dnase i (Worthington Biochemical)

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Deoxyribonuclease I

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Chromatographically purified A lyophilized powder with glycine as a stabilizer

Catalog Number:

ls002004

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5 mg

Source:

Bovine Pancreas

Cas Number:

9003.98.9

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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
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dnase i - by Bioz Stars, 2021-01

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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

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

Techniques Used: Binding Assay

Techniques Used: Hybridization, End Labeling

Techniques Used: In Vivo, Footprinting

Techniques Used: Binding Assay, Sequencing, Methylation

In Vivo:

Article Title: Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter
Article Snippet: .. In vivo DNase I footprint analysis was performed by treating permeabilized 4.12 and 8121 cells with increasing concentrations of DNase I, purifying the DNase I-treated genomic DNA, and examining the DNase I cleavage pattern in the region of interest by LMPCR. ..

Concentration Assay:

Article Title: A Cellular Protein Binds Vaccinia Virus Late Promoters and Activates Transcription In Vitro
Article Snippet: .. DNase I (Worthington Biochemicals) was added to a concentration of 8 ng/ml, and incubation was continued for an additional 2 min, after which the cleavage reaction was terminated by addition of an equal volume of a stop solution (0.2 M NaCl, 30 mM EDTA, 1% sodium dodecyl sulfate, and 100 μg of glycogen/ml). .. DNA cleavage products were extracted with phenol-chloroform, precipitated with ethanol, and analyzed on a 6% polyacrylamide DNA sequencing gel.

Incubation:

other:

Article Title: Structural and functional conservation at the boundaries of the chicken ?-globin domain
Article Snippet: The DNase I HS, 3′HS, was detected by digestion of nuclei with increasing amounts of DNase I as above followed by digestion of extracted DNA with Kpn I and probing with i112 (1000 bp; Kpn I –Pst I at 23.3–24.3 map units).

Article Title: Structural and functional conservation at the boundaries of the chicken ?-globin domain
Article Snippet: [ ] [ ] Stalder J., Larsen,A., Engel,J.D., Dolan,M., Groudine,M. and Weintraub,H. (1980) Tissue-specific DNA cleavages in the globin chromatin domain introduced by DNase I.

Activity Assay:

Article Title: Dynamic BRG1 Recruitment during T Helper Differentiation and Activation Reveals Distal Regulatory Elements ▿Dynamic BRG1 Recruitment during T Helper Differentiation and Activation Reveals Distal Regulatory Elements ▿ §
Article Snippet: .. Newly identified distal BRG1 binding regions in the GATA3 locus were specific with respect to fate and hypersensitive to DNase I and possessed BRG1-dependent enhancer-like activity. .. BRG1 binding to these regions was dependent on the presence of STAT6.

Sequencing:

Article Title: Role of the Promoter in Maintaining Transcriptionally Active Chromatin Structure and DNA Methylation Patterns In Vivo
Article Snippet: .. It is possible that the steeper slope detected by this probe is indicative of an intrinsically higher accessibility of the 5′flanking region to DNase I (or preferential DNase I cleavage of the underlying DNA sequence). ..

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.