dnase i  (New England Biolabs)


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    New England Biolabs dnase i
    Dnase I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 350 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 350 article reviews
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    dnase i - by Bioz Stars, 2020-04
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    New England Biolabs dnase i buffer
    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 <t>DNase</t> 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.
    Dnase I Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs dnase i treated dna
    A specifically positioned nucleosome covers the promoter of HPV-16. (A) The HPV-16 LCR cloned in pHPV-16-Luc was assembled into chromatin with Drosophila S190 extracts and treated with increasing amounts of <t>DNase</t> I, and the resulting fragments were purified and assayed by primer extension. Lanes 2 and 3, footprints originating from two nucleosomes that overlap with the promoter and the enhancer (large and small oval shapes on the right). Weak 10-bp-spaced bands (filled stars) indicate <t>DNase</t> I accessibility due to the rotational phasing of the nucleosomes, and a strong hypersensitive site (open star) suggests the center of the dyad symmetry of the nucleosome. As controls, lane 1 shows DNase I treatment of free HPV-16 LCR DNA and the left side of the panel indicates a sequencing ladder. Lane M, size marker with bands at 500, 400, 300, 200, and 100 bp. Symbols and nucleotides on the left identify the four cis -responsive elements of the E6 promoter, namely, binding sites for Sp1, the viral factor E2, and TBP. (B) Footprint obtained in a similar experiment and permitting similar interpretations. It highlights the 10-bp periodicity but does not permit clear mapping of the extent of nucleosomal protection.
    Dnase I Treated Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs t7e1 nuclease
    PTEN-KO validation of the MSCs. a The designed target site exon region. b The map of empty vector (from Addgene, Massachusetts, USA). c <t>T7E1</t> digestion products were analyzed by agarose gel electrophoresis. The pSpCas9(BB)-2A-GFP-T2 (px458-T2) plasmid showed the highest Knock-out performance. d DNA was extracted from plasmid-transfected BMSCs and amplified through PCR. The PTEN bands did not exist after transfection e Western blot confirmed PTEN was knocked out
    T7e1 Nuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    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

    A specifically positioned nucleosome covers the promoter of HPV-16. (A) The HPV-16 LCR cloned in pHPV-16-Luc was assembled into chromatin with Drosophila S190 extracts and treated with increasing amounts of DNase I, and the resulting fragments were purified and assayed by primer extension. Lanes 2 and 3, footprints originating from two nucleosomes that overlap with the promoter and the enhancer (large and small oval shapes on the right). Weak 10-bp-spaced bands (filled stars) indicate DNase I accessibility due to the rotational phasing of the nucleosomes, and a strong hypersensitive site (open star) suggests the center of the dyad symmetry of the nucleosome. As controls, lane 1 shows DNase I treatment of free HPV-16 LCR DNA and the left side of the panel indicates a sequencing ladder. Lane M, size marker with bands at 500, 400, 300, 200, and 100 bp. Symbols and nucleotides on the left identify the four cis -responsive elements of the E6 promoter, namely, binding sites for Sp1, the viral factor E2, and TBP. (B) Footprint obtained in a similar experiment and permitting similar interpretations. It highlights the 10-bp periodicity but does not permit clear mapping of the extent of nucleosomal protection.

    Journal: Journal of Virology

    Article Title: The Chromatin Structure of the Long Control Region of Human Papillomavirus Type 16 Represses Viral Oncoprotein Expression

    doi:

    Figure Lengend Snippet: A specifically positioned nucleosome covers the promoter of HPV-16. (A) The HPV-16 LCR cloned in pHPV-16-Luc was assembled into chromatin with Drosophila S190 extracts and treated with increasing amounts of DNase I, and the resulting fragments were purified and assayed by primer extension. Lanes 2 and 3, footprints originating from two nucleosomes that overlap with the promoter and the enhancer (large and small oval shapes on the right). Weak 10-bp-spaced bands (filled stars) indicate DNase I accessibility due to the rotational phasing of the nucleosomes, and a strong hypersensitive site (open star) suggests the center of the dyad symmetry of the nucleosome. As controls, lane 1 shows DNase I treatment of free HPV-16 LCR DNA and the left side of the panel indicates a sequencing ladder. Lane M, size marker with bands at 500, 400, 300, 200, and 100 bp. Symbols and nucleotides on the left identify the four cis -responsive elements of the E6 promoter, namely, binding sites for Sp1, the viral factor E2, and TBP. (B) Footprint obtained in a similar experiment and permitting similar interpretations. It highlights the 10-bp periodicity but does not permit clear mapping of the extent of nucleosomal protection.

    Article Snippet: DNase I-treated DNA was purified by standard procedures and used as a template for the extension reaction with Vent (exo-) polymerase (New England Biolabs).

    Techniques: Clone Assay, Purification, Sequencing, Marker, Binding Assay

    A specifically positioned nucleosome covers the replication origin of HPV-18 and extends into E6 promoter sequences. The cloned HPV-18 LCR was assembled into chromatin with Drosophila S190 extracts and treated with increasing amounts of DNase I, and the resulting fragments were assayed by primer extension. Lanes 3 to 7 show, with increasing DNase I treatment, the footprint of a nucleosome overlapping the replication origin (distal E2 and E1 binding site), indicated by a large hatched oval on the right. Weak 10-bp-spaced bands (filled stars) indicate DNase I accessibility due to the rotational phasing of the nucleosomal organization, and a strong hypersensitivity site (open star) suggests the center of the dyad symmetry of the nucleosome. As controls, lanes 1 and 2 show DNase I treatment of free HPV-18 LCR DNA, and the left side shows a sequencing ladder of this sequence. Lane M, size marker with bands at 500, 400, 300, 200, and 100 bp. Symbols and nucleotides on the right identify the third E2 binding site from the E6 promoter, the E1 binding site, and one of the four cis -responsive elements of the E6 promoter, namely, the binding site for Sp1.

    Journal: Journal of Virology

    Article Title: The Chromatin Structure of the Long Control Region of Human Papillomavirus Type 16 Represses Viral Oncoprotein Expression

    doi:

    Figure Lengend Snippet: A specifically positioned nucleosome covers the replication origin of HPV-18 and extends into E6 promoter sequences. The cloned HPV-18 LCR was assembled into chromatin with Drosophila S190 extracts and treated with increasing amounts of DNase I, and the resulting fragments were assayed by primer extension. Lanes 3 to 7 show, with increasing DNase I treatment, the footprint of a nucleosome overlapping the replication origin (distal E2 and E1 binding site), indicated by a large hatched oval on the right. Weak 10-bp-spaced bands (filled stars) indicate DNase I accessibility due to the rotational phasing of the nucleosomal organization, and a strong hypersensitivity site (open star) suggests the center of the dyad symmetry of the nucleosome. As controls, lanes 1 and 2 show DNase I treatment of free HPV-18 LCR DNA, and the left side shows a sequencing ladder of this sequence. Lane M, size marker with bands at 500, 400, 300, 200, and 100 bp. Symbols and nucleotides on the right identify the third E2 binding site from the E6 promoter, the E1 binding site, and one of the four cis -responsive elements of the E6 promoter, namely, the binding site for Sp1.

    Article Snippet: DNase I-treated DNA was purified by standard procedures and used as a template for the extension reaction with Vent (exo-) polymerase (New England Biolabs).

    Techniques: Clone Assay, Binding Assay, Sequencing, Marker

    PTEN-KO validation of the MSCs. a The designed target site exon region. b The map of empty vector (from Addgene, Massachusetts, USA). c T7E1 digestion products were analyzed by agarose gel electrophoresis. The pSpCas9(BB)-2A-GFP-T2 (px458-T2) plasmid showed the highest Knock-out performance. d DNA was extracted from plasmid-transfected BMSCs and amplified through PCR. The PTEN bands did not exist after transfection e Western blot confirmed PTEN was knocked out

    Journal: Cytotechnology

    Article Title: Generation of PTEN knockout bone marrow mesenchymal stem cell lines by CRISPR/Cas9-mediated genome editing

    doi: 10.1007/s10616-017-0183-3

    Figure Lengend Snippet: PTEN-KO validation of the MSCs. a The designed target site exon region. b The map of empty vector (from Addgene, Massachusetts, USA). c T7E1 digestion products were analyzed by agarose gel electrophoresis. The pSpCas9(BB)-2A-GFP-T2 (px458-T2) plasmid showed the highest Knock-out performance. d DNA was extracted from plasmid-transfected BMSCs and amplified through PCR. The PTEN bands did not exist after transfection e Western blot confirmed PTEN was knocked out

    Article Snippet: The mixture of duplexes was treated with T7E1 nuclease for 15 min at 37 °C (New England Biolabs, Beijing, China).

    Techniques: Plasmid Preparation, Agarose Gel Electrophoresis, Knock-Out, Transfection, Amplification, Polymerase Chain Reaction, Western Blot

    Proof of Concept of Anti-HBV Efficacy of TALENs or CRISPR/Cas9 (A) HEK293 cells were co-transfected with an HBV expression plasmid pTHBV2 and either of the complete nuclease systems. DNA was isolated after 4 days and examined for mutagenesis at target sites by T7E1 assay. Undigested and digested products were separated on an agarose gel side by side for comparison. Expected cleavage product sizes are indicated by arrowheads. “M” indicates the molecular weight marker lane. (B) Huh7 cells were co-transfected with an HBV expression plasmid pTHBV2 and TALEN or CRISPR/Cas9 nuclease systems. HBsAg concentrations in the supernatant were measured after 4 days by ELISA. Data are represented as means of S/CO (sample to control ratio) values and error bars indicate SD of three replicates. Statistically significant differences to HBV only are indicated by an asterisk (*p

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: One-Vector System for Multiplexed CRISPR/Cas9 against Hepatitis B Virus cccDNA Utilizing High-Capacity Adenoviral Vectors

    doi: 10.1016/j.omtn.2018.05.006

    Figure Lengend Snippet: Proof of Concept of Anti-HBV Efficacy of TALENs or CRISPR/Cas9 (A) HEK293 cells were co-transfected with an HBV expression plasmid pTHBV2 and either of the complete nuclease systems. DNA was isolated after 4 days and examined for mutagenesis at target sites by T7E1 assay. Undigested and digested products were separated on an agarose gel side by side for comparison. Expected cleavage product sizes are indicated by arrowheads. “M” indicates the molecular weight marker lane. (B) Huh7 cells were co-transfected with an HBV expression plasmid pTHBV2 and TALEN or CRISPR/Cas9 nuclease systems. HBsAg concentrations in the supernatant were measured after 4 days by ELISA. Data are represented as means of S/CO (sample to control ratio) values and error bars indicate SD of three replicates. Statistically significant differences to HBV only are indicated by an asterisk (*p

    Article Snippet: Mutation Detection For the T7 endonuclease 1 (T7E1) (New England Biolabs, MA) mutation detection assay, DNA sequences that span the target sites were amplified from purified genomic DNA by PCR using standard conditions for the OneTaq 2X Master Mix with Standard Buffer (New England Biolabs, MA), with the following primer sets: S/HBV-RT, S-T7 for 5′-ttcctcttcatcctgctgct-3′ and S rev 5′-tgtaaaaggggcagcaaaac-3′; X, No. 5-forw 5′-actcctagccgcttgttttg-3′ and No.5-rev 5′-ataagggtcgatgtccatgc-3′; C, C-T7 for 5′-ctgggtgggtgttaatttgg-3′ and No.6-rev 5′-tacccgccttccatagagtg-3′; P1, P1_F 5′-gctttcactttctcgccaac-3′ and P1_R 5′-accttgggcaatatttggtg-3′; and XCp, XCp_F 5′-actctctcgtccccttctcc-3′ and XCp_R 5′-gcctgagtgcagtatggtga-3′.

    Techniques: TALENs, CRISPR, Transfection, Expressing, Plasmid Preparation, Isolation, Mutagenesis, Agarose Gel Electrophoresis, Molecular Weight, Marker, Enzyme-linked Immunosorbent Assay