase I in vivo footprint over the five GC boxes in the human HPRT promoter; AP-2, position of a DNase I in vivo footprint over a putative consensus AP-2 site in the human HPRT promoter. All position numbers (left and right) are relative to the translation initiation site of the HPRT gene. (A) DNase I in vivo footprint analysis of the upper strand of the HPRT promoter using LMPCR primer set E. Ladder of arrows, apparent 10-bp ladder of DNase I cleavages in permeabilized cells consistent with rotationally positioned nucleosomes on the inactive HPRT promoter. (B) DNase I in vivo footprinting analysis of the lower strand of the HPRT promoter using LMPCR primer set A. All designations and symbols are as described above. This analysis identifies footprints over both a cluster of five GC boxes and a putative AP-2 site in the active HPRT promoter. (C) DNase I in vivo footprinting analysis of the upper strand using LMPCR primer set C. All designations and symbols are as described above. This analysis identifies a DNase in vivo footprint over a putative AP-2 site on the active HPRT promoter.
    Figure Legend Snippet: DNase I in vivo footprint analysis of the human HPRT promoter. Active, samples from cells containing an active HPRT gene on the active human X chromosome; inactive, samples from cells containing an inactive HPRT gene on the inactive human X chromosome; DNA , naked DNA treated with DNase I; cells, DNA from permeabilized cells treated with DNase I; GC boxes, position of a DNase I in vivo footprint over the five GC boxes in the human HPRT promoter; AP-2, position of a DNase I in vivo footprint over a putative consensus AP-2 site in the human HPRT promoter. All position numbers (left and right) are relative to the translation initiation site of the HPRT gene. (A) DNase I in vivo footprint analysis of the upper strand of the HPRT promoter using LMPCR primer set E. Ladder of arrows, apparent 10-bp ladder of DNase I cleavages in permeabilized cells consistent with rotationally positioned nucleosomes on the inactive HPRT promoter. (B) DNase I in vivo footprinting analysis of the lower strand of the HPRT promoter using LMPCR primer set A. All designations and symbols are as described above. This analysis identifies footprints over both a cluster of five GC boxes and a putative AP-2 site in the active HPRT promoter. (C) DNase I in vivo footprinting analysis of the upper strand using LMPCR primer set C. All designations and symbols are as described above. This analysis identifies a DNase in vivo footprint over a putative AP-2 site on the active HPRT promoter.

    Techniques Used: In Vivo, Footprinting

    Summary of the 10-base DNase I cleavage ladders of chromatin from the active and inactive HPRT promoters. Boldface letters, protein-coding region of the first exon; lowercase letters, nucleotides within the first intron; partial ovals, approximate positions of the translationally positioned nucleosomes on the active HPRT promoter as determined by MNase cleavage; open boxes, positions of transcription factor (TF) binding sites. From top to bottom, left to right, the TF binding sites are a putative AP-1 site (−271 to −264), five GC boxes (centered at −213, −201, −187, −177, and −166), and a putative initiator element (−94 to −86). Bent arrows, positions of the two major transcription initiation sites identified by Kim et al. (16); line between the nucleotide sequence of the upper and lower strands, region of multiple transcription initiation sites described by Patel et al. (32); black triangles above the sequence, positions of DNase I cleavage sites on the upper strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; gray triangles below the sequence, positions of DNase I cleavages on the lower strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; white triangles, positions of DNase I cleavages on the lower strand making up the 10-bp ladder, suggestive of rotational positioning of a nucleosome on the active promoter region in permeabilized cells; vertical ovals, positions of three CpG dinucleotides whose methylation is strongly correlated with transcriptional repression of the HPRT ).
    Figure Legend Snippet: Summary of the 10-base DNase I cleavage ladders of chromatin from the active and inactive HPRT promoters. Boldface letters, protein-coding region of the first exon; lowercase letters, nucleotides within the first intron; partial ovals, approximate positions of the translationally positioned nucleosomes on the active HPRT promoter as determined by MNase cleavage; open boxes, positions of transcription factor (TF) binding sites. From top to bottom, left to right, the TF binding sites are a putative AP-1 site (−271 to −264), five GC boxes (centered at −213, −201, −187, −177, and −166), and a putative initiator element (−94 to −86). Bent arrows, positions of the two major transcription initiation sites identified by Kim et al. (16); line between the nucleotide sequence of the upper and lower strands, region of multiple transcription initiation sites described by Patel et al. (32); black triangles above the sequence, positions of DNase I cleavage sites on the upper strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; gray triangles below the sequence, positions of DNase I cleavages on the lower strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; white triangles, positions of DNase I cleavages on the lower strand making up the 10-bp ladder, suggestive of rotational positioning of a nucleosome on the active promoter region in permeabilized cells; vertical ovals, positions of three CpG dinucleotides whose methylation is strongly correlated with transcriptional repression of the HPRT ).

    Techniques Used: Binding Assay, Sequencing, Methylation

    Related Articles

    Irradiation:

    Article Title: Characterization of the survival motor neuron (SMN) promoter provides evidence for complex combinatorial regulation in undifferentiated and differentiated P19 cells
    Article Snippet: .. Specifically, we used DMS, UVC irradiation and DNase I as DNA-modifying agents to map single-strand DNA breaks, comparing in vitro (naked DNA) and in vivo (living cells) footprints. .. In vivo footprints corresponding to nt −46 to +125 encompassing the minimal core promoter are presented in and summarized in .

    In Vivo:

    Article Title: Characterization of the survival motor neuron (SMN) promoter provides evidence for complex combinatorial regulation in undifferentiated and differentiated P19 cells
    Article Snippet: .. Specifically, we used DMS, UVC irradiation and DNase I as DNA-modifying agents to map single-strand DNA breaks, comparing in vitro (naked DNA) and in vivo (living cells) footprints. .. In vivo footprints corresponding to nt −46 to +125 encompassing the minimal core promoter are presented in and summarized in .

    In Vitro:

    Article Title: Characterization of the survival motor neuron (SMN) promoter provides evidence for complex combinatorial regulation in undifferentiated and differentiated P19 cells
    Article Snippet: .. Specifically, we used DMS, UVC irradiation and DNase I as DNA-modifying agents to map single-strand DNA breaks, comparing in vitro (naked DNA) and in vivo (living cells) footprints. .. In vivo footprints corresponding to nt −46 to +125 encompassing the minimal core promoter are presented in and summarized in .

    Produced:

    Article Title: Novel High-Throughput Deoxyribonuclease 1 Assay
    Article Snippet: .. The percentage of DNase I activity was calculated using Equation 1: DNase\u00a0I\u00a0activity (%) =\u00a0 (mean\u00a0velocity\u00a0of\u00a0a\u00a0compound/mean\u00a0velocity\u00a0of\u00a0DMSO)\u00a0\u00d7\u00a0100 (1) In similar assays, recombinant murine EndoG (produced in-house) was used at a concentration of 0.14 μM in 0.1 mM MgCl2 , 10 mM Tris-HCl, pH 7.4; and DNase II (Worthington, Lakewood, NJ) (3.32 nM) was tested in 100 mM sodium citrate buffer, pH 5.0. .. For evaluation of the quality of the assay, Z’ values were calculated using Equation 2: Z\u2019 =\u00a01\u00a0\u2212\u00a0(3SDC +\u00a03SDB )/(MC \u00a0\u2212\u00a0MB ) (2) where M = mean value; SD = standard deviation; C = control; and B = background.

    Concentration Assay:

    Article Title: Novel High-Throughput Deoxyribonuclease 1 Assay
    Article Snippet: .. The percentage of DNase I activity was calculated using Equation 1: DNase\u00a0I\u00a0activity (%) =\u00a0 (mean\u00a0velocity\u00a0of\u00a0a\u00a0compound/mean\u00a0velocity\u00a0of\u00a0DMSO)\u00a0\u00d7\u00a0100 (1) In similar assays, recombinant murine EndoG (produced in-house) was used at a concentration of 0.14 μM in 0.1 mM MgCl2 , 10 mM Tris-HCl, pH 7.4; and DNase II (Worthington, Lakewood, NJ) (3.32 nM) was tested in 100 mM sodium citrate buffer, pH 5.0. .. For evaluation of the quality of the assay, Z’ values were calculated using Equation 2: Z\u2019 =\u00a01\u00a0\u2212\u00a0(3SDC +\u00a03SDB )/(MC \u00a0\u2212\u00a0MB ) (2) where M = mean value; SD = standard deviation; C = control; and B = background.

    Incubation:

    Article Title: Identification of Viral Peptide Fragments for Vaccine Development
    Article Snippet: .. When the random digestion by DNase I is used for some genes, peculiarly a small amount of the full-length gene has been observed even after prolonged incubation. .. In this case, the digestion mixture should be passed through a column with an appropriate molecular weight cut-off to filter out the full-length gene, followed by a Microcon® YM-30 column to accomplish the buffer exchange.

    Article Title: Neutrophil Extracellular Traps Contain Calprotectin, a Cytosolic Protein Complex Involved in Host Defense against Candida albicans
    Article Snippet: .. As controls (i) NETs were mock-digested with nuclease-free RPMI and (ii) unstimulated neutrophils that did not release NETs were washed twice and incubated with RPMI containing 10 U/ml Dnase-1 for 20 min at 37°C. .. Four samples out of 4 wells were pooled, acetone precipitated, solubilized in 120 µl SDS loading buffer and boiled for 3 min. To account for potential protein loss due to proteolytic activity in the samples a complete purification procedure was performed in the presence of protease inhibitor cocktail (Sigma P1860; 1∶200) added to the wells 2 h after stimulation start as described above.

    other:

    Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver
    Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

    Article Title: Identification of Viral Peptide Fragments for Vaccine Development
    Article Snippet: In the random digestion step, the use of DNase I in the presence of MnCl2 is critical as this protocol will generate DNA fragments of relatively uniform sizes, which facilitates the reassembly step ( 17 , also see Note ).

    Article Title: Neutrophil Extracellular Traps Contain Calprotectin, a Cytosolic Protein Complex Involved in Host Defense against Candida albicans
    Article Snippet: Supernatants were removed, NETs were washed twice with 1 ml RPMI and digested with 500 µl 10 U/ml DNase-1 each.

    Activity Assay:

    Article Title: Novel High-Throughput Deoxyribonuclease 1 Assay
    Article Snippet: .. The percentage of DNase I activity was calculated using Equation 1: DNase\u00a0I\u00a0activity (%) =\u00a0 (mean\u00a0velocity\u00a0of\u00a0a\u00a0compound/mean\u00a0velocity\u00a0of\u00a0DMSO)\u00a0\u00d7\u00a0100 (1) In similar assays, recombinant murine EndoG (produced in-house) was used at a concentration of 0.14 μM in 0.1 mM MgCl2 , 10 mM Tris-HCl, pH 7.4; and DNase II (Worthington, Lakewood, NJ) (3.32 nM) was tested in 100 mM sodium citrate buffer, pH 5.0. .. For evaluation of the quality of the assay, Z’ values were calculated using Equation 2: Z\u2019 =\u00a01\u00a0\u2212\u00a0(3SDC +\u00a03SDB )/(MC \u00a0\u2212\u00a0MB ) (2) where M = mean value; SD = standard deviation; C = control; and B = background.

    Staining:

    Article Title: Constitutive Nucleosome Depletion and Ordered Factor Assembly at the GRP78 Promoter Revealed by Single Molecule Footprinting
    Article Snippet: .. These were then digested at 37 °C for 15 min using various concentrations of DNase I (Worthington, San Francisco, California, United States) to obtain a suitable range of digestion of genomic DNA as revealed by EtBr staining. .. Digested genomic DNA was purified, redigested by RsaI, resolved on a 1.5% agarose gel, and Southern blotted.

    Recombinant:

    Article Title: Novel High-Throughput Deoxyribonuclease 1 Assay
    Article Snippet: .. The percentage of DNase I activity was calculated using Equation 1: DNase\u00a0I\u00a0activity (%) =\u00a0 (mean\u00a0velocity\u00a0of\u00a0a\u00a0compound/mean\u00a0velocity\u00a0of\u00a0DMSO)\u00a0\u00d7\u00a0100 (1) In similar assays, recombinant murine EndoG (produced in-house) was used at a concentration of 0.14 μM in 0.1 mM MgCl2 , 10 mM Tris-HCl, pH 7.4; and DNase II (Worthington, Lakewood, NJ) (3.32 nM) was tested in 100 mM sodium citrate buffer, pH 5.0. .. For evaluation of the quality of the assay, Z’ values were calculated using Equation 2: Z\u2019 =\u00a01\u00a0\u2212\u00a0(3SDC +\u00a03SDB )/(MC \u00a0\u2212\u00a0MB ) (2) where M = mean value; SD = standard deviation; C = control; and B = background.

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    Worthington Biochemical alkaline phosphatase alp
    Optimization of hydrolysis conditions for detecting stable 4-OHEN-DNA adducts. A) Method I, incubation with NP1 and <t>ALP</t> together in 25 mM ammonium acetate (pH 5.3) for 45 min at 37 °C. Method II, the DNA solutions were incubated with NP1 for 4 h in ammonium acetate at 55 °C, and then ALP and <t>VPH</t> were added to mixture for 4 h at 37 °C after pH adjustment to 9.8 by 0.1 M diethanolamine. B) Equal amounts of calf thymus DNA were hydrolyzed using Method I and Method II. The hydrolysates were analyzed by LC-MS/MS and compared by total relative intensity of each adduct peak.
    Alkaline Phosphatase Alp, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Worthington Biochemical xue m
    Optimization of hydrolysis conditions for detecting stable 4-OHEN-DNA adducts. A) Method I, incubation with NP1 and <t>ALP</t> together in 25 mM ammonium acetate (pH 5.3) for 45 min at 37 °C. Method II, the DNA solutions were incubated with NP1 for 4 h in ammonium acetate at 55 °C, and then ALP and <t>VPH</t> were added to mixture for 4 h at 37 °C after pH adjustment to 9.8 by 0.1 M diethanolamine. B) Equal amounts of calf thymus DNA were hydrolyzed using Method I and Method II. The hydrolysates were analyzed by LC-MS/MS and compared by total relative intensity of each adduct peak.
    Xue M, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Worthington Biochemical hinks am
    Optimization of hydrolysis conditions for detecting stable 4-OHEN-DNA adducts. A) Method I, incubation with NP1 and <t>ALP</t> together in 25 mM ammonium acetate (pH 5.3) for 45 min at 37 °C. Method II, the DNA solutions were incubated with NP1 for 4 h in ammonium acetate at 55 °C, and then ALP and <t>VPH</t> were added to mixture for 4 h at 37 °C after pH adjustment to 9.8 by 0.1 M diethanolamine. B) Equal amounts of calf thymus DNA were hydrolyzed using Method I and Method II. The hydrolysates were analyzed by LC-MS/MS and compared by total relative intensity of each adduct peak.
    Hinks Am, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Worthington Biochemical munroe pb
    Optimization of hydrolysis conditions for detecting stable 4-OHEN-DNA adducts. A) Method I, incubation with NP1 and <t>ALP</t> together in 25 mM ammonium acetate (pH 5.3) for 45 min at 37 °C. Method II, the DNA solutions were incubated with NP1 for 4 h in ammonium acetate at 55 °C, and then ALP and <t>VPH</t> were added to mixture for 4 h at 37 °C after pH adjustment to 9.8 by 0.1 M diethanolamine. B) Equal amounts of calf thymus DNA were hydrolyzed using Method I and Method II. The hydrolysates were analyzed by LC-MS/MS and compared by total relative intensity of each adduct peak.
    Munroe Pb, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 90/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Optimization of hydrolysis conditions for detecting stable 4-OHEN-DNA adducts. A) Method I, incubation with NP1 and ALP together in 25 mM ammonium acetate (pH 5.3) for 45 min at 37 °C. Method II, the DNA solutions were incubated with NP1 for 4 h in ammonium acetate at 55 °C, and then ALP and VPH were added to mixture for 4 h at 37 °C after pH adjustment to 9.8 by 0.1 M diethanolamine. B) Equal amounts of calf thymus DNA were hydrolyzed using Method I and Method II. The hydrolysates were analyzed by LC-MS/MS and compared by total relative intensity of each adduct peak.

    Journal: Chemical research in toxicology

    Article Title: Development of a Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry Method for Analysis of Stable 4-Hydroxyequilenin-DNA Adducts in Human Breast Cancer Cells

    doi: 10.1021/tx900063g

    Figure Lengend Snippet: Optimization of hydrolysis conditions for detecting stable 4-OHEN-DNA adducts. A) Method I, incubation with NP1 and ALP together in 25 mM ammonium acetate (pH 5.3) for 45 min at 37 °C. Method II, the DNA solutions were incubated with NP1 for 4 h in ammonium acetate at 55 °C, and then ALP and VPH were added to mixture for 4 h at 37 °C after pH adjustment to 9.8 by 0.1 M diethanolamine. B) Equal amounts of calf thymus DNA were hydrolyzed using Method I and Method II. The hydrolysates were analyzed by LC-MS/MS and compared by total relative intensity of each adduct peak.

    Article Snippet: Alkaline phosphatase (ALP) and venom phosphodiesterase I (VPH) were purchased from Worthington (Lakewood, NJ).

    Techniques: Incubation, ALP Assay, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry